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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 Read source abstracts and check manuscript versions; preprints are not peer reviewed.

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At least 505 records · Page 28Linked to original sources

bioRxiv2018

Root meristem growth factor 1 controls root meristem size through reactive oxygen species signaling

Stem cell niche and root meristem size are maintained by intercellular interactions and signaling networks of a plant peptide hormone, Root Meristem Growth Factor 1 (RGF1). How RGF1 regulates root meristem development is an essential question to understand stem cell function. Although five receptors of RGF1 have recently been identified, the downstream signaling mechanism remains unknown. Here, we report a series of signaling events following RGF1 action. The RGF1-receptor pathway controls distribution of reactive oxygen species (ROS) along the developmental zones of the Arabidopsis root. We identify a novel transcription factor, RGF1 INDUCIBLE TRANSCRIPTION FACTOR 1 (RITF1), which plays a central role in mediating RGF1 signaling. Manipulating RITF1 expression leads to redistribution of ROS along the root developmental zones. Changes in ROS distribution, in turn, enhance the stability of the PLETHORA2 (PLT2) protein, a master regulator of root stem cells. Taken together, our study clearly depicts a signaling cascade initiated by RGF1 and links the RGF1 peptide to ROS regulatory mechanisms.

plant biology↗

bioRxiv2018

Arabidopsis HB52 mediates the crosstalk between ethylene and auxin signaling pathways by regulating PIN2, WAG1, and WAG2 during primary root elongation

The gaseous hormone ethylene participates in many physiological processes of plants. It is well known that ethylene-inhibited root elongation involves basipetal auxin delivery requiring PIN2. However, the molecular mechanism how ethylene regulates PIN2 is not well understood. Here, we report that the ethylene-responsive HD-Zip gene HB52 is involved in ethylene-mediated inhibition of primary root elongation. Using biochemical and genetic analyses, we demonstrated that HB52 is ethylene-responsive and acts immediately downstream of EIN3. HB52 knock-down mutants are insensitive to ethylene in primary root elongation while the overexpression lines have dramatically shortened roots like ethylene treated plants. Moreover, HB52 upregulates PIN2, WAG1, and WAG2 by directly binding to their promoter, leading to an enhanced basipetal auxin delivery to the elongation zone and thus inhibiting root growth. Our work uncovers HB52 as an important crosstalk node between ethylene signaling and auxin transport in root elongation.

plant biology↗

bioRxiv2018

Population structure of the Brachypodium species complex and genome wide association of agronomic traits in response to climate.

The development of model systems requires a detailed assessment of standing genetic variation across natural populations. The Brachypodium species complex has been promoted as a plant model for grass genomics with translational to small grain and biomass crops. To capture the genetic diversity within this species complex, thousands of Brachypodium accessions from around the globe were collected and sequenced using genotyping by sequencing (GBS). Overall, 1,897 samples were classified into two diploid or allopolyploid species and then further grouped into distinct inbred genotypes. A core set of diverse B. distachyon diploid lines were selected for whole genome sequencing and high resolution phenotyping. Genome-wide association studies across simulated seasonal environments was used to identify candidate genes and pathways tied to key life history and agronomic traits under current and future climatic conditions. A total of 8, 22 and 47 QTLs were identified for flowering time, early vigour and energy traits, respectively. Overall, the results highlight the genomic structure of the Brachypodium species complex and allow powerful complex trait dissection within this new grass model species.

plant biology↗

bioRxiv2018

A Transcriptomic Analysis of Xylan Mutants Does Not Support the Existence of A Secondary Cell Wall Integrity System in Arabidopsis

