Department of Plant Sciences

BACKGROUND: Development of transgenic rice overexpressing transcription factors involved in drought response has been previously reported to confer drought tolerance and therefore represents a means of crop improvement. We transformed lowland rice IR64 with OsTZF5, encoding a CCCH-tandem zinc finger protein, under the control of the rice LIP9 stress-inducible promoter and compared the drought response of transgenic lines and nulls to IR64 in successive screenhouse paddy and field trials up to the T6 generation. RESULTS: Compared to the well-watered conditions, the level of drought stress across experiments varied from a minimum of - 25 to - 75 kPa at a soil depth of 30 cm which reduced biomass by 30-55% and grain yield by 1-92%, presenting a range of drought severities. OsTZF5 transgenic lines showed high yield advantage under drought over IR64 in early generations, which was related to shorter time to flowering, lower shoot biomass and higher harvest index. However, the increases in values for yield and related traits in the transgenics became smaller over successive generations despite continued detection of drought-induced transgene expression as conferred by the LIP9 promoter. The decreased advantage of the transgenics over generations tended to coincide with increased levels of homozygosity. Background cleaning of the transgenic lines as well as introgression of the transgene into an IR64 line containing major-effect drought yield QTLs, which were evaluated starting at the BC3F1 and BC2F3 generation, respectively, did not result in consistently increased yield under drought as compared to the respective checks. CONCLUSIONS: Although we cannot conclusively explain the genetic factors behind the loss of yield advantage of the transgenics under drought across generations, our results help in distinguishing among potential drought tolerance mechanisms related to effectiveness of the transgenics, since early flowering and harvest index most closely reflected the levels of yield advantage in the transgenics across generations while reduced biomass did not.

There are more incidents of violence in summer and on hot days, a trend likely to be exacerbated by climate change. Urban areas experience additional temperature modulation due to the urban form, however, to date, no studies have considered the effect of the urban heat island (UHI) or green space with respect to the temperature-violence relationship. This study modelled the relationship between the number of daily violent crime incidents that occurred inside or outside between July 2013 and June 2018, and the average surface UHI or percentage greencover (including grasses, shrubs and trees) within each local government area in Greater Sydney, Australia. Panelised negative binomial time series regression models indicated that the violent crime rate was associated with higher surface UHI for crimes committed outside (p = 0.006) but not inside (p = 0.072). Greater percentage of all vegetation was associated with significantly lower rates of violent crime committed outside (p = 0.011) but was not associated with violent crimes committed inside (p = 0.430). More socio-economic disadvantage was associated with higher rates of violent crime committed inside (p = 0.002) but not outside (p = 0.145). Greater temperature was non-linearly associated with higher rates of violent crime committed both inside and outside (p < 0.001). The findings of this study are important because both violence and heat exposure are critical health issues and will be stressed by urbanisation and climate change. The expansion of green space and/or reduction in UHI may mitigate these effects.

The annual production of strawberry has increased by one million tonnes in the US and 8.4 million tonnes worldwide since 1960. Here we show that the US expansion was driven by genetic gains from Green Revolution breeding and production advances that increased yields by 2,755%. Using a California population with a century-long breeding history and phenotypes of hybrids observed in coastal California environments, we estimate that breeding has increased fruit yields by 2,974-6,636%, counts by 1,454-3,940%, weights by 228-504%, and firmness by 239-769%. Using genomic prediction approaches, we pinpoint the origin of the Green Revolution to the early 1950s and uncover significant increases in additive genetic variation caused by transgressive segregation and phenotypic diversification. Lastly, we show that the most consequential Green Revolution breeding breakthrough was the introduction of photoperiod-insensitive, PERPETUAL FLOWERING hybrids in the 1970s that doubled yields and drove the dramatic expansion of strawberry production in California.

In Arabidopsis thaliana, ARGONAUTE1 (AGO1) plays a central role in microRNA (miRNA) and small interfering RNA (siRNA)-mediated silencing. AGO1 associates to the rough endoplasmic reticulum to conduct miRNA-mediated translational repression, mRNA cleavage, and biogenesis of phased siRNAs. Here, we show that a 37°C heat stress (HS) promotes AGO1 protein accumulation in cytosolic condensates where it colocalizes with components of siRNA bodies and of stress granules. AGO1 contains a prion-like domain in its poorly characterized N-terminal Poly-Q domain, which is sufficient to undergo phase separation independently of the presence of SGS3. HS only moderately affects the small RNA repertoire, the loading of AGO1 by miRNAs, and the signatures of target cleavage, suggesting that its localization in condensates protects AGO1 rather than promoting or impairing its activity in reprogramming gene expression during stress. Collectively, our work sheds new light on the impact of high temperature on a main effector of RNA silencing in plants.

