SEARCH · Search bioRxiv

Results for “Plant Biology”

Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 703 records · Page 39Linked to original sources

bioRxiv2018

High-resolution genetic map and QTL analysis of growth-related traits of Hevea brasiliensis cultivated under suboptimal temperature and humidity conditions

Rubber tree (Hevea brasiliensis) cultivation is the main source of natural rubber worldwide and has been extended to areas with suboptimal climates and lengthy drought periods; this transition affects growth and latex production. High-density genetic maps with reliable markers support precise mapping of quantitative trait loci (QTL), which can help reveal the complex genome of the species, provide tools to enhance molecular breeding, and shorten the breeding cycle. In this study, QTL mapping of the stem diameter, tree height, and number of whorls was performed for a full-sibling population derived from a GT1 and RRIM701 cross. A total of 225 simple sequence repeats (SSRs) and 186 single-nucleotide polymorphism (SNP) markers were used to construct a base map with 18 linkage groups and to anchor 671 SNPs from genotyping by sequencing (GBS) to produce a very dense linkage map with small intervals between loci. The final map was composed of 1,079 markers, spanned 3,779.7 cM with an average marker density of 3.5 cM, and showed collinearity between markers from previous studies. Significant variation in phenotypic characteristics was found over a 59-month evaluation period with a total of 38 QTLs being identified through a composite interval mapping method. Linkage group 4 showed the greatest number of QTLs (7), with phenotypic explained values varying from 7.67% to 14.07%. Additionally, we estimated segregation patterns, dominance, and additive effects for each QTL. A total of 53 significant effects for stem diameter were observed, and these effects were mostly related to additivity in the GT1 clone. Associating accurate genome assemblies and genetic maps represents a promising strategy for identifying the genetic basis of phenotypic traits in rubber trees. Then, further research can benefit from the QTLs identified herein, providing a better understanding of the key determinant genes associated with growth of Hevea brasiliensis under limiting water conditions.

plant biology↗

bioRxiv2018

Seed Genome Hypomethylated Regions Are Enriched In Transcription Factor Genes

The precise mechanisms that control gene activity during seed development remain largely unknown. Previously, we showed that several genes essential for seed development, including those encoding storage proteins, fatty acid biosynthesis enzymes, and transcriptional regulators, such as ABI3 and FUS3, are located within hypomethylated regions of the soybean genome. These hypomethylated regions are similar to the DNA methylation valleys (DMVs), or canyons, found in mammalian cells. Here, we address the question of the extent to which DMVs are present within seed genomes, and what role they might play in seed development. We scanned soybean and Arabidopsis seed genomes from post-fertilization through dormancy and germination for regions that contain < 5% or < 0.4% bulk methylation in CG-, CHG-, and CHH-contexts over all developmental stages. We found that DMVs represent extensive portions of seed genomes, range in size from 5 to 76 kb, are scattered throughout all chromosomes, and are hypomethylated throughout the plant life cycle. Significantly, DMVs are enriched greatly in transcription factor genes, and other developmental genes, that play critical roles in seed formation. Many DMV genes are regulated with respect to seed stage, region, and tissue - and contain H3K4me3, H3K27me3, or bivalent marks that fluctuate during development. Our results indicate that DMVs are a unique regulatory feature of both plant and animal genomes, and that a large number of seed genes are regulated in the absence of methylation changes during development - probably by the action of specific transcription factors and epigenetic events at the chromatin level.\n\nSignificanceWe scanned soybean and Arabidopsis seed genomes for hypomethylated regions, or DNA Methylation Valleys (DMVs), present in mammalian cells. A significant fraction of seed genomes contain DMV regions that have < 5% bulk DNA methylation, or, in many cases, no detectable DNA methylation. Methylation levels of seed DMVs do not vary detectably during seed development with respect to time, region, and tissue, and are present prior to fertilization. Seed DMVs are enriched in transcription factor genes and other genes critical for seed development, and are also decorated with histone marks that fluctuate with developmental stage, resembling in significant ways their animal counterparts. We conclude that many genes playing important roles in seed formation are regulated in the absence of detectable DNA methylation events, and suggest that selective action of transcriptional activators and repressors, as well as chromatin epigenetic events play important roles in making a seed - particularly embryo formation.