Yeast have long been known to possess a cell wall integrity (CWI) system, and recently an analogous system has been described for the primary walls of plants (PCWI) that leads to changes in plant growth and cell wall composition. A similar system has been proposed to exist for secondary cell walls (SCWI). However, there is little data to support this. Here, we analysed the stem transcriptome of a set of cell wall biosynthetic mutants in order to investigate whether cell wall damage, in this case caused by aberrant xylan synthesis, activates a signalling cascade or changes in cell wall synthesis gene expression. Our data revealed remarkably few changes to the transcriptome. We hypothesise that this is because cells undergoing secondary cell wall thickening have entered a committed programme leading to cell death, and therefore a SCWI system would have limited impact. The absence of transcriptomic responses to secondary cell wall alterations may facilitate engineering of the secondary cell wall of plants.

plant biology↗

bioRxiv2018

Partial correlation analysis of transcriptomes helps detangle the growth and defense network in spruce

O_LIIn plants, there can be a trade-off between resource allocations to growth versus defense. Here, we use partial correlation analysis of gene expression to make inferences about the nature of this interaction.\nC_LIO_LIWe studied segregating progenies of Interior spruce subject to weevil attack. In a controlled experiment, we measured pre-attack plant growth and post-attack damage with several morphological measures, and profiled transcriptomes of 188 progeny.\nC_LIO_LIWe used partial correlations of individual transcripts (ESTs) with pairs of growth/defense traits to identify important nodes and edges in the inferred underlying gene network, e.g., those pairs of growth/defense traits with high mutual correlation with a single EST transcript. We give a method to identify such ESTs.\nC_LIO_LIA terpenoid ABC transporter gene showed strongest correlations (P=0.019); its transcript represented a hub within the compact 166-member gene-gene interaction network (P=0.004) of the negative genetic correlations between growth and subsequent pest attack. A small 21-member interaction network (P=0.004) represented the uncovered positive correlations.\nC_LIO_LIOur study demonstrates partial correlation analysis identifies important gene networks underlying growth and susceptibility to the weevil in spruce. In particular, we found transcripts that strongly modify the trade-off between growth and defense, and allow identification of networks more central to the trade-off.\nC_LI

plant biology↗

bioRxiv2018

Quantitative Trait Loci Controlling Phytophthora cactorum Resistance in the Cultivated Octoploid Strawberry (Fragaria x ananassa)

The cultivated strawberry, Fragaria x ananassa (Fragaria spp.) is the most economically important global soft fruit. Phytophthora cactorum, a water-borne oomycete causes economic losses in strawberry production globally. A bi-parental cross of octoploid cultivated strawberry segregating for resistance to P. cactorum, the causative agent of crown rot disease, was screened using artificial inoculation. Multiple resistance quantitative trait loci (QTL) were identified and mapped. Three major effect QTL (FaRPc6C, FaRPc6D and FaRPc7D) explained 36% of the variation observed and in total, the detected QTL explained 86% of the variation observed. There were no epistatic interactions detected between the three major QTLs. Testing a subset of the mapping population progeny against a range of P. cactorum isolates revealed no major differences in host response, however, some lines showed higher susceptibility than predicted, indicating that additional undetected factors may affect the expression of some quantitative resistance loci. Using historic crown rot disease score data from strawberry accessions, a preliminary genome-wide association study of 114 individuals revealed additional loci associated with resistance to P. cactorum. Mining of Fragaria vesca Hawaii 4 v1.1 genome revealed candidate resistance genes in the QTL regions.

plant biology↗

bioRxiv2018

In vivo monitoring of plant small GTPase activation using a Förster resonance energy transfer biosensor

Small GTPases act as molecular switches that regulate various plant responses such as disease resistance, pollen tube growth, root hair development, cell wall patterning and hormone responses. Thus, to monitor their activation status within plant cells is believed to be the key step in understanding their roles. We have established a plant version of a Forster resonance energy transfer (FRET) probe called Ras and interacting protein chimeric unit (Raichu) that can successfully monitor activation of the rice small GTPase OsRac1 during various defence responses in rice cells. Here, we describe the protocol for visualizing spatiotemporal activity of plant Rac/ROP GTPase in living plant cells, transfection of rice protoplasts with Raichu-OsRac1 and acquisition of FRET images. Our protocol should be widely adaptable for monitoring activation for other plant small GTPases and for other FRET sensors in various plant cells.

