Biology subjects

Sasidharan, R.

Publications and source records attributed to Sasidharan, R..

At least 19 recordsLinked to original sources

bioRxiv2025

Leaf-age specific flood resilience in Arabidopsis thaliana is determined by distinct processes contributing to post-submergence recovery

While the molecular mechanisms mediating submergence tolerance have been extensively studied, those underpinning age-dependent resilience remain poorly characterized. In Arabidopsis thaliana, submergence elicits a leaf-age dependent phenotype in which senescence and death progress across an age gradient starting with older leaves. Here we sought to investigate the mechanisms mediating this observed differential flood resilience by interrogating leaf age-specific transcriptome and proteome changes during submergence and recovery. Following submergence, most age-dependent differences were in the magnitude or speed of transcript abundance changes, whereas qualitative leaf-age dependent responses were most apparent during recovery. This included a strong desiccation response in old leaves despite a stronger ABA-signaling response. Physiological measurements suggested that faster dehydration was facilitated by a combination of submergence-mediated reduction of ABA sensitivity and higher conductance in old leaves. We also observed a stronger induction in young shoot tissue of genes associated with endoplasmic reticulum (ER) stress and the unfolded protein response (UPR). Mutants disabled in the two UPR signaling branches were affected in new leaf formation and the ability to restore the proteome, but not in senescence, suggesting that young tissues activate ER stress recovery to permit continuation of growth. Of the mitochondrial membrane proteins differentially regulated in young leaves, loss of mitochondrial voltage-dependent anion channel function impacted submergence-recovery tolerance. Our data reveal multiple mechanisms underlying leaf age-dependent differential submergence recovery and demonstrate how tolerance is determined by an interplay between age related developmental traits and stress signaling pathways.

plant biology↗

bioRxiv2025

Haplotype-resolved genome assembly of the tetraploid potato cultivar Desiree

Cultivar Desiree is an important model for potato functional genomics studies to assist breeding strategies. Here, we present a haplotype-resolved genome assembly of Desiree, achieved by assembling PacBio HiFi reads and Hi-C scaffolding, resulting in a high-contiguity chromosome-level assembly. We implemented a comprehensive annotation pipeline incorporating gene models and functional annotations from the Solanum tuberosum Phureja DM reference genome alongside RNA-seq reads to provide high-quality gene and transcript annotations. Additionally, we provide a genome-wide DNA methylation profile using Oxford Nanopore reads, enabling insights into potato epigenetics. The assembled genome, annotations, methylation and expression data are visualised in a publicly accessible genome browser (https://desiree.nib.si), providing a valuable resource for the potato research community.

plant biology↗

bioRxiv2024

Integration of multi-omics and deep phenotyping provides novel insights into multiple abiotic stress responses in potato

Potato is highly water and space efficient but susceptible to abiotic stresses such as heat, drought, or flooding, which are severely exacerbated by climate change. Understanding of crop acclimation to abiotic stress, however, remains limited. Here, we present a comprehensive molecular and physiological high-throughput profiling of potato (Solanum tuberosum, cv. Desiree) under heat, drought and waterlogging applied as single stresses or in combinations designed to mimic realistic future scenarios. Stress-responses were monitored via daily phenotyping and multi-omics analyses of leaf samples comprising transcriptomics, proteomics, metabolomics and hormonomics at several timepoints during and after stress treatments. Additionally, critical metabolites of tuber samples were analysed at the end of the stress period. Integrative analysis of multi-omics data was performed using a bioinformatic pipeline, which was established here, based on machine learning and knowledge networks. Overall, waterlogging had the most immediate and dramatic effects on potato plants, interestingly activating ABA-responses similar to drought stress. In addition, we observed distinct stress signatures at multiple molecular levels in response to heat or drought and to a combination of both. In response to all treatments, we found a downregulation of photosynthesis at different molecular levels, an accumulation of minor amino acids and diverse stress induced hormones. Our integrative multi-omics analysis provides global insights into plant stress responses, facilitating improved breeding strategies towards climate-adapted potato varieties. One Sentence SummaryIntegrated multi-omics analysis of high-throughput phenotyping in potato reveals distinct molecular signatures of acclimation to single and combined abiotic stresses related to climate change.

