Plant Direct最新文献

{"title":"Exome-based new allele-specific PCR markers and transferability for sodicity tolerance in bread wheat (<i>Triticum aestivum</i> L.).","authors":"Roopali Bhoite, Rosemary Smith, Urmil Bansal, Mirza Dowla, Harbans Bariana, Darshan Sharma","doi":"10.1002/pld3.520","DOIUrl":"10.1002/pld3.520","url":null,"abstract":"<p><p>Targeted exome-based genotype by sequencing (t-GBS), a sequencing technology that tags SNPs and haplotypes in gene-rich regions was used in previous genome-wide association studies (GWAS) for sodicity tolerance in bread wheat. Thirty-nine novel SNPs including 18 haplotypes for yield and yield-components were identified. The present study aimed at developing SNP-derived markers by precisely locating new SNPs on ~180 bp allelic sequence of t-GBS, marker validation, and SNP functional characterization based on its exonic location. We identified unknown locations of significant SNPs/haplotypes by aligning allelic sequences on to IWGSC RefSeqv1.0 on respective chromosomes. Eighteen out of the target 39 SNP locations fulfilled the criteria for producing PCR markers, among which only eight produced polymorphic signals. These eight markers associated with yield, plants m^-2, heads m^-2, and harvest index, including a pleiotropic marker for yield, harvest index, and grains/head were validated for its amplification efficiency and phenotypic effects in focused identification germplasm strategy (FIGS) wheat set and a doubled haploid (DH) population (Scepter/IG107116). The phenotypic variation explained by these markers are in the range of 4.1-37.6 in the FIGS population. High throughput PCR-based genotyping using new markers and association with phenotypes in FIGS wheat set and DH population validated the effect of functional SNP on closely associated genes-calcineurin B-like- and dirigent protein, basic helix-loop-helix (BHLH-), plant homeodomain (PHD-) and helix-turn-helix myeloblastosis (HTH myb) type -transcription factor. Further, genome-wide SNP annotation using SnpEff tool confirmed that these SNPs are in gene regulatory regions (upstream, 3'-UTR, and intron) modifying gene expression and protein-coding. This integrated approach of marker design for t-GBS alleles, SNP functional annotation, and high-throughput genotyping of functional SNP offers translation solutions across crops and complex traits in crop improvement programs.</p>","PeriodicalId":20230,"journal":{"name":"Plant Direct","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2023-08-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10435944/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10105523","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Differences in mucilage properties and stomatal sensitivity of locally adapted <i>Zea mays</i> in relation with precipitation seasonality and vapour pressure deficit regime of their native environment.","authors":"Bernd J Berauer, Asegidew Akale, Andreas H Schweiger, Mathilde Knott, Dörte Diehl, Marc-Philip Wolf, Ruairidh J H Sawers, Mutez A Ahmed","doi":"10.1002/pld3.519","DOIUrl":"10.1002/pld3.519","url":null,"abstract":"<p><p>With ongoing climate change and the increase in extreme weather events, especially droughts, the challenge of maintaining food security is becoming ever greater. Locally adapted landraces of crops represent a valuable source of adaptation to stressful environments. In the light of future droughts-both by altered soil water supply and increasing atmospheric water demand (vapor pressure deficit [VPD])-plants need to improve their water efficiency. To do so, plants can enhance their access to soil water by improving rhizosphere hydraulic conductivity via the exudation of mucilage. Furthermore, plants can reduce transpirational water loss via stomatal regulation. Although the role of mucilage and stomata regulation on plant water management have been extensively studied, little is known about a possible coordination between root mucilage properties and stomatal sensitivity as well as abiotic drivers shaping the development of drought resistant trait suits within landraces. Mucilage properties and stomatal sensitivity of eight Mexican landraces of <i>Zea mays</i> in contrast with one inbred line were first quantified under controlled conditions and second related to water demand and supply at their respective site of origin. Mucilage physical properties-namely, viscosity, contact angle, and surface tension-differed between the investigated maize varieties. We found strong influences of precipitation seasonality, thus plant water availability, on mucilage production (<i>R</i> ² = .88, <i>p</i> < .01) and mucilage viscosity (<i>R</i> ² = .93, <i>p</i> < .01). Further, stomatal sensitivity to increased atmospheric water demand was related to mucilage viscosity and contact angle, both of which are crucial in determining mucilage's water repellent, thus maladaptive, behavior upon soil drying. The identification of landraces with pre-adapted suitable trait sets with regard to drought resistance is of utmost importance, for example, trait combinations such as exhibited in one of the here investigated landraces. Our results suggest a strong environmental selective force of seasonality in plant water availability on mucilage properties as well as regulatory stomatal effects to avoid mucilage's maladaptive potential upon drying and likely delay critical levels of hydraulic dysfunction. By this, landraces from highly seasonal climates may exhibit beneficial mucilage and stomatal traits to prolong plant functioning under edaphic drought. These findings may help breeders to efficiently screen for local landraces with pre-adaptations to drought to ultimately increase crop yield resistance under future climatic variability.