plant biology↗

bioRxiv2018

The expa1-1 mutant reveals a new biophysical lateral root organogenesis checkpoint

In plants, post-embryonic formation of new organs helps shape the adult organism. This requires the tight regulation of when and where a new organ is formed, and a coordination of the underlying cell divisions. To build a root system, new lateral roots are continuously developing, and this process requires asymmetric cell division in adjacent pericycle cells. Characterization of an expansin a1 (expa1) mutant has revealed a novel checkpoint during lateral root formation. Specifically, a minimal pericycle width was found to be necessary and sufficient to trigger asymmetric pericycle cell divisions during auxin-driven lateral root formation. We conclude that a localized radial expansion of adjacent pericycle cells is required to position the asymmetric cell divisions and generate a core of small daughter cells, which is a prerequisite for lateral root organogenesis.\n\nSIGNFICANCE STATEMENTOrgan formation is an essential process in plants and animals, driven by cell division and cell identity establishment. Root branching, where lateral roots form along the primary root axis, increases the root system and aids capture of water and nutrients. We have discovered that tight control of cell width is necessary to co-ordinate asymmetric cell divisions in cells that give rise to a new lateral root organ. While biomechanical processes have been shown to play a role in plant organogenesis, including lateral root formation, our data give new mechanistic insights into the cell size checkpoint during lateral root initiation.

plant biology↗

bioRxiv2018

Criteria for evaluating molecular markers: Comprehensive quality metrics to improve marker-assisted selection

Despite strong interest over many years, the usage of quantitative trait loci in plant breeding has often failed to live up to expectations. A key weak point in the utilisation of QTLs is the \"quality\" of markers used during marker-assisted selection (MAS): unreliable markers result in variable outcomes, leading to a perception that MAS products fail to achieve reliable improvement. Most reports of markers used for MAS focus on markers derived from the mapping population. There are very few studies that examine the reliability of these markers in other genetic backgrounds, and critically, no metrics exist to describe and quantify this reliability. To improve the MAS process, this work proposes five core metrics that fully describe the reliability of a marker. These metrics give a comprehensive and quantitative measure of the ability of a marker to correctly classify germplasm as QTL[+]/[-], particularly against a background of high allelic diversity. Markers that score well on these metrics will have far higher reliability in breeding, and deficiencies in specific metrics give information on circumstances under which a marker may not be reliable. The metrics are applicable across different marker types and platforms, allowing an objective comparison of the performance of different markers irrespective of the platform. Evaluating markers using these metrics demonstrates that trait-specific markers consistently out-perform markers designed for other purposes. These metrics also provide a superb set of criteria for designing superior marker systems for a target QTL, enabling the selection of an optimal marker set before committing to design.

plant biology↗

bioRxiv2018

PILS6 is a temperature-sensitive regulator of nuclear auxin input and organ growth in Arabidopsis thaliana

Global warming is threatening plant productivity, because plant growth is highly sensitive to elevated temperatures. High temperature (HT) triggers the auxin biosynthesis-dependent growth in aerial tissues. On the other hand, the contribution of auxin to HT-induced root growth is currently under debate. Here we show that the putative intracellular auxin carrier PIN-LIKES 6 (PILS6) is a negative regulator of organ growth and that its abundance is highly sensitive to HT. PILS6 localises to the endoplasmic reticulum (ER) and limits the nuclear availability of auxin, consequently reducing the auxin signalling output. HT represses the transcription and protein abundance of PILS6 specifically in the root tip, which impacts on PILS6-dependent root organ growth rates. Accordingly, we hypothesize that PILS6 is part of a novel mechanism, linking HT to auxin responses in roots.