plant biology↗

bioRxiv2024

Deciphering Arabidopsis thaliana Acclimation to Sublethal Combined Abiotic Stresses

Plants are frequently exposed to environmental challenges. Responses to sub-lethal abiotic stress combinations are complex and often distinct from responses to individual stresses and remain poorly understood. Investigating traits and molecular factors mediating acclimation to stress combinations is essential for the development of climate change-resilient field crops. Here, we studied the morphological, physiological, and molecular responses of Arabidopsis thaliana to i) co-occurring high temperature and drought and ii) flooding sequentially followed by drought, both of which have increased in frequency due to climate change. A set of 15 physiological and morphological traits were assessed during single and combined stresses. By combining these comprehensive trait analyses with transcriptome characterization, we established the generally additive effects of simultaneous or sequential stresses on plant morphology and physiology compared to the corresponding individual stresses. Although drought had a mild effect in both stress combinations, a unique transcriptome signature emerged upon combination with high temperature simultaneously or flooding sequentially. Molecular processes identified as important for multi-stress resilience included plastid-nucleus communication, ABA signaling and photo-acclimation. Based on the RNA-seq data, a set of 39 genes was identified as potential multi-stress response regulators. Mutants were tested to validate their contribution to plant survival and phenotypic acclimation under combined stress. We confirmed the involvement of several genes in regulating phenotypic acclimation traits. Among the novel identified factors are EARLY FLOWERING 6 (ELF6) and ARABIDOPSIS TOXICOS EN LEVADURA (ATL80), with significant effects on plant growth, leaf development and plant survival (wilting) during high-temperature drought and post-submergence drought respectively.

plant biology↗

bioRxiv2024

Phylotranscriptomics provides a treasure trove of flood tolerance mechanisms in the Cardamineae tribe

Flooding events are highly detrimental to most terrestrial plant species. However, there is an impressive diversity of plant species that thrive in flood-prone regions and represent a treasure trove of unexplored flood-resilience mechanisms. Here we surveyed a panel of four species from the Cardamineae tribe representing a broad tolerance range. This included the flood-tolerant Cardamine pratensis, Rorippa sylvestris and Rorippa palustris and the flood-sensitive species Cardamine hirsuta. All four species displayed a quiescent strategy, evidenced by the repression of shoot growth underwater. Comparative transcriptomics analyses between the four species and the sensitive model species Arabidopsis thaliana were facilitated via de-novo transcriptome assembly and identification of 16,902 universal orthogroups at a high resolution. Our results suggest that tolerance likely evolved separately in the Cardamine and Rorippa species. While the Rorippa response was marked by a strong downregulation of cell-cycle genes, Cardamine minimized overall transcriptional regulation. However, a weak starvation signature was a universal trait of tolerant species, potentially achieved in multiple ways. It could result from a strong decline in cell-cycle activity, but is also intertwined with autophagy, senescence, day-time photosynthesis and night-time fermentation capacity. Our dataset provides a rich source to study adaptational mechanisms of flooding tolerance.

plant biology↗

bioRxiv2024

MEDIATOR SUBUNIT 25 modulates ERFVII-controlled hypoxia responses in Arabidopsis

Flooding impairs plant growth through oxygen deprivation, which activates plant survival and acclimation responses. Low-oxygen responses are generally associated with activation of group VII ETHYLENE-RESPONSE FACTOR (ERFVII) transcription factors. However, mechanism and molecular components by which ERFVII factors initiate gene expression are not fully elucidated. Here, we show that the Mediator complex subunit AtMED25 is recruited by RELATED TO APETALA 2.2 (RAP2.2) and RAP2.12 to coordinate gene expression during hypoxia in Arabidopsis thaliana.. The med25 mutants display reduced low-oxygen stress tolerance. AtMED25 associates with several ERFVII-controlled hypoxia core genes and its loss impairs transcription under hypoxia due to decreasing RNA polymerase II recruitment. Protein complex pulldown assays demonstrate that the Mediator complex built around AtMED25 is adjusted under low-oxygen conditions. Moreover, during hypoxia, no functional cooperation between AtMED25 and the two subunits AtMED8 and AtMED16 occurs, contrasting previous observations made for other conditions. In addition, AtMED25 function under hypoxia is independent from ethylene signalling. Finally, a functional conservation at the molecular level was found for the MED25-ERFVII module between Arabidopsis thaliana and the monocot Oryza sativa, pointing to a potentially universal role of MED25 in enabling ERFVII-dependent transcript responses to hypoxia in plants.