plant biology↗

bioRxiv2018

A Genome-Wide Association Study Reveals a Novel Regulator of Ovule Number and Fertility in Arabidopsis thaliana

Ovules contain the female gametophytes which are fertilized during pollination to initiate seed development. Thus, the number of ovules that are produced during flower development is an important determinant of seed crop yield and plant fitness. Mutants with pleiotropic effects on development often alter the number of ovules, but specific regulators of ovule number have been difficult to identify in traditional mutant screens. We used natural variation in Arabidopsis accessions to identify new genes involved in the regulation of ovule number. The ovule numbers per flower of 189 Arabidopsis accessions were determined and found to have broad phenotypic variation that ranged from 39 ovules to 84 ovules per pistil. Genome-Wide Association tests revealed several genomic regions that are associated with ovule number. T-DNA insertion lines in candidate genes from the most significantly associated loci were screened for ovule number phenotypes. The NEW ENHANCER of ROOT DWARFISM (NERD1) gene was found to have pleiotropic effects on plant fertility that include regulation of ovule number and both male and female gametophyte development. Overexpression of NERD1 increased ovule number per fruit in a background-dependent manner and more than doubled the total number of flowers produced in all backgrounds tested, indicating that manipulation of NERD1 levels can be used to increase plant productivity.\n\nAuthor SummaryOvules are the precursors of seeds in flowering plants. Each ovule contains an egg cell and a central cell that fuse with two sperm cells during double fertilization to generate seeds containing an embryo and endosperm. The number of ovules produced during flower development determines the maximum number of seeds that can be produced by a flower. In this paper, we used natural variation in Arabidopsis thaliana accessions to identify regions of the genome that are associated with ovule number. Polymorphisms in the plant-specific NERD1 gene on chromosome 3 were significantly associated with ovule number. Mutant and overexpression analyses revealed that NERD1 is a positive regulator of ovule number, lateral branching, and flower number in Arabidopsis. Manipulation of NERD1 expression levels could potentially be used to increase yield in crop plants.

plant biology↗

bioRxiv2018

Paralogues of the PXY and ER receptor kinases enforce radial patterning in plant vascular tissue.

Plant cell walls do not allow cells to migrate, thus plant growth and development is entirely the consequence of changes to cell division and cell elongation. Where tissues are arranged in concentric rings, expansion of inner tissue, such as that which occurs during vascular development, must be coordinated with cell division and/or expansion of the outer tissue layers, endodermis, cortex, and epidermis, in order for tissue integrity to be maintained. Little is known of how coordination between cell layers occurs, but non-cell autonomous signalling could provide an explanation. Endodermis-derived EPIDERMAL PATTERNING FACTOR-LIKE (EPFL) ligands have been shown to signal to the ERECTA (ER) receptor kinase present in the phloem. ER interacts with PHLOEM INTERCALLATED WITH XYLEM (PXY), a receptor present in the procambium. The PXY ligand, TRACHEARY ELEMENT DIFFERENTIATION INHIBITORY FACTOR (TDIF) is derived from CLE41 which is expressed in the phloem. These factors therefore represent a mechanism by which intertissue signalling could occur to control radial expansion between vascular and non-vascular tissue in plant stems. Here we show that ER regulates expression of PXY paralogues, PXL1 and PXL2, and that in turn PXY, PXL1 and PXL2 together with ER, regulate the expression of ERL1 and ERL2, genes paralogous to ER. PXY, PXL1, PXL2 and ER also regulate the expression of ER-ligands. Genetic analysis of these six receptor kinase genes demonstrated that they are required to control organisation, proliferation and cell size across multiple tissue layers. Taken together, our experiments demonstrate that ER signalling attenuates PXL expression in the stem, thus influencing vascular expansion and patterning. We anticipate that similar regulatory relationships, where tissue growth is controlled via cell signals moving across different tissue layers, will coordinate tissue layer expansion throughout the plant body.

plant biology↗

bioRxiv2018

Bulked-Segregant Analysis Coupled to Whole Genome Sequencing (BSA-Seq) for Rapid Gene Cloning in Maize

