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    <title>Recent ipnc items</title>
    <link>https://escholarship.org/uc/ipnc/rss</link>
    <description>Recent eScholarship items from Department of Plant Sciences</description>
    <pubDate>Mon, 14 Sep 2026 06:56:30 +0000</pubDate>
    <item>
      <title>Berry sugar accumulation and softening dynamics in a slow ripening genotype and its response to hormone application</title>
      <link>https://escholarship.org/uc/item/1w9352pc</link>
      <description>The onset and rate of sugar accumulation in wine grapes are important traits for wine style and quality attainment. As sugar accumulation rates increase due to the consequences of a rapidly changing environment, an uncoupling between the concentration of sugar and other compounds contributing to wine quality is often observed. Management practices can mitigate accelerated sugar accumulation only to a certain extent, while exploration of natural variants with fruit ripening traits of interest represents a more permanent solution. In this study, differences between two full siblings with extreme phenotypic variation in fruit ripening were investigated. Sugar accumulation, berry growth and softening over three years showed an unprecedented ripening delay of over 65&amp;nbsp;days. Hypothetical causes for the ripening failure were tested through a series of experiments. Leaf physiology was not impaired in the slow ripening genotype, and severe cluster thinning did not impact ripening time...</description>
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      <pubDate>Wed, 9 Sep 2026 00:00:00 +0000</pubDate>
      <author>
        <name>Previtali, Pietro</name>
      </author>
      <author>
        <name>Bellon, Oscar</name>
      </author>
      <author>
        <name>Green, Elizabeth</name>
      </author>
      <author>
        <name>Shackel, Kenneth</name>
        <uri>https://orcid.org/0000-0003-2637-5954</uri>
      </author>
      <author>
        <name>Fasoli, Marianna</name>
      </author>
      <author>
        <name>Zenoni, Sara</name>
      </author>
      <author>
        <name>Cousins, Peter</name>
      </author>
      <author>
        <name>Bartlett, Megan</name>
        <uri>https://orcid.org/0000-0003-0975-8777</uri>
      </author>
      <author>
        <name>Dokoozlian, Nick</name>
      </author>
    </item>
    <item>
      <title>Both inherent soil properties and management practices shape soil microbial communities under prolonged organic management</title>
      <link>https://escholarship.org/uc/item/9x4202rp</link>
      <description>The soil microbiome is recognized as a key component of soil health; however, microbial community responses to agricultural management can be inconsistent and context dependent. Here, we investigated the connections between soil microbial communities, soil properties, and agricultural practices in the Driftless Region of Wisconsin and Illinois, spanning 128 fields that have been under organic management for varying durations (from 3 to 51&amp;nbsp;years). Using structural equation modeling (SEM) we uncovered the effects of tillage, time under organic management, alfalfa use, and cover crop use on total carbon, nitrogen, and pH while quantifying their direct and indirect effects on bacterial biomass, bacterial diversity, relative abundance of arbuscular mycorrhizal fungi (AMF), and fungal diversity. We found that bacterial and fungal community compositions significantly varied among fields that recently transitioned to organic management but converged to a more consistent composition...</description>
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      <pubDate>Fri, 28 Aug 2026 00:00:00 +0000</pubDate>
      <author>
        <name>Messenger, Grayson M</name>
      </author>
      <author>
        <name>Potter, Teal S</name>
      </author>
      <author>
        <name>Lankau, Richard A</name>
      </author>
      <author>
        <name>Silva, Erin M</name>
      </author>
      <author>
        <name>Ruark, Matthew D</name>
      </author>
      <author>
        <name>Sikora, Miranda C</name>
      </author>
      <author>
        <name>Vereecke, Léa</name>
      </author>
    </item>
    <item>
      <title>Long-term yield dynamics of rice-rice and rice-wheat systems in South Asia: Evidence from 39 experiments</title>
      <link>https://escholarship.org/uc/item/8j63n6ss</link>
      <description>We assessed long-term yield trajectories in rice-rice (RR) and rice-wheat (RW) in South Asia, using multi-decadal records from 11 RR and 28 RW experiments under Control, NPK, and NPK + farmyard manure (FYM). Trends were classified as positive or declining using site-level regressions (slope ≠ 0, P ≤ 0.05). In RR, positive system productivity trends occurred at 10% of Control vs. 46% of NPK and 60% of NPK + FYM, while declines fell from 40% to 9–10%. In RW, corresponding shares of positive trends were 10%, 18%, and 44% for Control, NPK, and NPK + FYM, respectively, with declines dropping from 30% to 9–11%. Meta-analysis of crop yields showed consistent patterns: under NPK + FYM, the pooled correlations were positive for RR (kharif rice: r = 0.41, P = 0.001; rabi rice r = 0.28, P = 0.004), and RW (rice: r = 0.27, P = 0.011; wheat r = 0.18, P = 0.002), whereas NPK effects were less positive for RW-wheat (0.15, P = 0.048) and RR-rice (rabi rice: r = 0.29, P = 0.007) but near zero...</description>
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      <pubDate>Wed, 26 Aug 2026 00:00:00 +0000</pubDate>
      <author>
        <name>Chakraborty, Debashis</name>
      </author>
      <author>
        <name>Rana, Dharamvir Singh</name>
      </author>
      <author>
        <name>Ladha, Jagdish Kumar</name>
        <uri>https://orcid.org/0000-0001-6517-5379</uri>
      </author>
      <author>
        <name>Samanta, Suman</name>
      </author>
      <author>
        <name>Ansari, Meraj Alam</name>
      </author>
      <author>
        <name>Ravisankar, Natesan</name>
      </author>
      <author>
        <name>Banerjee, Saon</name>
      </author>
      <author>
        <name>Singh, Vinod Kumar</name>
      </author>
      <author>
        <name>Yuan, Shen</name>
      </author>
      <author>
        <name>Gathala, Mahesh K</name>
      </author>
    </item>
    <item>
      <title>Leveraging sustainable agronomic practices in smallholder maize production for environmental and economic gains: Evidence from the Erhai Lake Basin, China</title>
      <link>https://escholarship.org/uc/item/7s1037f5</link>
      <description>Context Global maize production faces multiple challenges of increasing food security, farmers’ profitability, and reducing environmental impacts, especially in smallholder-dominated, environmentally sensitive areas. Leveraging sustainable agronomic practices from high-performing smallholders holds the potential to reconcile crop production and environmental protection. Objective This study uses the Erhai Lake Basin, a typical lake basin in China surrounded by intensive crop production, as an example to illustrate how optimized agronomic practices can balance the environmental sustainability and economic benefits in maize production. Methods We conducted extensive farmer surveys across the Erhai Lake Basin, collecting 379 valid samples (comprising 226 grain maize and 153 sweet maize). From this dataset, we identified high yield and high N use efficiency (HH) maize farmers, and pinpointed key agronomic practices contributing to superior environmental and economic performance. Results...</description>
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      <pubDate>Wed, 26 Aug 2026 00:00:00 +0000</pubDate>
      <author>
        <name>Ying, Feiyu</name>
      </author>
      <author>
        <name>Huo, Yuewen</name>
      </author>
      <author>
        <name>Liang, Zhengyuan</name>
      </author>
      <author>
        <name>Müller, Torsten</name>
      </author>
      <author>
        <name>Ladha, Jagdish K</name>
        <uri>https://orcid.org/0000-0001-6517-5379</uri>
      </author>
      <author>
        <name>Ying, Hao</name>
      </author>
      <author>
        <name>Zhao, Zhengxiong</name>
      </author>
      <author>
        <name>Zhang, Fusuo</name>
      </author>
      <author>
        <name>Cong, Wen-Feng</name>
      </author>
    </item>
    <item>
      <title>Navigating challenges and unlocking future opportunities in cereal-based cropping systems in India</title>
      <link>https://escholarship.org/uc/item/75m6n446</link>
      <description>Cereal-based cropping systems, particularly in India, are vital for food and livelihood security. These systems, which mostly include rice-based, millet-based, and maize-based rotations, are crucial for meeting the growing food demands of over 1.4 billion people in the country. However, the sustainability of dominant cropping systems faces significant challenges, including soil degradation, declining groundwater, biodiversity loss, and environmental pollution due to faulty agronomic practices. These practices have led to increased greenhouse gas (GHG) emissions, climatic vulnerabilities, herbicide resistance in weed species, and outbreaks of biotic stresses. Sustainable agricultural practices such as multiple stress-tolerant crop varieties, organic amendments, efficient water and fertilizer management, and nature-friendly regenerative agriculture (RA)/conservation agriculture (CA), along with the adoption of digital tools and practices and decision support systems, are considered...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/75m6n446</guid>
      <pubDate>Wed, 26 Aug 2026 00:00:00 +0000</pubDate>
      <author>
        <name>Datta, Ashim</name>
      </author>
      <author>
        <name>Pradhan, Aliza</name>
      </author>
      <author>
        <name>Yadav, Arvind K</name>
      </author>
      <author>
        <name>Das, Abinash</name>
      </author>
      <author>
        <name>Nayak, Hari S</name>
      </author>
      <author>
        <name>Mandal, Surajit</name>
      </author>
      <author>
        <name>Das, Anup</name>
      </author>
      <author>
        <name>Gathala, Mahesh K</name>
      </author>
      <author>
        <name>Ladha, Jagdish K</name>
        <uri>https://orcid.org/0000-0001-6517-5379</uri>
      </author>
    </item>
    <item>
      <title>Global insights into nitrogen losses and efficiency in rice, wheat, and maize cultivation</title>
      <link>https://escholarship.org/uc/item/5z63p95w</link>
      <description>Context Nitrogen (N) use efficiency (NUE) and N losses in cereal systems are central to achieving the United Nations Sustainable Development Goals (SDGs) on food security and environmental sustainability. However, global variations in NUE across cereals, regions, and management conditions remain poorly quantified, especially in relation to the relative roles of synthetic and non-synthetic N inputs. Objectives This study aimed to (i) assess global differences in NUE and N losses among maize, rice, and wheat; (ii) compare efficiencies derived from synthetic versus total N inputs; (iii) evaluate regional and temporal patterns; and (iv) identify key drivers and management implications to enhance NUE and mitigate losses. Methods A global dataset was assembled to calculate NUE indicators including partial factor productivity of N (PFPN), agronomic efficiency of N (AEN), recovery efficiency of synthetic N (REN-S), recovery efficiency of total N (REN-T), and the fraction of N derived...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/5z63p95w</guid>
      <pubDate>Wed, 26 Aug 2026 00:00:00 +0000</pubDate>
      <author>
        <name>Chakraborty, Debashis</name>
      </author>
      <author>
        <name>Ladha, Jagdish Kumar</name>
        <uri>https://orcid.org/0000-0001-6517-5379</uri>
      </author>
      <author>
        <name>Das, Bappa</name>
      </author>
      <author>
        <name>Rana, Dharamvir Singh</name>
      </author>
      <author>
        <name>Gathala, Mahesh Kumar</name>
      </author>
      <author>
        <name>Jat, Mangi Lal</name>
      </author>
      <author>
        <name>Krupnik, Timothy J</name>
      </author>
    </item>
    <item>
      <title>Forecasting Urban Water Demand and Effects on Wastewater Management: An Integrated Systems Approach with Uncertainty</title>
      <link>https://escholarship.org/uc/item/2dk9h119</link>
      <description>Water demand forecasting is an important tool for integrated water management. Long-term demand predictions include inherent uncertainty, but few studies have investigated empirical methods to forecast water demand that include uncertainty from many driving factors or evaluate how changes in demand affect linked systems such as wastewater conveyance and treatment. This study presents a novel approach for long-term urban water demand forecasting that (1) integrates uncertainty in technology, behavior, and climate; and (2) estimates effects of demand changes on wastewater management systems. We demonstrate this using a case study of 350 urban water supply agencies and more than 300 wastewater treatment systems in California serving 31 million people. For the period from 2020 to 2030, we used modeling with Monte Carlo simulations to estimate future scenarios of urban water demand given changes in efficiency, climate, water rates, and population. Effects of demand changes on wastewater...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/2dk9h119</guid>
      <pubDate>Wed, 26 Aug 2026 00:00:00 +0000</pubDate>
      <author>
        <name>Porse, Erik</name>
      </author>
      <author>
        <name>Kaplan, Jonathan D</name>
      </author>
      <author>
        <name>Leverenz, Harold</name>
      </author>
      <author>
        <name>Leo, Caitlyn</name>
      </author>
      <author>
        <name>Solins, Joanna</name>
      </author>
      <author>
        <name>Cadenasso, Mary</name>
      </author>
      <author>
        <name>Pincetl, Stephanie</name>
        <uri>https://orcid.org/0000-0002-8660-4803</uri>
      </author>
      <author>
        <name>Keene, Dakota</name>
      </author>
      <author>
        <name>Babchanik, David</name>
      </author>
      <author>
        <name>Lezzaik, Khalil</name>
      </author>
      <author>
        <name>Maloney, Patrick</name>
      </author>
    </item>
    <item>
      <title>Integrating legumes to enhance cereal production: The relative inputs of fertiliser nitrogen and legume biological nitrogen fixation in major wheat and maize producing countries</title>
      <link>https://escholarship.org/uc/item/0n62k625</link>
      <description>BackgroundCereal crops dominate arable agriculture and underpin global food supply. Cereal grain yield is closely related to crop nitrogen (N) uptake. However, excessive inputs of N fertiliser in cereal production systems can have negative environmental consequences and represent high financial risk for farmers.ScopeThis review explores opportunities to reduce the current reliance of the global staples, wheat (Triticum aestivum) and maize (Zea mays), on N fertiliser by diversifying cereal-based cropping systems with legumes, in both time (rotation) and space (via intercropping). Increases in cereal grain yield and N uptake resulting from the inclusion of legumes in wheat and maize cropping systems are examined across different geographic regions. The role of grain legumes and legume-based forages, cover-crops and green manures is described for the 15 countries responsible for producing &amp;gt; 70% of the world’s wheat and maize and consuming &amp;gt; 80% of the global applications of...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/0n62k625</guid>
      <pubDate>Wed, 26 Aug 2026 00:00:00 +0000</pubDate>
      <author>
        <name>Peoples, Mark B</name>
      </author>
      <author>
        <name>Li, Xiaoxi</name>
      </author>
      <author>
        <name>Kirkegaard, John A</name>
      </author>
      <author>
        <name>Armstrong, Roger D</name>
      </author>
      <author>
        <name>Ciampitti, Ignacio A</name>
      </author>
      <author>
        <name>Franke, Angelinus C</name>
      </author>
      <author>
        <name>Giller, Ken E</name>
      </author>
      <author>
        <name>Hunt, James R</name>
      </author>
      <author>
        <name>Jeuffroy, Marie-Hélène</name>
      </author>
      <author>
        <name>Ladha, Jagdish K</name>
        <uri>https://orcid.org/0000-0001-6517-5379</uri>
      </author>
      <author>
        <name>Lemaire, Gilles</name>
      </author>
      <author>
        <name>Li, Long</name>
      </author>
      <author>
        <name>Palmero, Francisco</name>
      </author>
      <author>
        <name>Reckling, Moritz</name>
      </author>
      <author>
        <name>Salvagiotti, Fernando</name>
      </author>
      <author>
        <name>Sida, Tesfaye S</name>
      </author>
      <author>
        <name>Swan, Antony D</name>
      </author>
      <author>
        <name>Zhang, Siyu</name>
      </author>
      <author>
        <name>Herridge, David F</name>
      </author>
    </item>
    <item>
      <title>Correcting Apparent Priming Bias Unveils Fertilizer Nitrogen‐Risk Archetypes of Surplus and Depletion Across Asian Rice Systems</title>
      <link>https://escholarship.org/uc/item/0m66v8cq</link>
      <description>Accurate assessment of fertilizer nitrogen (N) fate is essential for optimizing rice production, yet regional-scale estimates remain limited. This progress has been fundamentally constrained by the prohibitive cost of isotopic tracing, which has not only limited large-scale deployment but also prevented the correction of apparent priming effect (APE)-induced bias, resulting in a systematic misestimation of soil N retention. To overcome this limitation, a continental-scale framework is developed to quantify fertilizer N fate across Asian rice systems. Ensemble modeling produces the first high-resolution (5 arcmin) maps of Net Residue and Loss, identifying Eastern andCentral China,&amp;nbsp;along with Northern India, as critical Loss hotspots. Accounting for APE reveals that positive priming suppresses the Net Residue of applied N to below 7% (-1%-15%), while 48% (43%-53%) of applied N is lost to the environment, leading to annual environmental costs of&amp;nbsp;US$98.53 (83.25-108.27)...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/0m66v8cq</guid>
      <pubDate>Wed, 26 Aug 2026 00:00:00 +0000</pubDate>
      <author>
        <name>Liu, Xiuyun</name>
      </author>
      <author>
        <name>Cai, Siyuan</name>
      </author>
      <author>
        <name>Xia, Longlong</name>
      </author>
      <author>
        <name>Ladha, Jagdish K</name>
        <uri>https://orcid.org/0000-0001-6517-5379</uri>
      </author>
      <author>
        <name>Yan, Xiaoyuan</name>
      </author>
      <author>
        <name>Zhao, Xu</name>
      </author>
    </item>
    <item>
      <title>Long-term balanced organic and synthetic nitrogen fertilization can realize sustainable crop production</title>
      <link>https://escholarship.org/uc/item/05p324dq</link>
      <description>CONTEXT Manure recycling to cropland reduces synthetic fertilizer use and nitrogen (N) waste while increasing soil carbon (C) sequestration, which is important for sustainable crop production. However, few studies have systematically integrated long-term N budgets with changes of soil C and N stocks and the greenhouse gas (GHG) balance. OBJECTIVE We aim to quantify the long-term responses of crop productivity, changes of soil C and N stock, reactive N losses and the GHG balance to various C and N management practices, thus providing evidence for sustainable crop production. METHODS We used a 15-year wheat-maize double cropping system in the North China Plain. The experiment included eight fertilization treatments with contrasting C and N management practices. Crop productivity, N losses, changes of soil C and N stock; and the GHG balance were evaluated. RESULTS AND CONCLUSIONS Compared with conventional fertilization with excess synthetic N, long-term balanced organic and synthetic...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/05p324dq</guid>
      <pubDate>Wed, 26 Aug 2026 00:00:00 +0000</pubDate>
      <author>
        <name>Zhang, Chong</name>
      </author>
      <author>
        <name>Zhang, Xin</name>
      </author>
      <author>
        <name>Rees, Robert M</name>
      </author>
      <author>
        <name>de Vries, Wim</name>
      </author>
      <author>
        <name>Lassaletta, Luis</name>
      </author>
      <author>
        <name>Ladha, Jagdish K</name>
        <uri>https://orcid.org/0000-0001-6517-5379</uri>
      </author>
      <author>
        <name>Ju, Xiaotang</name>
      </author>
    </item>
    <item>
      <title>Gradual increases in light intensity and photoperiod enhance light use efficiency and dry matter in indoor basil</title>
      <link>https://escholarship.org/uc/item/03n1k3vt</link>
      <description>Basil (&lt;i&gt;Ocimum basilicum&lt;/i&gt; L. Genovese) is a highly valued and economically important herb with significant culinary qualities. The quantity of light supplied to plants, including both light intensity and photoperiod, plays a critical role in regulating plant morphology and biomass accumulation. Optimizing these factors can simultaneously enhance yield and resource efficiency. This study assessed the effects of constant versus gradually increasing light intensity and photoperiod on basil growth, physiology, and light use efficiency (LUE), while maintaining an equivalent average daily light integral (DLI) over the 24-day growing period. Four different treatments were applied in a climate-controlled growth chamber: (CIP) constant light intensity (300 μmol m&lt;sup&gt;-&lt;/sup&gt;² s&lt;sup&gt;-&lt;/sup&gt;¹) and constant photoperiod (16&amp;nbsp;h), (CIDP) constant light intensity with a dynamic photoperiod (14-16-18 h), (DICP) dynamic light intensity (200-300-400 μmol m&lt;sup&gt;-&lt;/sup&gt;² s&lt;sup&gt;-&lt;/sup&gt;¹) with...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/03n1k3vt</guid>
      <pubDate>Wed, 29 Jul 2026 00:00:00 +0000</pubDate>
      <author>
        <name>Akter, Nazmin</name>
      </author>
      <author>
        <name>Ahamed, Shamim</name>
      </author>
      <author>
        <name>Taylor, Gail</name>
      </author>
      <author>
        <name>Cammarisano, Laura</name>
      </author>
    </item>
    <item>
      <title>Liquid organic fertilizers in soilless cultivation: a systematic review of production, performance, challenges, and future prospects</title>
      <link>https://escholarship.org/uc/item/1473n8t8</link>
      <description>Organic farming practices, including the use of organic growing media, biopesticides, and biological control, are increasingly gaining attention in soilless crop production under controlled environments, driven by rising environmental awareness and potential economic benefits. However, plant nutrition in soilless systems still relies heavily on synthetic fertilizers (SFs), whose production is energy-intensive and can contribute to environmental pollution when overapplied. Liquid organic fertilizers (LOFs), derived from plants, animals, and other organic waste materials, present a promising alternative. Despite this potential, their adoption remains limited due to insufficient awareness of production factors, uncertainty regarding performance, and challenges related to application. This systematic review synthesizes findings from more than 77 peer-reviewed studies, revealing substantial variability in LOF nutrient composition depending on formulation, feedstock, and processing...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/1473n8t8</guid>
      <pubDate>Wed, 15 Jul 2026 00:00:00 +0000</pubDate>
      <author>
        <name>Chand, Jonish</name>
      </author>
      <author>
        <name>Reza, Rubel</name>
      </author>
      <author>
        <name>Chowdhury, Milon</name>
      </author>
      <author>
        <name>Hager, Janelle V</name>
      </author>
      <author>
        <name>Dash, Prosanta K</name>
      </author>
      <author>
        <name>Akter, Nazmin</name>
      </author>
      <author>
        <name>Cammarisano, Laura</name>
      </author>
    </item>
    <item>
      <title>The annotated blueprint: integrated functional genomic resources for a model tetraploid wheat Triticum turgidum cv Kronos</title>
      <link>https://escholarship.org/uc/item/3094v8ct</link>
      <description>Triticum turgidum cv Kronos is a tetraploid wheat cultivar that underpins one of the most widely used community platforms for functional genomics. Over the past decade, researchers have generated c. 3000 exome-capture (EC) and promoter-capture (PC) datasets linked to mutagenized seed stocks, along with extensive transcriptomic and phenotypic resources. However, the absence of a reference genome has constrained their full utility. We assembled a chromosome-scale reference genome for Kronos, with high-confidence annotations, including manual curation of over 1000 disease resistance (nucleotide-binding leucine-rich repeat (NLR)) genes and genome-wide identification of microRNAs and phasiRNAs. We additionally reanalyzed EC and PC data to capture mutational landscapes across ethyl methane sulphonate-mutagenized Kronos populations. We revealed previously hidden NLR diversity and resolved their genomic organization at chromosomal ends. Re-analysis of capture datasets enabled high-resolution...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/3094v8ct</guid>
