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Open Access Publications from the University of California

Scholarly Works (38 results)

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UC Davis Electronic Theses and Dissertations (2023)

With the growing energy demand and global warming crisis, the world is in need of a more renewable and sustainable source of energy. Among the possible options, bioenergy is gaining more attention recently, as it can both act as a cleaner substitute for fossil fuels and sequester carbon from atmospheric CO2. Poplar (Populus trichocarpa) is a highly advantageous bioenergy crop, but since the production of bioenergy crops should minimize the diversion of cropland from food crop production, the marginal lands with greater susceptibility to drought are the main production sites for poplars. To increase the yield on marginal lands, the drought tolerance of poplars needs to be better quantified to determine their potential as an environmentally sustainable source of energy.In this experiment, we measured the leaf-level physiological and developmental traits from 1869 poplar trees of 471 unique genotypes. The genotypes originated from the western part of North America, covering latitudes with diverse rainfall conditions across most of the species’ range (38.9-54.3°N, 116-128.7°W). The leaf’s stomatal density, stomatal size, fresh weight, dry weight, relative water content, contact angle, spectral reflectance, leaf area, leaf perimeter, and compactness were measured to quantify the effect of drought during poplar’s early growth stage on different genotypes. Results indicated that most of the measured traits are significantly affected by drought, while the severity and duration of drought alter the drought response. The measurements of most traits decrease with drought, and genotype affects most traits significantly. Only a few traits show a significant interaction between genotype and treatment. Furthermore, many traits are affected by the latitude and precipitation of the warmest quarter of the genotype’s origin, and few are also affected by the precipitation of the coldest quarter. Several correlations have been noted among traits, such as a negative correlation between stomatal density and stomatal size, a negative correlation between dry weight and compactness, a positive correlation between adaxial and abaxial contact angle, and a positive correlation between NDVI and PRI. Overall, this thesis provides a quantitative assessment of how drought and geographical location impact the physiological and developmental traits of poplar. The findings have practical implications for identifying genotypes that are better suited for commercial cultivation in varying environmental conditions.

  • 3 supplemental ZIPs
  • Thesis
  • Peer Reviewed
UC Davis Electronic Theses and Dissertations (2021)

Watercress (Nasturtium officinale R. Br.; Brassicaceae) is a highly nutritious leafy green vegetable consumed by customers globally. The peppery taste of watercress is the indicator of mustard oils which help reduce inflammation and chronic damage in cells and has been shown to have a role in cancer prevention in vitro. Watercress has a rich health-related phytonutrient profile including secondary plant metabolites glucosinolates (GLS), especially gluconasturtiin and its hydrolysis product phenethyl isothiocyantate (PEITC). We describe the development of the 259 F2 progeny mapping population and explored the effects of G x E interactions on phenotypic traits for a set of F4 lines with extreme phenotypes for growth, morphology, antioxidant capacity, and glucosinolates produced in contrasting field locations. After identifying and grouping the "extreme" lines, they were bulked and transcriptome analysis performed to identify differentially expressed candidate genes (DEG) on the phenylpropanoid biosynthesis pathways. Results indicated that the environment has a great impact on plant morphology and nutritional quality between the CA and UK sites. Plants grown in the CA site had higher biomass, thicker main stem with more stems, and a higher concentration of aromatic GLS. In a bulk-segregant RNA-Seq analysis, we identified 22 DEG (FDR<0.05) between the "high" and "low" selected GLS phenotype bulks, and four gene families (IPR029063, IPR004813, IPR001128, IPR025610) encoding key regulators in GLS biosynthesis.