plant biology↗

bioRxiv2018

Expression of SULTR2;2 in the Arabidopsis bundle sheath is mediated by a highly conserved positive regulator

The bundle sheath provides a conduit linking veins and mesophyll cells. In C3 Arabidopsis thaliana it also plays important roles in oxidative stress and sulphur metabolism. However, the mechanisms responsible for the patterns of gene expression that underpin these metabolic specialisations are poorly understood. Here we used the A. thaliana SULTR2;2 gene as a model to better understand mechanisms that restrict expression to the bundle sheath. Deletion analysis indicated that the SULTR2;2 promoter contains a short region necessary for expression in the bundle sheath. This sequence acts as a positive regulator and is tolerant to multiple consecutive deletions indicating considerable redundancy in the cis-elements involved. It is highly conserved in SULTR2;2 genes of the Brassicaceae and is functional in the distantly related C4 species Flaveria bidentis that belongs to the Asteraceae. We conclude that expression of SULTR2;2 in the bundle sheath is underpinned by a highly redundant sequence that likely represents an ancient and conserved mechanism found in families as diverse as the Asteraceae and Brassicaceae.

plant biology↗

bioRxiv2018

Branch angle responses to photosynthesis are partially dependent on TILLER ANGLE CONTROL 1

Light serves as an important environmental cue in regulating plant architecture. Previous work had demonstrated that both photoreceptor-mediated signaling and photosynthesis play a role in determining the orientation of plant organs. TILLER ANGLE CONTROL 1 (TAC1) was recently shown to function in setting the orientation of lateral branches in diverse plant species, but the degree to which it plays a role in light-mediated phenotypes is unknown. Here, we demonstrated that TAC1 expression was light dependent, as expression was lost under dark or far-red growth conditions, but did not display any clear diurnal rhythm. Loss of TAC1 in the dark was gradual, and experiments with photoreceptor mutants indicated this was not dependent upon Red/Far-Red or Blue light signaling, but partially required the signaling integrator CONSTITUTIVE PHOTOMORPHGENESIS 1 (COP1). Over-expression of TAC1 partially prevented the narrowing of branch angles in the dark or under Far-Red light. Treatment with the carotenoid biosynthesis inhibitor Norflurazon or the PSII inhibitor DCMU led to loss of TAC1 expression similar to dark or far-red conditions, but surprisingly expression increased in response to the PSI inhibitor Paraquat. Our results indicate that TAC1 plays an important role in modulating plant architecture in response to photosynthetic signals.\n\nHIGHLIGHTBranch angles narrow in darkness or under far-red light. This response is partially mediated by TAC1 which responds to photosynthetic signals, providing a key link between photosynthesis and plant architecture.

plant biology↗

bioRxiv2018

Transcriptomic analyses with the progress of symbiosis in ‘crack-entry’ legume Arachis hypogaea highlight its contrast with ‘Infection thread’ adapted legumes

In root-nodule symbiosis, rhizobial invasion and nodule organogenesis is host controlled. In most legumes, rhizobia enter through infection-threads and nodule primordium in the cortex is induced from a distance. But in dalbergoid legumes like Arachis hypogaea, rhizobia directly invade cortical cells through epidermal cracks to generate the primordia. Herein we report the transcriptional dynamics with the progress of symbiosis in A. hypogaea at 1dpi: invasion; 4dpi: nodule primordia; 8dpi: spread of infection in nodule-like structure; 12dpi: immature nodules containing rod-shaped rhizobia; and 21dpi: mature nodules with spherical symbiosomes. Expression of putative orthologue of symbiotic genes in crack-entry legume A. hypogaea was compared with infection thread adapted model legumes. The contrasting features were (i) higher expression of receptors like LYR3, EPR3 as compared to canonical NFRs (ii) late induction of transcription factors like NIN, NSP2 and constitutive high expression of ERF1, EIN2, bHLH476 and (iii) induction of divergent pathogenesis responsive PR-1 genes. Additionally, symbiotic orthologues of SymCRK, FLOT4, ROP6, RR9, NOOT and SEN1 were not detectable and microsynteny analysis indicated the absence of RPG and DNF2 homologues in diploid parental genomes of A. hypogaea. The implications are discussed and a molecular framework that guide crack-entry symbiosis in A. hypogaea is proposed.