Forward genetics remains a powerful method for revealing the genes underpinning organismal form and function, and for revealing how these genes are tied together in gene networks. In maize, forward genetics has been tremendously successful, but the size and complexity of the maize genome made identifying mutant genes an often arduous process with traditional methods. The next generation sequencing revolution has allowed for the gene cloning process to be significantly accelerated in many organisms, even when genomes are large and complex. Here, we describe a bulked-segregant analysis sequencing (BSA-Seq) protocol for cloning mutant genes in maize. Our simple strategy can be used to quickly identify a mapping interval and candidate single nucleotide polymorphisms (SNPs) from whole genome sequencing of pooled F2 individuals. We employed this strategy to identify narrow odd dwarf as an enhancer of teosinte branched1, and to identify a new allele of defective kernel1. Our method provides a quick, simple way to clone genes in maize.\n\nReferences numbers for supporting data:figshare and NCBI SRA links to follow

plant biology↗

bioRxiv2018

Capturing auxin response factors syntax using DNA binding models

Auxin is a key hormone performing a wealth of functions throughout the plant life cycle. It acts largely by regulating genes at the transcriptional level through a family of transcription factors (TF) called auxin response factors (ARF). Even if all ARF monomers analysed so far bind a similar DNA sequence, there is evidence that ARFs differ in their target genomic regions and regulated genes. Here we use position weight matrices (PWM) to model ARF DNA binding specificity based on published DNA affinity purification sequencing (DAP-seq) data. We find that the genome binding of two ARFs (ARF2 and ARF5/Monopteros/MP) differ largely because these two factors have different preferred ARF binding site (ARFbs) arrangements (orientation and spacing). We illustrate why PWMs are more versatile to reliably identify ARFbs than the widely used consensus sequences and demonstrate their power with biochemical experiments on the regulatory regions of the IAA19 model gene. Finally, we combined gene regulation by auxin with ARF-bound regions and identified specific ARFbs configurations that are over-represented in auxin up-regulated genes, thus deciphering the ARFbs syntax functional for regulation. This provides a general method to exploit the potential of genome-wide DNA binding assays and decode gene regulation.

plant biology↗

bioRxiv2018

LEAFY maintains apical stem cell activity during shoot development in the fern Ceratopteris richardii

During land plant evolution, determinate spore-bearing axes (retained in extant bryophytes such as mosses) were progressively transformed into indeterminate branching shoots with specialized reproductive axes that form flowers. The LEAFY transcription factor, which is required for the first zygotic cell division in mosses and primarily for floral meristem identity in flowering plants, may have facilitated developmental innovations during these transitions. Mapping the LEAFY evolutionary trajectory has been challenging, however, because there is no functional overlap between mosses and flowering plants, and no functional data from intervening lineages. Here, we report a transgenic analysis in the fern Ceratopteris richardii that reveals a role for LEAFY in maintaining cell divisions in the apical stem cells of both haploid and diploid phases of the lifecycle. These results support an evolutionary trajectory in which an ancestral LEAFY module that promotes cell proliferation was progressively co-opted, adapted and specialized as novel shoot developmental contexts emerged.

plant biology↗

bioRxiv2018

Genetic mapping with allele dosage information in tetraploid Urochloa decumbens (Stapf) R.D. Webster reveals insights into spittlebug (Notozulia entreriana Berg) resistance

