Genome-Wide Analysis of the MADS-box Gene Family Involved in Salt and Waterlogging Tolerance in Barley (Hordeum Vulgare. L)
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ABSTRACT:
ORGANISM(S): Hordeum vulgare
PROVIDER: GSE230751 | GEO | 2023/05/31
REPOSITORIES: GEO
Similar Datasets
Project description:Waterlogging is a major abiotic stress causing oxygen depletion and carbon dioxide accumulation in the rhizosphere. Barley is more susceptible to waterlogging stress than other cereals. To gain a better understanding of the effect of waterlogging stress in barley, we carried out a genome-wide gene expression analysis in roots of Yerong and Deder2 barley genotypes under waterlogging and control (well-watered) conditions by RNA-Sequencing, using Illumina HiSeq™ 4000 platform.
2020-02-14 | GSE144077 | GEO
Project description: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 QTLs 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.
2023-07-29 | GSE220532 | GEO
Project description:Waterlogging is one of the major abiotic stresses that affects barley production and yield quality. Proteomics techniques have been widely utilized to explore the mechanisms involved in the responses to abiotic stress. In this study, two barley genotypes with contrasting responses to waterlogging stress were analyzed with proteomic technology. The waterlogging treatment caused a greater reduction in biomass and photosynthetic performance in the waterlogging-sensitive genotype TF57 than that in the waterlogging-tolerant genotype TF58. Under waterlogging stress, 30, 30, 20 and 20 differentially expressed proteins were identified through tandem mass spectrometry analysis in the leaves, adventitious roots, nodal roots and seminal roots, respectively. Among these proteins, photosynthesis-, metabolism- and energy-related proteins were differentially expressed in the leaves, with oxygen-evolving enhancer protein 1, ATP synthase subunit and heat shock protein 70 being up-regulated in TF58. Pyruvate decarboxylase (PDC), 1-amino cyclopropane 1-carboxylic acid oxidase (ACO), glutamine synthetase (GS), glutathione S-transferases (GST) and beta-1, 3-glucanase in adventitious, nodal and seminal roots were more abundant in TF58 than those in TF57 under waterlogging stress. Ten representative genes were selected for validation by qRT-PCR in different genotypes with known waterlogging tolerance, and the expression levels of three candidate genes (PDC, ACO and GST) increased in the roots of all genotypes in response to the waterlogging stress. These three genes might play a significant role in the adaptation process of barley under waterlogging stress. The current results partially determined the mechanisms of waterlogging tolerance and provided valuable information for the breeding of barley with enhanced tolerance to waterlogging.
| S-EPMC6018542 | biostudies-literature
Project description:Background: Waterlogging was one of the most serious abiotic stresses in wheat-growing regions of China. There were great differences in waterlogging tolerance among different wheat varieties, and the mechanism of waterlogging tolerance of wheat seeds during germination was unclear. Methods: In order to reveal the adaptability of wheat to waterlogging stress during germination, we analyzed the germination rate and anatomical structure of three wheat seeds, ‘Zhoumai 22’, ‘Bainong 207’ and ‘Bainong 607’. At the same time, Illumina sequencing technology was used to determine the transcriptome of these three wheat varieties during germination. Results: The results showed that there was no significant difference between the germination rate of ‘Bainong 207’ after 3 days of waterlogging treatment and that of the control seeds. However, under waterlogging stress, the degree of emulsification and degradation of endosperm cells was higher than that of the control treatment, and starch granules in endosperm were significantly reduced. Transcriptome data were obtained from seed samples (a total of 18 samples) of three wheat varieties under waterlogging and control treatment. A total of 2,775 differentially expressed genes (DEGs) were identified by comprehensive analysis. In addition, by analyzing the correlation between the expression levels of DEGs and seed germination rates in three wheat varieties under waterlogging stress, it was found that the relative expression levels of 563 and 398 genes were positively and negatively correlated with the germination rate of wheat seeds, respectively. The GO and KEGG analysis found that the difference in waterlogging tolerance of the three wheat varieties was related to the abundance of key genes involved in the glycolysis pathway, the starch and sucrose metabolism pathway, and the lactose metabolism pathway. The ethanol dehydrogenase (ADH) gene in the endosperm of ‘Bainong 607’ was immediately induced after a short period of waterlogging, and the energy provided by glycolysis pathway enabled the seeds of ‘Bainong 607’ to germinate as early as possible, while the expression level of AP2/ERF transcription factor was up-regulated to further enhance its waterlogging tolerance. Conclusions: In general, this study provided a deeper understanding of the mechanisms by which different wheat varieties respond to waterlogging stress during germination.