plant biology↗

bioRxiv2018

Elongator is required for root stem cell maintenance by regulating SHORT ROOT transcription

SHORTROOT (SHR) is essential for stem cell maintenance and radial patterning in Arabidopsis thaliana roots, but how its expression is regulated is still unknown. Here, we report that Elongator regulates the transcription of SHR. The depletion of Elongator drastically reduced SHR expression and led to defective root stem cell maintenance and radial patterning. The importance of the nuclear localization of Elongator for its functioning, together with the insensitivity of the elp1 mutant to the transcription elongation inhibitor 6-azauracil and the direct interaction of the ELP4 subunit with the C-terminal domain of RNA polymerase II (RNAPII CTD), support the notion that Elongator plays important roles in transcription elongation. Indeed, we found that ELP3 associates with the pre-mRNA of SHR and that mutation of Elongator reduces the enrichment of RNAPII on the SHR gene body. Moreover, Elongator interacted in vivo with SUPPRESSOR OF Ty4 (SPT4), a well-established transcription elongation factor that was recruited to the SHR locus. Together, these results demonstrate that Elongator acts in concert with SPT4 to regulate the transcription of SHR.

plant biology↗

bioRxiv2018

Crystal structures of two tandem malectin-like receptor kinases involved in plant reproduction

A complex cell-to-cell communication between the male pollen tube and the female reproductive organs is required for plant fertilization. A family of Catharanthus roseus Receptor Kinase-1 ( CrRLK1L) membrane receptors has been genetically implicated in this process. Here we present crystal structures of the CrRLK1Ls ANXUR1 and 2 at 1.48 and 1.1 [A] resolution, respectively. Our structures reveal a novel arrangement of two malectin-like domains connected by a short {beta}hairpin linker and stabilized by calcium ions. The canonical carbohydrate interaction surfaces of related animal and bacterial carbohydrate binding modules are not conserved among plant CrRLK1Ls. In line with this, we failed to detect binding of chemically diverse oligosaccharides to ANXUR1 and HERCULES1. Instead, CrRLK1Ls have evolved a protein-protein interface between their malectin domains, which forms a deep cleft lined by highly conserved aromatic and polar residues. Analysis of the glycosylation pattern of different CrRLK1Ls and their oligomeric states together suggests that this cleft could resemble a binding site for a ligand required for CrRLK1Ls receptor activation.

plant biology↗

bioRxiv2018

Fine-tuning of ABA responses by the protein kinase WNK8

The phytohormone abscisic acid (ABA) regulates various growth- and developmental processes in response to limiting water conditions. ABA functions through an established signaling pathway consisting of PYR1/PYL/RCAR ABA receptors that inhibit group A type 2C protein phosphatases (PP2Cs) in an ABA-dependent manner. Inhibition of PP2Cs enables the activation of SnRK2-type protein kinases that phosphorylate downstream targets including transcription factors and ion channels. However, ABA-dependent signals have to be integrated into other growth- and developmental programs to ensure a successful life cycle. Here, we have characterized the role of the protein kinase WNK8 in the ABA signalling pathway. Two T-DNA insertion alleles wnk8-1 and wnk8-4 exhibited contrasting ABA responses during seed germination and young seedling growth. However, reciprocal crossings with wild type plants suggested that wnk8-1 that still expressed the WNK8 kinase domain functioned in a hypermorphic and dominant manner. WNK8 directly interacted with the PP2C PP2CA in planta and was negatively regulated by this phosphatase in vitro. WNK8 also phosphorylated the ABA receptor PYR1 in vitro. Double mutant analyses revealed that the dominant allele wnk8-1 suppressed the ABA- and glucose hypersensitivity of the pp2ca-1 T-DNA allele. In transient protoplast assays WNK8 suppressed ABA-induced reporter gene expression that was dependent on a functional kinase. In summary, we have identified the protein kinase WNK8 as a negative regulator of ABA responses during young seedling establishment through its direct interaction with core ABA signaling components.\n\nSIGNIFICANCE STATEMENTThe phytohormone abscisic acid regulates the water household of plants through a defined core signaling pathway. Here we have identified the protein kinase WNK8 as a direct interactor of core abscisic acid signalling components and as a negative modulator of abscisic acid responses during young seedling development in Arabidopsis.