plant biology↗

bioRxiv2023

Flower visitor groups show differential responses to individual and plot-level chemodiversity with consequences for plant fitness

O_LIChemodiversity, the diversity of specialised metabolites, plays a crucial role in mediating interactions between plants and animals, including insect herbivores and mutualists. Chemodiversity can be observed at both the individual and the population level. However, the impacts of chemodiversity at these two levels on interactions between plants and floral visitors, mainly pollinators and floral herbivores (florivores), are only poorly understood. C_LIO_LIThis study aimed to investigate the effects of chemodiversity at both individual and plot level on pollinators and florivores, examining their mutual interactions. To investigate these questions, we used individuals of the perennial Tanacetum vulgare differing in their terpenoid composition, representing so-called chemotypes. We planted individuals of five distinct chemotypes in a common garden design with homogeneous (five plants of the same chemotype) and heterogeneous (five different chemotypes) plots and observed flower visits in dependence of individual chemotype and plot type. Seeds were collected from a subset of plants and germination rates determined. C_LIO_LIOur findings revealed that chemodiversity at the plot level significantly influenced pollinator visitation, with more visits on plants of heterogeneous plots. We also observed marginally more pollinators on one of the chemotypes grown in homogeneous plots. In contrast, chemotype but not plot type had a significant effect on florivore visits. Pollinator and florivore species richness did not vary with plot type. Furthermore, a negative correlation was observed between pollinator and florivore visits in one year, suggesting competitive interactions between these two groups. Germination rates were positively correlated with pollinator visits and affected by chemotype but not by florivore visits or plot type. C_LIO_LISynthesis. Our study emphasizes the significance of the scale at which different chemical profiles are perceived by flower visitors, potentially influencing the reproductive fitness of plants. Exploring the ecology of these visitors and the varying selection pressures they exert on floral chemistry can help elucidating the evolutionary processes that maintain chemodiversity in natural environments. C_LI

ecology↗

bioRxiv2023

Chemodiversity in flowers of Tanacetum vulgare has consequences on a florivorous beetle

O_LIThe chemical composition of plant individuals can vary, leading to high intraspecific chemodiversity. Diversity of floral chemistry may impact the responses of flower-feeding insect visitors. C_LIO_LIPlants of Tanacetum vulgare vary significantly in their leaf terpenoid composition, resulting in distinct chemotypes. We investigated the composition of terpenoids and nutritents of flower heads and pollen in plants belonging to three chemotypes, dominated either by {beta}-thujone (BThu), artemisia ketone (Keto) or a mixture of (Z)-myroxide, santolina triene and artemisyl acetate (Myrox). Moreover, we tested the effects of these differences on preferences, weight gain and performance of adults of the shining flower beetle, Olibrus aeneus. C_LIO_LIThe terpenoid composition and diversity of flower heads and pollen significantly differed among individuals belonging to these chemotypes, while total concentrations of terpenoids, sugars, amino acids or lipids of the pollen did not differ. Beetles preferred the BThu over the Myrox chemotype in both olfactory and contact choice assays, while the Keto chemotype was marginally repellent in olfactory assays. The beetles gained the least weight within 48 h and their initial mortality was highest when feeding exclusively on floral tissues of the Myrox chemotype. Short-term weight gain and long-term performance were highest on the BThu chemotype. C_LIO_LIIn conclusion, the beetles showed chemotype-specific responses towards different T. vulgare chemotypes, which may be attributed to the terpenoid composition in flower heads and pollen rather than to differences in nutrient profiles. Both richness and overall diversity are important factors when determining chemodiversity of individual plants and their consequences on interacting insects. C_LI SHORT SUMMARYWe demonstrate that Tanacetum vulgare chemotypes distinguished by their leaf terpenoid profiles also show unique floral and pollen chemotypes based on terpenoid composition and diversity, which affect the preference and performance of a beetle florivore.

