Department of Plant Sciences

In this study, we explore spectral heterogeneity within plant canopies, a characteristic often observed in stressed plants where certain leaves or intra-leaf regions exhibit stress symptoms while others remain unaffected. Considering this variability in spectral signatures holds promise for enhancing remote sensing methodologies aimed at plant stress detection. Typically, remote sensing techniques analyze the plant as a whole, potentially overlooking stress-related spectral signatures due to the inclusion of unaffected pixels. We used a clustering-based technique, which incorporates semi-supervised learning elements for tuning hyper-parameters, to differentiate spectral patterns associated with and unique to pixels from broomrape-infected (Orobanche spp. and Phelipanche spp.) carrots from unrelated patterns. Ground-based hyperspectral (400–1000 nm) images of broomrape-infected and non-infected carrot canopies were used in an agglomerative clustering procedure followed by spectral angle mapper (SAM) analysis to identify a spectral endmember indicative of broomrape infection symptoms. Pixels from this cluster constituted an average of 8.5–11.5 % from the canopies of infected plants. Subsequently, we: (a) examined the relationship between carrot leaf mineral content and the percentage of symptomatic pixels to explore stress-induced alterations creating the unique spectral signatures of infected plants; and (b) utilized the inverse mode of PROSPECT, a radiative transfer model (RTM), to derive primary plant traits from the distinct spectral data of each cluster. We found that deficits in two macro elements, phosphorous and potassium, along with two pigments, chlorophyll and carotenoid, were correlated with the symptomatic cluster in infected plants. The methodology presented in this study paves the way for further research into broomrape detection in various crop species, as well as other plant stressors.

Mutants lacking functional HYD2 homoeologs showed improved seedling growth, but comparable or increased susceptibility to salt stress in tillering plants, suggesting a developmentally restricted role of HYD2 in salt response. Salinity stress threatens global food security by reducing the yield of staple crops such as wheat (Triticum ssp.). Understanding how wheat responds to salinity stress is crucial for developing climate resilient varieties. In this study, we examined the interplay between carotenoid metabolism and the response to salt (NaCl) stress, a specific form of salinity stress, in tetraploid wheat plants with mutations in carotenoid β-hydroxylase 1 (HYD1) and HYD2. Our investigation encompassed both the vulnerable seedling stage and the more developed tillering stage of wheat plant growth. Mutant combinations lacking functional HYD2 homoeologs, including hyd-A2 hyd-B2, hyd-A1 hyd-A2 hyd-B2, hyd-B1 hyd-A2 hyd-B2, and hyd-A1 hyd-B1 hyd-A2 hyd-B2, had longer first true leaves and slightly enhanced root growth during germination under salt stress compared to the segregate wild-type (control) plants. Interestingly, these mutant seedlings also showed decreased levels of neoxanthin and violaxanthin (xanthophylls derived from β-carotene) and an increase in β-carotene in roots. However, tillering hyd mutant and segregate wild-type plants generally did not differ in their height, tiller count, and biomass production under acute or prolonged salt stress, except for decreases in these parameters observed in the hyd-A1 hyd-B1 hyd-A2 hyd-B2 mutant that indicate its heightened susceptibility to salt stress. Taken together, these findings suggest a significant, yet developmentally restricted role of HYD2 homoeologs in salt-stress response in tetraploid wheat. They also show that hyd-A2 hyd-B2 mutant plants, previously demonstrated for possessing enriched nutritional (β-carotene) content, maintain an unimpaired ability to withstand salt stress.

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.

Duckweeds are among the fastest reproducing plants, able to clonally divide at exponential rates. However, the genetic and epigenetic impact of clonality on plant genomes is poorly understood. 5-methylcytosine (5mC) is a modified base often described as necessary for the proper regulation of certain genes and transposons and for the maintenance of genome integrity in plants. However, the extent of this dogma is limited by the current phylogenetic sampling of land plant species diversity. Here we analyzed DNA methylomes, small RNAs, mRNA-seq, and H3K9me2 histone modification for Spirodela polyrhiza. S. polyrhiza has lost highly conserved genes involved in de novo methylation of DNA at sites often associated with repetitive DNA, and within genes, however, symmetrical DNA methylation and heterochromatin are maintained during cell division at certain transposons and repeats. Consequently, small RNAs that normally guide methylation to silence repetitive DNA like retrotransposons are diminished. Despite the loss of a highly conserved methylation pathway, and the reduction of small RNAs that normally target repetitive DNA, transposons have not proliferated in the genome, perhaps due in part to the rapid, clonal growth lifestyle of duckweeds.

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.

Successful alien species may experience a period of quiescence, known as the lag phase, before becoming invasive and widespread. The existence of lags introduces severe uncertainty in risk analyses of aliens as the present state of species is a poor predictor of future distributions, invasion success and impact. Predicting a species' ability to invade and pose negative impacts requires a quantitative understanding of the commonality and magnitude of lags, environmental factors and mechanisms likely to terminate lag. Using herbarium and climate data, we analysed over 5,700 time series (species × regions) in 3,505 naturalized plant species from nine regions in temperate and tropical climates to quantify lags and test whether there have been shifts in the species' climatic space during the transition from the lag phase to the expansion phase. Lags were identified in 35% of the assessed invasion events. We detected phylogenetic signals for lag phases in temperate climate regions and that annual self-fertilizing species were less likely to experience lags. Where lags existed, they had an average length of 40 years and a maximum of 320 years. Lengthy lags (>100 years) were more likely to occur in perennial plants and less frequent in self-pollinating species. For 98% of the species with a lag phase, the climate spaces sampled during the lag period differed from those in the expansion phase based on the assessment of centroid shifts or degree of climate space overlap. Our results highlight the importance of functional traits for the onset of the expansion phase and suggest that climate discovery may play a role in terminating the lag phase. However, other possibilities, such as sampling issues and climate niche shifts, cannot be ruled out.

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.