plant biology↗

bioRxiv2018

Ethylene mitigates waterlogging stress by regulating glutathione biosynthesis-related transcripts in soybeans

Waterlogging stress is a restrictive factors in soybean productivity worldwide. Plants utilize various physio-chemical changes to mitigate waterlogging stress. In current study, the regulatory roles of seven kinds of plant growth regulators, including abscisic acid (ABA), ethylene (ethephon, ETP), gibberellins (GA4), indole-3-acetic acid (IAA), kinetine (KT), jasmonic acid (JA) and salicylic acid (SA), were determined for soybeans under waterlogging conditions. Based on the results, the donor source of ethylene was selected and its role was further examined regarding physiochemical alteration and glutathione biosynthesis-related transcripts through application of exogenous ETP. ETP application mitigated waterlogging stress and significantly improved the efficiency of photosynthesis and increased bioactive GA4 contents compared to that of untreated plants. Element and amino acid contents among the treatments were significantly different. Total elements and amino acid contents were increased in 100 M ETP-treated soybean plants. ETP application induced adventitious root initiation, improved root surface area, and significantly increased glutathione transferases expression and glutathione relative to that of non-ETP treated soybean plants. Finally, 100 M-ETP application induced up-regulated protein content and glutathione s-transferase DHAR2 as compared to that of soybeans under waterlogging-conditions only. ETP could induce various biochemical and transcriptional modulations that strengthen plant growth and mitigate waterlogging stress.\n\nHighlightEthylene application to soybean plants after waterlogging up-regulates glutathione transferase genes. Higher glutathione activity, as well as increased glutathione s-transferase DHAR2 protein content was induced to scavenge reactive oxygen species.

plant biology↗

bioRxiv2018

Natural variation in stomata size contributes to the local adaptation of water-use efficiency in Arabidopsis thaliana

Stomata control gas exchanges between the plant and the atmosphere. How natural variation in stomata size and density contributes to resolve trade-offs between carbon uptake and water-loss in response to local climatic variation is not yet understood. We developed an automated confocal microscopy approach to characterize natural genetic variation in stomatal patterning in 330 fully-sequenced Arabidopsis thaliana accessions collected throughout the European range of the species. We compared this to variation in water-use efficiency, measured as carbon isotope discrimination ({delta}13C). We detect substantial genetic variation for stomata size and density segregating within Arabidopsis thaliana. A positive correlation between stomata size and {delta}13C further suggests that this variation has consequences on water-use efficiency. Genome-wide association analyses indicate a complex genetic architecture underlying not only variation in stomata patterning but also to its co-variation with carbon uptake parameters. Yet, we report two novel QTL affecting {delta}13C independently of stomata patterning. This suggests that, in A. thaliana, both morphological and physiological variants contribute to genetic variance in water-use efficiency. Patterns of regional differentiation and co-variation with climatic parameters indicate that natural selection has contributed to shape some of this variation, especially in Southern Sweden, where water availability is more limited in spring relative to summer. These conditions are expected to favor the evolution of drought avoidance mechanisms over drought escape strategies.

plant biology↗