ecology↗

bioRxiv2023

Understanding the phytochemical diversity of plants: Quantification, variation and ecological function

Plants produce a great number of phytochemical compounds mediating a variety of different functions. Recently, phytochemical diversity (chemodiversity), a way which to quantify the complex phenotype formed by sets of phytochemicals, has been suggested to be important for function. However, no study has systematically examined the potential (in)direct functional importance of chemodiversity on a general level, partly due to a lack of an agreement on how to quantify this aspect of the plant phenotype. This paper has four aims: 1) We discuss how chemodiversity (deconstructed into components of richness, evenness and disparity) may quantify different aspects of the phenotype that are ecologically relevant. 2) We systematically review the literature on chemodiversity to examine methodological practices, explore ecological patterns of variability in diversity across different levels of biological organization, and investigate the functional role of this diversity in interactions between plants and other organisms. 3) We provide a framework facilitating decisions on which measure of chemodiversity is best used in different contexts. 4) We outline open questions and avenues for future research in this area. A more thorough understanding of phytochemical diversity will increase our knowledge on the functional role phytochemical compounds, and how they shape ecological interactions between plants and their environment.

ecology↗

bioRxiv2023

Inter-laboratory comparison of plant volatile analyses in the light of intra-specific chemodiversity

IntroductionAssessing intraspecific variation in plant volatile organic compounds (VOCs) involves pitfalls that may bias biological interpretation, particularly when several laboratories collaborate on joint projects. Comparative, inter-laboratory ring trials can inform on the reproducibility of such analyses. ObjectivesIn a ring trial involving five laboratories, we investigated the reproducibility of VOC collections with polydimethylsiloxane (PDMS) and analyses by thermal desorption-gas chromatography-mass spectrometry (TD-GC-MS). As model plant we used Tanacetum vulgare, which shows a remarkable diversity in terpenoids, forming so-called chemotypes. We performed our ring-trial with two chemotypes to examine the sources of technical variation in plant VOC measurements during pre-analytical, analytical, and post-analytical steps. MethodsMonoclonal root cuttings were generated in one laboratory and distributed to five laboratories, in which plants were grown under laboratory-specific conditions. VOCs were collected on PDMS tubes from all plants before and after a jasmonic acid (JA) treatment. Thereafter, each laboratory (donors) sent a subset of tubes to four of the other laboratories (recipients), which performed TD-GC-MS with their own established procedures. ResultsChemotype-specific differences in VOC profiles were detected but with an overall high variation both across donor and recipient laboratories. JA-induced changes in VOC profiles were not reproducible. Laboratory-specific growth conditions led to phenotypic variation that affected the resulting VOC profiles. ConclusionOur ring trial shows that despite large efforts to standardise each VOC measurement step, the outcomes differed both qualitatively and quantitatively. Our results reveal sources of variation in plant VOC research and may help to avoid systematic errors in similar experiments.

plant biology↗

bioRxiv2023

Floral volatiles evoke partially similar responses in both florivores and pollinators and are correlated with non-volatile reward chemicals