      <pubDate>Tue, 30 Jun 2026 00:00:00 +0000</pubDate>
      <author>
        <name>Seong, Kyungyong</name>
      </author>
      <author>
        <name>Kumar, Rakesh</name>
      </author>
      <author>
        <name>Prigozhin, Daniil M</name>
        <uri>https://orcid.org/0000-0003-2075-0231</uri>
      </author>
      <author>
        <name>Lunde, China</name>
      </author>
      <author>
        <name>Ribeiro, Thales Henrique Cherubino</name>
      </author>
      <author>
        <name>Bélanger, Sébastien</name>
      </author>
      <author>
        <name>Hsieh, Jo‐Wei Allison</name>
      </author>
      <author>
        <name>Tang, McCree</name>
      </author>
      <author>
        <name>Meyers, Blake C</name>
        <uri>https://orcid.org/0000-0003-3436-6097</uri>
      </author>
      <author>
        <name>Krasileva, Ksenia V</name>
        <uri>https://orcid.org/0000-0002-1679-0700</uri>
      </author>
    </item>
    <item>
      <title>Decoupled carbon assimilation and growth responses to aridity in temperate deciduous oaks.</title>
      <link>https://escholarship.org/uc/item/2jn5z25x</link>
      <description>The magnitude of the terrestrial carbon sink remains a key uncertainty in future climate projections, in part due to poorly understood links between carbon uptake and its allocation to woody biomass in vegetation. Here, in this study, we show that photosynthesis and aboveground growth occur asynchronously across diel to seasonal scales in eight North American oak species. Across 137 tree ring sites, current-year annual growth was insensitive to climate variability after midsummer despite 26 to 36% of annual gross primary productivity (GPP) occurring during this period. Hourly GPP flux and growth measurements at four sites spanning seven site years further demonstrate that wood formation ceases earlier than photosynthesis and is restricted to periods of low atmospheric aridity and temperature. This photosynthesis-growth decoupling intensifies with interannual variability in vapor pressure deficit (&lt;i&gt;r&lt;/i&gt; = 0.86, &lt;i&gt;P&lt;/i&gt; &amp;lt; 0.05), suggesting that by assuming tight coupling...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/2jn5z25x</guid>
      <pubDate>Mon, 22 Jun 2026 00:00:00 +0000</pubDate>
      <author>
        <name>Rao, Mukund</name>
      </author>
      <author>
        <name>Pacheco-Solana, Arturo</name>
      </author>
      <author>
        <name>Li, Rong</name>
      </author>
      <author>
        <name>Oryan, Bar</name>
      </author>
      <author>
        <name>Jensen, Johanna</name>
      </author>
      <author>
        <name>Rodriguez-Caton, Milagros</name>
      </author>
      <author>
        <name>Klinek, Lily</name>
      </author>
      <author>
        <name>Pierrat, Zoe</name>
      </author>
      <author>
        <name>Ruehr, Sophie</name>
      </author>
      <author>
        <name>Oelkers, Rose</name>
      </author>
      <author>
        <name>Boeschoten, Laura</name>
      </author>
      <author>
        <name>Griffin, Kevin</name>
      </author>
      <author>
        <name>McCormack, M</name>
      </author>
      <author>
        <name>Yang, Xi</name>
      </author>
      <author>
        <name>Verfaillie, Joseph</name>
      </author>
      <author>
        <name>Baldocchi, Dennis</name>
      </author>
      <author>
        <name>Hise, Jeremy</name>
      </author>
      <author>
        <name>Turner, Alexander</name>
      </author>
      <author>
        <name>Scanlon, Todd</name>
      </author>
      <author>
        <name>Andreu-Hayles, Laia</name>
      </author>
      <author>
        <name>Eitel, Jan</name>
      </author>
      <author>
        <name>Pederson, Neil</name>
      </author>
      <author>
        <name>Griffin, Daniel</name>
      </author>
      <author>
        <name>Stahle, David</name>
      </author>
      <author>
        <name>Maxwell, Justin</name>
      </author>
      <author>
        <name>Voelker, Steven</name>
      </author>
      <author>
        <name>Kannenberg, Steven</name>
      </author>
      <author>
        <name>Peñuelas, Josep</name>
      </author>
      <author>
        <name>Magney, Troy</name>
      </author>
    </item>
    <item>
      <title>Invasion stress mitigates climate stress in a brackish marsh amphipod</title>
      <link>https://escholarship.org/uc/item/9128q07n</link>
      <description>Abstract     Organisms in coastal brackish ecosystems face not only highly variable environmental conditions, but the intensity and stochasticity of these environmental conditions are anticipated to increase due to climate change. While environmental changes are often presented unilaterally as stressors, there are some anthropogenic environmental transformations, such as the introduction of habitat forming plant species, that may mitigate physiological stress imposed by warming. In Suisun Marsh in the California Delta, native plant canopies allow light and heat to penetrate to the understory yet the canopies of the introduced Phragmites australis reed block out sunlight and heat for organisms living below.     We set out to understand the physiological performance of mud‐dwelling invertebrates in this context: can invasion stress mitigate climate stress? We raised field collected Gammarus amphipods in the laboratory under simulated ‘native canopy’ and ‘ Phragmites canopy’ temperature/light...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/9128q07n</guid>
      <pubDate>Thu, 18 Jun 2026 00:00:00 +0000</pubDate>
      <author>
        <name>Haworth, Lorna E</name>
      </author>
      <author>
        <name>Nancollas, Sarah</name>
      </author>
      <author>
        <name>Landa, Susie N</name>
      </author>
      <author>
        <name>Todgham, Anne E</name>
        <uri>https://orcid.org/0000-0003-1439-6985</uri>
      </author>
      <author>
        <name>Tanner, Richelle L</name>
      </author>
    </item>
    <item>
      <title>Thirty Years of Changes in How We Understand and Steward California’s Grasslands</title>
      <link>https://escholarship.org/uc/item/664506k2</link>
      <description>The California Native Grassland Association’s (CNGA’s) leadership in the restoration of California grasslands has extended far beyond incorporating the latest science into restoration techniques, it’s also pushed the frontiers of research—forging new directions and recruiting and collaborating with researchers to explore novel ways of understanding these grasslands, addressing critical knowledge gaps in our stewardship. This is a short review of some of the major changes in our understanding of California’s grasslands in the last 30 years.</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/664506k2</guid>
      <pubDate>Tue, 16 Jun 2026 00:00:00 +0000</pubDate>
      <author>
        <name>Eviner, Valerie</name>
        <uri>https://orcid.org/0000-0001-5530-9417</uri>
      </author>
    </item>
    <item>
      <title>Interactive effects of electrical conductivity and light intensity on growth, yield, and nutrient dynamics of hydroponic lettuce</title>
      <link>https://escholarship.org/uc/item/152340mg</link>
      <description>Abstract Precise management of nutrient solution properties, such as electrical conductivity (EC), and environmental factors, such as light intensity (LI), is essential for optimizing crop yield and quality in hydroponic production. This study evaluated the individual and combined effects of two EC ranges (EC1: 1.5–2.0&amp;nbsp;dS m-1; EC2: 4.5–6.0&amp;nbsp;dS m-1) and three LI levels (L1 = 145, L2 = 185, and L3 = 240 $$\mu$$mol m-2&amp;nbsp;s-1) on the growth, yield, leaf mineral uptake, and nitrate accumulation of butterhead lettuce grown in hydroponic system under artificial lighting. The greatest leaf area (1338.31&amp;nbsp;cm2) and yield (57.97&amp;nbsp;g plant-1) were observed in EC1L3 treatment, corresponding to reductions of 75% and 77.2%, respectively, compared to EC2L3 (330.79&amp;nbsp;cm2 and 13.98&amp;nbsp;g plant-1), indicating the adverse effects of salinity stress. Furthermore, within the same EC1 level, LI positively impacted yield, which increased by 47% under EC1L3 compared to EC1L1. Mineral...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/152340mg</guid>
      <pubDate>Wed, 3 Jun 2026 00:00:00 +0000</pubDate>
      <author>
        <name>Akter, Nazmin</name>
      </author>
      <author>
        <name>Cammarisano, Laura</name>
      </author>
      <author>
        <name>Ahamed, Md Shamim</name>
        <uri>https://orcid.org/0000-0003-1970-0050</uri>
      </author>
    </item>
    <item>
      <title>The psyI and psyR Genes of Pseudomonas syringae pv. tomato DC3000 Contribute to Bacterial Virulence on Tomato.</title>
      <link>https://escholarship.org/uc/item/9h629134</link>
      <description>The LuxI/LuxR system, which produces and perceives &lt;i&gt;N&lt;/i&gt;-acyl homoserine lactones (AHLs), plays a significant role in regulating pathogenesis and communication in gram-negative bacteria. A homologous system exists in &lt;i&gt;Pseudomonas syringae&lt;/i&gt; pv. &lt;i&gt;tomato&lt;/i&gt; (&lt;i&gt;Pst&lt;/i&gt;) DC3000, which is encoded by the single-copy genes &lt;i&gt;psyI/psyR&lt;/i&gt;. We created a double-knockout mutant of the AHL synthase (&lt;i&gt;psyI&lt;/i&gt;) and the AHL receptor (&lt;i&gt;psyR&lt;/i&gt;) genes in &lt;i&gt;Pst&lt;/i&gt; DC3000 and a corresponding complemented strain to gain insights into their role in plant-pathogen interactions and the metabolic processes associated with this system in vitro. We observed that the mutant strain &lt;i&gt;psyI&lt;sup&gt;-&lt;/sup&gt;R&lt;sup&gt;-&lt;/sup&gt;&lt;/i&gt; can overcome stomatal immunity as the parental strain &lt;i&gt;Pst&lt;/i&gt; DC3000. However, the &lt;i&gt;psyI&lt;sup&gt;-&lt;/sup&gt;R&lt;sup&gt;-&lt;/sup&gt;&lt;/i&gt; apoplastic population is significantly smaller than that of &lt;i&gt;Pst&lt;/i&gt; DC3000 at 3 days postinoculation. Furthermore, PsyI and PsyR are required for...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/9h629134</guid>
      <pubDate>Thu, 21 May 2026 00:00:00 +0000</pubDate>
      <author>
        <name>Yeemin, Jirachaya</name>
      </author>
      <author>
        <name>Rossidivito, Gabrielle</name>
      </author>
      <author>
        <name>Bridges, David F</name>
      </author>
      <author>
        <name>Panchal, Shweta</name>
      </author>
      <author>
        <name>Rodrigues, Jorge L Mazza</name>
        <uri>https://orcid.org/0000-0002-6446-6462</uri>
      </author>
      <author>
        <name>Melotto, Maeli</name>
        <uri>https://orcid.org/0000-0001-6021-9803</uri>
      </author>
    </item>
    <item>
      <title>Structure and sequence evolution in the pennycress (Thlaspi arvense) pangenome</title>
      <link>https://escholarship.org/uc/item/8gb9j1gf</link>
      <description>Eukaryotic genomes harbor many forms of variation, including nucleotide diversity and structural polymorphisms, which experience natural selection and contribute to genome evolution and biodiversity. Harnessing this variation for agriculture hinges on our ability to detect, quantify, catalog, and deploy genetic diversity. Here, we explore seven complete genomes of the emerging biofuel crop pennycress (Thlaspi arvense) drawn from across the species' current genetic diversity to catalog variation in genome structure and content. Across this new pangenome resource, we find contrasting evolutionary modes in different genomic zones. Gene-poor, repeat-rich pericentromeric regions experience frequent rearrangements, including repeated centromere repositioning. By contrast, conserved gene-dense chromosome arms maintain large-scale synteny across accessions even in fast-evolving NOD-like receptor immune genes, where microsynteny breaks down across species, but gene cluster positioning...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/8gb9j1gf</guid>
      <pubDate>Fri, 15 May 2026 00:00:00 +0000</pubDate>
      <author>
        <name>Bird, Kevin A</name>
      </author>
      <author>
        <name>Rifkin, Joanna L</name>
      </author>
      <author>
        <name>McLaughlin, Chloee M</name>
      </author>
      <author>
        <name>Harder, Avril M</name>
      </author>
      <author>
        <name>Basnet, Pawan</name>
      </author>
      <author>
        <name>Katz, Ella</name>
      </author>
      <author>
        <name>Brůna, Tomáš</name>
      </author>
      <author>
        <name>Barry, Kerrie</name>
        <uri>https://orcid.org/0000-0002-8999-6785</uri>
      </author>
      <author>
        <name>Boston, LoriBeth</name>
      </author>
      <author>
        <name>Daum, Christopher</name>
        <uri>https://orcid.org/0000-0003-3895-5892</uri>
      </author>
      <author>
        <name>Guo, Jie</name>
      </author>
      <author>
        <name>Lipzen, Anna</name>
        <uri>https://orcid.org/0000-0003-2293-9329</uri>
      </author>
      <author>
        <name>Plott, Christopher</name>
      </author>
      <author>
        <name>Jenkins, Jerry W</name>
      </author>
      <author>
        <name>Walstead, Rachel</name>
      </author>
      <author>
        <name>Rajasekar, Shanmugam</name>
      </author>
      <author>
        <name>Talag, Jayson</name>
      </author>
      <author>
        <name>Frels, Katherine</name>
      </author>
      <author>
        <name>Greenham, Kathleen</name>
      </author>
      <author>
        <name>Ellison, Shelby</name>
      </author>
      <author>
        <name>Grimwood, Jane</name>
      </author>
      <author>
        <name>Schmutz, Jeremy</name>
      </author>
      <author>
        <name>Edger, Patrick P</name>
      </author>
      <author>
        <name>Pires, J Chris</name>
      </author>
      <author>
        <name>Lovell, John T</name>
      </author>
      <author>
        <name>Kliebenstein, Daniel J</name>
        <uri>https://orcid.org/0000-0001-5759-3175</uri>
      </author>
    </item>
    <item>
      <title>Labile carbon dynamics under initial transition to regenerative agriculture</title>
      <link>https://escholarship.org/uc/item/3rp4j5th</link>
      <description>Understanding the dynamics of labile organic carbon (LOC) is critical for evaluating the short-term impacts of regenerative agricultural practices on soil health. We assessed changes in key LOC fractions such as permanganate oxidizable carbon (POXC) measured by 0.01 M, 0.02 M, 0.033 M potassium permanganate, microbial biomass carbon (MBC), and very labile carbon (CVL) across four long-term conservation agriculture (CA) experiment sites located in contrasting agro-ecological zones of South Asia namely Karnal, Patna, Aduthurai, and Gazipur. At each site, four cropping system scenarios (S) were evaluated: S1, current farmers practice; S2, current farmers cropping system with partial CA; S3, current farmers cropping system with full CA; and S4, diversified crop rotation with full CA. Soil samples were collected from 0–15 and 15–30 cm depth after two cropping cycles. Results showed that POXC, MBC, CVL, oxidizable organic carbon (SOC) and total organic carbon (TOC) increased following...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/3rp4j5th</guid>
      <pubDate>Sun, 26 Apr 2026 00:00:00 +0000</pubDate>
      <author>
        <name>Roy, Dibakar</name>
      </author>
      <author>
        <name>Kundu, Ritesh</name>
      </author>
      <author>
        <name>Datta, Ashim</name>
      </author>
      <author>
        <name>Mandal, Biswapati</name>
      </author>
      <author>
        <name>Paul, Subhadip</name>
      </author>
      <author>
        <name>Sharma, Sheetal</name>
      </author>
      <author>
        <name>Ladha, Jagdish Kumar</name>
        <uri>https://orcid.org/0000-0001-6517-5379</uri>
      </author>
    </item>
    <item>
      <title>No-till in rice systems: A global meta-analysis of key agronomic practices impacting yields</title>
      <link>https://escholarship.org/uc/item/3h10m6jn</link>
      <description>Context While no-till (NT), one of the pillars of conservation agriculture, is widely practiced in upland crops, considerably less research has been conducted in rice systems. While adoption has been limited, numerous field experiments have evaluated NT rice across diverse regions and management contexts yet reported yield responses to key agronomic practices, soil properties, and climatic conditions remain inconsistent and poorly synthesized at a global scale. Objective Our objective was to conduct a global meta-analysis comparing the effects of NT to conventional tillage (CT) on rice yields and to identify the agronomic practices, soil characteristics, and climate factors most strongly associated with yield changes under NT. Methods We performed a global meta-analysis of 115 studies (579 paired observations) comparing rice yields under NT and CT. Yield response ratios (lnRR) were analyzed using mixed-effects meta-analysis to estimate overall effects. Meta-regression and Random...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/3h10m6jn</guid>
      <pubDate>Fri, 24 Apr 2026 00:00:00 +0000</pubDate>
      <author>
        <name>Godbey, Mia</name>
      </author>
      <author>
        <name>Macedo, Ignacio</name>
      </author>
      <author>
        <name>Pittelkow, Cameron M</name>
        <uri>https://orcid.org/0000-0001-8654-9552</uri>
      </author>
      <author>
        <name>Linquist, Bruce</name>
        <uri>https://orcid.org/0000-0002-0750-8427</uri>
      </author>
    </item>
    <item>
      <title>Association Between Observed Climate Change and Cardiovascular Disease in the United States</title>
      <link>https://escholarship.org/uc/item/0gn8w4x6</link>
      <description>Climate change is affecting nearly all social and environmental determinants of health. However, the extent of resulting cumulative impacts on cardiovascular and other noncommunicable diseases is not known. To address this gap and inform future research, we conducted an ecological evaluation of associations between 14 long-term climate anomaly metrics and prevalence of coronary heart disease (CHD) and stroke in the United States. We calculated long-term anomaly metrics as the difference between their respective 1970-1979 baseline mean and 2013-2022 modern mean values. With fitted random effects regression analysis, we evaluated associations between each anomaly metric, individually and collectively, and census tract-level 2020-2022 mean prevalence of CHD and stroke. In adjusted models with all noncollinear anomaly metrics, we found a net association of all metrics with 0.59% higher CHD prevalence and 0.88% higher stroke prevalence (9.8% and 27.9% relative prevalence, respectively)....</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/0gn8w4x6</guid>
      <pubDate>Thu, 23 Apr 2026 00:00:00 +0000</pubDate>
      <author>
        <name>Yeager, R</name>
      </author>
      <author>
        <name>Tuholske, C</name>
      </author>
      <author>
        <name>Browning, MHEM</name>
      </author>
      <author>
        <name>Mattingly, C</name>
      </author>
      <author>
        <name>Olmsted, S</name>
      </author>
      <author>
        <name>Ossola, A</name>
        <uri>https://orcid.org/0000-0002-0507-6026</uri>
      </author>
      <author>
        <name>Locke, DH</name>
      </author>
    </item>
    <item>
      <title>Target-site mechanism confers resistance pattern of ACCase inhibitors in bearded sprangletop (Leptochloa fusca ssp. fascicularis) from California</title>
      <link>https://escholarship.org/uc/item/99f3k2hk</link>
      <description>Abstract  Bearded sprangletop is a problematic native grass weed in California’s rice fields. The widespread and extensive use of acetyl-CoA carboxylase (ACCase)–inhibiting herbicides, such as cyhalofop- p -butyl (cyhalofop), has led to speculation that biotypes of bearded sprangletop have developed herbicide resistance to ACCase. The aim of this study was to evaluate suspected resistant bearded sprangletop biotypes, R1, R2, R3, and the susceptible biotype, S1, in terms of their levels of resistance to three ACCase-inhibiting herbicides and to characterize the molecular mechanisms of resistance. Dose–response experiments suggested that the biotype R1, R2, and R3 had high-level resistance to cyhalofop and to quizalofop- p -ethyl (quizalofop), but not clethodim. The study determined that the resistance to ACCase inhibitors was a target-site mechanism resulting from nucleotide substitution. The carboxyl transferase (CT) domain of the ACCase gene’s sequence analysis revealed the substitutions...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/99f3k2hk</guid>
      <pubDate>Wed, 22 Apr 2026 00:00:00 +0000</pubDate>
      <author>
        <name>Unan, Rasim</name>
      </author>
      <author>
        <name>Becerra-Alvarez, Aaron</name>
      </author>
      <author>
        <name>Al-Khatib, Kassim</name>
        <uri>https://orcid.org/0000-0002-9214-6714</uri>
      </author>
    </item>
    <item>
      <title>DNA methylation is conserved between vegetative propagules in almond (&lt;i&gt;Prunus dulcis&lt;/i&gt; Mill DA Webb)</title>
      <link>https://escholarship.org/uc/item/8t91t08g</link>
      <description>DNA methylation is conserved between vegetative propagules in almond (&lt;i&gt;Prunus dulcis&lt;/i&gt; Mill DA Webb)</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/8t91t08g</guid>
      <pubDate>Wed, 22 Apr 2026 00:00:00 +0000</pubDate>
      <author>
        <name>Hazzard, William</name>
      </author>
      <author>
        <name>Fresnedo-Ramirez, Jonathan</name>
      </author>
      <author>
        <name>Anderson, Elizabeth</name>
      </author>
      <author>
        <name>Brown, Patrick J</name>
      </author>
      <author>
        <name>Gradziel, Thomas</name>
      </author>
    </item>
    <item>
      <title>Multi-environment evaluation and genomic prediction of agronomic traits in the southern US rice genepool.</title>
      <link>https://escholarship.org/uc/item/0p5295j0</link>
      <description>The southern United States is responsible for 80% of the countrys production of rice, approximately half of which is exported. Understanding genotypic and environmental factors impacting the historical performance of rice (Oryza sativa L.) is important for directing research efforts to optimize production of this globally important crop. A set of 429 rice genotypes including globally diverse historical parents and advanced japonica breeding lines from southern US breeding programs was phenotyped in 2008 for eight agronomic traits in Arkansas, Louisiana, and Mississippi. They were also genotyped using a single-nucleotide polymorphism set optimized for genomic prediction/selection. Genotypic and phenotypic data were analyzed via clustering techniques and principal component analysis. Single-trait and multi-trait genomic prediction were used to predict genetic values on a per-plant basis. We found that contemporary germplasm from the southern state breeding programs was highly interrelated...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/0p5295j0</guid>
      <pubDate>Wed, 8 Apr 2026 00:00:00 +0000</pubDate>
      <author>
        <name>LaPorte, Mary-Francis</name>
      </author>
      <author>
        <name>Hu, Haixiao</name>
      </author>
      <author>
        <name>Solomon, Walter</name>
      </author>
      <author>
        <name>Oard, James</name>
      </author>
      <author>
        <name>Knapp, Steven</name>
      </author>
      <author>
        <name>Runcie, Daniel</name>
      </author>
      <author>
        <name>Edwards, Jeremy</name>
      </author>
      <author>
        <name>McClung, Anna</name>
      </author>
      <author>
        <name>Diepenbrock, Christine</name>
      </author>
    </item>
    <item>
      <title>Effect of physiological priming on stored coffee seeds</title>
      <link>https://escholarship.org/uc/item/9cw6j7md</link>
      <description>Abstract: The physiological priming has been used to standardize and increase the speed of development of seed lots. The use of this technique is essential in coffee cultivation, as the crop has low longevity associated with slow and uneven germination. The objective was to evaluate the effect of physiological priming on the physiological quality of coffee seeds stored with different water contents. Seeds of two cultivars of Coffea arabica were used: cv. Catuaí Vermelho IAC144 and Topázio MG1190. A portion of the seeds were dried in the shade until reaching 12% moisture, and the other did not undergo drying. The seeds were stored in a cold chamber at 10 °C for nine months. Every three months, the physiological priming technique was performed with subsequent evaluation of the physiological quality by germination tests, root protrusion, normal seedlings at fifteen days, strong normal seedlings, seedlings with expanded cotyledonary leaves and seedling dry weight. Seeds that did not...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/9cw6j7md</guid>