    • Article
    • Peer Reviewed
    UC Davis Previously Published Works (2022)
    Watercress is a nutrient-dense leafy green crop, traditionally grown in aquatic outdoor systems and increasingly seen as well-suited for indoor hydroponic systems. However, there is concern that this crop has a detrimental impact on the environment through direct phosphate additions causing environmental pollution. Phosphate-based fertilisers are supplied to enhanced crop yield, but their use may contribute to eutrophication of waterways downstream of traditional watercress farms. One option is to develop a more phosphate use efficient (PUE) crop. This review identifies the key traits for this aquatic crop (the ideotype), for future selection, marker development and breeding. Traits identified as important for PUE are (i) increased root surface area through prolific root branching and adventitious root formation, (ii) aerenchyma formation and root hair growth. Functional genomic traits for improved PUE are (iii) efficacious phosphate remobilisation and scavenging strategies and (iv) the use of alternative metabolic pathways. Key genomic targets for this aquatic crop are identified as: PHT phosphate transporter genes, global transcriptional regulators such as those of the SPX family and genes involved in galactolipid and sulfolipid biosynthesis such as MGD2/3, PECP1, PSR2, PLDζ1/2 and SQD2. Breeding for enhanced PUE in watercress will be accelerated by improved molecular genetic resources such as a full reference genome sequence that is currently in development.
      Cover page: Improving phosphate use efficiency in the aquatic crop watercress (Nasturtium officinale)
      • Article
      • Peer Reviewed
      UC Davis Previously Published Works (2019)
      Rising atmospheric CO2 concentration is a key driver of enhanced global greening, thought to account for up to 70% of increased global vegetation in recent decades. CO2 fertilization effects have further profound implications for ecosystems, food security and biosphere-atmosphere feedbacks. However, it is also possible that current trends will not continue, due to ecosystem level constraints and as plants acclimate to future CO2 concentrations. Future predictions of plant response to rising [CO2 ] are often validated using single-generation short-term FACE (Free Air CO2 Enrichment) experiments but whether this accurately represents vegetation response over decades is unclear. The role of transgenerational plasticity and adaptation in the multigenerational response has yet to be elucidated. Here, we propose that naturally occurring high CO2 springs provide a proxy to quantify the multigenerational and long-term impacts of rising [CO2 ] in herbaceous and woody species respectively, such that plasticity, transgenerational effects and genetic adaptation can be quantified together in these systems. In this first meta-analysis of responses to elevated [CO2 ] at natural CO2 springs, we show that the magnitude and direction of change in eight of nine functional plant traits are consistent between spring and FACE experiments. We found increased photosynthesis (49.8% in spring experiments, comparable to 32.1% in FACE experiments) and leaf starch (58.6% spring, 84.3% FACE), decreased stomatal conductance (gs , 27.2% spring, 21.1% FACE), leaf nitrogen content (6.3% spring, 13.3% FACE) and Specific Leaf Area (SLA, 9.7% spring, 6.0% FACE). These findings not only validate the use of these sites for studying multigenerational plant response to elevated [CO2 ], but additionally suggest that long-term positive photosynthetic response to rising [CO2 ] are likely to continue as predicted by single-generation exposure FACE experiments.
        Cover page: FACE facts hold for multiple generations; Evidence from natural CO2 springs
        • Article
        • Peer Reviewed
        UC Davis Previously Published Works (2011)

        Background

        There is an increasing demand for renewable resources to replace fossil fuels. However, different applications such as the production of secondary biofuels or combustion for energy production require different wood properties. Therefore, high-throughput methods are needed for rapid screening of wood in large scale samples, e.g., to evaluate the outcome of tree breeding or genetic engineering. In this study, we investigated the intra-specific variability of lignin and energy contents in extractive-free wood of hybrid poplar progenies (Populus trichocarpa × deltoides) and tested if the range was sufficient for the development of quantitative prediction models based on Fourier transform infrared spectroscopy (FTIR). Since lignin is a major energy-bearing compound, we expected that the energy content of wood would be positively correlated with the lignin content.