Water-seeded rice (Oryza sativa L.) in California is produced near growing urban centers and a variety of neighboring high-value crops, which make water quality a paramount concern because of potential herbicide residue contamination in downstream surface waters. Pendimethalin is a potential herbicide for use in California water-seeded rice. A study was conducted to characterize pendimethalin's dissipation in water of a water-seeded rice field. A capsule suspension (CS), emulsifiable concentrate (EC), and granule (GR) pendimethalin were applied onto flooded rice plots at 1.1, 2.3, and 3.4 kg ai ha−1 rates. Water samples were collected periodically and analyzed with an high pressure liquid chromatography tandem mass spectrometry system for residues. Pendimethalin dissipation differed across formulations. The initial sampled concentrations recorded values from 3.0 to 125.6 parts per billion (ppb). First-order dissipation resulted in half-lives for the CS from 2.3 to 3.5 days, the EC from 0.6 to 0.7 days, and the GR from 3.5 to 6.9 days. Pendimethalin use in water-seeded rice is at low risk of contaminating downstream surface waters; however, early sampled residue concentrations could be concerning. The results can assist in generating management tactics like water-holding periods to avoid potential downstream off-target effects and ensure herbicidal activity in the applied area after a pendimethalin application in a water-seeded rice field.

Autophagy in eukaryotes functions to maintain homeostasis by degradation and recycling of long-lived and unwanted cellular materials. Autophagy plays important roles in pathogenicity of various fungal pathogens, suggesting that autophagy is a novel target for development of antifungal compounds. Here, we describe bioluminescence resonance energy transfer (BRET)-based high-throughput screening (HTS) strategy to identify compounds that inhibit fungal ATG4 cysteine protease-mediated cleavage of ATG8 that is critical for autophagosome formation. We identified ebselen (EB) and its analogs ebselen oxide (EO) and 2-(4-methylphenyl)-1,2-benzisothiazol-3(2H)-one (PT) as inhibitors of fungal pathogens Botrytis cinerea and Magnaporthe oryzae ATG4-mediated ATG8 processing. The EB and its analogs inhibit spore germination, hyphal development, and appressorium formation in Ascomycota pathogens, B. cinerea, M. oryzae, Sclerotinia sclerotiorum and Monilinia fructicola. Treatment with EB and its analogs significantly reduced fungal pathogenicity. Our findings provide molecular insights to develop the next generation of antifungal compounds by targeting autophagy in important fungal pathogens.

BACKGROUND: The most aggressive form of breast cancer is triple-negative breast cancer (TNBC), which lacks expression of the estrogen receptor (ER) and progesterone receptor (PR), and does not have overexpression of the human epidermal growth factor receptor 2 (HER2). Treatment options for women with TNBC tumors are limited, unlike those with ER-positive tumors that can be treated with hormone therapy, or those with HER2-positive tumors that can be treated with anti-HER2 therapy. Therefore, we have sought to identify novel targeted therapies for TNBC. In this study, we investigated the potential of a novel phosphatase, NUDT5, as a potential therapeutic target for TNBC. METHODS: The mRNA expression levels of NUDT5 in breast cancers were investigated using TCGA and METABRIC (Curtis) datasets. NUDT5 ablation was achieved through siRNA targeting and NUDT5 inhibition with the small molecule inhibitor TH5427. Xenograft TNBC animal models were employed to assess the effect of NUDT5 inhibition on in vivo tumor growth. Proliferation, death, and DNA replication assays were conducted to investigate the cellular biological effects of NUDT5 loss or inhibition. The accumulation of 8-oxo-guanine (8-oxoG) and the induction of γH2AX after NUDT5 loss was determined by immunofluorescence staining. The impact of NUDT5 loss on replication fork was assessed by measuring DNA fiber length. RESULTS: In this study, we demonstrated the significant role of an overexpressed phosphatase, NUDT5, in regulating oxidative DNA damage in TNBCs. Our findings indicate that loss of NUDT5 results in suppressed growth of TNBC both in vitro and in vivo. This growth inhibition is not attributed to cell death, but rather to the suppression of proliferation. The loss or inhibition of NUDT5 led to an increase in the oxidative DNA lesion 8-oxoG, and triggered the DNA damage response in the nucleus. The interference with DNA replication ultimately inhibited proliferation. CONCLUSIONS: NUDT5 plays a crucial role in preventing oxidative DNA damage in TNBC cells. The loss or inhibition of NUDT5 significantly suppresses the growth of TNBCs. These biological and mechanistic studies provide the groundwork for future research and the potential development of NUDT5 inhibitors as a promising therapeutic approach for TNBC patients.