      <pubDate>Wed, 25 Mar 2026 00:00:00 +0000</pubDate>
      <author>
        <name>Penido, Amanda Carvalho</name>
      </author>
      <author>
        <name>de Rezende, Édila Maria</name>
      </author>
      <author>
        <name>de Sousa Pereira, Diego</name>
      </author>
      <author>
        <name>Reis, Venícius Urbano Vilela</name>
      </author>
      <author>
        <name>Rocha, Debora Kelli</name>
      </author>
      <author>
        <name>Oliveira, João Almir</name>
      </author>
    </item>
    <item>
      <title>Trait‐based approaches to restoration ecology: Synthesizing insights from diverse systems</title>
      <link>https://escholarship.org/uc/item/94c6d3gt</link>
      <description>Under accelerating global change, trait-based approaches are emerging as essential tools in the ecological restoration toolbox. Where restoration has traditionally focused on the recovery of focal species in isolated systems, trait-based methods can provide a common language that extends beyond species- or system-specific contexts, allowing scientists and practitioners to translate insights across organisms and ecosystems and predict functional variation critical to resilience in the face of rapidly changing environmental conditions. Trait-based insights can thus help achieve restoration that is both adaptable and scalable as future climate scenarios unfold. To date, trait-based approaches to restoration have developed and proceeded independently across habitats and ecosystems, limiting information sharing and innovation. Here, we synthesize diverse perspectives and research on trait-informed restoration across ecosystems, distilling our findings into three key insights. First,...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/94c6d3gt</guid>
      <pubDate>Wed, 25 Mar 2026 00:00:00 +0000</pubDate>
      <author>
        <name>Briand, Julia K</name>
      </author>
      <author>
        <name>Hosler, Sheryl C</name>
      </author>
      <author>
        <name>Merchant, Thomas K</name>
      </author>
      <author>
        <name>Vinebrooke, Rolf D</name>
      </author>
      <author>
        <name>Ostertag, Rebecca</name>
      </author>
      <author>
        <name>Symons, Celia C</name>
        <uri>https://orcid.org/0000-0003-4120-0327</uri>
      </author>
      <author>
        <name>Cadotte, Marc W</name>
      </author>
      <author>
        <name>Eviner, Valerie T</name>
        <uri>https://orcid.org/0000-0001-5530-9417</uri>
      </author>
      <author>
        <name>Bracken, Matthew ES</name>
        <uri>https://orcid.org/0000-0002-0068-7485</uri>
      </author>
      <author>
        <name>Carlson, Rachel R</name>
      </author>
      <author>
        <name>Henn, Jonathan J</name>
      </author>
      <author>
        <name>Garbowski, Magda</name>
      </author>
      <author>
        <name>Bauer, Jonathan T</name>
      </author>
      <author>
        <name>Luong, Justin C</name>
        <uri>https://orcid.org/0000-0003-2118-4788</uri>
      </author>
      <author>
        <name>Atkinson, Joe</name>
      </author>
      <author>
        <name>Hughes, A Randall</name>
      </author>
      <author>
        <name>Adams, Carrie Reinhardt</name>
      </author>
      <author>
        <name>Bates, Amanda E</name>
      </author>
      <author>
        <name>Funk, Jennifer L</name>
        <uri>https://orcid.org/0000-0002-1916-5513</uri>
      </author>
      <author>
        <name>Love, Allegra E</name>
      </author>
      <author>
        <name>Zheng, Liting</name>
      </author>
      <author>
        <name>Galloway, Emily</name>
      </author>
      <author>
        <name>Green, Stephanie J</name>
      </author>
    </item>
    <item>
      <title>Vigor of maize seeds and its effects on plant stand establishment, crop development and grain yield</title>
      <link>https://escholarship.org/uc/item/42b9g3z3</link>
      <description>Vigor of maize seeds and its effects on plant stand establishment, crop development and grain yield</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/42b9g3z3</guid>
      <pubDate>Wed, 25 Mar 2026 00:00:00 +0000</pubDate>
      <author>
        <name>Vilela Reis, Venicius Urbano</name>
      </author>
      <author>
        <name>Penido, Amanda Carvalho</name>
      </author>
      <author>
        <name>Carvalho, Everson Reis</name>
      </author>
      <author>
        <name>Rocha, Debora Kelli</name>
      </author>
      <author>
        <name>Reis, Leandro Vilela</name>
      </author>
      <author>
        <name>Zanqueta Semolini, Pedro Henrique</name>
      </author>
    </item>
    <item>
      <title>Lignin content, morphoanatomical traits and antioxidant activity as determinants of soybean seed storage tolerance and quality</title>
      <link>https://escholarship.org/uc/item/0pj2c9pz</link>
      <description>The storage of soybean seeds is a critical aspect of the production process, making it essential for genotypes to show tolerance during this phase to maintain seed quality. This study aimed to examine and correlate lignin content in the seed coat, enzyme activity expression, and morphoanatomical characteristics of soybean cultivars with the preservation of physiological quality and storage tolerance. Eight soybean cultivars were selected, produced, and harvested under uniform edaphoclimatic conditions. Physiological quality assessments were conducted at six storage intervals: 0, 60, 120, 180, 240, and 360 days. Evaluations included tests for germination, emergence, accelerated aging, electrical conductivity, and lignin content in the seed coat. Additionally, biochemical and enzymatic analyses of antioxidant metabolism and morphoanatomical examinations were performed using light microscopy on seeds stored for 0 and 360 days. The experiment used an 8 × 6 factorial arrangement, encompassing...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/0pj2c9pz</guid>
      <pubDate>Wed, 25 Mar 2026 00:00:00 +0000</pubDate>
      <author>
        <name>Nardelli, ACP</name>
      </author>
      <author>
        <name>Reis, VUV</name>
      </author>
      <author>
        <name>de Souza, GA</name>
      </author>
      <author>
        <name>Pires, RMDO</name>
      </author>
      <author>
        <name>Rocha, DK</name>
      </author>
      <author>
        <name>Carvalho, ER</name>
        <uri>https://orcid.org/0000-0003-4925-4100</uri>
      </author>
    </item>
    <item>
      <title>Comparative genomics of six Juglans species reveals disease‐associated gene family contractions</title>
      <link>https://escholarship.org/uc/item/9rc2m526</link>
      <description>Juglans (walnuts), the most speciose genus in the walnut family (Juglandaceae), represents most of the family's commercially valuable fruit and wood-producing trees. It includes several species used as rootstock for their resistance to various abiotic and biotic stressors. We present the full structural and functional genome annotations of six Juglans species and one outgroup within Juglandaceae (Juglans regia, J. cathayensis, J. hindsii, J. microcarpa, J. nigra, J. sigillata and Pterocarya stenoptera) produced using BRAKER2 semi-unsupervised gene prediction pipeline and additional tools. For each annotation, gene predictors were trained using 19 tissue-specific J. regia transcriptomes aligned to the genomes. Additional functional evidence and filters were applied to multi-exonic and mono-exonic putative genes to yield between 27&amp;nbsp;000 and 44&amp;nbsp;000 high-confidence gene models per species. Comparison of gene models to the BUSCO embryophyta dataset suggested that, on average,...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/9rc2m526</guid>
      <pubDate>Wed, 11 Mar 2026 00:00:00 +0000</pubDate>
      <author>
        <name>Trouern‐Trend, Alexander J</name>
      </author>
      <author>
        <name>Falk, Taylor</name>
      </author>
      <author>
        <name>Zaman, Sumaira</name>
      </author>
      <author>
        <name>Caballero, Madison</name>
      </author>
      <author>
        <name>Neale, David B</name>
      </author>
      <author>
        <name>Langley, Charles H</name>
        <uri>https://orcid.org/0000-0001-6160-5503</uri>
      </author>
      <author>
        <name>Dandekar, Abhaya M</name>
        <uri>https://orcid.org/0000-0001-7925-4086</uri>
      </author>
      <author>
        <name>Stevens, Kristian A</name>
      </author>
      <author>
        <name>Wegrzyn, Jill L</name>
      </author>
    </item>
    <item>
      <title>A Sugar Transporter Takes Up both Hexose and Sucrose for Sorbitol-Modulated In Vitro Pollen Tube Growth in Apple[OPEN]</title>
      <link>https://escholarship.org/uc/item/9pp50282</link>
      <description>Rapid pollen tube growth requires uptake of Suc or its hydrolytic products, hexoses, from the apoplast of surrounding tissues in the style. Due to species-specific sugar requirements, reliance of pollen germination and tube growth on cell wall invertase and Suc or hexose transporters varies between species, but it is not known if plants have a sugar transporter that mediates the uptake of both hexose and Suc for pollen tube growth. Here, we show that a sugar transporter protein in apple (&lt;i&gt;Malus domestica&lt;/i&gt;), MdSTP13a, takes up both hexose and Suc when expressed in yeast, and is essential for pollen tube growth on Glc and Suc but not on maltose. MdSTP13a-mediated direct uptake of Suc is primarily responsible for apple pollen tube growth on Suc medium. Sorbitol, a major photosynthate and transport carbohydrate in apple, modulates pollen tube growth via the MYB transcription factor MdMYB39L, which binds to the promoter of &lt;i&gt;MdSTP13a&lt;/i&gt; to activate its expression. Antisense...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/9pp50282</guid>
      <pubDate>Wed, 11 Mar 2026 00:00:00 +0000</pubDate>
      <author>
        <name>Li, Chunlong</name>
      </author>
      <author>
        <name>Meng, Dong</name>
      </author>
      <author>
        <name>Piñeros, Miguel A</name>
      </author>
      <author>
        <name>Mao, Yuxin</name>
      </author>
      <author>
        <name>Dandekar, Abhaya M</name>
        <uri>https://orcid.org/0000-0001-7925-4086</uri>
      </author>
      <author>
        <name>Cheng, Lailiang</name>
      </author>
    </item>
    <item>
      <title>Exploring multitasking proteins in Xanthomonas secretomes: Insights into mechanisms of plant-pathogen interactions</title>
      <link>https://escholarship.org/uc/item/8k66c7gz</link>
      <description>Recent advances in large-scale functional genomic analysis have significantly increased interest in multitask proteins. The role of these proteins in Xanthomonas phytopathogens, a model for plant-pathogen interaction studies, remains largely underexplored. In this study, we introduce an innovative systematic comparative analysis of secretomes from 18 different Xanthomonas species, integrating data from multiple proteomic studies to identify potential multitasking proteins. This approach led to the identification of 93 proteins primarily involved in central metabolism that are secreted under various physiological conditions, including 16 previously characterized moonlighting proteins. Promiscuity analysis of five selected enzymes revealed that three (asparaginase, chorismate mutase, and phosphoenolpyruvate synthase) exhibit high potential for catalyzing reactions with non-canonical substrates, suggesting additional functional roles beyond their primary enzymatic activities. Additionally,...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/8k66c7gz</guid>
      <pubDate>Wed, 11 Mar 2026 00:00:00 +0000</pubDate>
      <author>
        <name>de Almeida Barbosa Assis, Renata</name>
      </author>
      <author>
        <name>Ferreira, Rafael Marini</name>
      </author>
      <author>
        <name>de Oliveira, Amanda Carolina Paulino</name>
      </author>
      <author>
        <name>Carvalho, Flávia Maria Souza</name>
      </author>
      <author>
        <name>Ferro, Jesus Aparecido</name>
      </author>
      <author>
        <name>de Souza, Robson Francisco</name>
      </author>
      <author>
        <name>Orellano, Elena Graciela</name>
      </author>
      <author>
        <name>Almeida, Nalvo Franco</name>
      </author>
      <author>
        <name>Garcia, Camila Carrião Machado</name>
      </author>
      <author>
        <name>Dandekar, Abhaya M</name>
        <uri>https://orcid.org/0000-0001-7925-4086</uri>
      </author>
      <author>
        <name>Chakraborty, Sandeep</name>
      </author>
      <author>
        <name>Varani, Alessandro M</name>
      </author>
      <author>
        <name>Moreira, Leandro Marcio</name>
      </author>
    </item>
    <item>
      <title>SnRK1 kinase-mediated phosphorylation of transcription factor bZIP39 regulates sorbitol metabolism in apple</title>
      <link>https://escholarship.org/uc/item/8hv721tx</link>
      <description>Sorbitol is a major photosynthate produced in leaves and transported through the phloem of apple (Malus domestica) and other tree fruits in Rosaceae. Sorbitol stimulates its own metabolism, but the underlying molecular mechanism remains unknown. Here, we show that sucrose nonfermenting 1 (SNF1)-related protein kinase 1 (SnRK1) is involved in regulating the sorbitol-responsive expression of both SORBITOL DEHYDROGENASE 1 (SDH1) and ALDOSE-6-PHOSPHATE REDUCTASE (A6PR), encoding 2 key enzymes in sorbitol metabolism. SnRK1 expression is increased by feeding of exogenous sorbitol but decreased by sucrose. SnRK1 interacts with and phosphorylates the basic leucine zipper (bZIP) transcription factor bZIP39. bZIP39 binds to the promoters of both SDH1 and A6PR and activates their expression. Overexpression of SnRK1 in 'Royal Gala' apple increases its protein level and activity, upregulating transcript levels of both SDH1 and A6PR without altering the expression of bZIP39. Of all the sugars...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/8hv721tx</guid>
      <pubDate>Wed, 11 Mar 2026 00:00:00 +0000</pubDate>
      <author>
        <name>Meng, Dong</name>
      </author>
      <author>
        <name>Cao, Hongyan</name>
      </author>
      <author>
        <name>Yang, Qing</name>
      </author>
      <author>
        <name>Zhang, Mengxia</name>
      </author>
      <author>
        <name>Borejsza-Wysocka, Ewa</name>
      </author>
      <author>
        <name>Wang, Huicong</name>
      </author>
      <author>
        <name>Dandekar, Abhaya M</name>
        <uri>https://orcid.org/0000-0001-7925-4086</uri>
      </author>
      <author>
        <name>Fei, Zhangjun</name>
      </author>
      <author>
        <name>Cheng, Lailiang</name>
      </author>
    </item>
    <item>
      <title>Deploying Genome Editing Tools for Dissecting the Biology of Nut Trees</title>
      <link>https://escholarship.org/uc/item/8gw0b43w</link>
      <description>Walnuts are among the most important nut crops grown in temperate regions of the world. Commercial production in California, and increasingly worldwide, relies on only few clonally grafted scion genotypes, particularly “Chandler,” and more recently clonally propagated disease-resistant rootstocks. Diseases, nematodes, insect pests, abiotic stresses, and other nutritional and environmental factors, can reduce walnut productivity and quality, affecting grower profitability. The California Walnut Breeding Program at UC Davis has developed and released scion cultivars and rootstocks to help address some of these problems. Sequencing of the walnut genome is expected to speed walnut breeding by facilitating development of molecular markers that can be linked to phenotypic traits, and by reducing the time needed to screen new genotypes. Nonetheless, conventional breeding of tree crops is still a long-term proposition. Here we describe a toolkit that utilizes the CRISPR-Cas9 system to...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/8gw0b43w</guid>
      <pubDate>Wed, 11 Mar 2026 00:00:00 +0000</pubDate>
      <author>
        <name>Walawage, Sriema L</name>
      </author>
      <author>
        <name>Zaini, Paulo A</name>
        <uri>https://orcid.org/0000-0001-6495-7942</uri>
      </author>
      <author>
        <name>Mubarik, Muhammad S</name>
      </author>
      <author>
        <name>Martinelli, Federico</name>
      </author>
      <author>
        <name>Balan, Bipin</name>
      </author>
      <author>
        <name>Caruso, Tiziano</name>
      </author>
      <author>
        <name>Leslie, Charles A</name>
      </author>
      <author>
        <name>Dandekar, Abhaya M</name>
        <uri>https://orcid.org/0000-0001-7925-4086</uri>
      </author>
    </item>
    <item>
      <title>A Rapid In Vitro Phenotypic Assay of Walnut Shoots for Prescreening Resistance to Phytophthora pini</title>
      <link>https://escholarship.org/uc/item/8f30f81f</link>
      <description>Phytophthora species cause crown, root, and aerial canker diseases in diverse horticultural crops, resulting in a loss of yield, loss of quality, and plant death. Breeding programs are interested in developing genotypes resistant to these and other pathogens, but current screening methods for tree crops are time-consuming, potentially spanning many years. Here we present a rapid in&amp;nbsp;vitro assay in which walnut shoots obtained from tissue culture can be challenged with Phytophthora zoospores and monitored for symptom development within a week. As a proof of concept, two cultivars, scion variety ‘Chandler’ and clonal rootstock ‘RX1’, with known different degrees of crown rot susceptibility, were inoculated in&amp;nbsp;vitro with P. pini (formerly included in P. citricola complex), and results of the assay reproducibly matched the differences in disease susceptibility generally observed for these two walnut selections under greenhouse and orchard conditions. In addition, when the...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/8f30f81f</guid>
      <pubDate>Wed, 11 Mar 2026 00:00:00 +0000</pubDate>
      <author>
        <name>Zaini, Paulo A</name>
        <uri>https://orcid.org/0000-0001-6495-7942</uri>
      </author>
      <author>
        <name>Lee, Steven H</name>
      </author>
      <author>
        <name>Leslie, Charles A</name>
      </author>
      <author>
        <name>Walawage, Sriema L</name>
      </author>
      <author>
        <name>Jiang, Cai-Zhong</name>
        <uri>https://orcid.org/0000-0002-5972-7963</uri>
      </author>
      <author>
        <name>Browne, Gregory T</name>
      </author>
      <author>
        <name>Dandekar, Abhaya M</name>
        <uri>https://orcid.org/0000-0001-7925-4086</uri>
      </author>
      <author>
        <name>Kasuga, Takao</name>
      </author>
    </item>
    <item>
      <title>Development of a deep proteomic pipeline for recalcitrant olive leaf tissue</title>
      <link>https://escholarship.org/uc/item/77x9k4ps</link>
      <description>Proteomic analysis is a powerful tool to unravel the complexity of plant cellular processes that underpin the regulation of plant immunity. A major challenge is the improvement of the detectable fraction of the crop proteome that is still markedly lower compared to other omics, such as next generation sequencing technologies. This is due in part to the occurrence of large amounts of secondary compounds, which co-precipitate with proteins and severely interfere with the analysis. Olive leaf tissue is notoriously recalcitrant to common protein extraction methods due to high levels of interfering compounds, hence hampering deep proteomic investigations. Our study aims to overcome these hurdles and expand the application of deep proteomic analyses to olive leaves. We developed a complete proteomic pipeline, from sample preparation to LC-HRMS and data analyses, allowing the first comparative proteomic study among three Italian olive cultivars, 'Leccino', 'Ogliarola' and 'Coratina',...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/77x9k4ps</guid>
      <pubDate>Wed, 11 Mar 2026 00:00:00 +0000</pubDate>
      <author>
        <name>Abbattista, R</name>
      </author>
      <author>
        <name>Zaini, PA</name>
        <uri>https://orcid.org/0000-0001-6495-7942</uri>
      </author>
      <author>
        <name>Salemi, M</name>
      </author>
      <author>
        <name>Phinney, BS</name>
        <uri>https://orcid.org/0000-0003-3870-3302</uri>
      </author>
      <author>
        <name>Cataldi, TRI</name>
      </author>
      <author>
        <name>Losito, I</name>
      </author>
      <author>
        <name>Dandekar, AM</name>
        <uri>https://orcid.org/0000-0001-7925-4086</uri>
      </author>
    </item>
    <item>
      <title>A fine‐scale genetic linkage map reveals genomic regions associated with economic traits in walnut (Juglans regia)</title>
      <link>https://escholarship.org/uc/item/73q3w67f</link>
      <description>Abstract  A genetic linkage map of walnut containing 2,220 single nucleotide polymorphisms (SNPs) in 16 linkage groups (LGs) was constructed using an F 1 mapping population from a cross between “Chandler” and “Idaho,” two contrasting heterozygous parents. Five quantitative yield traits, lateral fruitfulness, harvest date and three nut traits (shell thickness, nut weight and kernel fill) were then mapped on to linkage groups. A significant quantitative trait locus (QTL) in LG 11 with negative additive effects suggested heterozygote superiority in the expression of lateral bearing. A set of three QTLs explaining ~10% of the variation in harvest date was located in LG 1. Shell thickness, nut weight and kernel fill were under the control of two to three linked pleiotropic QTLs in LG 1 segregating from “Idaho.” The marginal positive additive effects of QTLs for harvest date, shell thickness and nut weight and small negative additive effects for kernel fill suggested that the QTLs had...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/73q3w67f</guid>
      <pubDate>Wed, 11 Mar 2026 00:00:00 +0000</pubDate>
      <author>
        <name>Aradhya, Mallikarjuna K</name>
      </author>
      <author>
        <name>Velasco, Dianne</name>
      </author>
      <author>
        <name>Wang, Ji‐Rui</name>
      </author>
      <author>
        <name>Ramasamy, Ramesh</name>
      </author>
      <author>
        <name>You, Frank M</name>
      </author>
      <author>
        <name>Leslie, Chuck</name>
      </author>
      <author>
        <name>Dandekar, Abhaya</name>
        <uri>https://orcid.org/0000-0001-7925-4086</uri>
      </author>
      <author>
        <name>Luo, Ming‐Cheng</name>
        <uri>https://orcid.org/0000-0002-9744-5887</uri>
      </author>
      <author>
        <name>Dvorak, Jan</name>
      </author>
    </item>
    <item>
      <title>Reduced Sorbitol Genotype Alters Postharvest Microbiomes of ‘Greensleeves’ Apples</title>
      <link>https://escholarship.org/uc/item/73k5n90n</link>
      <description>Fruit microbiomes are capable of protecting their hosts from harmful pathogens and aiding in biocontrol; therefore, it is important to understand how differences in host genotype shape fruit microbial communities. The fruit species and even cultivars within a species can harbor different fruit microbiomes, but it has been difficult to establish how a single host gene can shape the microbiome structure. We investigated two genotypes of ‘Greensleeves’ apples with reduced sorbitol biosynthesis through antisense suppression of aldose 6-phosphate reductase with the wild type (WT) to assess how sugar composition of the fruit surface impacts microbial communities. We hypothesized that reduced sorbitol genotypes A4 and A10 would show an epiphytic microbiome different from that of the WT that corresponds to a difference in sugar composition on the fruit surface at harvest and during storage with and without postharvest treatment of fruit with 1-methycyclopropene (1-MCP), which is an inhibitor...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/73k5n90n</guid>
      <pubDate>Wed, 11 Mar 2026 00:00:00 +0000</pubDate>
      <author>
        <name>Lane, Connor</name>
      </author>
      <author>
        <name>Al Shoffe, Yosef</name>
      </author>
      <author>
        <name>Brown, Michael G</name>
      </author>
      <author>
        <name>Cheng, Lailiang</name>
      </author>
      <author>
        <name>Kao-Kniffin, Jenny T</name>
      </author>
      <author>
        <name>Peck, Gregory M</name>
      </author>
      <author>
        <name>Dandekar, Abhaya</name>
        <uri>https://orcid.org/0000-0001-7925-4086</uri>
      </author>
      <author>
        <name>Watkins, Christopher B</name>
      </author>
    </item>
    <item>
      <title>De Novo Arginine Synthesis Is Required for Full Virulence of Xanthomonas arboricola pv. juglandis During Walnut Bacterial Blight Disease.</title>