</p>","PeriodicalId":20230,"journal":{"name":"Plant Direct","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2023-08-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10435965/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10049416","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptional analysis in multiple barley varieties identifies signatures of waterlogging response.","authors":"Alexandra Miricescu, Ailbhe Jane Brazel, Joseph Beegan, Frank Wellmer, Emmanuelle Graciet","doi":"10.1002/pld3.518","DOIUrl":"10.1002/pld3.518","url":null,"abstract":"<p><p>Waterlogging leads to major crop losses globally, particularly for waterlogging-sensitive crops such as barley. Waterlogging reduces oxygen availability and results in additional stresses, leading to the activation of hypoxia and stress response pathways that promote plant survival. Although certain barley varieties have been shown to be more tolerant to waterlogging than others and some tolerance-related quantitative trait loci have been identified, the molecular mechanisms underlying this trait are mostly unknown. Transcriptomics approaches can provide very valuable information for our understanding of waterlogging tolerance. Here, we surveyed 21 barley varieties for the differential transcriptional activation of conserved hypoxia-response genes under waterlogging and selected five varieties with different levels of induction of core hypoxia-response genes. We further characterized their phenotypic response to waterlogging in terms of shoot and root traits. RNA sequencing to evaluate the genome-wide transcriptional responses to waterlogging of these selected varieties led to the identification of a set of 98 waterlogging-response genes common to the different datasets. Many of these genes are orthologs of the so-called \"core hypoxia response genes,\" thus highlighting the conservation of plant responses to waterlogging. Hierarchical clustering analysis also identified groups of genes with intrinsic differential expression between varieties prior to waterlogging stress. These genes could constitute interesting candidates to study \"predisposition\" to waterlogging tolerance or sensitivity in barley.</p>","PeriodicalId":20230,"journal":{"name":"Plant Direct","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2023-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10422865/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9990490","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptome analyses of leaf architecture in <i>Sansevieria</i> support a common genetic toolkit in the parallel evolution of unifacial leaves in monocots.","authors":"Edward M Golenberg, Aleksandar Popadić, Weilong Hao","doi":"10.1002/pld3.511","DOIUrl":"10.1002/pld3.511","url":null,"abstract":"<p><p>Planar structures dramatically increase the surface-area-to-volume ratio, which is critically important for multicellular organisms. In this study, we utilize naturally occurring phenotypic variation among three <i>Sansivieria</i> species (Asperagaceae) to investigate leaf margin expression patterns that are associated with mediolateral and adaxial/abaxial development. We identified differentially expressed genes (DEGs) between center and margin leaf tissues in two planar-leaf species <i>Sansevieria subspicata</i> and <i>Sansevieria trifasciata</i> and compared these with expression patterns within the cylindrically leaved <i>Sansevieria cylindrica</i>. Two <i>YABBY</i> family genes, homologs of <i>FILAMENTOUS FLOWER</i> and <i>DROOPING LEAF</i>, are overexpressed in the center leaf tissue in the planar-leaf species and in the tissue of the cylindrical leaves. As mesophyll structure does not indicate adaxial versus abaxial differentiation, increased leaf thickness results in more water-storage tissue and enhances resistance to aridity. This suggests that the cylindrical-leaf in <i>S. cylindrica</i> is analogous to the central leaf tissue in the planar-leaf species. Furthermore, the congruence of the expression patterns of these <i>YABBY</i> genes in <i>Sansevieria</i> with expression patterns found in other unifacial monocot species suggests that patterns of parallel evolution may be the result of similar solutions derived from a limited developmental toolbox.</p>","PeriodicalId":20230,"journal":{"name":"Plant Direct","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2023-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/9a/f7/PLD3-7-e511.PMC10407180.