BackgroundPlants use floral displays to attract mutualists, but simultaneously need to prevent attacks by antagonists. Chemical displays detectable from a distance include attractive or repellent floral volatile organic compounds (FVOCs). Post-landing, visitors perceive contact chemicals including nutrients, but also deterrent or toxic constituents in pollen and nectar, protecting flowers from overexploitation. The composition of FVOCs and pollen chemistry is well known to vary among and within species. However, we lack knowledge about differences and similarities in the detectability of and behavioural responses towards these compounds for insect flower visitor groups of key importance, i.e., mutualistic pollinators versus antagonistic florivores, as well as the correlation between FVOCs and pollen chemodiversity. ScopeWe reviewed how FVOCs and non-volatile floral chemical displays, i.e., nutrients and toxins of pollen, vary in composition and how they affect the detection and behaviour of insect flower visitors. Moreover, we used a meta-analytic approach to evaluate the detection of and responses towards FVOCs by pollinators vs. florivores within the same plant genera. Furthermore, we tested whether the chemodiversity of FVOCs as well as nutrients and toxins stored in pollen are correlated and hence informative about each other. Key ResultsAccording to the available data, florivores are more likely to detect FVOCs than pollinators. Common FVOCs such as linalool and methyl salicylate were often reported as attractive to pollinators and repellent towards florivores. A higher number of FVOCs was found to be attractive to both mutualists and antagonists compared to shared repellent compounds. Furthermore, a negative correlation between FVOC richness and the number of pollen toxin classes was revealed, besides a trend towards a positive correlation between pollen protein amount and the number of pollen toxins. ConclusionsPlants face critical trade-offs when producing floral chemicals, as these partly mediate the same information, particularly attraction but also repellence or toxicity, to both mutualists and antagonists. Moreover, chemodiversity of different floral parts is partly correlated and thus highly relevant for investigations of flower-insect interactions. Further research is needed on more different wild and cultivated plant species and mutualistic and antagonistic interaction partners to test for generalisation of these patterns.

ecology↗

bioRxiv2022

Ethylene-mediated phosphorylation of ORESARA1 induces sequential leaf death during flooding in Arabidopsis

The volatile phytohormone ethylene is a major regulator of plant adaptive responses to flooding. In flooded plant tissues, it quickly increases to high concentrations due to its low solubility and diffusion rates in water. The passive, quick and consistent accumulation of ethylene in submerged plant tissues makes it a reliable cue to trigger flood-acclimative responses, including metabolic adjustments to cope with flood-induced hypoxia. However, persistent ethylene accumulation also accelerates leaf senescence. Stress-induced senescence hampers the photosynthetic capacity and stress recovery. In submerged Arabidopsis shoots, senescence follows a strict age-dependent pattern starting with the older leaves. Although mechanisms underlying ethylene-mediated senescence have been uncovered, it is unclear how submerged plants avoid an indiscriminate breakdown of leaves despite high systemic ethylene accumulation. Here we demonstrate in Arabidopsis plants that even though submergence triggers a leaf-age independent activation of ethylene signaling via EIN3, senescence was initiated only in the old leaves, and independent of the N-degron pathway of oxygen sensing. This EIN3 stabilization also led to the overall transcript and protein accumulation of the senescence-promoting transcription factor ORESARA1 (ORE1). ORE1 protein accumulated in both old and young leaves during submergence. However, leaf age-dependent senescence could be explained by ORE1 protein activation specifically in old leaves, independent of the previously identified age-dependent control of ORE1 via miR164. Our results unravel a mechanism by which plants regulate the speed and pattern of senescence during environmental stresses like flooding. The age-dependent activity of ORE1 ensures that older expendable leaves are dismantled first, thus prolonging the life of younger leaves and meristematic tissues vital to whole plant survival. Significance statementFlooded plants systemically accumulate saturating concentrations of the senescence promoting volatile hormone ethylene. Yet, leaf senescence follows a strict age-dependent gradient, thus prolonging the survival of young leaves and meristematic tissue. Here we show that in flooded plants, age-independent activation of ethylene signaling via EIN3, induces the systemic accumulation of the senescence-inducing transcription factor ORE1. Premature senescence of younger tissues is prevented by the posttranslational activation of ORE1 specifically in old leaves, where it induces the transcription of senescence-associated genes. Our results highlight how a systemic stress signal (ethylene accumulation upon flooding) induces a signaling cascade that diverges in an age-dependent manner, and eventually leads to an age-dependent physiological output (leaf senescence).

plant biology↗

bioRxiv2022

Arabidopsis latent virus 1, a comovirus widely spread in Arabidopsis thaliana collections