      <link>https://escholarship.org/uc/item/6373k4f5</link>
      <description>Walnut blight (WB) disease caused by &lt;i&gt;Xanthomonas arboricola&lt;/i&gt; pv. &lt;i&gt;juglandis&lt;/i&gt; (Xaj) threatens orchards worldwide. Nitrogen metabolism in this bacterial pathogen is dependent on arginine, a nitrogen-enriched amino acid that can either be synthesized or provided by the plant host. The arginine biosynthetic pathway uses argininosuccinate synthase (&lt;i&gt;argG&lt;/i&gt;), associated with increased bacterial virulence. We examined the effects of bacterial arginine and nitrogen metabolism on the plant response during WB by proteomic analysis of the mutant strain Xaj &lt;i&gt;argG&lt;sup&gt;-&lt;/sup&gt;&lt;/i&gt;. Phenotypically, the mutant strain produced 42% fewer symptoms and survived in the plant tissue with 2.5-fold reduced growth compared with wild type, while showing itself to be auxotrophic for arginine in&amp;nbsp;vitro. Proteomic analysis of infected tissue enabled the profiling of 676 Xaj proteins and 3,296 walnut proteins using isobaric labeling in a data-dependent acquisition approach. Comparative...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/6373k4f5</guid>
      <pubDate>Wed, 11 Mar 2026 00:00:00 +0000</pubDate>
      <author>
        <name>Sagawa, Cíntia HD</name>
      </author>
      <author>
        <name>Assis, Renata de AB</name>
        <uri>https://orcid.org/0000-0002-2075-9319</uri>
      </author>
      <author>
        <name>Zaini, Paulo A</name>
        <uri>https://orcid.org/0000-0001-6495-7942</uri>
      </author>
      <author>
        <name>Saxe, Houston</name>
      </author>
      <author>
        <name>Wilmarth, Phillip A</name>
      </author>
      <author>
        <name>Salemi, Michelle</name>
      </author>
      <author>
        <name>Phinney, Brett S</name>
        <uri>https://orcid.org/0000-0003-3870-3302</uri>
      </author>
      <author>
        <name>Dandekar, Abhaya M</name>
        <uri>https://orcid.org/0000-0001-7925-4086</uri>
      </author>
    </item>
    <item>
      <title>Primary metabolism changes in transgenic apple plants with reduced activity of sorbitol dehydrogenase</title>
      <link>https://escholarship.org/uc/item/5wr9h6fz</link>
      <description>Background - Sorbitol is the main translocated carbohydrate in species belonging to Rosaceae. It is thought to be a key molecule for the measurement of sink strength in apple. The quantity of sorbitol in plant tissues depends on the different factors such as species, development and physiological status, and type of tissues. Objective - An analysis of metabolic changes in primary metabolism was conducted in vegetative sinks of apple transgenic plants with altered sorbitol dehydrogenase (SDH) activity. The aim of this study was to determine the effects of the transgenic modulation of the SDH gene in carbohydrate partitioning and primary metabolism. Methods - Three antisenses and one sense transgenic line of cv. 'Greensleaves' were obtained for sorbi-tol dehydrogenase and grown in pots in a controlled environment. Results - The two antisense lines A041703/H and A111802/25 showed a reduced SDH activity similarly to antisense lines previously characterized. The three antisense lines...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/5wr9h6fz</guid>
      <pubDate>Wed, 11 Mar 2026 00:00:00 +0000</pubDate>
      <author>
        <name>Martinelli, F</name>
      </author>
      <author>
        <name>Uratsu, S</name>
      </author>
      <author>
        <name>Yousefi, S</name>
      </author>
      <author>
        <name>Teo, G</name>
      </author>
      <author>
        <name>Dandekar, AM</name>
        <uri>https://orcid.org/0000-0001-7925-4086</uri>
      </author>
    </item>
    <item>
      <title>The plant-based chimeric antimicrobial protein SlP14a-PPC20 protects tomato against bacterial wilt disease caused by Ralstonia solanacearum</title>
      <link>https://escholarship.org/uc/item/5qz87477</link>
      <description>Cecropin-B (CecB) is a peptide with well-established antimicrobial properties against different phytopathogenic bacteria. Despite modest action against Ralstonia solanacearum, its animal source limits the acceptance in transgenic applications. To overcome this, we selected eight alpha-helical (AH) cationic peptides derived from plant protein sequences and investigated their antimicrobial properties against R. solanacearum. Remarkably, PPC20 (a linear AH-peptide present in phosphoenolpyruvate carboxylase) has a three-fold lower lethal dose on R. solanacearum than CecB and lower toxicity to human intestinal epithelial cells. Linking PPC20 to SlP14a (part of a pathogenesis-related protein) established an apoplast-targeted protein providing a means of secreting and stabilizing the antimicrobial peptide in the plant compartment colonized by the pathogen. SlP14a is also a potential antimicrobial, homologous to a human elastase which likely targets outer membrane proteins in Gram-negative...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/5qz87477</guid>
      <pubDate>Wed, 11 Mar 2026 00:00:00 +0000</pubDate>
      <author>
        <name>Morais, Tâmara P</name>
      </author>
      <author>
        <name>Zaini, Paulo A</name>
        <uri>https://orcid.org/0000-0001-6495-7942</uri>
      </author>
      <author>
        <name>Chakraborty, Sandeep</name>
      </author>
      <author>
        <name>Gouran, Hossein</name>
      </author>
      <author>
        <name>Carvalho, Camila P</name>
      </author>
      <author>
        <name>Almeida-Souza, Hebréia O</name>
      </author>
      <author>
        <name>Souza, Jessica B</name>
      </author>
      <author>
        <name>Santos, Paula S</name>
      </author>
      <author>
        <name>Goulart, Luiz R</name>
      </author>
      <author>
        <name>Luz, José MQ</name>
      </author>
      <author>
        <name>Nascimento, Rafael</name>
      </author>
      <author>
        <name>Dandekar, Abhaya M</name>
        <uri>https://orcid.org/0000-0001-7925-4086</uri>
      </author>
    </item>
    <item>
      <title>Expression and Characterization of SARS-CoV-2 Spike Protein in Thermothelomyces heterothallica C1</title>
      <link>https://escholarship.org/uc/item/56g4x8nm</link>
      <description>Abstract  The COVID-19 pandemic demonstrated a pressing need for rapid, adaptive, and scalable manufacturing of vaccines and reagents. With the transition into an endemic disease and rising threats of other emerging pandemics, production of these biologicals requires a stable and sustainable supply chain and accessible distribution methods. In this study, we demonstrate the strength of an engineered filamentous fungal platform, Thermothelomyces heterothallica C1, for high volumetric productivity of the full-length spike glycoprotein. Spike protein produced in this system is highly thermostable and immunization of mice with spike made in C1 or mammalian platforms resulted in a similar humoral response. Additionally, it was shown that the native N-glycan profile can be redecorated with complex sialylated structures, if necessary, resulting in a more human-like glycan profile, without impacting binding characteristics as shown experimentally and in simulations. Through extensive...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/56g4x8nm</guid>
      <pubDate>Wed, 11 Mar 2026 00:00:00 +0000</pubDate>
      <author>
        <name>Ophir, Yakir</name>
      </author>
      <author>
        <name>Wong, Justin</name>
      </author>
      <author>
        <name>Haddad, Katherine R</name>
      </author>
      <author>
        <name>Huuskonen, Anne</name>
      </author>
      <author>
        <name>Karmaker, Anindya</name>
        <uri>https://orcid.org/0000-0002-9374-7327</uri>
      </author>
      <author>
        <name>Gore, Varun</name>
      </author>
      <author>
        <name>Jung, Seongwon</name>
      </author>
      <author>
        <name>Oloumi, Armin</name>
      </author>
      <author>
        <name>Liu, Yiyun</name>
      </author>
      <author>
        <name>Fu, Jingxin</name>
      </author>
      <author>
        <name>Zhang, Libo</name>
      </author>
      <author>
        <name>Huang, Peishan</name>
      </author>
      <author>
        <name>Minami, Shiaki Arnett</name>
      </author>
      <author>
        <name>Garimella, Shruthi Satya</name>
      </author>
      <author>
        <name>Thyagatur, Anugraha</name>
      </author>
      <author>
        <name>Zaini, Paulo A</name>
      </author>
      <author>
        <name>Vitikainen, Marika</name>
      </author>
      <author>
        <name>Tchelet, Ronen</name>
      </author>
      <author>
        <name>Valbuena, Noelia</name>
      </author>
      <author>
        <name>Fuerst, Thomas R</name>
      </author>
      <author>
        <name>Korkmaz, Emrullah</name>
      </author>
      <author>
        <name>Falo, Louis D</name>
      </author>
      <author>
        <name>Balmert, Stephen C</name>
      </author>
      <author>
        <name>Mahendiratta, Saniya</name>
      </author>
      <author>
        <name>Emalfarb, Mark</name>
      </author>
      <author>
        <name>Shah, Priya S</name>
        <uri>https://orcid.org/0000-0001-7518-2839</uri>
      </author>
      <author>
        <name>Siegel, Justin</name>
      </author>
      <author>
        <name>Dandekar, Abhaya M</name>
        <uri>https://orcid.org/0000-0001-7925-4086</uri>
      </author>
      <author>
        <name>Chen, Xi</name>
      </author>
      <author>
        <name>Lebrilla, Carlito</name>
      </author>
      <author>
        <name>Faller, Roland</name>
      </author>
      <author>
        <name>Saloheimo, Markku</name>
      </author>
      <author>
        <name>McDonald, Karen A</name>
      </author>
      <author>
        <name>Nandi, Somen</name>
      </author>
    </item>
    <item>
      <title>Functional analysis of walnut polyphenol oxidase gene (JrPPO1) in transgenic tobacco plants and PPO induction in response to walnut bacterial blight</title>
      <link>https://escholarship.org/uc/item/4v07h7n3</link>
      <description>Abstract  Walnut ( Juglans regia ) is economically important for both its wood and nut nutritional value, but it is susceptible to diseases such as walnut bacterial blight, caused by Xanthomonas arboricola pv. juglandis ( Xaj ). Walnuts contain many phenolic compounds, providing a good model on which to study polyphenol oxidase (PPO). We inoculated the detached walnut fruits of cultivars Ford, Chandler, Franquette, Robert Livermore, and Payne with Xaj and measured the induction of PPO activity in infected&amp;nbsp;sites and adjacent to infected sites. Compared to infected and uninfected sites,&amp;nbsp;PPO activity was induced significantly in areas adjacent to infected sites in all cultivars except Ford. Ford and Franquette, presenting the lowest and highest PPO activity, showed the largest and smallest mean diameter spots in response to Xaj , respectively. Polyacrylamide gel electrophoresis confirmed monophenol oxidase activity of walnut PPO in the assessed tissues. Then, we revealed...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/4v07h7n3</guid>
      <pubDate>Wed, 11 Mar 2026 00:00:00 +0000</pubDate>
      <author>
        <name>Khodadadi, Fatemeh</name>
      </author>
      <author>
        <name>Tohidfar, Masoud</name>
      </author>
      <author>
        <name>Vahdati, Kourosh</name>
      </author>
      <author>
        <name>Dandekar, Abhaya M</name>
        <uri>https://orcid.org/0000-0001-7925-4086</uri>
      </author>
      <author>
        <name>Leslie, Charles A</name>
      </author>
    </item>
    <item>
      <title>Nanopore RNA direct sequencing identifies that m6A modification is essential for sorbitol-controlled resistance to Alternaria alternata in apple</title>
      <link>https://escholarship.org/uc/item/48k25865</link>
      <description>Sorbitol, a main photosynthate and transport carbohydrate in all tree fruit species in Rosaceae, acts as a signal controlling resistance against Alternaria (A.) alternata in apple by altering the expression of the MdNLR16 resistance gene via the MdWRKY79 transcription factor. However, it is not known if N&lt;sup&gt;6&lt;/sup&gt;-methyladenosine (m&lt;sup&gt;6&lt;/sup&gt;A) methylation of the mRNAs of these genes participates in the process. Here, we found that decreased sorbitol synthesis in apple leaves leads to a transcriptome-wide reduction in the m&lt;sup&gt;6&lt;/sup&gt;A modification, with fewer transcripts containing two or more methylation sites. We identified two methyltransferases, MdVIR1 and MdVIR2, that respond to sorbitol and A. alternata inoculation and positively control resistance to A. alternata. MdVIR1 and MdVIR2 act on MdWRKY79 and MdNLR16 mRNAs, and the resulting m&lt;sup&gt;6&lt;/sup&gt;A modification stabilizes their mRNAs and improves translation efficiency. These data identify that m&lt;sup&gt;6&lt;/sup&gt;A modification...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/48k25865</guid>
      <pubDate>Wed, 11 Mar 2026 00:00:00 +0000</pubDate>
      <author>
        <name>Song, Zhihua</name>
      </author>
      <author>
        <name>Yang, Qing</name>
      </author>
      <author>
        <name>Dong, Biying</name>
      </author>
      <author>
        <name>Wang, Shengjie</name>
      </author>
      <author>
        <name>Xue, Jingyi</name>
      </author>
      <author>
        <name>Liu, Ni</name>
      </author>
      <author>
        <name>Zhou, Xiaomiao</name>
      </author>
      <author>
        <name>Li, Na</name>
      </author>
      <author>
        <name>Dandekar, Abhaya M</name>
        <uri>https://orcid.org/0000-0001-7925-4086</uri>
      </author>
      <author>
        <name>Cheng, Lailiang</name>
      </author>
      <author>
        <name>Meng, Dong</name>
      </author>
      <author>
        <name>Fu, Yujie</name>
      </author>
    </item>
    <item>
      <title>A comparative genomic analysis of Xanthomonas arboricola pv. juglandis strains reveal hallmarks of mobile genetic elements in the adaptation and accelerated evolution of virulence</title>
      <link>https://escholarship.org/uc/item/3qk2x2h2</link>
      <description>Xanthomonas arboricola pv. juglandis (Xaj) is the most significant aboveground walnut bacterial pathogen. Disease management uses copper-based pesticides which induce pathogen resistance. We examined the genetic repertoire associated with adaptation and virulence evolution in Xaj. Comparative genomics of 32 Xaj strains reveal the possible acquisition and propagation of virulence factors via insertion sequences (IS). Fine-scale annotation revealed a Tn3 transposon (TnXaj417) encoding copper resistance genes acquired by horizontal gene transfer and associated with adaptation and tolerance to metal-based pesticides commonly used to manage pathogens in orchard ecosystems. Phylogenomic analysis reveals IS involvement in acquisition and diversification of type III effector proteins ranging from two to eight in non-pathogenic strains, 16 to 20 in pathogenic strains, besides six other putative effectors with a reduced identity degree found mostly among pathogenic strains. Yersiniabactin,...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/3qk2x2h2</guid>
      <pubDate>Wed, 11 Mar 2026 00:00:00 +0000</pubDate>
      <author>
        <name>Assis, Renata AB</name>
      </author>
      <author>
        <name>Varani, Alessandro M</name>
      </author>
      <author>
        <name>Sagawa, Cintia HD</name>
      </author>
      <author>
        <name>Patané, José SL</name>
      </author>
      <author>
        <name>Setubal, João Carlos</name>
      </author>
      <author>
        <name>Uceda-Campos, Guillermo</name>
      </author>
      <author>
        <name>da Silva, Aline Maria</name>
      </author>
      <author>
        <name>Zaini, Paulo A</name>
        <uri>https://orcid.org/0000-0001-6495-7942</uri>
      </author>
      <author>
        <name>Almeida, Nalvo F</name>
      </author>
      <author>
        <name>Moreira, Leandro Marcio</name>
      </author>
      <author>
        <name>Dandekar, Abhaya M</name>
        <uri>https://orcid.org/0000-0001-7925-4086</uri>
      </author>
    </item>
    <item>
      <title>Deep learning neural network prediction method improves proteome profiling of vascular sap of grapevines during Pierce’s disease development</title>
      <link>https://escholarship.org/uc/item/3dj1f8ns</link>
      <description>Abstract  Plant secretome studies have shown the importance of plant defense proteins in the vascular system against pathogens. Studies on Pierce’s disease of grapevines caused by the xylem-limited bacteria Xylella fastidiosa ( Xf ) have detected proteins and pathways associated to its pathobiology. Despite the biological importance of the secreted proteins in the extracellular space to plant survival and development, proteome studies are scarce due to technical and technological challenges. Deep learning neural network prediction methods can provide powerful tools for improving proteome profiling by data-independent acquisition (DIA). We aimed to explore the potential of this strategy by combining it with in silico spectral library prediction tool, Prosit, to analyze the proteome of vascular leaf sap of grapevines with Pierce’s disease. The results demonstrate that the combination of DIA and Prosit increased the total number of identified proteins from 145 to 360 for grapevines...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/3dj1f8ns</guid>
      <pubDate>Wed, 11 Mar 2026 00:00:00 +0000</pubDate>
      <author>
        <name>Sagawa, Cíntia HD</name>
      </author>
      <author>
        <name>Zaini, Paulo A</name>
        <uri>https://orcid.org/0000-0001-6495-7942</uri>
      </author>
      <author>
        <name>de A. B. Assis, Renata</name>
      </author>
      <author>
        <name>Saxe, Houston</name>
      </author>
      <author>
        <name>Salemi, Michelle</name>
      </author>
      <author>
        <name>Jacobson, Aaron</name>
      </author>
      <author>
        <name>Phinney, Brett S</name>
        <uri>https://orcid.org/0000-0003-3870-3302</uri>
      </author>
      <author>
        <name>Dandekar, Abhaya M</name>
        <uri>https://orcid.org/0000-0001-7925-4086</uri>
      </author>
    </item>
    <item>
      <title>Generation and In-planta expression of a recombinant single chain antibody with broad neutralization activity on Bothrops pauloensis snake venom</title>
      <link>https://escholarship.org/uc/item/2bj8r949</link>
      <description>The main systemic alterations present in bothropic envenomation are hemostasis disorders, for which the conventional treatment is based on animal-produced antiophidic sera. We have developed a neutralizing antibody against Bothrops pauloensis (B. pauloensis) venom, which is member of the genus most predominant in snakebite accidents in Brazil. Subsequently, we expressed this antibody in plants to evaluate its enzymatic and biological activities. The ability of single-chain variable fragment (scFv) molecules to inhibit fibrinogenolytic, azocaseinolytic, coagulant and hemorrhagic actions of snake venom metalloproteinases (SVMPs) contained in B. pauloensis venom was verified through proteolytic assays. The antibody neutralized the toxic effects of envenomation, particularly those related to systemic processes, by interacting with one of the predominant classes of metalloproteinases. This novel molecule is a potential tool with great antivenom potential and provides a biotechnological...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/2bj8r949</guid>
      <pubDate>Wed, 11 Mar 2026 00:00:00 +0000</pubDate>
      <author>
        <name>Souza, Jessica B</name>
      </author>
      <author>
        <name>Cardoso, Rone</name>
      </author>
      <author>
        <name>Almeida-Souza, Hebréia O</name>
      </author>
      <author>
        <name>Carvalho, Camila P</name>
      </author>
      <author>
        <name>Correia, Lucas Ian Veloso</name>
      </author>
      <author>
        <name>Faria, Paula Cristina B</name>
      </author>
      <author>
        <name>Araujo, Galber R</name>
      </author>
      <author>
        <name>Mendes, Mirian M</name>
      </author>
      <author>
        <name>Rodrigues, Renata Santos</name>
      </author>
      <author>
        <name>Rodrigues, Veridiana M</name>
      </author>
      <author>
        <name>Dandekar, Abhaya M</name>
        <uri>https://orcid.org/0000-0001-7925-4086</uri>
      </author>
      <author>
        <name>Goulart, Luiz Ricardo</name>
      </author>
      <author>
        <name>Nascimento, Rafael</name>
      </author>
    </item>
    <item>
      <title>Advanced in Rootstock Breeding of Nut Trees: Objectives and Strategies</title>
      <link>https://escholarship.org/uc/item/293729fq</link>
      <description>The production and consumption of nuts are increasing in the world due to strong economic returns and the nutritional value of their products. With the increasing role and importance given to nuts (i.e., walnuts, hazelnut, pistachio, pecan, almond) in a balanced and healthy diet and in the prevention of various diseases, breeding of the nuts species has also been stepped up. Most recent fruit breeding programs have focused on scion genetic improvement. However, the use of locally adapted grafted rootstocks also enhanced the productivity and quality of tree fruit crops. Grafting is an ancient horticultural practice use in nut crops to manipulate scion phenotype and productivity and overcome biotic and abiotic stresses. There are complex rootstock breeding objectives and physiological and molecular aspects of rootstock–scion interactions in nut crops. In this review, we provide an overview of these, considering the mechanisms involved in nutrient and water uptake, regulation of...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/293729fq</guid>
      <pubDate>Wed, 11 Mar 2026 00:00:00 +0000</pubDate>
      <author>
        <name>Vahdati, Kourosh</name>
      </author>
      <author>
        <name>Sarikhani, Saadat</name>
      </author>
      <author>
        <name>Arab, Mohammad Mehdi</name>
      </author>
      <author>
        <name>Leslie, Charles A</name>
      </author>
      <author>
        <name>Dandekar, Abhaya M</name>
        <uri>https://orcid.org/0000-0001-7925-4086</uri>
      </author>
      <author>
        <name>Aletà, Neus</name>
      </author>
      <author>
        <name>Bielsa, Beatriz</name>
      </author>
      <author>
        <name>Gradziel, Thomas M</name>
      </author>
      <author>
        <name>Montesinos, Álvaro</name>
      </author>
      <author>
        <name>Rubio-Cabetas, María José</name>
      </author>
      <author>
        <name>Sideli, Gina M</name>
      </author>
      <author>
        <name>Serdar, Ümit</name>
      </author>
      <author>
        <name>Akyüz, Burak</name>
      </author>
      <author>
        <name>Beccaro, Gabriele Loris</name>
      </author>
      <author>
        <name>Donno, Dario</name>
      </author>
      <author>
        <name>Rovira, Mercè</name>
      </author>
      <author>
        <name>Ferguson, Louise</name>
      </author>
      <author>
        <name>Akbari, Mohammad</name>
      </author>
      <author>
        <name>Sheikhi, Abdollatif</name>
        <uri>https://orcid.org/0000-0002-2221-2536</uri>
      </author>
      <author>
        <name>Sestras, Adriana F</name>
      </author>
      <author>
        <name>Kafkas, Salih</name>
      </author>
      <author>
        <name>Paizila, Aibibula</name>
      </author>
      <author>
        <name>Roozban, Mahmoud Reza</name>
      </author>
      <author>
        <name>Kaur, Amandeep</name>
      </author>
      <author>
        <name>Panta, Srijana</name>
      </author>
      <author>
        <name>Zhang, Lu</name>
      </author>
      <author>
        <name>Sestras, Radu E</name>
      </author>
      <author>
        <name>Mehlenbacher, Shawn A</name>
      </author>
    </item>
    <item>
      <title>Advancements in Persian walnut tissue culture and genetic engineering: bridging traditional methods with modern biotechnology</title>
      <link>https://escholarship.org/uc/item/244541d8</link>
      <description>Main conclusionThis review summarizes major advances in Persian walnut biotechnology, emphasizing progress in propagation, somatic embryogenesis, genome editing, and computational tools while outlining key challenges for large-scale propagation and genetic improvement.AbstractIn vitro culture is fundamental for uniform and large-scale propagation of Persian walnut. Over the past decades, significant improvements have enhanced plant adaptability and survival during transfer to ex vitro environments. Commonly used explants, such as shoot buds, nodal segments, and shoot tips, show variable success depending on genetic, physiological, and environmental factors, as well as culture media composition. Somatic embryogenesis and plant regeneration form the basis for several biotechnological approaches, including haploid production for genomic mapping, mutation analysis, and hybrid development. Recent advances in genome editing, particularly CRISPR/Cas9, have accelerated the creation of...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/244541d8</guid>