Urochloa decumbens (Stapf) R.D. Webster is one of the most important African forage grasses in Brazilian beef production. Currently available genetic-genomic resources for this species are restricted mainly due to polyploidy and apomixis. Therefore, crucial genomic-molecular studies such as the construction of genetic maps and the mapping of quantitative trait loci (QTLs) are very challenging and consequently affect the advancement of molecular breeding. The objectives of this work were to (i) construct an integrated U. decumbens genetic map for a full-sibling progeny using GBS-based markers with allele dosage information, (ii) detect QTLs for spittlebug (Notozulia entreriana) resistance, and (iii) seek putative candidate genes involved in resistance/defense against pathogens. We used the Setaria viridis genome as reference to align GBS reads and selected 4,240 high-quality SNPs markers with allele dosage information. Of these markers, 1,000 were distributed throughout nine homologous groups with a cumulative map length of 1,335.09 cM and an average marker density of 1.33 cM. We detected QTLs for resistance to spittlebug, an important pasture insect pest, that explained between 4.66% and 6.24% of the phenotypic variation. These QTLs are in regions containing putative candidate genes related to resistance/defense against pathogens. Because this is the first genetic map with SNP autotetraploid dosage data and QTL detection in U. decumbens, it will be useful for future evolutionary studies, genome assembly, and other QTL analyses in Urochloa spp. Moreover, the results might facilitate the isolation of spittlebug-related candidate genes and help clarify the mechanism of spittlebug resistance. These approaches will improve selection efficiency and accuracy in U. decumbens molecular breeding and shorten the breeding cycle.

plant biology↗

bioRxiv2018

Linkage Disequilibrium and Population Structure in Wild and Cultivated Populations of Rubber Tree (Hevea brasiliensis)

Among rubber tree species, which belong to the Hevea genus of the Euphorbiaceae family, Hevea brasiliensis (Willd. ex Adr.de Juss.) Muell. Arg. is the main commercial source of natural rubber production worldwide. Knowledge of the population structure and linkage disequilibrium (LD) of this species is essential for the efficient organization and exploitation of genetic resources. Here, we obtained single-nucleotide polymorphisms (SNPs) using a genotyping-by-sequencing (GBS) approach and then employed the SNPs for the following objectives: (i) to identify the positions of SNPs on a genetic map of a segregating mapping population, (ii) to evaluate the population structure of a germplasm collection, and (iii) to detect patterns of LD decay among chromosomes for future genetic association studies in rubber tree. A total of 626 genotypes, including both germplasm accessions (368) and individuals from a genetic mapping population (254), were genotyped. A total of 77,660 and 21,283 SNPs were detected by GBS in the germplasm and mapping populations, respectively. The mapping population, which was previously mapped, was constructed with 1,062 markers, among which only 576 SNPs came from GBS, reducing the average interval between two adjacent markers to 4.4 cM. SNPs from GBS genotyping were used for the analysis of genetic structure and LD estimation in the germplasm accessions. Two groups, which largely corresponded to the cultivated and wild populations, were detected using STRUCTURE and via principal coordinate analysis (PCoA). LD analysis, also using the mapped SNPs, revealed that non-random associations varied along chromosomes, with regions of high LD interspersed with regions of low LD. Considering the length of the genetic map (4,693 cM) and the mean LD (0.49 for cultivated and 0.02 for wild populations), a large number of evenly spaced SNPs would be needed to perform genome-wide association studies in rubber tree, and the wilder the genotypes used, the more difficult the mapping saturation.

plant biology↗

bioRxiv2018

Tracking disease resistance deployment in potato breeding by enrichment sequencing

Following the molecular characterisation of functional disease resistance genes in recent years, methods to track and verify the integrity of multiple genes in varieties are needed for crop improvement through resistance stacking. Diagnostic resistance gene enrichment sequencing (dRenSeq) enables the high-confidence identification and complete sequence validation of known functional resistance genes in crops. As demonstrated for tetraploid potato varieties, the methodology is more robust and cost-effective in monitoring resistances than whole-genome sequencing and can be used to appraise (trans)gene integrity efficiently. All currently known NB-LRRs effective against viruses, nematodes and the late blight pathogen Phytophthora infestans can be tracked with dRenSeq in potato and hitherto unknown polymorphisms have been identified. The methodology provides a means to improve the speed and efficiency of future disease resistance breeding in crops by directing parental and progeny selection towards effective combinations of resistance genes.

plant biology↗

bioRxiv2018

Genetic variation in a complex polyploid: unveiling the dynamic allelic features of sugarcane