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9972767","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mechanosensitive ion channels MSL8, MSL9, and MSL10 have environmentally sensitive intrinsically disordered regions with distinct biophysical characteristics in vitro.","authors":"Aidan J Flynn, Kari Miller, Jennette M Codjoe, Matthew R King, Elizabeth S Haswell","doi":"10.1002/pld3.515","DOIUrl":"10.1002/pld3.515","url":null,"abstract":"<p><p>Intrinsically disordered protein regions (IDRs) are highly dynamic sequences that rapidly sample a collection of conformations over time. In the past several decades, IDRs have emerged as a major component of many proteomes, comprising ~30% of all eukaryotic protein sequences. Proteins with IDRs function in a wide range of biological pathways and are notably enriched in signaling cascades that respond to environmental stresses. Here, we identify and characterize intrinsic disorder in the soluble cytoplasmic N-terminal domains of MSL8, MSL9, and MSL10, three members of the MscS-like (MSL) family of mechanosensitive ion channels. In plants, MSL channels are proposed to mediate cell and organelle osmotic homeostasis. Bioinformatic tools unanimously predicted that the cytosolic N-termini of MSL channels are intrinsically disordered. We examined the N-terminus of MSL10 (MSL10^N) as an exemplar of these IDRs and circular dichroism spectroscopy confirms its disorder. MSL10^N adopted a predominately helical structure when exposed to the helix-inducing compound trifluoroethanol (TFE). Furthermore, in the presence of molecular crowding agents, MSL10^N underwent structural changes and exhibited alterations to its homotypic interaction favorability. Lastly, interrogations of collective behavior via in vitro imaging of condensates indicated that MSL8^N, MSL9^N, and MSL10^N have sharply differing propensities for self-assembly into condensates, both inherently and in response to salt, temperature, and molecular crowding. Taken together, these data establish the N-termini of MSL channels as intrinsically disordered regions with distinct biophysical properties and the potential to respond uniquely to changes in their physiochemical environment.</p>","PeriodicalId":20230,"journal":{"name":"Plant Direct","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2023-08-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10400277/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10007352","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identifying developmental QTL alleles with favorable effect on grain yield components under late-terminal drought in spring barley MAGIC population.","authors":"Nazanin P Afsharyan,&nbsp;Wiebke Sannemann,&nbsp;Agim Ballvora,&nbsp;Jens Léon","doi":"10.1002/pld3.516","DOIUrl":"10.1002/pld3.516","url":null,"abstract":"<p><p>Barley is the fourth most cultivated cereal worldwide, and drought is a major cause of its yield loss by negatively affecting its development. Hence, better understanding developmental mechanisms that control complex polygenic yield-related traits under drought is essential to uncover favorable yield regulators. This study evaluated seven above-ground yield-related traits under well-watered (WW) and late-terminal drought (TD) treatment using 534 spring barley multiparent advanced generation intercross double haploid (DH) lines. The analysis of quantitative trait loci (QTL) for WW, TD, marker by treatment interaction, and drought stress tolerance identified 69, 64, 25, and 25 loci, respectively, for seven traits from which 15 loci were common for at least three traits and 17 were shared by TD and drought stress tolerance. Evaluation of allelic effects for a QTL revealed varying effect of parental alleles. Results showed prominent QTL located on major flowering time gene <i>Ppd-H1</i> with favorable effects for grain weight under TD when flowering time was not significantly affected, suggesting that this gene might be linked with increasing grain weight by ways other than timing of flowering under late-terminal drought stress. Furthermore, a desirable novel QTL allele was identified on chromosome 5H for grain number under TD nearby sucrose transporter gene <i>HvSUT2</i>. The findings indicated that spring barley multiparent advanced generation intercross population can provide insights to improve yield under complex condition of drought.</p>","PeriodicalId":20230,"journal":{"name":"Plant Direct","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2023-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10394678/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9992828","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Overexpression of AHL proteins enhances root hair production by altering the transcription of RHD6-downstream genes.","authors":"Qike Zeng, Li Song, Mingzhe Xia, Zai Zheng, Ziang Chen, Ximing Che, Dong Liu","doi":"10.1002/pld3.517","DOIUrl":"10.1002/pld3.517","url":null,"abstract":"<p><p>AT-HOOK MOTIF NUCLEAR LOCALIZED (AHL) proteins occur in all sequenced plant species. They bind to the AT-rich DNA sequences in chromosomes and regulate gene transcription related to diverse biological processes. However, the molecular mechanism underlying how AHL proteins regulate gene transcription is poorly understood. In this research, we used root hair production as a readout to study the function of two Arabidopsis AHL proteins, AHL17, and its closest homolog AHL28. Overexpression of <i>AHL17</i> or <i>AHL28</i> greatly enhanced root hair production by increasing the transcription of an array of genes downstream of RHD6. RHD6 is a key transcription factor that regulates root hair development. Mutation of <i>RHD6</i> completely suppressed the overproduction of root hairs by blocking the transcription of <i>AHL17</i>-activated genes. The overexpression of <i>AHL17</i> or <i>AHL28</i>, however, neither affected the transcription of <i>RHD6</i> nor the accumulation of RHD6 protein. These two AHL proteins also did not directly interact with RHD6. Furthermore, we found that three members of the Heat Shock Protein70 family, which have been annotated as the subunits of the plant Mediator complex, could form a complex with both AHL17 and RHD6. Our research might reveal a previously unrecognized mechanism of how AHL proteins regulate gene transcription.