      <pubDate>Wed, 11 Mar 2026 00:00:00 +0000</pubDate>
      <author>
        <name>Deligani, Zahra Makari</name>
      </author>
      <author>
        <name>Arab, Mohammad M</name>
      </author>
      <author>
        <name>Dejahang, Ata</name>
      </author>
      <author>
        <name>Eftekhari, Maliheh</name>
      </author>
      <author>
        <name>Younessi-Hamzekhanlu, Mehdi</name>
      </author>
      <author>
        <name>Leslie, Charles A</name>
      </author>
      <author>
        <name>Dandekar, Abhaya M</name>
        <uri>https://orcid.org/0000-0001-7925-4086</uri>
      </author>
      <author>
        <name>Vahdati, Kourosh</name>
      </author>
    </item>
    <item>
      <title>A Link Between Cell Wall Biogenesis, Pathogenesis, and Vigor in Walnut Root and Trunk Diseases</title>
      <link>https://escholarship.org/uc/item/0965m4hv</link>
      <description>Crown gall (Agrobacterium tumefaciens), crown/root rot (Phytophthora spp.), root lesion disease (Pratylenchus vulnus), and tree vigor are key traits affecting productivity and quality of walnuts in California. Non-inoculated hybrid rootstocks were analyzed by RNA-seq to examine pre-formed factors affecting these traits. Enrichment analysis of the differentially expressed genes revealed that increased expression of cell wall biogenesis-related genes plays a key role in susceptibility to A. tumefaciens, Phytophthora spp., increased vigor, but not P. vulnus. Analysis of the predicted subcellular loci of the encoded proteins revealed that many gene products associated with vigor and susceptibility were targeted to the plasma membrane and extracellular space, connecting these traits to sustaining barrier function. We observed that RNA processing and splicing, along with predicted nuclear targeting, were associated with resistance to A. tumefaciens, Phytophthora spp., low vigor, but...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/0965m4hv</guid>
      <pubDate>Wed, 11 Mar 2026 00:00:00 +0000</pubDate>
      <author>
        <name>Saxe, Houston J</name>
      </author>
      <author>
        <name>Walawage, Sriema L</name>
      </author>
      <author>
        <name>Balan, Bipin</name>
      </author>
      <author>
        <name>Leslie, Charles A</name>
      </author>
      <author>
        <name>Brown, Patrick J</name>
      </author>
      <author>
        <name>Browne, Gregory T</name>
      </author>
      <author>
        <name>Kluepfel, Daniel A</name>
      </author>
      <author>
        <name>Westphal, Andreas M</name>
      </author>
      <author>
        <name>Dandekar, Abhaya M</name>
        <uri>https://orcid.org/0000-0001-7925-4086</uri>
      </author>
    </item>
    <item>
      <title>Genome-wide association study of rice vegetative growth under ammonium or nitrate nutrition</title>
      <link>https://escholarship.org/uc/item/4rd3647n</link>
      <description>Rice is the most important source of daily calories in human diets and second only to wheat as the most important protein source. Rice is generally exposed to high ammonium (NH&lt;sub&gt;4&lt;/sub&gt;&lt;sup&gt;+&lt;/sup&gt;) levels in the rhizosphere but may employ both NH&lt;sub&gt;4&lt;/sub&gt;&lt;sup&gt;+&lt;/sup&gt; and nitrification-derived nitrate (NO&lt;sub&gt;3&lt;/sub&gt;&lt;sup&gt;-&lt;/sup&gt;) as major sources of nitrogen. However, the genetic basis underlying rice adaptation to different nitrogen forms remains poorly characterized. Here, we assessed biomass under either NH&lt;sub&gt;4&lt;/sub&gt;&lt;sup&gt;+&lt;/sup&gt; or NO&lt;sub&gt;3&lt;/sub&gt;&lt;sup&gt;-&lt;/sup&gt; as a sole nitrogen source in 390 accessions from the USDA Rice Diversity Panel 1. Rice effectively used either form of nitrogen to support early growth. Tolerance to a high-NH&lt;sub&gt;4&lt;/sub&gt;&lt;sup&gt;+&lt;/sup&gt; exposure was correlated with biomass under NO&lt;sub&gt;3&lt;/sub&gt;&lt;sup&gt;-&lt;/sup&gt; and lower NH&lt;sub&gt;4&lt;/sub&gt;&lt;sup&gt;+&lt;/sup&gt; levels. Both genotype and nitrogen source strongly influenced biomass accumulation and partitioning between...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/4rd3647n</guid>
      <pubDate>Tue, 10 Mar 2026 00:00:00 +0000</pubDate>
      <author>
        <name>Kasemsap, Pornpipat</name>
        <uri>https://orcid.org/0000-0002-9322-8682</uri>
      </author>
      <author>
        <name>Cohen, Itay</name>
      </author>
      <author>
        <name>Bloom, Arnold J</name>
        <uri>https://orcid.org/0000-0001-6006-1495</uri>
      </author>
    </item>
    <item>
      <title>MoGAAAP: a modular Snakemake workflow for automated genome assembly and annotation with quality assessment</title>
      <link>https://escholarship.org/uc/item/6dk6c7rk</link>
      <description>With the current speed of sequencing, there is a desire for standardized and automated genome assembly and annotation to produce high-quality genomes as input for comparative (pan)genomics. Therefore, we created a convenience pipeline using existing tools that creates annotated genome assemblies from HiFi (and optionally ultra-long ONT and/or Hi-C) reads for a set of related individuals as well as a related reference genome. Our pipeline is species-agnostic and generates an extensive quality assessment report that can be used for manual filtering and refinement of the assembly and annotation. It includes statistics for individual completeness and contamination assessments as well as a concise pangenome view. The pipeline is implemented in Snakemake and available with a GPLv3 licence at GitHub under github.com/dirkjanvw/MoGAAAP, at Zenodo under doi.org/10.5281/zenodo.14833021, and can be installed through Bioconda.</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/6dk6c7rk</guid>
      <pubDate>Thu, 12 Feb 2026 00:00:00 +0000</pubDate>
      <author>
        <name>van Workum, Dirk-Jan M</name>
      </author>
      <author>
        <name>Dey, Kuntal K</name>
      </author>
      <author>
        <name>Kozik, Alexander</name>
      </author>
      <author>
        <name>Lavelle, Dean O</name>
      </author>
      <author>
        <name>de Ridder, Dick</name>
      </author>
      <author>
        <name>Schranz, M Eric</name>
      </author>
      <author>
        <name>Michelmore, Richard W</name>
      </author>
      <author>
        <name>Smit, Sandra</name>
      </author>
    </item>
    <item>
      <title>Rapid Design and Production of Alpha-1 Antitrypsin Fusion Proteins in a Plant-Based Cell-Free Expression System</title>
      <link>https://escholarship.org/uc/item/8bn2m2mq</link>
      <description>Alpha-1 antitrypsin deficiency (AATD) is a rare disease, causing significant lung damage, that is currently treated with FDA approved replacement therapy comprised of weekly infusions of costly plasma-derived AAT. Fusing AAT with a crystallizable fragment (Fc) region could potentially extend the plasma half-life, reducing dose frequency. However, computational structural simulations predict steric hinderance of the Fc domain with the linker that effects the binding of AAT-Fc to neutrophil elastase and require functional experimental evaluation. Using the Nicotiana tabacum BY-2 cell derived "Almost Living Cell Free Expression" (ALiCE®) platform, we rapidly produced AAT and AAT-Fc variants and tested their anti-elastase functionality. AAT and AAT-Fc titers were 0.92 mg/mL and 0.57 mg/mL in the ALiCE® reaction lysate after 48-hour reactions respectively, AAT showing anti-elastase activity in a band-shift assay. In contrast, AAT-Fc variants lacked band-shift assay activity and had...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/8bn2m2mq</guid>
      <pubDate>Wed, 11 Feb 2026 00:00:00 +0000</pubDate>
      <author>
        <name>Karmaker, Anindya</name>
        <uri>https://orcid.org/0000-0002-9374-7327</uri>
      </author>
      <author>
        <name>Alyami, Faris</name>
      </author>
      <author>
        <name>Randolph, Connor A</name>
      </author>
      <author>
        <name>Ranade, Saee</name>
      </author>
      <author>
        <name>Liu, Yiyun</name>
      </author>
      <author>
        <name>Thyagatur, Anugraha</name>
      </author>
      <author>
        <name>Wong, Justin</name>
      </author>
      <author>
        <name>Zaini, Paulo A</name>
        <uri>https://orcid.org/0000-0001-6495-7942</uri>
      </author>
      <author>
        <name>Williams, Charles</name>
      </author>
      <author>
        <name>Dandekar, Abhaya M</name>
        <uri>https://orcid.org/0000-0001-7925-4086</uri>
      </author>
      <author>
        <name>Cross, Carroll E</name>
      </author>
      <author>
        <name>Faller, Roland</name>
      </author>
      <author>
        <name>Lebrilla, Carlito B</name>
      </author>
      <author>
        <name>McCormick, Alison A</name>
      </author>
      <author>
        <name>Nandi, Somen</name>
      </author>
      <author>
        <name>McDonald, Karen A</name>
        <uri>https://orcid.org/0000-0002-5145-9968</uri>
      </author>
    </item>
    <item>
      <title>The Walnut’s Dark Secret: Polyphenol Oxidase and the Enigmatic Pathway to Melanin</title>
      <link>https://escholarship.org/uc/item/7v45c85h</link>
      <description>The biosynthesis of melanin in plants remains an enduring biochemical enigma. Unlike the well-characterized pathways of animals and fungi that produce the canonical “true melanins”, the enzymatic origins and physiological functions of melanin-like pigments in plants are poorly described. Recent advances in Juglans regia (walnut) have begun to illuminate this “dark metabolism,” revealing a dual polyphenol oxidase (PPO) system, constitutive JrPPO1 and stress-inducible JrPPO2, that orchestrates the oxidation of phenolics into amorphous, heterogeneous polymeric pigments. Functional studies demonstrate that JrPPO1 maintains tyrosine and redox homeostasis, while silencing triggers a lesion-mimic phenotype, highlighting the enzyme’s role in detoxifying reactive intermediates. In contrast, JrPPO2 responds to redox and pathogen stress, driving pigment formation as part of the defense response. The integration of biological evidence, encompassing genomics, genetics, and phenotyping, reveals...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/7v45c85h</guid>
      <pubDate>Wed, 11 Feb 2026 00:00:00 +0000</pubDate>
      <author>
        <name>Dandekar, Abhaya M</name>
        <uri>https://orcid.org/0000-0001-7925-4086</uri>
      </author>
      <author>
        <name>Feinberg, Noah G</name>
        <uri>https://orcid.org/0000-0002-7710-6298</uri>
      </author>
      <author>
        <name>Zaini, Paulo A</name>
        <uri>https://orcid.org/0000-0001-6495-7942</uri>
      </author>
      <author>
        <name>Abbattista, Ramona</name>
      </author>
      <author>
        <name>de Almeida Barbosa Assis, Renata</name>
        <uri>https://orcid.org/0000-0002-2075-9319</uri>
      </author>
      <author>
        <name>Walawage, Sriema L</name>
      </author>
    </item>
    <item>
      <title>Trapping Failure Leads to Discovery of Potent Semiochemical Repellent for the Walnut Twig Beetle</title>
      <link>https://escholarship.org/uc/item/78k8q56b</link>
      <description>The walnut twig beetle, Pityophthorus juglandis Blackman, and its associated fungal pathogen that causes thousand cankers disease, currently threaten the viability of walnut trees across much of North America. During a 2011 assessment of seasonal flight patterns of P. juglandis with yellow sticky traps baited with the male-produced aggregation pheromone component, 3-methyl-2-buten-1-ol, dramatically reduced catches were recorded when Tree Tanglefoot adhesive was used to coat the traps. In summer 2011, two trap adhesives were tested for potential repellency against P. juglandis in a field trapping bioassay. SuperQ extracts of volatiles from the most repellent adhesive were analyzed by gas chromatography-mass spectrometry, and limonene and α-pinene were identified as predominant components. In field-based, trapping experiments both enantiomers of limonene at a release rate of ~700 mg/d conferred 91-99% reduction in trap catches of P. juglandis to pheromone-baited traps. (+)- and...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/78k8q56b</guid>
      <pubDate>Wed, 11 Feb 2026 00:00:00 +0000</pubDate>
      <author>
        <name>Audley, Jackson P</name>
      </author>
      <author>
        <name>Dallara, Paul L</name>
      </author>
      <author>
        <name>Nelson, Lori J</name>
      </author>
      <author>
        <name>Hamud, Shakeeb M</name>
      </author>
      <author>
        <name>Bostock, Richard M</name>
        <uri>https://orcid.org/0000-0001-9928-4610</uri>
      </author>
      <author>
        <name>Seybold, Steven J</name>
      </author>
    </item>
    <item>
      <title>Host selection behavior mediated by differential landing rates of the walnut twig beetle, Pityophthorus juglandis, and associated subcortical insect species, on two western North American walnut species, Juglans californica and J. major</title>
      <link>https://escholarship.org/uc/item/5v91q7s1</link>
      <description>Abstract  The walnut twig beetle, Pityophthorus juglandis Blackman (Coleoptera: Scolytidae), vectors a phytopathogenic fungus, Geosmithia morbida Kolařík et al. (Hypocreales), which causes thousand cankers disease (TCD) in walnut ( Juglans sp.) and wingnut ( Pterocarya sp., both Juglandaceae) trees. We investigated an early point in disease inception in two walnut species – Juglans californica S. Wats. and Juglans major (Torr. ex Sitsgr.) Heller – native to riparian forests of the western USA by comparing P.&amp;nbsp;juglandis flight and landing responses to small‐diameter branch sections. Twenty unbaited branch sections (10 each of J.&amp;nbsp;californica and J.&amp;nbsp;major ) were presented in a completely randomized design to populations of P.&amp;nbsp;juglandis at the USDA Agricultural Research Service, National Clonal Germplasm Repository (NCGR) Juglans collection located at Wolfskill Experimental Orchards (Winters, CA, USA) and at the California State University, Chico, Agricultural Teaching...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/5v91q7s1</guid>
      <pubDate>Wed, 11 Feb 2026 00:00:00 +0000</pubDate>
      <author>
        <name>Lona, Irene D</name>
      </author>
      <author>
        <name>Miller, Donald G</name>
      </author>
      <author>
        <name>Hatfield, Colleen A</name>
      </author>
      <author>
        <name>Rosecrance, Richard C</name>
      </author>
      <author>
        <name>Nelson, Lori J</name>
      </author>
      <author>
        <name>Audley, Jackson P</name>
      </author>
      <author>
        <name>Siefker, Megan A</name>
      </author>
      <author>
        <name>Chen, Yigen</name>
      </author>
      <author>
        <name>Seybold, Steven J</name>
      </author>
    </item>
    <item>
      <title>Walnut twig beetle landing rates differ between host and nonhost hardwood trees under the influence of aggregation pheromone in a northern California riparian forest</title>
      <link>https://escholarship.org/uc/item/4s04c6mv</link>
      <description>Abstract    Host selection behaviour of the walnut twig beetle (WTB) among hardwood trees was investigated in a riparian forest in northern California by monitoring the landing rate of the beetle with sticky traps on branches baited with 3‐methyl‐2‐buten‐1‐ol, the male‐produced aggregation pheromone.    The assay was conducted over 7 days (22 May to 29 May 2017) and compared landing rates on branches of six nonhost species paired with northern California black walnut, Juglans hindsii (the host).     A total of 2242/1192 WTB were collected on branches of host/nonhost pairs, and more WTB landed on J. hindsii than on nonhosts in 42 of 58 instances. Female landing rate generally exceeded male landing rate, which underscores the influence of the male‐produced synthetic pheromone in this system.     Landing rates of WTB males, females, and the combined sexes on boxelder, Acer negundo , and valley oak, Quercus lobata , did not differ significantly from the landing rates on J. hindsii...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/4s04c6mv</guid>
      <pubDate>Wed, 11 Feb 2026 00:00:00 +0000</pubDate>
      <author>
        <name>Homicz, Crystal S</name>
      </author>
      <author>
        <name>Audley, Jackson P</name>
      </author>
      <author>
        <name>Chen, Yigen</name>
      </author>
      <author>
        <name>Bostock, Richard M</name>
        <uri>https://orcid.org/0000-0001-9928-4610</uri>
      </author>
      <author>
        <name>Tauber, Catherine A</name>
      </author>
      <author>
        <name>Seybold, Steven J</name>
      </author>
    </item>
    <item>
      <title>Bark Colonization of Kiln-Dried Wood by the Walnut Twig Beetle: Effect of Wood Location and Pheromone Presence</title>
      <link>https://escholarship.org/uc/item/18z1r3p0</link>
      <description>The walnut twig beetle (Pityophthorus juglandis Blackman) (Coleoptera: Curculionidae) is a regulated pest in the United States due to its causal role in thousand cankers disease of walnut trees, including the commercially valuable eastern black walnut (Juglans nigra L.). Several state quarantines designed to limit spread of P. juglandis regulate movement of kiln-dried walnut lumber that contains bark. Previous research demonstrated that P. juglandis will enter and re-emerge from bark of kiln-dried, J. nigra slabs subjected to extreme beetle pressure (baited with a pheromone lure and hung in infested J. nigra trees). This study evaluated P. juglandis bark colonization of both kiln-dried and fresh J. nigra slabs, varying the presence of aggregation pheromone and relative proximity to a beetle source. Wood treatment, slab location, and pheromone presence all significantly affected P. juglandis colonization, as assessed by subsequent beetle emergence. When placed on the ground directly...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/18z1r3p0</guid>
      <pubDate>Wed, 11 Feb 2026 00:00:00 +0000</pubDate>
      <author>
        <name>Mayfield, Albert E</name>
      </author>
      <author>
        <name>Audley, Jackson</name>
      </author>
      <author>
        <name>Camp, Robert</name>
      </author>
      <author>
        <name>Mudder, Bryan T</name>
      </author>
      <author>
        <name>Taylor, Adam</name>
      </author>
    </item>
    <item>
      <title>Applied Chemical Ecology of Spruce Beetle in Western North America</title>
      <link>https://escholarship.org/uc/item/0hg9x9mf</link>
      <description>Spruce beetle (Dendroctonus rufipennis (Kirby)) is a major cause of spruce (Picea spp.) mortality in western North America. We synthesized the literature on the chemical ecology of spruce beetle, focusing on efforts to reduce host tree losses. This literature dates back to the mid-20th century and focuses on spruce beetle populations in Alaska, U.S., western Canada, and the central and southern Rocky Mountains, U.S. Spruce beetle aggregation pheromone components include frontalin (1,5-dimethyl-6,8-dioxabicyclo[3.2.1]octane), seudenol (3-methyl-2-cyclohexen-1-ol), MCOL (1-methyl-2-cyclohexen-1-ol), and verbenene (4-methylene-6,6-dimethylbicyclo[3.1.1]hept-2-ene). The attraction of spruce beetle to one aggregation pheromone component is enhanced by the co-release of other aggregation pheromones and host compounds (e.g., α-pinene). Several baits that attract spruce beetles are commercially available and are used for survey and detection, population suppression, snag creation, and...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/0hg9x9mf</guid>
      <pubDate>Wed, 11 Feb 2026 00:00:00 +0000</pubDate>
      <author>
        <name>Fettig, Christopher J</name>
      </author>
      <author>
        <name>Audley, Jackson P</name>
      </author>
      <author>
        <name>Munson, Allen Steven</name>
      </author>
    </item>
    <item>
      <title>Developing semiochemical repellents for protecting Picea from Dendroctonus rufipennis (Coleoptera: Curculionidae) in Alaska and Utah, USA</title>
      <link>https://escholarship.org/uc/item/0hg001g2</link>
      <description>Spruce beetle, Dendroctonus rufipennis (Kirby) (Coleoptera: Curculionidae), is the most destructive pest of mature spruce (Picea) in western North America. Recent outbreaks in Alaska and other western US states highlight the need for tools to protect Picea from D. rufipennis. The primary antiaggregation pheromone of D. rufipennis (3-methylcyclohex-2-en-1-one, MCH) and various combinations of potential repellents (1-octen-3-ol, exo-brevicomin, endo-brevicomin, ipsdienol, ipsenol, limonene, and verbenone) were tested for their ability to disrupt the response of D. rufipennis to attractant-baited multiple-funnel traps. Two assays were conducted on the Kenai Peninsula, Alaska, in June and July 2021. All treatments significantly reduced the mean number of D. rufipennis caught compared to the baited control. No other significant differences were observed among treatments. Informed by these and other data, tree protection studies were established in Lutz spruce, Picea × lutzii, on the...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/0hg001g2</guid>
      <pubDate>Wed, 11 Feb 2026 00:00:00 +0000</pubDate>
      <author>
        <name>Audley, Jackson P</name>
      </author>
      <author>
        <name>Fettig, Christopher J</name>
      </author>
      <author>
        <name>Moan, Jason E</name>
      </author>
      <author>
        <name>Moan, Jessie</name>
      </author>
      <author>
        <name>Swenson, Steve</name>
      </author>
      <author>
        <name>Munson, A Steven</name>
      </author>
      <author>
        <name>Mortenson, Leif A</name>
      </author>
      <author>
        <name>Blackford, Darren C</name>
      </author>
      <author>
        <name>Graham, Elizabeth E</name>
      </author>
      <author>
        <name>Mafra-Neto, Agenor</name>
      </author>
    </item>
    <item>
      <title>Dendroctonus rufipennis (Coleoptera: Curculionidae) responses to 4 doses of 3-methylcyclohex-2-en-1-one (MCH) in baited trapping assays</title>
      <link>https://escholarship.org/uc/item/0g25z9wc</link>
      <description>Spruce beetle, Dendroctonus rufipennis (Kirby) (Coleoptera: Curculionidae), is the most significant pest of spruce, Picea spp. (Pinales: Pinaceae), in western North America. Several doses of 3-methylcyclohex-2-en-1-one (MCH), the primary antiaggregation pheromone of D. rufipennis, alone and combined with non-host volatiles have been demonstrated effective for Picea protection. Herein, we evaluate the effects of MCH dose on D. rufipennis captures in baited trapping assays in Alaska and Colorado, United States. Twenty-five, 12-unit, multiple-funnel traps were baited with a D. rufipennis lure (frontalin + MCOL + spruce terpenes; Synergy Semiochemical Corp., Delta, British Columbia, Canada) and randomly assigned to one of 5 treatments in each assay: SBL (baited control); SBL + 1 g MCH; SBL + 3.5 g MCH; SBL + 7 g MCH; and SBL + 10 g MCH. SPLAT MCH (experimental formulation ISR: MCH-001R1, ISCA Inc., Riverside, California, United States), a flowable matrix containing 10.0% MCH by weight,...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/0g25z9wc</guid>
      <pubDate>Wed, 11 Feb 2026 00:00:00 +0000</pubDate>
      <author>
        <name>Audley, Jackson P</name>
      </author>
      <author>
        <name>Fettig, Christopher J</name>
      </author>
      <author>
        <name>Moan, Jason E</name>
      </author>
      <author>
        <name>Moan, Jessie</name>
      </author>
      <author>
        <name>Mortenson, Leif A</name>
      </author>
      <author>
        <name>Mafra-Neto, Agenor</name>
      </author>
    </item>
    <item>
      <title>Storage of halved strawberry fruits affects aroma, phytochemical content and gene expression, and is affected by pre-harvest factors</title>
      <link>https://escholarship.org/uc/item/3fr5v0d2</link>
      <description>Introduction: Strawberry fruit are highly valued for their aroma which develops during ripening. However, they have a short shelf-life. Low temperature storage is routinely used to extend shelf-life for transport and storage in the supply chain,&amp;nbsp;however cold storage can also affect fruit aroma. Some fruit continue to ripen during chilled storage; however, strawberries are a non-climacteric fruit and hence ripening postharvest is limited. Although most strawberry fruit is sold whole, halved fruit is also used in ready to eat fresh fruit salads which are of increasing consumer demand and pose additional challenges to fresh fruit&amp;nbsp;storage.
Methods: To better understand the effects of cold storage, volatilomic and transcriptomic analyses were applied to halved &lt;i&gt;Fragaria x ananassa&lt;/i&gt; cv. Elsanta fruit stored at 4 or 8°C for up to 12 days over two growing seasons.