Southeast Asia (SEA) is a key producer and exporter of rice, accounting for around 28% of rice produced globally. To effectively mitigate greenhouse gas (GHG) emissions in SEA rice systems, field methane (CH4) and nitrous oxide (N2O) emissions have been intensively studied. However, an integrated assessment of system-level GHG emissions which includes other carbon (C) balance components, such as soil organic carbon (SOC) or energy use, that can positively or negatively influence the net capacity for climate change mitigation is lacking. We conducted a systematic review of published research in SEA rice systems to synthesize findings across four main components of net system emissions: (1) field GHG emissions, (2) energy inputs, (3) residue utilization beyond the field, and (4) SOC change. The objectives were to highlight effective mitigation opportunities and explore cross-component effects to identify tradeoffs and key knowledge gaps. Field GHG emissions were the largest contributor to net system emissions in agreement with existing scientific consensus, with results showing that practices such as floodwater drainage and residue removal are sound options for CH4 mitigation. On the other hand, increasing SOC potentially provides a large GHG mitigation opportunity, with long-term continuous rice cropping and practices such as residue incorporation and biochar application promoting SOC increase. A reduction in energy inputs was mainly achieved by optimizing agrochemical use, especially N fertilizers. For residue utilization beyond the field, GHG emission mitigation mainly came from preventing open field burning through residue removal. Removed residue can subsequently be used for producing energy that offsets GHG emissions associated with conventional fuel sources (e.g. fossil fuel-based electricity generation) or substituting material used in other production systems. Integrating all four components of net system emissions into one analysis underscores the following two main takeaways. First, the components of field GHG emissions and SOC change are the biggest opportunities for reducing net system emissions and need to be considered for effective climate change mitigation. Second, the reduction of C inputs through residue removal and increased soil aeration through multiple drainage will lower CH4 emissions but may also potentially decrease SOC stocks over time. Hence, we argue that future research needs to consider cross-component effects to optimize net system emissions, specifically the “stacking” of best management practices for mitigation related to field GHG emissions or SOC change in long-term experiments.

Powdery mildew (PM) is one of the most destructive diseases that threaten cucumber production globally. Efficient breeding of novel PM-resistant cultivars will require a robust understanding of the molecular mechanisms of cucumber resistance against PM. Using a genome-wide association study, we detected a locus significantly correlated with PM resistance in cucumber stem, pm-s5.1. A 1449-bp insertion in the CsMLO8 coding region at the pm-s5.1 locus resulted in enhanced stem PM resistance. Knockout mutants of CsMLO8 and CsMLO11 generated by CRISPR/Cas9 both showed improved PM resistance in the stem, hypocotyl, and leaves, and the double mutant mlo8mlo11 displayed even stronger resistance. We found that reactive oxygen species (ROS) accumulation was higher in the stem of these mutants. Protein interaction assays suggested that CsMLO8 and CsMLO11 could physically interact with CsRbohD and CsCRK2, respectively. Further, we showed that CsMLO8 and CsCRK2 competitively interact with the C-terminus of CsRbohD to affect CsCRK2-CsRbohD module-mediated ROS production during PM defense. These findings provide new insights into the understanding of CsMLO proteins during PM defense responses.

Microbial competition within plant tissues affects invading pathogens fitness. Metabolomics is a great tool for studying their biochemical interactions by identifying accumulated metabolites. Xylella fastidiosa, a Gram-negative bacterium causing Pierces disease (PD) in grapevines, secretes various virulence factors including cell wall-degrading enzymes, adhesion proteins, and quorum-sensing molecules. These factors, along with outer membrane vesicles, contribute to its pathogenicity. Previous studies demonstrated that co-inoculating X. fastidiosa with the Paraburkholderia phytofirmans strain PsJN suppressed PD symptoms. Here, we further investigated the interaction between the phytopathogen and the endophyte by analyzing the exometabolome of wild-type X. fastidiosa and a diffusible signaling factor (DSF) mutant lacking quorum sensing, cultivated with 20% P. phytofirmans spent media. Liquid chromatography-mass spectrometry (LC-MS) and the Method for Metabolite Annotation and Gene Integration (MAGI) were used to detect and map metabolites to genomes, revealing a total of 121 metabolites, of which 25 were further investigated. These metabolites potentially relate to host adaptation, virulence, and pathogenicity. Notably, this study presents the first comprehensive profile of X. fastidiosa in the presence of a P. phytofirmans spent media. The results highlight that P. phytofirmans and the absence of functional quorum sensing affect the ratios of glutamine to glutamate (Gln:Glu) in X. fastidiosa. Additionally, two compounds with plant metabolism and growth properties, 2-aminoisobutyric acid and gibberellic acid, were downregulated when X. fastidiosa interacted with P. phytofirmans. These findings suggest that P. phytofirmans-mediated disease suppression involves modulation of the exometabolome of X. fastidiosa, impacting plant immunity.