</p>","PeriodicalId":20230,"journal":{"name":"Plant Direct","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2023-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10416611/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9990492","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correction to \"NDH-1L with a truncated NdhM subunit is unstable under stress conditions in cyanobacteria\".","authors":"","doi":"10.1002/pld3.525","DOIUrl":"https://doi.org/10.1002/pld3.525","url":null,"abstract":"<p><p>[This corrects the article DOI: 10.1002/pld3.502.].</p>","PeriodicalId":20230,"journal":{"name":"Plant Direct","volume":null,"pages":null},"PeriodicalIF":3.0,"publicationDate":"2023-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10457548/pdf/PLD3-7-.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10088187","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification of a xyloglucan beta-xylopyranosyltransferase from <i>Vaccinium corymbosum</i>.","authors":"Ronja Immelmann, Niklas Gawenda, Vicente Ramírez, Markus Pauly","doi":"10.1002/pld3.514","DOIUrl":"10.1002/pld3.514","url":null,"abstract":"<p><p>Plant cell walls contain the hemicellulose xyloglucan, whose fine structure may vary depending on cell type, tissue, and/or plant species. Most but not all of the glycosyltransferases involved in the biosynthesis of xyloglucan sidechains have been identified. Here, we report the identification of several functional glycosyltransferases from blueberry (<i>Vaccinium corymbosum</i> bluecrop). Among those transferases is a hitherto elusive <b>X</b>yloglucan:<b>B</b>eta-xylosyl<b>T</b>ransferase (XBT). Heterologous expression of <i>VcXBT</i> in the <i>Arabidopsis thaliana</i> double mutant <i>mur3 xlt2</i>, where xyloglucan consists only of an unsubstituted xylosylated glucan core structure, results in the production of the xylopyranose-containing \"U\" sidechain as characterized by mass spectrometry, glycosidic linkage, and NMR analysis. The introduction of the additional xylopyranosyl residue rescues the dwarfed phenotype of the untransformed Arabidopsis <i>mur3 xlt2</i> mutant to wild-type height. Structural protein analysis using Alphafold of this and other related xyloglucan glycosyltransferase family 47 proteins not only identifies potential domains that might influence the regioselectivity of these enzymes but also gives hints to specific amino acids that might determine the donor-substrate specificity of these glycosyltransferases.</p>","PeriodicalId":20230,"journal":{"name":"Plant Direct","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2023-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/02/79/PLD3-7-e514.PMC10368651.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9877960","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Simulation of microtubule-cytoplasm interaction revealed the importance of fluid dynamics in determining the organization of microtubules.","authors":"Mohammad Murshed, Donghui Wei, Ying Gu, Jin Wang","doi":"10.1002/pld3.505","DOIUrl":"10.1002/pld3.505","url":null,"abstract":"<p><p>Although microtubules in plant cells have been extensively studied, the mechanisms that regulate the spatial organization of microtubules are poorly understood. We hypothesize that the interaction between microtubules and cytoplasmic flow plays an important role in the assembly and orientation of microtubules. To test this hypothesis, we developed a new computational modeling framework for microtubules based on theory and methods from the fluid-structure interaction. We employed the immersed boundary method to track the movement of microtubules in cytoplasmic flow. We also incorporated details of the encounter dynamics when two microtubules collide with each other. We verified our computational model through several numerical tests before applying it to the simulation of the microtubule-cytoplasm interaction in a growing plant cell. Our computational investigation demonstrated that microtubules are primarily oriented in the direction orthogonal to the axis of cell elongation. We validated the simulation results through a comparison with the measurement from laboratory experiments. We found that our computational model, with further calibration, was capable of generating microtubule orientation patterns that were qualitatively and quantitatively consistent with the experimental results. The computational model proposed in this study can be naturally extended to many other cellular systems that involve the interaction between microstructures and the intracellular fluid.</p>","PeriodicalId":20230,"journal":{"name":"Plant Direct","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2023-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/10/94/PLD3-7-e505.PMC10368657.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9884503","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}