Results and discussion: The volatile organic compound (VOC) profile differed between 4 or 8°C on most days...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/3fr5v0d2</guid>
      <pubDate>Wed, 28 Jan 2026 00:00:00 +0000</pubDate>
      <author>
        <name>Baldwin, Ashley</name>
      </author>
      <author>
        <name>Dhorajiwala, Rakhee</name>
      </author>
      <author>
        <name>Roberts, Callum</name>
      </author>
      <author>
        <name>Dimitrova, Simone</name>
      </author>
      <author>
        <name>Tu, Sarah</name>
      </author>
      <author>
        <name>Jones, Stephanie</name>
      </author>
      <author>
        <name>Ludlow, Richard A</name>
      </author>
      <author>
        <name>Cammarisano, Laura</name>
      </author>
      <author>
        <name>Davoli, Daniela</name>
      </author>
      <author>
        <name>Andrews, Robert</name>
      </author>
      <author>
        <name>Kent, Nicholas A</name>
      </author>
      <author>
        <name>Spadafora, Natasha D</name>
      </author>
      <author>
        <name>Müller, Carsten T</name>
      </author>
      <author>
        <name>Rogers, Hilary J</name>
      </author>
    </item>
    <item>
      <title>The Global Spectra-Trait Initiative: A database of paired leaf spectroscopy and functional traits associated with leaf photosynthetic capacity</title>
      <link>https://escholarship.org/uc/item/9kn473ng</link>
      <description>Abstract. Accurate assessment of leaf functional traits is crucial for a diverse range of applications from crop phenotyping to parameterizing global climate models. Leaf reflectance spectroscopy offers a promising avenue to advance ecological and agricultural research by complementing traditional, time-consuming gas exchange measurements. However, the development of robust hyperspectral models for predicting leaf photosynthetic capacity and associated traits from reflectance data has been hindered by limited data availability across species and environments. Here we introduce the Global Spectra-Trait Initiative (GSTI), a collaborative repository of paired leaf hyperspectral and gas exchange measurements from diverse ecosystems. The GSTI repository currently encompasses over 7500 observations from 397 species and 41 sites gathered from 36 published and unpublished studies, thereby offering a key resource for developing and validating hyperspectral models of leaf photosynthetic...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/9kn473ng</guid>
      <pubDate>Tue, 27 Jan 2026 00:00:00 +0000</pubDate>
      <author>
        <name>Lamour, Julien</name>
      </author>
      <author>
        <name>Serbin, Shawn P</name>
      </author>
      <author>
        <name>Rogers, Alistair</name>
        <uri>https://orcid.org/0000-0001-9262-7430</uri>
      </author>
      <author>
        <name>Acebron, Kelvin T</name>
      </author>
      <author>
        <name>Ainsworth, Elizabeth</name>
      </author>
      <author>
        <name>Albert, Loren P</name>
      </author>
      <author>
        <name>Alonzo, Michael</name>
      </author>
      <author>
        <name>Anderson, Jeremiah</name>
      </author>
      <author>
        <name>Atkin, Owen K</name>
      </author>
      <author>
        <name>Barbier, Nicolas</name>
      </author>
      <author>
        <name>Barnes, Mallory L</name>
      </author>
      <author>
        <name>Bernacchi, Carl J</name>
      </author>
      <author>
        <name>Besson, Ninon</name>
      </author>
      <author>
        <name>Burnett, Angela C</name>
      </author>
      <author>
        <name>Caplan, Joshua S</name>
      </author>
      <author>
        <name>Chave, Jérôme</name>
      </author>
      <author>
        <name>Cheesman, Alexander W</name>
      </author>
      <author>
        <name>Clocher, Ilona</name>
      </author>
      <author>
        <name>Coast, Onoriode</name>
      </author>
      <author>
        <name>Coste, Sabrina</name>
      </author>
      <author>
        <name>Croft, Holly</name>
      </author>
      <author>
        <name>Cui, Boya</name>
      </author>
      <author>
        <name>Dauvissat, Clément</name>
      </author>
      <author>
        <name>Davidson, Kenneth J</name>
      </author>
      <author>
        <name>Doughty, Christopher</name>
      </author>
      <author>
        <name>Ely, Kim S</name>
      </author>
      <author>
        <name>Evans, John R</name>
      </author>
      <author>
        <name>Féret, Jean-Baptiste</name>
      </author>
      <author>
        <name>Filella, Iolanda</name>
      </author>
      <author>
        <name>Fortunel, Claire</name>
      </author>
      <author>
        <name>Fu, Peng</name>
      </author>
      <author>
        <name>Furbank, Robert T</name>
      </author>
      <author>
        <name>Garcia, Maquelle</name>
      </author>
      <author>
        <name>Gimenez, Bruno O</name>
      </author>
      <author>
        <name>Guan, Kaiyu</name>
      </author>
      <author>
        <name>Guo, Zhengfei</name>
      </author>
      <author>
        <name>Heckmann, David</name>
      </author>
      <author>
        <name>Heuret, Patrick</name>
      </author>
      <author>
        <name>Isaac, Marney</name>
      </author>
      <author>
        <name>Kothari, Shan</name>
      </author>
      <author>
        <name>Kumagai, Etsushi</name>
      </author>
      <author>
        <name>Kyaw, Thu Ya</name>
      </author>
      <author>
        <name>Liu, Liangyun</name>
      </author>
      <author>
        <name>Liu, Lingli</name>
      </author>
      <author>
        <name>Liu, Shuwen</name>
      </author>
      <author>
        <name>Llusià, Joan</name>
      </author>
      <author>
        <name>Magney, Troy</name>
        <uri>https://orcid.org/0000-0002-9033-0024</uri>
      </author>
      <author>
        <name>Maréchaux, Isabelle</name>
      </author>
      <author>
        <name>Martin, Adam R</name>
      </author>
      <author>
        <name>Meacham-Hensold, Katherine</name>
      </author>
      <author>
        <name>Montes, Christopher M</name>
      </author>
      <author>
        <name>Ogaya, Romà</name>
      </author>
      <author>
        <name>Ojo, Joy</name>
      </author>
      <author>
        <name>Oliveira, Regison</name>
      </author>
      <author>
        <name>Paquette, Alain</name>
      </author>
      <author>
        <name>Peñuelas, Josep</name>
      </author>
      <author>
        <name>Placido, Antonia Debora</name>
      </author>
      <author>
        <name>Posada, Juan M</name>
      </author>
      <author>
        <name>Qian, Xiaojin</name>
      </author>
      <author>
        <name>Renninger, Heidi J</name>
      </author>
      <author>
        <name>Rodriguez-Caton, Milagros</name>
      </author>
      <author>
        <name>Rojas-González, Andrés</name>
      </author>
      <author>
        <name>Schlüter, Urte</name>
      </author>
      <author>
        <name>Sellan, Giacomo</name>
      </author>
      <author>
        <name>Siegert, Courtney M</name>
      </author>
      <author>
        <name>Silva-Perez, Viridiana</name>
      </author>
      <author>
        <name>Song, Guangqin</name>
      </author>
      <author>
        <name>Southwick, Charles D</name>
      </author>
      <author>
        <name>Souza, Daisy C</name>
      </author>
      <author>
        <name>Stahl, Clément</name>
      </author>
      <author>
        <name>Su, Yanjun</name>
      </author>
      <author>
        <name>Sujeeun, Leeladarshini</name>
      </author>
      <author>
        <name>Ting, To-Chia</name>
      </author>
      <author>
        <name>Vasquez, Vicente</name>
      </author>
      <author>
        <name>Vijayakumar, Amrutha</name>
      </author>
      <author>
        <name>Vilas-Boas, Marcelo</name>
      </author>
      <author>
        <name>Wang, Diane R</name>
      </author>
      <author>
        <name>Wang, Sheng</name>
      </author>
      <author>
        <name>Wang, Han</name>
      </author>
      <author>
        <name>Wang, Jing</name>
      </author>
      <author>
        <name>Wang, Xin</name>
      </author>
      <author>
        <name>Weber, Andreas PM</name>
      </author>
      <author>
        <name>Wong, Christopher YS</name>
      </author>
      <author>
        <name>Wu, Jin</name>
      </author>
      <author>
        <name>Wu, Fengqi</name>
      </author>
      <author>
        <name>Wu, Shengbiao</name>
      </author>
      <author>
        <name>Yan, Zhengbing</name>
      </author>
      <author>
        <name>Yang, Dedi</name>
      </author>
      <author>
        <name>Zhao, Yingyi</name>
      </author>
    </item>
    <item>
      <title>Crop diversification improves water-use efficiency and regional water sustainability</title>
      <link>https://escholarship.org/uc/item/1fs9d7kw</link>
      <description>As global water scarcity intensifies, identifying agricultural practices that enhance sustainable water management is critical. Temporal crop diversification-rotating multiple species over time-has been proposed to improve soil health and water retention based on field-scale experiments. However, widespread adoption remains limited on farms, in part due to unverified benefits at larger scales. Here, we assess the influence of crop diversification on agricultural water-use efficiency (WUE, ratio of gross primary productivity to evapotranspiration) along a spectrum of monoculture to complex species rotations in California. Leveraging new high-resolution remote sensing datasets, we show that crop diversification is a key driver of agricultural WUE, and increasing the number of species planted in the previous 6 years from two to four increases WUE by ∼20% after accounting for differences between crops. Our results provide spatially explicit, large-scale quantification of crop diversification’s...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/1fs9d7kw</guid>
      <pubDate>Wed, 21 Jan 2026 00:00:00 +0000</pubDate>
      <author>
        <name>Ruehr, Sophie</name>
      </author>
      <author>
        <name>Bassiouni, Maoya</name>
        <uri>https://orcid.org/0000-0001-5795-9894</uri>
      </author>
      <author>
        <name>Kang, Yanghui</name>
      </author>
      <author>
        <name>Socolar, Yvonne</name>
      </author>
      <author>
        <name>Magney, Troy</name>
        <uri>https://orcid.org/0000-0002-9033-0024</uri>
      </author>
      <author>
        <name>Keenan, Trevor F</name>
        <uri>https://orcid.org/0000-0002-3347-0258</uri>
      </author>
    </item>
    <item>
      <title>Short-duration high blue light at night enhances phytochemicals and morphology without yield loss in three lettuce cultivars</title>
      <link>https://escholarship.org/uc/item/4c88q200</link>
      <description>Controlled environment agriculture (CEA) enables precise regulation of plant physiological processes through environmental control. Among these, the spectral composition of photosynthetically active radiation (PAR), particularly the proportion, dose, and duration of blue light exposure, has a strong effect in enhancing plant nutritional quality. This study investigated how end-of-production (EoP) light spectrum (PAR vs. PAR with high blue portion) and application mode (daily continuous for 18&amp;nbsp;h vs. 18&amp;nbsp;h plus 2-h nighttime exposure) affect the growth, morphology and nutritional quality of three red leaf lettuce cultivars (Lactuca sativa var. crispa 'Xandra', 'Alaine' and 'Haflex'). Plants grown in climate-controlled conditions for 29 days, were exposed to four light treatments (Ctrl, HB, Night, NightB) with a Daily Light Integral (DLI) of 24.3&amp;nbsp;mol&amp;nbsp;m&lt;sup&gt;-2&lt;/sup&gt; d&lt;sup&gt;-1&lt;/sup&gt; during the final seven days. Light spectrum and application mode significantly affected...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/4c88q200</guid>
      <pubDate>Wed, 14 Jan 2026 00:00:00 +0000</pubDate>
      <author>
        <name>Cammarisano, Laura</name>
      </author>
      <author>
        <name>Correa Galvis, Viviana</name>
      </author>
      <author>
        <name>Charalambous, Filippos</name>
      </author>
      <author>
        <name>Heyneke, Elmien</name>
      </author>
      <author>
        <name>Villar Alegria, Emilio</name>
      </author>
      <author>
        <name>Sugiarto Teng, Ricky</name>
      </author>
      <author>
        <name>Körner, Oliver</name>
      </author>
      <author>
        <name>Kalaitzoglou, Pavlos</name>
      </author>
    </item>
    <item>
      <title>Drone methods and educational resources for plant science and agriculture</title>
      <link>https://escholarship.org/uc/item/4tf5m57w</link>
      <description>Technological advances have made drones (UAVs) increasingly important tools for the collection of trait data in plant science. Many costs for the analysis of plant populations have dropped precipitously in recent decades, particularly for genetic sequencing. Similarly, hardware advances have made it increasingly simple and practical to capture drone imagery of plant populations. However, converting this imagery into high-precision and high-throughput tabular data has become a major bottleneck in plant science. Here, we describe high-throughput phenotyping methods for the analysis of numerous plant traits based on imagery from diverse sensor types. Methods can be flexibly combined to extract data related to canopy temperature, area, height, volume, vegetation indices, and summary statistics derived from complex segmentations and classifications including using methods based on artificial intelligence (AI), computer vision, and machine learning. We then describe educational and...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/4tf5m57w</guid>
      <pubDate>Wed, 7 Jan 2026 00:00:00 +0000</pubDate>
      <author>
        <name>Parker, Travis A</name>
        <uri>https://orcid.org/0000-0002-1233-7829</uri>
      </author>
      <author>
        <name>Celebioglu, Burcu</name>
      </author>
      <author>
        <name>Watson, Mark</name>
      </author>
      <author>
        <name>Gepts, Paul</name>
        <uri>https://orcid.org/0000-0002-1056-4665</uri>
      </author>
    </item>
    <item>
      <title>Unveiling distinct storage composition and starch properties in developing indica rice grains via transcriptional profiling and enzymatic activity analysis</title>
      <link>https://escholarship.org/uc/item/9cd2g1fs</link>
      <description>The starch and protein in rice grains determine their nutritional value, eating and cooking quality (ECQ), and potential applications as a biopolymer. Building on previously identified functional differences between two Thai indica cultivars, waxy RD6 and high-amylose RD57, we examined the transcriptional regulation of their storage polymers by profiling key starch-biosynthetic and storage-protein genes in developing endosperms at 7-, 14-, 21-, and 28-days post-anthesis (DPA). Major differentially expressed genes were cross-validated with enzymatic activities and grain starch and storage-protein composition. Transcriptome dynamics varied significantly between cultivars, and were predominant at 14 DPA, which coincided with the period of active expression of the starch biosynthetic genes, while for storage protein gene expression, it was strongest at 7 DPA. At 21 and 28 DPA, most starch and glutelin biosynthesis genes in RD6 showed stronger expression than those in RD57. However,...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/9cd2g1fs</guid>
      <pubDate>Mon, 5 Jan 2026 00:00:00 +0000</pubDate>
      <author>
        <name>Sangwongchai, Wichian</name>
      </author>
      <author>
        <name>Wanichthanarak, Kwanjeera</name>
      </author>
      <author>
        <name>In-on, Ammarin</name>
      </author>
      <author>
        <name>Natee, Supidcha</name>
      </author>
      <author>
        <name>Champasri, Chamaiporn</name>
      </author>
      <author>
        <name>Sa-ingthong, Nutcha</name>
      </author>
      <author>
        <name>Beckles, Diane M</name>
        <uri>https://orcid.org/0000-0001-6336-1186</uri>
      </author>
      <author>
        <name>Khoomrung, Sakda</name>
      </author>
      <author>
        <name>Thitisaksakul, Maysaya</name>
      </author>
    </item>
    <item>
      <title>Comparison of simulated gastrointestinal digestion platforms with varying complexity and sample mass requirements, using common bean (Phaseolus vulgaris L.) as a model</title>
      <link>https://escholarship.org/uc/item/43r6j535</link>
      <description>BACKGROUND: Measuring bioaccessible nutrient levels during digestion in a physiologically relevant (dynamic) manner is a bottleneck in plant breeding and food product development. The first aim of this study was to develop and compare four simulated gastric digestion models paired with a static small-intestinal phase for use with small sample masses. The four gastric models tested included three dynamic models, which emulate peristaltic contractions with or without additional emulation of enzymatic secretion and flow of food, and one static model. The second aim was to examine bioaccessible nutrient levels in common bean (Phaseolus vulgaris L.) samples representing four genotype by growing environment combinations with differing seed coat coloration, patterning, and phenolic profiles.
RESULTS: While the highest bioaccessible nutrient levels (starch and protein hydrolysis, total phenolics, and antioxidant power) were observed from more complex dynamic digestion models, even simple...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/43r6j535</guid>
      <pubDate>Mon, 5 Jan 2026 00:00:00 +0000</pubDate>
      <author>
        <name>Bolt, Tayah M</name>
      </author>
      <author>
        <name>Riggs, Margaret</name>
      </author>
      <author>
        <name>Sun, Weiyi</name>
      </author>
      <author>
        <name>Yu, Shu</name>
      </author>
      <author>
        <name>Lerno, Larry</name>
      </author>
      <author>
        <name>Tian, Li</name>
        <uri>https://orcid.org/0000-0001-6461-6072</uri>
      </author>
      <author>
        <name>Gepts, Paul</name>
        <uri>https://orcid.org/0000-0002-1056-4665</uri>
      </author>
      <author>
        <name>Palkovic, Antonia</name>
      </author>
      <author>
        <name>Parker, Travis A</name>
        <uri>https://orcid.org/0000-0002-1233-7829</uri>
      </author>
      <author>
        <name>Bornhorst, Gail M</name>
      </author>
      <author>
        <name>Diepenbrock, Christine H</name>
        <uri>https://orcid.org/0000-0001-8411-0343</uri>
      </author>
    </item>
    <item>
      <title>Tomato</title>
      <link>https://escholarship.org/uc/item/2jv3j44g</link>
      <description>Tomato is both one of the most consumed horticultural crops and the model species for fleshy fruits. While impressive yields are now obtained, the tomato sector must face the numerous threats to these advances in productivity due to the consequences of climate change. Since the first draft genome sequence in 2012, our understanding of tomato genetics has advanced dramatically, greatly facilitating the identification of mechanisms involved in growth, development, resistance to stress, and organoleptic quality. This intensive investigation has broadened our understanding of the integration and coordination of these mechanisms by phytohormones and transcription factors, as well as the roles played by metabolism, particularly in establishing fruit quality, with the aim to better target breeding programmes and to develop innovative cultivation practices.</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/2jv3j44g</guid>
      <pubDate>Mon, 5 Jan 2026 00:00:00 +0000</pubDate>
      <author>
        <name>Gibon, Yves</name>
      </author>
      <author>
        <name>Beckles, Diane M</name>
        <uri>https://orcid.org/0000-0001-6336-1186</uri>
      </author>
      <author>
        <name>Osorio, Sonia</name>
      </author>
      <author>
        <name>Ezura, Hiroshi</name>
      </author>
    </item>
    <item>
      <title>Urban Farms as Social and Resiliency Spaces in San Juan, Puerto Rico Following Hurricane Maria</title>
      <link>https://escholarship.org/uc/item/8625t4sp</link>
      <description>Puerto Rico imports most of its food. In 2017, it was estimated the archipelago imported 90 to 95 percent of its food (Carro-Figueroa 2002; Robles and Ferré-Sadurní 2017). As a result, the few urban farms (huertos urbanos) provide some of the only locally produced fresh produce for Puerto Ricans. In 2017, Hurricane Maria struck the island of Puerto Rico and devastated agricultural production, including urban farms. In this article, urban farms are conceptualized as social infrastructure to analyze their significance in communities. This research, conducted in July 2019, investigates how women experienced the impacts of Hurricane Maria on their urban farms. Social infrastructure theory influenced the way we analyzed data and feminist standpoint theory informed the methodology used in our research. The findings demonstrate that many women enjoy urban farming and that it provides fresh and healthy produce for their families and communities. Almost all the women farmers experienced...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/8625t4sp</guid>
      <pubDate>Fri, 2 Jan 2026 00:00:00 +0000</pubDate>
      <author>
        <name>Zepeda, Ana</name>
      </author>
      <author>
        <name>Ortíz-Rivera, Maria C</name>
      </author>
      <author>
        <name>Cannon, Clare EB</name>
      </author>
      <author>
        <name>Crump, Amanda</name>
        <uri>https://orcid.org/0000-0002-9710-2956</uri>
      </author>
    </item>
    <item>
      <title>Piloting of the Concerns-based Adoption Model: Farmer Concerns About the Participatory Guarantee System in Cambodia</title>
      <link>https://escholarship.org/uc/item/2d54s3f4</link>
      <description>Piloting of the Concerns-based Adoption Model: Farmer Concerns About the Participatory Guarantee System in Cambodia</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/2d54s3f4</guid>
      <pubDate>Fri, 2 Jan 2026 00:00:00 +0000</pubDate>
      <author>
        <name>Mize, Meghan</name>
      </author>
      <author>
        <name>Trexler, Cary J</name>
      </author>
      <author>
        <name>Crump, Amanda</name>
        <uri>https://orcid.org/0000-0002-9710-2956</uri>
      </author>
      <author>
        <name>Young, Glenn M</name>
      </author>
      <author>
        <name>Buntong, Borarin</name>
      </author>
      <author>
        <name>LeGrand, Karen</name>
      </author>
    </item>
    <item>
      <title>Monitoring the stability of transgene expression in lettuce using the RUBY reporter</title>
      <link>https://escholarship.org/uc/item/8vm2v82s</link>
      <description>Key messageThe RUBY reporter enabled the evaluation of different transgene expression constructs in lettuce, revealing that the lettuce ubiquitin promoter and terminator had strong expression that was stable over multiple generations.AbstractNearly four decades after the first transgenic lettuce was reported, constructs for stable transgene expression remain limited. Notably, the 35S promoter from the Cauliflower Mosaic Virus (35S), which drives strong expression of transgenes in several plant species, has often shown silencing and instability in lettuce. Other promoter/terminator combinations that are commonly used in plant expression vectors have not been extensively studied in lettuce. In this study, we evaluated three different expression constructs in two different horticultural types of lettuce using the non-invasive RUBY reporter, which allowed for the monitoring of transgene expression throughout the process of regeneration during tissue culture, throughout development...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/8vm2v82s</guid>
      <pubDate>Fri, 12 Dec 2025 00:00:00 +0000</pubDate>
      <author>
        <name>Rowan, Beth A</name>
      </author>
      <author>
        <name>Reeves, Megan</name>
      </author>
      <author>
        <name>Hays, Claire</name>
      </author>
      <author>
        <name>Shirley, Cana</name>
      </author>
      <author>
        <name>Rajapakse, Wathsala</name>
      </author>
      <author>
        <name>Taran, Katrine A</name>
      </author>
      <author>
        <name>Bull, Tawni</name>
      </author>
      <author>
        <name>Wong, Dylan A</name>
      </author>
      <author>
        <name>Michelmore, Richard W</name>
      </author>
    </item>
    <item>
      <title>Bleeding green: California's schools are rapidly losing tree canopy cover</title>
      <link>https://escholarship.org/uc/item/7v05b0dg</link>
      <description>For many students in California, schoolyards are often the only accessible green space in their daily lives. Maintaining and expanding schoolyard canopies is critical infrastructure for children’s health and resilience. As such, they represent a strategic site for both climate adaptation and environmental justice. We assessed changes in tree canopy cover between 2018 and 2022 across 7262 public urban schools using data from the CALFIRE Urban Tree Canopy Map. Our findings reveal that, at the state level, the mean net canopy change was –1.8 %, with 85 % of schools experiencing canopy loss during this period. However, the canopy decline was particularly acute in some districts, exceeding 25 %. Central Valley emerged as the most dynamic region, exhibiting both pronounced losses and gains. These trends reflect the combined effects of redevelopment, environmental pressures, and uneven greening efforts. Overall, the decline in canopy cover is particularly troubling as climate change...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/7v05b0dg</guid>
      <pubDate>Wed, 3 Dec 2025 00:00:00 +0000</pubDate>
      <author>
        <name>Velasquez-Camacho, Luisa</name>
      </author>
      <author>
        <name>Willaredt, Moreen</name>
      </author>
      <author>
        <name>Singh, Pooja</name>
      </author>
      <author>
        <name>Ossola, Alessandro</name>
        <uri>https://orcid.org/0000-0002-0507-6026</uri>
      </author>
    </item>
    <item>
      <title>Canopy seed survival through extreme fire in non‐serotinous conifers: An unexpected source of forest resilience</title>
      <link>https://escholarship.org/uc/item/6gt0g45m</link>
      <description>Across much of the semiarid conifer forests of western North America (“dry conifer forests”), the dominant tree species are non‐serotinous, lack soil seedbanks, and rarely disperse seeds much farther than 100 m, so tree regeneration in large, high‐severity burned patches is expected to be highly seed‐limited. Conifer seedlings do, however, sometimes establish at high densities deep within high‐severity patches in these forests, implying that seeds can sometimes survive intense wildfire even when all overstory trees die. Does seed survival in the canopies of non‐serotinous trees provide an unexpected source of forest resilience? To answer this question, we surveyed tree survival, fire severity, and seedling abundance across two very large wildfires in the first year after fire. Several of the study species had a good seed cone production year at the time of the fires. We stratified many of our plots deep within high‐severity patches far from surviving trees, where existing models...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/6gt0g45m</guid>
      <pubDate>Fri, 28 Nov 2025 00:00:00 +0000</pubDate>
      <author>
        <name>Young, Derek JN</name>
      </author>
      <author>
        <name>Venuti, Nina E</name>
      </author>
      <author>
        <name>Greene, David F</name>
      </author>
      <author>
        <name>Latimer, Andrew M</name>
        <uri>https://orcid.org/0000-0001-8098-0448</uri>
      </author>
    </item>
    <item>
      <title>Convergence and constraint in glucosinolate evolution across the Brassicaceae</title>
      <link>https://escholarship.org/uc/item/9hm0k3vk</link>