        Results

        Lignin contents of extractive-free poplar wood samples determined by the acetyl bromide method ranged from 23.4% to 32.1%, and the calorific values measured with a combustion calorimeter varied from 17260 to 19767 J g-1. For the development of calibration models partial least square regression and cross validation was applied to correlate FTIR spectra determined with an attenuated total reflectance (ATR) unit to measured values of lignin or energy contents. The best models with high coefficients of determination (R2 (calibration) = 0.91 and 0.90; R2 (cross-validation) = 0.81 and 0.79) and low root mean square errors of cross validation (RMSECV = 0.77% and 62 J g-1) for lignin and energy determination, respectively, were obtained after data pre-processing and automatic wavenumber restriction. The calibration models were validated by analyses of independent sets of wood samples yielding R2 = 0.88 and 0.86 for lignin and energy contents, respectively.

        Conclusions

        These results show that FTIR-ATR spectroscopy is suitable as a high-throughput method for lignin and energy estimations in large data sets. Our study revealed that the intra-specific variations in lignin and energy contents were unrelated to each other and that the lignin content, therefore, was no predictor of the energy content. Employing principle component analyses we showed that factor loadings for the energy content were mainly associated with carbohydrate ring vibrations, whereas those for lignin were mainly related to aromatic compounds. Therefore, our analysis suggests that it may be possible to optimize the energy content of trees without concomitant increase in lignin.
          Cover page: FTIR-ATR-based prediction and modelling of lignin and energy contents reveals independent intra-specific variation of these traits in bioenergy poplars
          • Article
          • Peer Reviewed
          UC Davis Previously Published Works (2015)
          Identifying processes underlying the genetic and morphological differences among populations is a central question of evolutionary biology. Forest trees typically contain high levels of neutral genetic variation, and genetic differences are often correlated with geographic distance between populations [isolation by distance (IBD)] or are due to historic vicariance events [isolation by colonization (IBC)]. In contrast, morphological differences are largely due to local adaptation. Here, we examined genetic (microsatellite) and morphological (from a common garden experiment) variation in Populus nigra L., European black poplar, collected from 13 sites across western Europe and grown in a common garden in Belgium. Significant genetic differentiation was observed, with populations from France displaying greater admixture than the distinct Spanish and central European gene pools, consistent with previously described glacial refugia (IBC). Many quantitative traits displayed a bimodal distribution, approximately corresponding to small-leaf and large-leaf ecotypes. Examination of nine climatic variables revealed the sampling locations to have diverse climates, and although the correlation between morphological and climatic differences was significant, the pattern was not consistent with strict local adaptation. Partial Mantel tests based on multivariate summary statistics identified significant residual correlation in comparisons of small-leaf to large-leaf ecotypes, and within the small-leaf samples, but not within large-leaf ecotypes, indicating that variation within the small-leaf morphotype in particular may be adaptive. Some small-leaf populations experience climates very similar to those in large-leaf sites. We conclude that adaptive differentiation and persistent IBC acted in combination to produce the genetic and morphological patterns observed in P. nigra.
            Cover page: Genetic and morphological differentiation in Populus nigra L.: isolation by colonization or isolation by adaptation?
            • Article
            • Peer Reviewed
            UC Davis Previously Published Works (2009)

            Background

            This work explores the potential contribution of bioenergy technologies to 60% and 80% carbon reductions in the UK energy system by 2050, by outlining the potential for accelerated technological development of bioenergy chains. The investigation was based on insights from MARKAL modelling, detailed literature reviews and expert consultations. Due to the number and complexity of bioenergy pathways and technologies in the model, three chains and two underpinning technologies were selected for detailed investigation: (1) lignocellulosic hydrolysis for the production of bioethanol, (2) gasification technologies for heat and power, (3) fast pyrolysis of biomass for bio-oil production, (4) biotechnological advances for second generation bioenergy crops, and (5) the development of agro-machinery for growing and harvesting bioenergy crops. Detailed literature searches and expert consultations (looking inter alia at research and development needs and economic projections) led to the development of an 'accelerated' dataset of modelling parameters for each of the selected bioenergy pathways, which were included in five different scenario runs with UK-MARKAL (MED). The results of the 'accelerated runs' were compared with a low-carbon (LC-Core) scenario, which assesses the cheapest way to decarbonise the energy sector.