O_LITranscriptome studies of Illumina RNA-seq datasets of different Arabidopsis thaliana natural accessions and T-DNA mutants revealed the presence of two virus-like RNA sequences which showed the typical two segmented genome characteristics of a comovirus. C_LIO_LIThis comovirus did not induce any visible symptoms in infected Arabidopsis plants cultivated under standard laboratory conditions. Hence it was named Arabidopsis latent virus 1 (ArLV1). Virus infectivity in Arabidopsis plants was confirmed by RT-qPCR, transmission electron microscopy and mechanical inoculation. ArLV1 can also mechanically infect Nicotiana benthamiana, causing distinct mosaic symptoms. C_LIO_LIA bioinformatics investigation of Arabidopsis RNA-Seq repositories, including nearly 6500 Sequence Read Archives (SRAs) in the NCBI SRA database, revealed the presence of ArLV1 in 25% of all archived natural Arabidopsis accessions and in 8.5% of all analyzed SRAs. ArLV1 could also be detected in Arabidopsis plants collected from the wild. C_LIO_LIArLV1 is highly seed-transmissible with up to 40% incidence on the progeny derived from infected Arabidopsis plants. This has likely led to a worldwide distribution in the model plant Arabidopsis with yet unknown effects on plant performance in a substantial number of studies. C_LI Plain language summaryWe identified Arabidopsis latent virus 1 (ArLV1), a comovirus that infects the model plant Arabidopsis thaliana without causing any visible symptoms. It is efficiently spread by transmission via seeds to the plant progeny. ArLV1 is infectious to Arabidopsis plants and another model plant, Nicotiana benthamiana. By analyzing public sequencing data, we found that ArLV1 is widely spread in Arabidopsis laboratory collections worldwide. Moreover, it was also detected in wild Arabidopsis plants collected from different locations in the Netherlands and Spain, suggesting that it is a virus that naturally occurs in Arabidopsis.

plant biology↗

bioRxiv2022

Ethylene augments root hypoxia tolerance through amelioration of reactive oxygen species and growth cessation

Flooded plants experience impaired gas diffusion underwater, leading to oxygen deprivation (hypoxia). The volatile plant hormone ethylene is rapidly trapped in submerged plant cells and is instrumental for enhanced hypoxia acclimation. However, the precise mechanisms underpinning ethylene-enhanced hypoxia survival remain unclear. We studied the effect of ethylene pre-treatment on hypoxia survival of primary Arabidopsis thaliana root tips. Both hypoxia itself and re-oxygenation following hypoxia are highly damaging to root tip cells and ethylene pre-treatments reduced this damage. Ethylene pre-treatment alone altered the abundance of transcripts and proteins involved in hypoxia responses, root growth, translation and reactive oxygen species (ROS) homeostasis. Through imaging and manipulating ROS abundance in planta, we demonstrate that ethylene limits excessive ROS formation during hypoxia and subsequent re-oxygenation and improves oxidative stress survival. In addition, we show that ethylene leads to rapid root growth cessation and this quiescence behaviour contributes to enhanced hypoxia tolerance. Collectively, our results show that the early flooding signal ethylene modulates a variety of processes that all contribute to hypoxia survival.

plant biology↗

bioRxiv2021

Effects of sub-lethal single, simultaneous, and sequential abiotic stresses on phenotypic traits of Arabidopsis thaliana

Plant responses to abiotic stresses are complex and dynamic, and involve changes in different traits, either as the direct consequence of the stress, or as an active acclimatory response. Abiotic stresses frequently occur simultaneously or in succession, rather than in isolation. Despite this, most studies have focused on a single stress and single or few plant traits. To address this gap, our study comprehensively and categorically quantified the individual and combined effects of three major abiotic stresses associated with climate change (flooding, progressive drought and high temperature) on 12 phenotypic traits related to morphology, development, growth and fitness, at different developmental stages in four Arabidopsis thaliana accessions. Combined sub-lethal stresses were applied either simultaneously (high temperature and drought) or sequentially (flooding followed by drought). In total, we analyzed the phenotypic responses of 1782 individuals across these stresses and different developmental stages. Overall, abiotic stresses and their combinations resulted in distinct patterns of effects across the traits analyzed, with both quantitative and qualitative differences across accessions. Stress combinations had additive effects on some traits, whereas clear positive and negative interactions were observed for other traits: 9 out of 12 traits for high temperature and drought, 6 out of 12 traits for post-submergence and drought showed significant interactions. In many cases where the stresses interacted, the strength of interactions varied across accessions. Hence, our results indicated a general pattern of response in most phenotypic traits to the different stresses and stress combinations, but it also indicated a natural genetic variation in the strength of these responses. Overall, our study provides a rich characterization of trait responses of Arabidopsis plants to sub-lethal abiotic stresses at the phenotypic level and can serve as starting point for further in-depth physiological research and plant modelling efforts.