      <description>Diversity in plant specialized metabolites plays critical roles in plant-environment interactions. In longer evolutionary scales, e.g. between families or orders, this diversity arises from whole-genome and tandem duplication events. Less is known about the evolutionary patterns that shape chemical diversity at shorter scales, e.g. within a family. Utilizing the aliphatic glucosinolate pathway, we explored how the genes encoding the terminal structural modification enzyme GSL-OH evolved across the Brassicaceae and the genomic processes that control presence-absence variation of its products (R)-2-hydroxy-but-3-enyl and (S)-2-hydroxy-but-3-enyl glucosinolate. We implemented a phylo-functional approach to functionally validate GSL-OH orthologs across the Brassicaceae and used that information to map the genomic origin and trajectory of the locus. This uncovered a complex mechanism involving at least 3 ancestral loci with extensive gene loss across all species, creating unequal retention...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/9hm0k3vk</guid>
      <pubDate>Sat, 22 Nov 2025 00:00:00 +0000</pubDate>
      <author>
        <name>Ramos, Amanda Agosto</name>
      </author>
      <author>
        <name>Bird, Kevin A</name>
      </author>
      <author>
        <name>Jain, Annanya</name>
      </author>
      <author>
        <name>Sumo, Gabriel Philip</name>
      </author>
      <author>
        <name>Okegbe, Odinaka</name>
      </author>
      <author>
        <name>Holland, Lucy</name>
      </author>
      <author>
        <name>Kliebenstein, Daniel J</name>
        <uri>https://orcid.org/0000-0001-5759-3175</uri>
      </author>
    </item>
    <item>
      <title>Global genomic population structure of wild and cultivated oat reveals signatures of chromosome rearrangements</title>
      <link>https://escholarship.org/uc/item/8zn8773j</link>
      <description>The genus Avena consists of approximately 30 wild and cultivated oat species. Cultivated oat is an important food crop, yet the broader genetic diversity within the Avena gene pool remains underexplored and underexploited. Here, we characterize over 9000 wild and cultivated hexaploid oat accessions of global origin using genotyping-by-sequencing and explore population structure using multidimensional scaling and population-based clustering methods. We also conduct analyses to reveal chromosome regions associated with local adaptation, sometimes resulting from large-scale chromosome rearrangements. We report four distinct genetic populations within the wild species A. sterilis, a distinct population of cultivated A. byzantina, and multiple populations within cultivated A. sativa. Some chromosome regions associated with local adaptation are also associated with confirmed structural rearrangements on chromosomes 1A, 1C, 3C, 4C, and 7D. This work provides evidence suggesting multiple...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/8zn8773j</guid>
      <pubDate>Thu, 20 Nov 2025 00:00:00 +0000</pubDate>
      <author>
        <name>Bekele, Wubishet A</name>
      </author>
      <author>
        <name>Avni, Raz</name>
      </author>
      <author>
        <name>Birkett, Clayton L</name>
      </author>
      <author>
        <name>Itaya, Asuka</name>
      </author>
      <author>
        <name>Wight, Charlene P</name>
      </author>
      <author>
        <name>Bellavance, Justin</name>
      </author>
      <author>
        <name>Brodführer, Sophie</name>
      </author>
      <author>
        <name>Canales, Francisco J</name>
      </author>
      <author>
        <name>Carlson, Craig H</name>
      </author>
      <author>
        <name>Fiebig, Anne</name>
      </author>
      <author>
        <name>Li, Yongle</name>
      </author>
      <author>
        <name>Michel, Steve</name>
      </author>
      <author>
        <name>Nandety, Raja Sekhar</name>
      </author>
      <author>
        <name>Waring, David J</name>
      </author>
      <author>
        <name>Arbelaez, Juan D</name>
      </author>
      <author>
        <name>Beattie, Aaron D</name>
      </author>
      <author>
        <name>Caffe, Melanie</name>
      </author>
      <author>
        <name>del Blanco, Isabel A</name>
        <uri>https://orcid.org/0000-0002-6305-6461</uri>
      </author>
      <author>
        <name>Fiedler, Jason D</name>
      </author>
      <author>
        <name>Gupta, Rajeev</name>
      </author>
      <author>
        <name>Gutierrez, Lucia</name>
      </author>
      <author>
        <name>Harris, John C</name>
      </author>
      <author>
        <name>Harrison, Stephen A</name>
      </author>
      <author>
        <name>Herrmann, Matthias H</name>
      </author>
      <author>
        <name>Huang, Yung-Fen</name>
      </author>
      <author>
        <name>Isidro y Sanchez, Julio</name>
      </author>
      <author>
        <name>McMullen, Michael S</name>
      </author>
      <author>
        <name>Mitchell Fetch, Jennifer W</name>
      </author>
      <author>
        <name>Nilsen, Kirby T</name>
      </author>
      <author>
        <name>Parkin, Isobel AP</name>
      </author>
      <author>
        <name>Peng, YuanYing</name>
      </author>
      <author>
        <name>Smith, Kevin P</name>
      </author>
      <author>
        <name>Sutton, Tim</name>
      </author>
      <author>
        <name>Yan, Weikai</name>
      </author>
      <author>
        <name>Zwer, Pamela</name>
      </author>
      <author>
        <name>Diederichsen, Axel</name>
      </author>
      <author>
        <name>Esvelt Klos, Kathy</name>
      </author>
      <author>
        <name>Fu, Yong-Bi</name>
      </author>
      <author>
        <name>Howarth, Catherine J</name>
      </author>
      <author>
        <name>Jannink, Jean-Luc</name>
      </author>
      <author>
        <name>Jellen, Eric N</name>
      </author>
      <author>
        <name>Langdon, Tim</name>
      </author>
      <author>
        <name>Maughan, Peter J</name>
      </author>
      <author>
        <name>Paczos-Grzeda, Edyta</name>
      </author>
      <author>
        <name>Prats, Elena</name>
      </author>
      <author>
        <name>Sen, Taner Z</name>
        <uri>https://orcid.org/0000-0002-5553-6190</uri>
      </author>
      <author>
        <name>Mascher, Martin</name>
      </author>
      <author>
        <name>Tinker, Nicholas A</name>
      </author>
    </item>
    <item>
      <title>Spectrally selective quantum dot laminated glass for photonic modulation and climate regulation in greenhouses</title>
      <link>https://escholarship.org/uc/item/7zm4t3tm</link>
      <description>The spectral and thermal environment in greenhouses is critical for optimizing crop performance, particularly during low-light winter periods. This study evaluated laminated glass integrated with CuInS2/ZnS quantum dots (QDs) that passively convert ultraviolet and blue photons into orange-red light (590–620 nm), enhancing the spectral quality of transmitted sunlight without requiring active energy input. Compared to a control glass, the QD-glazing increased relative red photon flux by 29% and increased the Red:Blue ratio by 57%, with negligible losses in total PAR (photosynthetically active radiation). Experimental trials conducted from January to February demonstrated that the QD-glazed greenhouse maintained a higher internal air temperature, averaging 0.68 °C warmer than the control. Root zone (nutrient solution) temperature also exhibited consistent thermal advantages, averaging 1–2 °C higher under the QD glazing, contributing to enhanced nutrient uptake. Vapor pressure deficit...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/7zm4t3tm</guid>
      <pubDate>Wed, 19 Nov 2025 00:00:00 +0000</pubDate>
      <author>
        <name>Thakur, Amrit Kumar</name>
      </author>
      <author>
        <name>Akter, Nazmin</name>
      </author>
      <author>
        <name>Ahamed, Shamim</name>
      </author>
      <author>
        <name>Hebert, Damon</name>
      </author>
      <author>
        <name>Ganley, Emily</name>
      </author>
      <author>
        <name>Gurchiek, JK</name>
      </author>
      <author>
        <name>Cammarisano, Laura</name>
      </author>
      <author>
        <name>Li, Zhian</name>
      </author>
      <author>
        <name>Ahsan, TM Abir</name>
      </author>
      <author>
        <name>Kabir, Sazzadul</name>
      </author>
    </item>
    <item>
      <title>Plants and microplastics: Growing impacts in the terrestrial environment</title>
      <link>https://escholarship.org/uc/item/3xx3q4n1</link>
      <description>Microplastic pollution is a largely unexplored yet pervasive environmental problem, in terrestrial environments, including impacts on plants and food crops. Plant growth and function are most often negatively impacted by plastic exposure, but these pollutants can also stimulate plant processes such as root growth and there is a tentative suggestion that monocotyledonous may be less sensitive to microplastics than dicotyledonous plants. Toxic effects include reduced plant biomass, chlorophyll content, photosynthesis, and changes to antioxidants, metabolites, and nutrients, with stimulatory effects often found at lower concentrations of exposure. There is strong evidence that roots can directly uptake and translocate plastic particles at 1 µm and under in size. Indirect effects include interactions of microplastics with other pollutants, soil properties, and soil organisms. These findings have potentially wide-ranging implications for terrestrial ecosystem function and human health....</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/3xx3q4n1</guid>
      <pubDate>Wed, 19 Nov 2025 00:00:00 +0000</pubDate>
      <author>
        <name>Wong, Amanda E</name>
        <uri>https://orcid.org/0000-0002-5145-5780</uri>
      </author>
      <author>
        <name>Taylor, Gail</name>
      </author>
    </item>
    <item>
      <title>A Consensus Statement for Ecological Medicine: Moving Toward Connection-Based Medicine</title>
      <link>https://escholarship.org/uc/item/3gd3s20g</link>
      <description>Mounting evidence across multiple disciplines supports the health benefits of connection to nature. Although this trend suggests that the human-nature relationship is integral to health, its importance is often overlooked in clinical practice due, in part, to lack of consensus on its scope, limits, and terminology. To fill a needed gap, we developed a consensus statement on an inter-connectivity based view of health termed Ecological Medicine. The study recruited an expert working group and used modified Delphi technique and focus groups. The Ecological Medicine Working Group was directed toward Ecological Medicine consensus goals that included: (1) a consensus definition and framework, (2) priorities for practice, research, education, and policy, and (3) Ecological Medicine’s implications. A consensus definition and framework for Ecological Medicine was reached, focusing on the importance of human inter-connections (to self, others, non-human species, and natural environment)...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/3gd3s20g</guid>
      <pubDate>Wed, 19 Nov 2025 00:00:00 +0000</pubDate>
      <author>
        <name>Makhinson, Michael</name>
        <uri>https://orcid.org/0000-0001-6493-9699</uri>
      </author>
      <author>
        <name>Pollack, Landon</name>
      </author>
      <author>
        <name>Hallowell, Ronan</name>
      </author>
      <author>
        <name>Murray, Conor H</name>
        <uri>https://orcid.org/0000-0001-9954-7601</uri>
      </author>
      <author>
        <name>Maddock, Jay E</name>
      </author>
      <author>
        <name>Stewart, Stephanie Michael</name>
      </author>
      <author>
        <name>Basu, Avik</name>
      </author>
      <author>
        <name>King, David</name>
      </author>
      <author>
        <name>Hansen, Helena</name>
      </author>
    </item>
    <item>
      <title>Erratum: Corrigendum: The Type II Secreted Lipase/Esterase LesA is a Key Virulence Factor Required for Xylella fastidiosa Pathogenesis in Grapevines</title>
      <link>https://escholarship.org/uc/item/9hk9551h</link>
      <description>Scientific Reports 6: Article number: 18598; published online: 12 January 2016; updated: 25 February 2016. The Acknowledgements section in this Article is incomplete. “The authors acknowledge research support obtained from the Citrus Research Board and the CDFA PD Board of California. RN is gratefulto Brazilian agency CAPES for scholarship’s support.</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/9hk9551h</guid>
      <pubDate>Wed, 22 Oct 2025 00:00:00 +0000</pubDate>
      <author>
        <name>Nascimento, Rafael</name>
      </author>
      <author>
        <name>Gouran, Hossein</name>
      </author>
      <author>
        <name>Chakraborty, Sandeep</name>
      </author>
      <author>
        <name>Gillespie, Hyrum W</name>
      </author>
      <author>
        <name>Almeida-Souza, Hebréia O</name>
      </author>
      <author>
        <name>Tu, Aye</name>
      </author>
      <author>
        <name>Rao, Basuthkar J</name>
      </author>
      <author>
        <name>Feldstein, Paul A</name>
      </author>
      <author>
        <name>Bruening, George</name>
      </author>
      <author>
        <name>Goulart, Luiz R</name>
      </author>
      <author>
        <name>Dandekar, Abhaya M</name>
        <uri>https://orcid.org/0000-0001-7925-4086</uri>
      </author>
    </item>
    <item>
      <title>Microbial biotherapeutic metabolite alleviates liver injury by restoring hepatic lipid metabolism through PPARα across the gut-liver axis</title>
      <link>https://escholarship.org/uc/item/80n8n8f7</link>
      <description>Infectious and non-infectious liver diseases are marked by disrupted liver metabolism and are frequently accompanied by gut epithelial barrier dysfunction and microbial dysbiosis, reflecting the compromised gut-liver axis. Despite the pivotal role of the gut-liver axis in health, transformative therapeutic interventions that simultaneously target both the liver and gut remain underexplored. Peroxisome proliferator-activated receptor alpha (PPARα) suppression drives both gut and liver metabolic diseases. In this study, we report on the therapeutic impact of microbial metabolite, 10-hydroxystearic acid (10-HSA), on restoring lipid metabolism and liver regeneration through PPARα activation, leading to a functional gut-liver axis in an &lt;i&gt;in vivo&lt;/i&gt; liver injury model. We previously identified 10-HSA, a known PPARα agonist, in &lt;i&gt;Lactiplantibacillus plantarum-&lt;/i&gt;treated intestine. Here, we report that oral administration of 10-HSA prevented AFB1-induced gut epithelial barrier disruption...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/80n8n8f7</guid>
      <pubDate>Wed, 22 Oct 2025 00:00:00 +0000</pubDate>
      <author>
        <name>Kramer, Dylan J</name>
      </author>
      <author>
        <name>Wang, Weicang</name>
      </author>
      <author>
        <name>Loque, Ikaika</name>
      </author>
      <author>
        <name>Walters-Laird, Chara J</name>
      </author>
      <author>
        <name>Morisseau, Christophe</name>
        <uri>https://orcid.org/0000-0002-5672-6631</uri>
      </author>
      <author>
        <name>Xiao, Xiaoyue</name>
      </author>
      <author>
        <name>Nearing, Marie</name>
      </author>
      <author>
        <name>Rocha, Clarissa Santos</name>
      </author>
      <author>
        <name>Dandekar, Abhaya</name>
        <uri>https://orcid.org/0000-0001-7925-4086</uri>
      </author>
      <author>
        <name>Hammock, Bruce</name>
        <uri>https://orcid.org/0000-0003-1408-8317</uri>
      </author>
      <author>
        <name>Dandekar, Satya</name>
        <uri>https://orcid.org/0000-0002-6346-8028</uri>
      </author>
    </item>
    <item>
      <title>Expression and characterization of SARS-CoV-2 spike protein in Thermothelomyces heterothallica C1</title>
      <link>https://escholarship.org/uc/item/07v1x8sh</link>
      <description>The COVID-19 pandemic demonstrated a pressing need for rapid, adaptive, and scalable manufacturing of vaccines and reagents. With the transition into an endemic disease and rising threats of other emerging pandemics, production of these biologicals requires a stable and sustainable supply chain and accessible distribution methods. In this study, we demonstrate the strength of an engineered filamentous fungal platform, Thermothelomyces heterothallica C1, for high volumetric productivity of the full-length spike glycoprotein. Spike protein produced in this system is highly thermostable and immunization of mice with spike made in C1 or mammalian platforms resulted in a similar humoral response. Additionally, it was shown that the native N-glycan profile can be redecorated with complex sialylated structures, if necessary, resulting in a more human-like glycan profile, without impacting binding characteristics as shown experimentally and in simulations. Through extensive physicochemical...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/07v1x8sh</guid>
      <pubDate>Wed, 22 Oct 2025 00:00:00 +0000</pubDate>
      <author>
        <name>Ophir, Yakir</name>
      </author>
      <author>
        <name>Wong, Justin H</name>
      </author>
      <author>
        <name>Haddad, Katherine R</name>
      </author>
      <author>
        <name>Huuskonen, Anne</name>
      </author>
      <author>
        <name>Karmaker, Anindya</name>
        <uri>https://orcid.org/0000-0002-9374-7327</uri>
      </author>
      <author>
        <name>Gore, Varun</name>
      </author>
      <author>
        <name>Jung, Seongwon</name>
      </author>
      <author>
        <name>Oloumi, Armin</name>
      </author>
      <author>
        <name>Liu, Yiyun</name>
      </author>
      <author>
        <name>Fu, Jingxin</name>
      </author>
      <author>
        <name>Zhang, Libo</name>
      </author>
      <author>
        <name>Huang, Peishan</name>
      </author>
      <author>
        <name>Minami, Shiaki Arnett</name>
      </author>
      <author>
        <name>Garimella, Shruthi Satya</name>
      </author>
      <author>
        <name>Thyagatur, Anugraha</name>
      </author>
      <author>
        <name>Zaini, Paulo A</name>
        <uri>https://orcid.org/0000-0001-6495-7942</uri>
      </author>
      <author>
        <name>Vitikainen, Marika</name>
      </author>
      <author>
        <name>Tchelet, Ronen</name>
      </author>
      <author>
        <name>Valbuena, Noelia</name>
      </author>
      <author>
        <name>Fuerst, Thomas R</name>
      </author>
      <author>
        <name>Korkmaz, Emrullah</name>
      </author>
      <author>
        <name>Falo, Louis D</name>
      </author>
      <author>
        <name>Balmert, Stephen C</name>
      </author>
      <author>
        <name>Mahendiratta, Saniya</name>
      </author>
      <author>
        <name>Emalfarb, Mark</name>
      </author>
      <author>
        <name>Shah, Priya S</name>
        <uri>https://orcid.org/0000-0001-7518-2839</uri>
      </author>
      <author>
        <name>Siegel, Justin</name>
      </author>
      <author>
        <name>Dandekar, Abhaya M</name>
        <uri>https://orcid.org/0000-0001-7925-4086</uri>
      </author>
      <author>
        <name>Chen, Xi</name>
      </author>
      <author>
        <name>Lebrilla, Carlito</name>
        <uri>https://orcid.org/0000-0001-7190-5323</uri>
      </author>
      <author>
        <name>Faller, Roland</name>
      </author>
      <author>
        <name>Saloheimo, Markku</name>
      </author>
      <author>
        <name>McDonald, Karen A</name>
        <uri>https://orcid.org/0000-0002-5145-9968</uri>
      </author>
      <author>
        <name>Nandi, Somen</name>
      </author>
    </item>
    <item>
      <title>On the suitability of non-dormant alfalfa to tolerate off-season groundwater recharge during winter and spring periods</title>
      <link>https://escholarship.org/uc/item/2gk4134h</link>
      <description>Winter groundwater recharge, which involves flooding farmland with excess surface water during the dormant season to replenish underlying aquifers, is a promising water conservation strategy, and alfalfa represents a particularly promising crop for this practice. In this study, we investigated yield and forage quality effects of intentional winter or spring flooding of non-dormant alfalfa (Medicago sativa L.) for groundwater recharge. A replicated randomized complete block design study was implemented at the University of California Kearney Research and Extension Center (KARE) in Parlier, CA testing three treatments (3 days of flooding followed by 4 days without flooding, 4 days of flooding followed by 10 days without flooding, and control) for a duration of 6 weeks in winter 2019 and spring 2020. A total of 1.6 and 3.6 m3 m−2 (2019) and 1.3 and 2.2 m3 m−2 (2020) were recharged in the 4 on 10 off and 3 on 4 off flood treatments at a recharge efficiency of &amp;gt; 88 % (81 % – 217 %...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/2gk4134h</guid>
      <pubDate>Thu, 9 Oct 2025 00:00:00 +0000</pubDate>
      <author>
        <name>Dahlke, Helen E</name>
        <uri>https://orcid.org/0000-0001-8757-6982</uri>
      </author>
      <author>
        <name>Ganot, Yonatan</name>
      </author>
      <author>
        <name>Clark, Nicholas</name>
      </author>
      <author>
        <name>Bali, Khaled</name>
      </author>
      <author>
        <name>Putnam, Daniel H</name>
      </author>
    </item>
    <item>
      <title>Predictability of Cottonwood Recruitment Along a Dynamic, Regulated River</title>
      <link>https://escholarship.org/uc/item/81r5m4hv</link>
      <description>Riparian vegetation planting and management are vital to river engineering projects. To inform of these activities, science needs to provide practitioners with a better understanding of influences on recruitment and where vegetation will most likely establish and survive. This study investigated whether the spatially explicit recruitment of Populus fremontii (Fremont cottonwood), a dominant riparian species in the western United States, could be predicted along a dynamic, alluvial regulated river. We used a ~34-km segment of the Yuba River in California, United States, which was mapped in 2017 after a large flood reset the terrain. Five years later from August through November 2022, a field campaign characterised precise locations of juvenile cottonwoods. We evaluated predictions from deterministic and statistical models. For the deterministic test, a spatially distributed riparian seedling recruitment model was used with expert-estimated parameters. The model was not accurate...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/81r5m4hv</guid>
      <pubDate>Thu, 25 Sep 2025 00:00:00 +0000</pubDate>
      <author>
        <name>Wright, Rachel E</name>
      </author>
      <author>
        <name>Phillips, Sierra J</name>
      </author>
      <author>
        <name>Diaz‐Gomez, Romina</name>
      </author>
      <author>
        <name>Jin, Yufang</name>
        <uri>https://orcid.org/0000-0002-9049-9807</uri>
      </author>
      <author>
        <name>Cadenasso, Mary L</name>
      </author>
      <author>
        <name>Pasternack, Gregory B</name>
        <uri>https://orcid.org/0000-0002-1977-4175</uri>
      </author>
    </item>
    <item>
      <title>Oregon Wolfe barley genetic stocks – Research and teaching tools for next generation scientists</title>
      <link>https://escholarship.org/uc/item/2kw46178</link>
      <description>Abstract: 
The Oregon Wolfe Barley (OWB) mapping population (Reg. no. MP‐4, NSL 554937 MAP) is a resource for genetics research and instruction. The OWBs are a set of doubled haploid barley (Hordeum vulgare L.) lines developed at Oregon State University from the F1 of a cross between Dr. Robert Wolfe's dominant and recessive marker stocks. Exhibiting a high level of genetic and phenotypic diversity, the OWBs are used throughout the world as a research tool for barley genetics. To date, these endeavors have led to 56 peer‐reviewed publications, as well as three reports in the Barley Genetics Newsletter. At the same time, the OWBs are widely used as an instructor resource at the K–12, undergraduate, graduate, and professional levels. They are currently used at universities and/or institutes in German, Italy, Norway, Spain, and the United States and are currently being developed further for educational use in other countries. Genotype and phenotype data, lesson plans, and seed availability...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/2kw46178</guid>
      <pubDate>Wed, 24 Sep 2025 00:00:00 +0000</pubDate>
      <author>
        <name>Krause, Margaret R</name>
      </author>
      <author>
        <name>Arbelaez, Juan David</name>
      </author>
      <author>
        <name>Asdal, Åsmund</name>
      </author>
      <author>
        <name>Belkodja, Ramzi</name>
      </author>
      <author>
        <name>Boury, Nancy</name>
      </author>
      <author>
        <name>Blake, Victoria C</name>
      </author>
      <author>
        <name>Brown, Patrick J</name>
      </author>
      <author>
        <name>Casas, Ana</name>
      </author>
      <author>
        <name>Cistué, Luis</name>
      </author>
      <author>
        <name>Farré‐Martínez, Alba</name>
      </author>
      <author>
        <name>Fisk, Scott</name>
      </author>
      <author>
        <name>Fuerst, Gregory S</name>
      </author>
      <author>
        <name>Giménez, Estela</name>
      </author>
      <author>
        <name>Guijarro‐Real, Carla</name>
      </author>
      <author>
        <name>Guthrie, Katy</name>
      </author>
      <author>
        <name>Halstead, Margaret</name>
      </author>
      <author>
        <name>Helgerson, Laura</name>
      </author>
      <author>
        <name>Hisano, Hiroshi</name>
      </author>
      <author>
        <name>Igartua, Ernesto</name>
      </author>
      <author>
        <name>Lillemo, Morten</name>
      </author>
      <author>
        <name>Martínez‐García, Marina</name>
      </author>
      <author>
        <name>Martínez‐Subirà, Mariona</name>
      </author>
      <author>
        <name>McCouch, Susan</name>
      </author>
      <author>
        <name>McGhee, Laurie</name>
      </author>
      <author>
        <name>Nickols, Travis</name>
      </author>
      <author>
        <name>Peters, Nick</name>
      </author>
      <author>
        <name>Porter, Raymond</name>
      </author>
      <author>
        <name>Romagosa, Ignacio</name>
      </author>
      <author>
        <name>Ruud, Anja Karine</name>
      </author>
      <author>
        <name>Sato, Kazuhiro</name>
      </author>
      <author>
        <name>Salvi, Silvio</name>
      </author>
      <author>
        <name>Sangiorgi, Giuseppe</name>
      </author>
      <author>
        <name>Schüller, Rebekka</name>
      </author>
      <author>
        <name>Sen, Taner Z</name>
        <uri>https://orcid.org/0000-0002-5553-6190</uri>
      </author>
      <author>
        <name>Soriano, José Miguel</name>
      </author>
      <author>
        <name>Stupar, Robert M</name>
      </author>
      <author>
        <name>Ting, To‐Chia</name>
      </author>
      <author>
        <name>Vining, Kelly</name>
      </author>
      <author>
        <name>von Korff, Maria</name>
      </author>
      <author>
        <name>Walla, Agatha</name>
      </author>
      <author>
        <name>Wang, Diane R</name>
      </author>
      <author>
        <name>Waugh, Robbie</name>
      </author>
      <author>
        <name>Wise, Roger P</name>
      </author>
      <author>
        <name>Wolfe, Robert</name>
      </author>
      <author>
        <name>Yao, Eric</name>
      </author>
      <author>
        <name>Hayes, Patrick M</name>
      </author>
    </item>
    <item>
      <title>Breeding for plant‐based proteins in pulse and legume crops: Perspectives, challenges and opportunities</title>
      <link>https://escholarship.org/uc/item/51p102v1</link>
      <description>The consumption of plant proteins is increasing worldwide as a viable alternative to animal-derived proteins in the marketplace. The projected increase in global population to at least 10 billion by 2050 is placing greater pressure on the food supply, particularly due to the rising demand for large-scale protein production. This protein transition is caused by macro-drivers such as changing consumer demographics, environmental sustainability, animal ethics, regulatory influences, and changing dietary patterns. Research efforts worldwide have explored various food applications for plant protein ingredients, including meat analogs, dairy alternatives, beverages, bakery products, and hybrid products. We provide here a review of the potential for legume breeding programs to incorporate traits that target the emerging plant-based protein market and aim to promote discussion among (but not limited to) plant breeders and geneticists, plant physiologists, agricultural economists, food...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/51p102v1</guid>