            Results

            Bioenergy was deployed in larger quantities in the bioenergy accelerated technological development scenario compared with the LC-Core scenario. In the electricity sector, solid biomass was highly utilised for energy crop gasification, displacing some deployment of wind power, and nuclear and marine to a lesser extent. Solid biomass was also deployed for heat in the residential sector from 2040 in much higher quantities in the bioenergy accelerated technological development scenario compared with LC-Core. Although lignocellulosic ethanol increased, overall ethanol decreased in the transport sector in the bioenergy accelerated technological development scenario due to a reduction in ethanol produced from wheat.

            Conclusion

            There is much potential for future deployment of bioenergy technologies to decarbonise the energy sector. However, future deployment is dependent on many different factors including investment and efforts towards research and development needs, carbon reduction targets and the ability to compete with other low carbon technologies as they become deployed. All bioenergy technologies should become increasingly more economically competitive with fossil-based technologies as feedstock costs and flexibility are reduced in line with technological advances.
              Cover page: How can accelerated development of bioenergy contribute to the future UK energy mix? Insights from a MARKAL modelling exercise
              • Article
              • Peer Reviewed
              UC Davis Previously Published Works (2013)
              Watercress (Rorippa nasturtium-aquaticum), wild rocket (Diplotaxis tenuifolia), and spinach (Spinacia oleracea) are commercial crops reported to have high concentrations of antioxidants, possibly contributing to disease prevention following human consumption. Following analysis of supermarket-purchased salad leaves, we report the antioxidant content potential of these species using two comparable techniques assessing the consistency between the assays - by the ferric reducing antioxidant power (FRAP) assay and the oxygen radical absorbance capacity (ORAC) assay. The leaves were harvested from both conventionally and organically managed crops, to investigate whether organic agriculture results in improved crop quality. Watercress had the highest FRAP and ability to scavenge free radicals, followed by spinach and rocket. For watercress and rocket, there was no significant effect of organic agriculture on FRAP and ORAC, but for spinach, the antioxidant potential was reduced and this was significant at the 5% level of probability for FRAP but not ORAC, although the trend was clear in both tests. We conclude that there is variation in salad crop antioxidant potential and that FRAP and ORAC are useful techniques for measuring antioxidants in these salad crops with similar ranking for each salad crop studied.
                Cover page: Antioxidant assays – consistent findings from FRAP and ORAC reveal a negative impact of organic cultivation on antioxidant potential in spinach but not watercress or rocket leaves
                • Article
                • Peer Reviewed
                UC Davis Previously Published Works (2021)
                  Cover page: Embrace open-source sensors for local climate studies
                  • Article
                  • Peer Reviewed
                  UC Davis Previously Published Works (2022)
                  Protected areas and renewable energy generation are critical tools to combat biodiversity loss and climate change, respectively. Over the coming decades, expansion of the protected area network to meet conservation objectives will be occurring alongside rapid deployment of renewable energy infrastructure to meet climate targets, driving potential conflict for a finite land resource. Renewable energy infrastructure can have negative effects on wildlife, and co-occurrence may mean emissions targets are met at the expense of conservation objectives. Here, we assess current and projected overlaps of wind and solar photovoltaic installations and important conservation areas across nine global regions using spatially explicit wind and solar data and methods for predicting future renewable expansion. We show similar levels of co-occurrence as previous studies but demonstrate that once area is accounted for, previous concerns about overlaps in the Northern Hemisphere may be largely unfounded, although they are high in some biodiverse countries (e.g., Brazil). Future projections of overlap between the two land uses presented here are generally dependent on priority threshold and region and suggest the risk of future conflict can be low. We use the best available data on protected area degradation to corroborate this level of risk. Together, our findings indicate that while conflicts between renewables and protected areas inevitably do occur, renewables represent an important option for decarbonization of the energy sector that would not significantly affect area-based conservation targets if deployed with appropriate policy and regulatory controls.
                    Cover page: Predicted wind and solar energy expansion has minimal overlap with multiple conservation priorities across global regions
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