plant biology↗

bioRxiv2021

Towards increased shading potential: a combined phenotypic and genetic analysis of rice shoot architecture

Rice feeds more than half of the worlds human population. In modern rice farming, a major constraint for productivity is weed proliferation and the ecological impact of herbicide application. Increased weed competitiveness of commercial rice varieties requires enhanced shade casting to limit growth of shade-sensitive weeds and the need for herbicide. We aimed to identify traits that enhance rice shading capacity based on the canopy architecture and the underlying genetic components. We performed a phenotypic screen of a rice diversity panel comprised of 344 varieties, examining 13 canopy architecture traits linked with shading capacity in 4-week-old plants. The analysis revealed a vast range of phenotypic variation across the diversity panel. We used trait correlation and clustering to identify core traits that define shading capacity to be shoot area, number of leaves, culm and solidity (the compactness of the shoot). To simplify the complex canopy architecture, these traits were combined into a Shading Rank metric that is indicative of a plants ability to cast shade. Genome wide association study (GWAS) revealed genetic loci underlying canopy architecture traits, out of which five loci were substantially contributing to shading potential. Subsequent haplotype analysis further explored allelic variation and identified seven haplotypes associated with increased shading. Identification of traits contributing to shading capacity and underlying allelic variation presented in this study will serve future genomic assisted breeding programmes. The investigated diversity panel, including widely grown varieties, shows that there is big potential and genetic resources for improvement of elite breeding lines. Implementing increased shading in rice breeding will make its farming less dependent on herbicides and contribute towards more environmentally sustainable agriculture. One sentence summaryThrough screening a rice diversity panel for variation in shoot architecture, we identified traits corresponding to plant shading potential and their genetic constituents.

plant biology↗

bioRxiv2019

Ethylene-mediated nitric oxide depletion pre-adapts plants to hypoxia stress

Timely perception of adverse environmental changes is critical for survival. Dynamic changes in gases are important cues for plants to sense environmental perturbations, such as submergence. In Arabidopsis thaliana, changes in oxygen and nitric oxide (NO) control the stability of ERFVII transcription factors. ERFVII proteolysis is regulated by the N-degron pathway and mediates adaptation to flooding-induced hypoxia. However, how plants detect and transduce early submergence signals remains elusive. Here we show that plants can rapidly detect submergence through passive ethylene entrapment and use this signal to pre-adapt to impending hypoxia. Ethylene can enhance ERFVII stability prior to hypoxia by increasing the NO-scavenger PHYTOGLOBIN1. This ethylene-mediated NO depletion and consequent ERFVII accumulation pre-adapts plants to survive subsequent hypoxia. Our results reveal the biological link between three gaseous signals for the regulation of flooding survival and identifies novel regulatory targets for early stress perception that could be pivotal for developing flood-tolerant crops.

plant biology↗

bioRxiv2019

Cytokinin functions as an asymmetric and anti-gravitropic signal in lateral roots

Directional organ growth allows the plant root system to strategically cover its surroundings. Intercellular auxin transport is aligned with the gravity vector in the primary root tips, facilitating downward organ bending at the lower root flank. Here we show that cytokinin signaling functions as a lateral root specific anti-gravitropic component, promoting the radial distribution of the root system. We performed a genome-wide association study and revealed that signal peptide processing of Cytokinin Oxidase 2 (CKX2) affects its enzymatic activity and, thereby, determines the degradation of cytokinins in natural Arabidopsis thaliana accessions. Cytokinin signaling interferes with growth at the upper lateral root flank and thereby prevents downward bending. Our interdisciplinary approach revealed that two phytohormonal cues at opposite organ flanks counterbalance each others negative impact on growth, suppressing organ growth towards gravity and allow for radial expansion of the root system.

plant biology↗