BackgroundSugarcane (Saccharum spp.) is highly polyploid and aneuploid. Modern cultivars are derived from hybridization between S. officinarum and S. spontaneum. This combination results in a genome exhibiting variable ploidy among different loci, a huge genome size (approximately 10 Gb) and a high content of repetitive regions. Gene expression mechanisms are poorly understood in these cultivars. An approach using genomic, transcriptomic and genetic mapping can improve our knowledge of the behavior of genetics in sugarcane.\n\nResultsThe hypothetical HP600 and centromere protein C (CENP-C) genes from sugarcane were used to elucidate the allelic expression and genomic and genetic behavior of this complex polyploid. The genomically side-by-side genes HP600 and CENP-C were found in two different homeologous chromosome groups with ploidies of eight and ten. The first region (Region01) was a Sorghum bicolor ortholog with all haplotypes of HP600 and CENP- C expressed, but HP600 exhibited an unbalanced haplotype expression. The second region (Region02) was a scrambled sugarcane sequence formed from different noncollinear genes containing duplications of HP600 and CENP-C (paralogs). This duplication occurred before the Saccharum genus formation and after the separation of sorghum and sugarcane, resulting in a nonexpressed HP600 pseudogene and a recombined fusion version of CENP-C and orthologous gene Sobic.003G299500 with at least two chimerical gene haplotypes expressed. The genetic map construction supported the difficulty of mapping markers located in duplicated regions of complex polyploid genomes.\n\nConclusionAll these findings describe a low synteny region in sugarcane, formed by events occurring in all members of the Saccharum genus. Additionally, evidence of duplicated and truncate gene expression and the behavior of genetic markers in a duplicated region was found. Thus, we describe the complexity involved in sugarcane genetics and genomics and allelic dynamics, which can be useful for understanding the complex polyploid genome.

plant biology↗

bioRxiv2018

Lateral root priming synergystically arises from root growth and auxin transport dynamics

The root system is a major determinant of plant fitness. Its capacity to supply the plant with sufficient water and nutrients strongly depends on root system architecture, which arises from the repeated branching off of lateral roots. A critical first step in lateral root formation is priming, which prepatterns sites competent of forming a lateral root. Priming is characterized by temporal oscillations in auxin, auxin signalling and gene expression in the root meristem, which through growth become transformed into a spatially repetitive pattern of competent sites. Previous studies have demonstrated the importance of auxin synthesis, transport and perception for the amplitude of these oscillations and their chances of producing an actual competent site. Additionally, repeated lateral root cap apoptosis was demonstrated to be strongly correlated with repetitive lateral root priming. Intriguingly, no single mutation has been identified that fully abolishes lateral root formation, and thusfar the mechanism underlying oscillations has remained unknown. In this study, we investigated the impact of auxin reflux loop properties combined with root growth dynamics on priming, using a computational approach. To this end we developed a novel multi-scale root model incorporating a realistic root tip architecture and reflux loop properties as well as root growth dynamics. Excitingly, in this model, repetitive auxin elevations automatically emerge. First, we show that root tip architecture and reflux loop properties result in an auxin loading zone at the start of the elongation zone, with preferential auxin loading in narrow vasculature cells. Second, we demonstrate how meristematic root growth dynamics causes regular alternations in the sizes of cells arriving at the elongation zone, which subsequently become amplified during cell expansion. These cell size differences translate into differences in cellular auxin loading potential. Combined, these properties result in temporal and spatial fluctuations in auxin levels in vasculature and pericycle cells. Our model predicts that temporal priming frequency predominantly depends on cell cycle duration, while cell cycle duration together with meristem size control lateral root spacing.

plant biology↗

bioRxiv2018

Of puzzles and pavements: a quantitative exploration of leaf epidermal cell shape