      <pubDate>Wed, 10 Sep 2025 00:00:00 +0000</pubDate>
      <author>
        <name>Cordoba, HA</name>
      </author>
      <author>
        <name>Sadohara, R</name>
      </author>
      <author>
        <name>Gali, KK</name>
      </author>
      <author>
        <name>Zhou, J</name>
      </author>
      <author>
        <name>Hart, J</name>
      </author>
      <author>
        <name>Alexandre, AC Silveira</name>
      </author>
      <author>
        <name>Cichy, K</name>
      </author>
      <author>
        <name>Wilker, J</name>
      </author>
      <author>
        <name>Dohle, S</name>
      </author>
      <author>
        <name>Mukankusi, C</name>
      </author>
      <author>
        <name>Warkentin, TD</name>
      </author>
      <author>
        <name>Rajcan, I</name>
      </author>
      <author>
        <name>Eskandari, M</name>
      </author>
      <author>
        <name>Marsolais, F</name>
      </author>
      <author>
        <name>Vandemark, G</name>
      </author>
      <author>
        <name>von Wettberg, E</name>
      </author>
      <author>
        <name>Palanichamy, D</name>
      </author>
      <author>
        <name>Thomassin, P</name>
      </author>
      <author>
        <name>Diepenbrock, CH</name>
        <uri>https://orcid.org/0000-0001-8411-0343</uri>
      </author>
      <author>
        <name>Nickerson, M</name>
      </author>
      <author>
        <name>Orsat, V</name>
      </author>
      <author>
        <name>Osorno, JM</name>
      </author>
      <author>
        <name>Hoyos‐Villegas, V</name>
      </author>
    </item>
    <item>
      <title>Distinct classes of 21‐ and 24‐nt phasiRNAs suggests diverse mechanisms of biogenesis and function in rice anther development</title>
      <link>https://escholarship.org/uc/item/266259kf</link>
      <description>PhasiRNAs (phased small interfering RNAs) are a major class of plant small RNAs (sRNA) known to be key regulators in male reproductive development of maize (Zea mays) and rice (Oryza sativa), among other plants. Earlier research focused primarily on premeiotic 21-nucleotide (nt) phasiRNAs and meiotic 24-nt phasiRNAs, while new studies uncovered a premeiotic class of 24-nt phasiRNAs. The biogenesis and function of these phasiRNAs remain unclear. We conducted an integrative analysis combining sRNA sequencing and transcriptomic profiling of sRNA-associated genes across 10 developmental stages of anther in Kitaake rice to map associations between expression of the transcripts encoding sRNA-related proteins and accumulation of phasiRNA classes. We identified previously undescribed classes of postmeiotic 21- and 24-nt phasiRNA-producing loci and characterized their unique accumulation patterns. Additionally, our findings reveal distinct nucleotide composition and register accumulation...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/266259kf</guid>
      <pubDate>Mon, 8 Sep 2025 00:00:00 +0000</pubDate>
      <author>
        <name>Jouni, Rachel</name>
      </author>
      <author>
        <name>Henry, Caroline</name>
      </author>
      <author>
        <name>Bélanger, Sébastien</name>
      </author>
      <author>
        <name>Baldrich, Patricia</name>
        <uri>https://orcid.org/0000-0003-4669-6632</uri>
      </author>
      <author>
        <name>Meyers, Blake C</name>
        <uri>https://orcid.org/0000-0003-3436-6097</uri>
      </author>
    </item>
    <item>
      <title>Integration of crop modeling and sensing into molecular breeding for nutritional quality and stress tolerance</title>
      <link>https://escholarship.org/uc/item/1f36k0x1</link>
      <description>Integrating innovative technologies into plant breeding is critical to bolster food and nutritional security under biotic and abiotic stresses in changing climates. While breeding efforts have focused primarily on yield and stress tolerance, emerging evidence highlights the need to also prioritize nutritional quality. Advanced molecular breeding approaches have enhanced our ability to develop improved crop varieties and could be substantially informed by the routine integration of crop modeling and remote sensing technologies. This review article discusses the potential of combining crop modeling and sensing with molecular breeding to address the dual challenge of nutritional quality and stress tolerance. We provide overviews of stress response strategies, challenges in breeding for quality traits, and the use of environmental data in genomic prediction. We also describe the status of crop modeling and sensing technologies in grain legumes, rice, and leafy greens, alongside the...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/1f36k0x1</guid>
      <pubDate>Wed, 27 Aug 2025 00:00:00 +0000</pubDate>
      <author>
        <name>Berlingeri, Jonathan</name>
      </author>
      <author>
        <name>Fuentes, Abelina</name>
      </author>
      <author>
        <name>Ranario, Earl</name>
      </author>
      <author>
        <name>Yun, Heesup</name>
      </author>
      <author>
        <name>Rim, Ellen Y</name>
      </author>
      <author>
        <name>Garrett, Oscar</name>
      </author>
      <author>
        <name>Howard, Alexander</name>
      </author>
      <author>
        <name>LaPorte, Mary-Francis</name>
      </author>
      <author>
        <name>Lo, Sassoum</name>
      </author>
      <author>
        <name>Pauli, Duke</name>
      </author>
      <author>
        <name>Hershberger, Jenna</name>
      </author>
      <author>
        <name>Earles, Mason</name>
      </author>
      <author>
        <name>Van Deynze, Allen</name>
      </author>
      <author>
        <name>Brummer, Edward Charles</name>
      </author>
      <author>
        <name>Michelmore, Richard</name>
      </author>
      <author>
        <name>Wong, Christopher YS</name>
      </author>
      <author>
        <name>Magney, Troy S</name>
        <uri>https://orcid.org/0000-0002-9033-0024</uri>
      </author>
      <author>
        <name>Ronald, Pamela C</name>
        <uri>https://orcid.org/0000-0002-4107-1345</uri>
      </author>
      <author>
        <name>Runcie, Daniel E</name>
        <uri>https://orcid.org/0000-0002-3008-9312</uri>
      </author>
      <author>
        <name>Bailey, Brian N</name>
      </author>
      <author>
        <name>Diepenbrock, Christine H</name>
        <uri>https://orcid.org/0000-0001-8411-0343</uri>
      </author>
    </item>
    <item>
      <title>Hands on the land: prioritizing inclusivity and continued intervention in restoration</title>
      <link>https://escholarship.org/uc/item/1gx6w2f8</link>
      <description>Restoration is a powerful tool to ameliorate global change, but unreached goals cast doubt on its efficacy. Here, we call for prioritizing long-term, continued intervention and increased inclusivity within the field of restoration, particularly in North America. Many have called to re-examine the field of restoration; we are not the first. The prevailing paradigm, though, of applying discrete restoration interventions to achieve a final “restored” state yields inconsistent outcomes. Additionally, collaboration gaps between researchers, managers, and the community do little to garner restoration success. To answer the call for continued intervention and increased inclusivity, the authors founded Hands on the Land (HOTL), an organization that gives all people free, repeated restoration experience. HOTL prioritizes inclusion through socio-ecological thinking, equity, safety, and support. Lastly, we address challenges to adopting the HOTL model. Ultimately, the benefits of combining...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/1gx6w2f8</guid>
      <pubDate>Wed, 20 Aug 2025 00:00:00 +0000</pubDate>
      <author>
        <name>Luzzio, Alana M</name>
      </author>
      <author>
        <name>Wainwright, Brooke E</name>
      </author>
      <author>
        <name>Dodd, Doshia</name>
      </author>
      <author>
        <name>Nelson, Rebecca</name>
      </author>
      <author>
        <name>Simon, Sophia</name>
      </author>
      <author>
        <name>Flynn, Margot Tai‐Yi</name>
      </author>
      <author>
        <name>Mabe, Lauren</name>
      </author>
    </item>
    <item>
      <title>Breeding indoor watercress for enhanced crop biofortification: harnessing natural variation of wild germplasm</title>
      <link>https://escholarship.org/uc/item/5418k1t6</link>
      <description>We quantified the natural genetic variation of a diverse collection of wild watercress germplasm, consisting of 32 accessions collected from 16 locations in nine countries worldwide and grown in a controlled indoor environment with contrasting blue light regimes. Significant phenotypic diversity was identified for all three categories of traits: morphology and yield varied by 68% across the population (leaf size, biomass production, and stem length), with sensory (sugar content and brix), and nutritional quality (glucosinolates, vitamin C, carotenoids) varying by 45% and 43% respectively. Using two LED light regimes, control and additional blue light exposure, revealed that the watercress nutritional profile is plastic, and that the magnitude and direction of plastic responses vary depending on genotype and trait. Two glucosinolate compounds responded differently to blue light, as indolyl-3-methyl-glucosinolate increased while 4-phenylbutyl-glucosinolate decreased, but the other...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/5418k1t6</guid>
      <pubDate>Wed, 13 Aug 2025 00:00:00 +0000</pubDate>
      <author>
        <name>Qian, Yufei</name>
      </author>
      <author>
        <name>Katz, Ella</name>
      </author>
      <author>
        <name>Kliebenstein, Daniel J</name>
      </author>
      <author>
        <name>Taylor, Gail</name>
      </author>
    </item>
    <item>
      <title>Global synthesis and regional insights for mainstreaming urban nature-based solutions</title>
      <link>https://escholarship.org/uc/item/9g89c6qm</link>
      <description>Nature-based solutions (NbS) have emerged as a key strategy for sustainably addressing multiple urban challenges, with rapidly increasing knowledge production requiring synthesis to better understand whether and how NbS work in different social, ecological, economic, or governance contexts. Insights in this Perspective are drawn from a thematic review of 61 NbS review articles supported by an expert assessment of NbS knowledge in seven global regions to examine key challenges, fill gaps in Global South assessment, and provide insights for scaling up NbS for impact in cities. Eight NbS challenges emerged from our review of NbS reviews including conceptual, thematic, geographic, ecological, inclusivity, health, governance, and systems challenges. An additional expert assessment reviewing literature and cases in seven global regions further revealed the following: 1) Local context-based ecological knowledge is essential for NbS success; 2) Improved technical knowledge is required...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/9g89c6qm</guid>
      <pubDate>Wed, 30 Jul 2025 00:00:00 +0000</pubDate>
      <author>
        <name>McPhearson, Timon</name>
      </author>
      <author>
        <name>Frantzeskaki, Niki</name>
      </author>
      <author>
        <name>Ossola, Alessandro</name>
        <uri>https://orcid.org/0000-0002-0507-6026</uri>
      </author>
      <author>
        <name>Diep, Loan</name>
      </author>
      <author>
        <name>Anderson, Pippin ML</name>
      </author>
      <author>
        <name>Blatch, Timothy</name>
      </author>
      <author>
        <name>Collier, Marcus J</name>
      </author>
      <author>
        <name>Cook, Elizabeth M</name>
      </author>
      <author>
        <name>Fatti, Christina Culwick</name>
      </author>
      <author>
        <name>Grabowski, Zbigniew J</name>
      </author>
      <author>
        <name>Grimm, Nancy B</name>
      </author>
      <author>
        <name>Haase, Dagmar</name>
      </author>
      <author>
        <name>Herreros-Cantis, Pablo</name>
      </author>
      <author>
        <name>Kavonic, Jessica</name>
      </author>
      <author>
        <name>Lin, Brenda B</name>
      </author>
      <author>
        <name>Meneses, Duván H Lopez</name>
      </author>
      <author>
        <name>Matsler, A Marissa</name>
      </author>
      <author>
        <name>Moglia, Magnus</name>
      </author>
      <author>
        <name>Morató, Jordi</name>
      </author>
      <author>
        <name>O’Farrell, Patrick</name>
      </author>
      <author>
        <name>Roy, Parama</name>
      </author>
      <author>
        <name>Singh, Chandni</name>
      </author>
      <author>
        <name>Wang, Jing</name>
      </author>
      <author>
        <name>Zhou, Weiqi</name>
      </author>
    </item>
    <item>
      <title>Comprehensive transcriptional analysis of ethylene and softening regulation in plums with distinct climacteric ripening behaviors</title>
      <link>https://escholarship.org/uc/item/8ns2s5hz</link>
      <description>Understanding the molecular mechanisms underlying variations across climacteric categories in tree crops remains challenging, particularly due to the limitations of applying conventional genetic approaches. In this study, we examined genetically related Japanese plum (Prunus salicina Lindl.) cultivars with distinct ethylene production and responses during ripening: ‘Santa Rosa’ (climacteric fruit), ‘Casselman’ (suppressed-climacteric fruit), and ‘Sweet Miriam’ (non-climacteric fruit). Our primary objective was to comprehensively investigate transcriptional differences related to ethylene and fruit softening across three on-tree developmental stages: “Green” (early development), “Mature” (pre-climacteric or early climacteric), and “Ripe” (climacteric). By integrating information from Phytozome and Dicot PLAZA databases, we identified complete gene families for six ethylene-related and seven softening-related genes. Multi-developmental stage RNA-seq clustering revealed that “Late”...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/8ns2s5hz</guid>
      <pubDate>Wed, 30 Jul 2025 00:00:00 +0000</pubDate>
      <author>
        <name>Huang, Po-Kai</name>
      </author>
      <author>
        <name>Manganaris, George A</name>
      </author>
      <author>
        <name>Gasic, Ksenija</name>
      </author>
      <author>
        <name>Saski, Christopher A</name>
      </author>
      <author>
        <name>Beckles, Diane M</name>
        <uri>https://orcid.org/0000-0001-6336-1186</uri>
      </author>
      <author>
        <name>Crisosto, Carlos H</name>
      </author>
    </item>
    <item>
      <title>Tree Nut Crop Response to Simulated Florpyrauxifen-benzyl and Triclopyr Herbicide Drift</title>
      <link>https://escholarship.org/uc/item/6343434g</link>
      <description>California is the nation’s primary producer of almonds, pistachios, and walnuts, and an important producer of rice. Because of California’s diverse cropping systems, off-target herbicide drift can be a considerable problem, particularly from aerial applications that are commonly used in flooded rice production systems. Triclopyr is an auxin-mimic type herbicide that has been commonly used in rice for many years for control of broadleaf weeds and the industry is familiar with symptoms of off-target triclopyr drift. Florpyrauxifen-benzyl is a newly registered auxin-mimic herbicide in California rice with activity on key weeds and is being rapidly adopted. Although symptoms typically are similar among auxinic herbicides, it is important to understand subtle differences and risks among these herbicides as stewardship for newly registered products. This research was conducted in 2020 and 2021 to determine the relative sensitivity of almond, pistachio, and walnut trees to simulated...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/6343434g</guid>
      <pubDate>Wed, 30 Jul 2025 00:00:00 +0000</pubDate>
      <author>
        <name>Inci, Deniz</name>
      </author>
      <author>
        <name>Hanson, Bradley D</name>
        <uri>https://orcid.org/0000-0003-4462-5339</uri>
      </author>
      <author>
        <name>Al-Khatib, Kassim</name>
        <uri>https://orcid.org/0000-0002-9214-6714</uri>
      </author>
    </item>
    <item>
      <title>Ectopic overexpression of ShCBF1 and SlCBF1 in tomato suggests an alternative view of fruit responses to chilling stress postharvest.</title>
      <link>https://escholarship.org/uc/item/3j12p9c0</link>
      <description>Postharvest chilling injury (PCI) is a physiological disorder that often impairs tomato fruit ripening; this reduces fruit quality and shelf-life, and even accelerates spoilage at low temperatures. The CBF gene family confers cold tolerance in Arabidopsis thaliana, and constitutive overexpression of CBF in tomato increases vegetative chilling tolerance, in part by retarding growth, but, whether CBF increases PCI tolerance in fruit is unknown. We hypothesized that CBF1 overexpression (OE) would be induced in the cold and increase resistance to PCI. We induced high levels of CBF1 in fruit undergoing postharvest chilling by cloning it from S. lycopersicum and S. habrochaites, using the stress-inducible RD29A promoter. Harvested fruit were cold-stored (2.5°C) for up to three weeks, then rewarmed at 20°C for three days. Transgene upregulation was triggered during cold storage from 8.6- to 28.6-fold in SlCBF1-OE, and between 3.1- to 8.3-fold in ShCBF1-OE fruit, but developmental abnormalities...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/3j12p9c0</guid>
      <pubDate>Wed, 30 Jul 2025 00:00:00 +0000</pubDate>
      <author>
        <name>Albornoz, Karin</name>
      </author>
      <author>
        <name>Zhou, Jiaqi</name>
      </author>
      <author>
        <name>Zakharov, Florence</name>
      </author>
      <author>
        <name>Grove, Jonas</name>
      </author>
      <author>
        <name>Wang, Minmin</name>
      </author>
      <author>
        <name>Beckles, Diane</name>
      </author>
    </item>
    <item>
      <title>Reinventing Inheritance: Clonal Propagation of Crops Through Seeds with Apomixis</title>
      <link>https://escholarship.org/uc/item/2t51161c</link>
      <description>Hybrid crops play a crucial role in modern agriculture, offering higher yields, improved disease resistance, and greater adaptability to environmental challenges. However, the need for repeated hybridization each generation makes hybrid seed production costly and labor-intensive. Synthetic apomixis, an innovative breakthrough in plant biotechnology, enables clonal propagation through seeds, allowing hybrid plants to produce genetically identical offspring. This technology has the potential to revolutionize crop breeding because it preserves hybrid vigor across generations and significantly reduces seed production costs. By eliminating dependence on traditional hybrid seed production methods, synthetic apomixis could facilitate broader hybrid cultivar adoption and cultivation worldwide. It has the potential to ensure global food security, promote sustainable agriculture, and accelerate the breeding of climate-resilient crops. In this review, we discuss recent advances in synthetic...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/2t51161c</guid>
      <pubDate>Wed, 30 Jul 2025 00:00:00 +0000</pubDate>
      <author>
        <name>Reed, Reagan C</name>
      </author>
      <author>
        <name>Iqbal, Rasheeba</name>
      </author>
      <author>
        <name>Sundaresan, Venkatesan</name>
        <uri>https://orcid.org/0000-0002-4670-0630</uri>
      </author>
      <author>
        <name>Khanday, Imtiyaz</name>
        <uri>https://orcid.org/0000-0003-1460-3577</uri>
      </author>
    </item>
    <item>
      <title>Co‐domestication of cold tolerance and female flower is determined by CsEIN2 in cucumber</title>
      <link>https://escholarship.org/uc/item/18f4x5z9</link>
      <description>Survive and successful reproduction at cold stress&amp;nbsp;are critical for cucumber adaptation to environmental conditions in high-latitude regions. However, the molecular basis for the co-domestication of cold adaptation and reproductive success in cucumber remains unknown. Here, we demonstrate that CsEIN2 acts as an indispensable hub in regulating both cold tolerance and female flower percentage (FFP) in cucumber. Specifically, we discover that three completely linked natural variations at the C-terminus of CsEIN2, that is, the CsEIN2&lt;sup&gt;CTC&lt;/sup&gt; and CsEIN2&lt;sup&gt;TCG&lt;/sup&gt; haplotypes determine the differences in cold tolerance and FFP. These variations affect the interaction of CsEIN2 with the transcription factor CsEIN3, which activates the expression of target genes such as CsCBF2 and CsERF31 to regulate cold tolerance and FFP, respectively. Interestingly, the geographical distribution analyses show that the CsEIN2&lt;sup&gt;CTC&lt;/sup&gt; haplotype, conferring higher cold tolerance and...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/18f4x5z9</guid>
      <pubDate>Wed, 30 Jul 2025 00:00:00 +0000</pubDate>
      <author>
        <name>Li, Caixia</name>
      </author>
      <author>
        <name>Dong, Shaoyun</name>
      </author>
      <author>
        <name>Liu, Xiaoping</name>
      </author>
      <author>
        <name>Guan, Jiantao</name>
      </author>
      <author>
        <name>Beckles, Diane M</name>
        <uri>https://orcid.org/0000-0001-6336-1186</uri>
      </author>
      <author>
        <name>Gu, Xingfang</name>
      </author>
      <author>
        <name>Sun, Jiaqiang</name>
      </author>
      <author>
        <name>Miao, Han</name>
      </author>
      <author>
        <name>Zhang, Shengping</name>
      </author>
    </item>
    <item>
      <title>Turning the page on front matter: Wishing Nan Eckardt a joyful retirement</title>
      <link>https://escholarship.org/uc/item/65r567g2</link>
      <description>Turning the page on front matter: Wishing Nan Eckardt a joyful retirement</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/65r567g2</guid>
      <pubDate>Tue, 15 Jul 2025 00:00:00 +0000</pubDate>
      <author>
        <name>Quatrano, Ralph S</name>
      </author>
      <author>
        <name>Jorgensen, Richard A</name>
      </author>
      <author>
        <name>Martin, Cathie</name>
      </author>
      <author>
        <name>Merchant, Sabeeha S</name>
      </author>
      <author>
        <name>Meyers, Blake C</name>
        <uri>https://orcid.org/0000-0003-3436-6097</uri>
      </author>
    </item>
    <item>
      <title>Identification of drought and heat tolerant tepary beans in a multi‐environment trial study</title>
      <link>https://escholarship.org/uc/item/8gt8d90k</link>
      <description>Abiotic constraints, such as drought and heat driven by climate change, negatively impact the production of the common bean (Phaseolus vulgaris L.), an essential grain legume worldwide. The ability to tolerate drought and heat stress in common bean can be improved by introducing genetic variation from related species, such as tepary bean (Phaseolus acutifolius A. Gray), which has recently gained attention because of its adaptation to drought and heat stresses and potential use as a genetic resource and alternative crop. To better understand the phenotypic response of tepary bean to drought and heat stress in multiple environments and trials and to select highly adapted tepary beans, we conducted two field experiments. In Experiment 1, we compared the adaptation to drought stress of tepary bean (n&amp;nbsp;=&amp;nbsp;10), common bean (n&amp;nbsp;=&amp;nbsp;10), and Lima bean (Phaseolus lunatus L.; n&amp;nbsp;=&amp;nbsp;9) by assessing the reduction in grain yield under terminal drought compared to well-irrigated...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/8gt8d90k</guid>
      <pubDate>Mon, 14 Jul 2025 00:00:00 +0000</pubDate>
      <author>
        <name>Barrera, Santos</name>
      </author>
      <author>
        <name>Mier y Teran, Jorge C Berny</name>
      </author>
      <author>
        <name>Aparicio, Johan</name>
      </author>
      <author>
        <name>Diaz, Jairo</name>
      </author>
      <author>
        <name>Leon, Rommel</name>
      </author>
      <author>
        <name>Beebe, Steve</name>
      </author>
      <author>
        <name>Urrea, Carlos A</name>
      </author>
      <author>
        <name>Gepts, Paul</name>
        <uri>https://orcid.org/0000-0002-1056-4665</uri>
      </author>
    </item>
    <item>
      <title>Phylogenetic systematics of Vigna sensu stricto in the context of Physostigma and allies</title>
      <link>https://escholarship.org/uc/item/87z8v9fd</link>
      <description>PREMISE: Vigna includes economically vital crops and wild species. Molecular systematic studies of Vigna species resulted in generic segregates of many New World (NW) species. However, limited Old World (OW) sampling left questions regarding inter- and intraspecific relationships in Vigna s.s.
METHODS: African species, including the putative sister genus Physostigma, were comprehensively sampled within the context of NW relatives. Maximum likelihood and Bayesian inference analyses of the chloroplast matK-trnK and nuclear ribosomal ITS/5.8 S (ITS) DNA regions were undertaken to resolve OW Vigna taxonomic questions. Divergence dates were estimated using BEAST to date key nodes in the phylogeny.
RESULTS: Analyses of matK and ITS data supported five clades of Vigna s.s.: subg. Lasiospron, a reduced subg. Vigna, subg. Haydonia, subg. Ceratotropis, an enlarged subg. Plectrotropis, and a clade including V. kirkii and V. stenophylla. Genome size estimates of 601 Mb for V. kirkii are near...</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/87z8v9fd</guid>
      <pubDate>Mon, 14 Jul 2025 00:00:00 +0000</pubDate>
      <author>
        <name>Horton, Dasha M</name>
      </author>
      <author>
        <name>Feleke, Yonas</name>
      </author>
      <author>
        <name>Pasquet, Remy S</name>
      </author>
      <author>
        <name>Javadi, Firouzeh</name>
      </author>
      <author>
        <name>Melville, Kaycie A</name>
      </author>
      <author>
        <name>Delgado‐Salinas, Alfonso</name>
      </author>
      <author>
        <name>Thulin, Mats</name>
      </author>
      <author>
        <name>Mithen, Richard F</name>
      </author>
      <author>
        <name>Gepts, Paul</name>
        <uri>https://orcid.org/0000-0002-1056-4665</uri>
      </author>
      <author>
        <name>Egan, Ashley N</name>
      </author>
    </item>
    <item>
      <title>Exploitation of rhizosphere microbiome biodiversity in plant breeding</title>
      <link>https://escholarship.org/uc/item/5wf1j1tk</link>
      <description>Climate change-induced stresses are perceived by plants at the root-soil interface, where they are alleviated through interactions between the host plant and the rhizosphere microbiome. The recruitment of specific microbiomes helps mitigate stress, increases resistance to pathogens, and promotes plant growth, development, and reproduction. The structure of the rhizosphere microbiome is shaped by crop domestication and variations in ploidy levels. Here we list key genes that regulate rhizosphere microbiomes and host genetic traits. We also discuss the prospects for rigorous analysis of symbiotic interactions, research needs, and strategies for systematically utilizing microbe-crop interactions to improve crop performance. Finally, we highlight challenges of maintaining live rhizosphere microbiome collections and mining heritable variability to enhance interactions between host plants and their rhizosphere microbiomes.</description>
      <guid isPermaLink="true">https://escholarship.org/uc/item/5wf1j1tk</guid>
      <pubDate>Mon, 14 Jul 2025 00:00:00 +0000</pubDate>
      <author>
        <name>Dwivedi, Sangam L</name>
      </author>
      <author>
        <name>Vetukuri, Ramesh Raju</name>
      </author>
      <author>
        <name>Kelbessa, Bekele Gelena</name>
      </author>
      <author>
        <name>Gepts, Paul</name>
        <uri>https://orcid.org/0000-0002-1056-4665</uri>
      </author>
      <author>
        <name>Heslop-Harrison, Pat</name>
      </author>
      <author>
        <name>Araujo, Ademir SF</name>
      </author>
      <author>
        <name>Sharma, Shilpi</name>
      </author>
      <author>
        <name>Ortiz, Rodomiro</name>
      </author>
    </item>
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