SummaryThe epidermal cells of leaves lend themselves readily to observation and display many shapes and types: tabular pavement cells, complex trichomes, and stomatal complexes1. Pavement cells from Zea mays (maize) and Arabidopsis thaliana (arabidopsis) both have highly undulate anticlinal walls and are held as representative of monocots and eudicots, respectively. In these two model species, we have a nuanced understanding of the molecular mechanisms that generate undulating pavement cell shape2-9. This model-system dominance has led to two common assumptions: first, that particular plant lineages are characterized by particular pavement cell shapes; and second, that undulatory pavement cell shapes are common enough to be model shapes. To test these assumptions, we quantified pavement cell shape in the leaves of 278 vascular plant taxa and assessed cell shape metrics across large taxonomic groups. We settled on two metrics that described cell shape diversity well in this dataset: aspect ratio (degree of cell elongation) and solidity (a proxy for margin undulation). We found that pavement cells in the monocots tended to have weakly undulating margins, pavement cells in ferns had strongly undulating margins, and pavement cells in the eudicots showed no particular degree of undulation. Indeed, we found that cells with strongly undulating margins, like those of arabidopsis and maize, were in the minority in seed plants. At the organ level, we found a trend towards cells with more undulating margins on the abaxial leaf surface vs. the adaxial surface. We also detected a correlation between cell and leaf aspect ratio: highly elongated leaves tended to have highly elongated cells (low aspect ratio), but not in the eudicots. This indicates that while plant anatomy and plant morphology can be connected, superficially similar leaves can develop through very different underlying growth dynamics (cell expansion and division patterns). This work reveals the striking diversity of pavement cell shapes across vascular plants, and lays the quantitative groundwork for testing hypotheses about pavement cell form and function.\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=139 SRC=\"FIGDIR/small/361717_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (83K):\norg.highwire.dtl.DTLVardef@1a571a8org.highwire.dtl.DTLVardef@c8cf7dorg.highwire.dtl.DTLVardef@1ae3090org.highwire.dtl.DTLVardef@f666ce_HPS_FORMAT_FIGEXP M_FIG C_FIG

plant biology↗

bioRxiv2018

Heliaphen, an outdoor high-throughput phenotyping platform designed to integrate genetics and crop modeling

Heliaphen is an outdoor pot platform designed for high-throughput phenotyping. It allows automated management of drought scenarios and plant monitoring during the whole plant cycle. A robot moving between plants growing in 15L pots monitors plant water status and phenotypes plant or leaf morphology, from which we can compute more complex traits such as the response of leaf expansion (LE) or plant transpiration (TR) to water deficit. Here, we illustrate the platform capabilities for sunflower on two practical cases: a genetic and genomics study for the response to drought of yield-related traits and a simulation study, where we use measured parameters as inputs for a crop simulation model. For the genetic study, classical measurements of thousand-kernel weight (TKW) were done on a sunflower bi-parental population under water stress and control conditions managed automatically. The association study using the TKW drought-response highlighted five genetic markers. A complementary transcriptomic experiment identified closeby candidate genes differentially expressed in the parental backgrounds in drought conditions. For the simulation study, we used the SUNFLO crop simulation model to assess the impact of two traits measured on the platform (LE and TR) on crop yield in a large population of environments. We conducted simulations in 42 contrasted locations across Europe and 21 years of climate data. We defined the pattern of abiotic stresses occurring at this continental scale and identified ideotypes (i.e. genotypes with specific traits values) that are more adapted to specific environment types. This study exemplifies how phenotyping platforms can help with the identification of the genetic architecture of complex response traits and the estimation of eco-physiological model parameters in order to define ideotypes adapted to different environmental conditions.

plant biology↗

bioRxiv2018

Triazole ureas covalently bind to strigolactone receptors and regulate signaling

Strigolactones (SLs), a class of plant hormones with multiple functions, mediate plant-plant and plant-microorganism communications in the rhizosphere. In this study, we developed potent strigolactone antagonists, which covalently bind to the strigolactone receptor D14, by preparing an array of triazole urea compounds. Using yeast two-hybrid assays and rice tillering assays, we identified a triazole urea compound KK094 as a potent inhibitor of strigolactone receptors. The LC-MS/MS analysis and X-ray crystallography concluded that KK094 was hydrolyzed by D14, and that a reaction product of this degradation covalently binds to the Ser residue of the catalytic triad of D14. We also identified KK052 and KK073, whose effects on D14-D53/D14-SLR1 complex formation were opposite due to a trifluoromethyl group on its benzene ring. These results demonstrate that triazole urea compounds are potentially powerful tools for agricultural application and may be useful for the elucidation of the complicated mechanism underlying SL-perception.

plant biology↗

bioRxiv2018

The contrasting response to drought and waterlogging is underpinned by divergent DNA methylation programs associated with gene expression in sesame

DNA methylation is a heritable epigenetic mechanism that participates in gene regulation under abiotic stresses in plants. Sesame (Sesamum indicum L.) is typically considered a drought-tolerant crop but highly susceptible to waterlogging, a property attributed to its presumed origin in Africa or India. Understanding DNA methylation patterns in sesame under drought and waterlogging conditions can provide insights into the regulatory mechanisms underlying its contrasting responses to these principal abiotic stresses. Here, we combined Methylation-Sensitive Amplified Polymorphism and transcriptome analyses to profile cytosine methylation patterns, gene expression alteration, and their interplay in drought-tolerant and waterlogging-tolerant sesame genotypes under control, stress and recovery conditions. Our data showed that drought stress strongly induced de novo methylation (DNM) whereas most of the loci were demethylated (DM) during the recovery phase. In contrast, waterlogging decreased the level of methylation under stress but during the recovery phase, both DM and DNM were concomitantly deployed. In both stresses, the differentially expressed genes (DEGs) were highly correlated with the methylation patterns. We observed that DM was associated with the up-regulation of the DEGs while DNM was correlated with the down-regulation of the DEGs. In addition, we sequenced 44 differentially methylated regions of which 90% overlapped with the promoters and coding sequences of the DEGs. Altogether, we demonstrated that sesame has divergent epigenetic programs that respond to drought and waterlogging stresses. Our results also highlighted the possible interplay among DNA methylation and gene expression, which may modulate the contrasting responses to drought and waterlogging in sesame.

plant biology↗

bioRxiv2018

An EDS1 EP-domain surface mediating timely transcriptional reprogramming of immunity genes

Plant intracellular NLR receptors recognize pathogen interference to trigger immunity. NLR signalling mechanisms have not been resolved. Enhanced disease susceptibility 1 (EDS1) heterodimers are recruited by Toll-interleukin1-receptor domain NLRs (TNLs) to transcriptionally mobilize resistance pathways. Using an Arabidopsis EDS1 heterodimer crystal structure we interrogate the conserved but functionally uncharacterized EDS1 -helical EP-domain. We identify EP-domain positively charged residues lining a cavity that are essential for TNL immunity signalling, beyond heterodimer formation. Mutating arginine (R493) to alanine creates a weak EDS1 allele which disables TNL immunity against bacteria producing a virulence factor, coronatine (COR). Arabidopsis plants expressing EDS1R493A are slow to mobilize defence gene expression changes, independently of COR. The transcriptional delay has severe consequences for pathogen resistance and for countering bacterial COR. We uncover a set of host immunity genes whose repression by COR is blocked by wild-type EDS1 but not by EDS1R493A in the TNL response. These data uncover an EDS1 signalling surface lining the heterodimer EP-domain cavity which confers timely transcriptional reprogramming of host defence pathways and blocks bacterial virulence in NLR receptor immunity.

plant biology↗

bioRxiv2018

Sensing Plant Physiology and Environmental Stress by Automatically Tracking Fj and Fi Features in PSII Chlorophyll Fluorescence Induction

Following a step excitation, chlorophyll fluorescence (ChlF) from photosystem II of a dark-adapted plant leaf exhibits the well-known OJIP pattern. The OJIP induction has been widely applied in plant science, agriculture engineering, and environmental engineering. While the J and I phases are related to transitions of photochemical reaction redox states, characteristic fluorescence intensities for the two phases (Fj and Fi) are often treated as fixed time points in routine measurement and thus do not account for variations in plant and experimental conditions, which (1) neglects the time differences, potentially useful information for characterizing plant status and environmental factors, and (2) leads to errors in measured Fj and Fi values. In this work, a method for consistent measurement of Fj and Fi was developed through polynomial fitting and curvature analysis. The method measures the curvatures in the OJIP curve and automatically tracks the characteristic transition points under variable sample and experimental conditions. Experiments were carried out to demonstrate the concept and classification capabilities of the developed method. This research established a new framework to analyze ChlF and enhanced the applications of ChlF.

plant biology↗