2020-01-31 | GSE144554 | GEO
Project description:Waterlogging is a major abiotic stress causing oxygen depletion and carbon dioxide accumulation in the rhizosphere. Barley is more susceptible to waterlogging stress than other cereals. To gain a better understanding, the genome-wide gene expression responses in roots of waterlogged barley seedlings of Yerong and Deder2 were analyzed by RNA-Sequencing. A total of 6736, 5482, and 4538 differentially expressed genes (DEGs) were identified in waterlogged roots of Yerong at 72 h and Deder2 at 72 and 120 h, respectively, compared with the non-waterlogged control. Gene Ontology (GO) enrichment analyses showed that the most significant changes in GO terms, resulted from these DEGs observed under waterlogging stress, were related to primary and secondary metabolism, regulation, and oxygen carrier activity. In addition, more than 297 transcription factors, including members of MYB, AP2/EREBP, NAC, WRKY, bHLH, bZIP, and G2-like families, were identified as waterlogging responsive. Tentative important contributors to waterlogging tolerance in Deder2 might be the highest up-regulated DEGs: Trichome birefringence, α/β-Hydrolases, Xylanase inhibitor, MATE efflux, serine carboxypeptidase, and SAUR-like auxin-responsive protein. The study provides insights into the molecular mechanisms underlying the response to waterlogging in barley, which will be of benefit for future studies of molecular responses to waterlogging and will greatly assist barley genetic research and breeding.
| S-EPMC7076447 | biostudies-literature
Project description:Waterlogging is one of the main abiotic stresses severely reducing barley grain yield. Barley breeding programs focusing on waterlogging tolerance require an understanding of genetic loci and alleles in the current germplasm. In this study, 247 worldwide spring barley genotypes grown under controlled field conditions were genotyped with 35,926 SNPs with minor allele frequency (MAF) > 0.05. Significant phenotypic variation in each trait, including biomass, spikes per plant, grains per plant, kernel weight per plant, plant height and chlorophyll content, was observed. A genome-wide association study (GWAS) based on linkage disequilibrium (LD) for waterlogging tolerance was conducted. Population structure analysis divided the population into three subgroups. A mixed linkage model using both population structure and kinship matrix (Q+K) was performed. We identified 17 genomic regions containing 51 significant waterlogging-tolerance-associated markers for waterlogging tolerance response, accounting for 5.8-11.5% of the phenotypic variation, with a majority of them localized on chromosomes 1H, 2H, 4H, and 5H. Six novel QTL were identified and eight potential candidate genes mediating responses to abiotic stresses were located at QTL associated with waterlogging tolerance. To our awareness, this is the first GWAS for waterlogging tolerance in a worldwide barley collection under controlled field conditions. The marker-trait associations could be used in the marker-assisted selection of waterlogging tolerance and will facilitate barley breeding.
| S-EPMC8427447 | biostudies-literature
Project description:Shoot tissue from 17 day old barley plants was used for expression analysis. Targets from three biological replicates of each were generated and the expression profiles were determined using Affymetrix Barley1 Genechip arrays. Comparisons between the control and stressed samples at three time points (3, 8 and 27 h) allow the identification of salt stress responsive genes. Experiment Overall Design: 3 control and 3 salt stressed biological replicates were analyzed at 3, 8 and 27 h.
2007-10-04 | E-GEOD-3097 | biostudies-arrayexpress
Project description:Gene expression in plastids of higher plants is dependent on two different transcription machineries, a plastid-encoded bacterial-type RNA polymerase (PEP) and a nuclear-encoded phage-type RNA polymerase (NEP), which recognize distinct types of promoters. The division of labor between PEP and NEP during plastid development and in mature chloroplasts is unclear due to a lack of comprehensive information on promoter usage. Here we present a thorough investigation into the distribution of PEP and NEP promoters within the plastid genome of barley (Hordeum vulgare L). Using a novel differential RNA sequencing approach, which discriminates between primary and processed transcripts, we obtained a genome-wide map of transcription start sites in plastids of mature first leaves. PEP-lacking plastids of the albostrians mutant allowed for the unambiguous identifications of NEP promoters. We observed that the chloroplast genome contains many more promoters than genes. According to our data, most genes (including genes coding for photosynthesis proteins) have both PEP and NEP promoters. We also detected numerous transcription start sites within operons indicating transcriptional uncoupling of genes in polycistronic gene clusters. Moreover, we mapped many transcription start sites in intergenic regions, as well as opposite to annotated genes demonstrating the existence of numerous non-coding RNA candidates.
2011-11-23 | GSE33773 | GEO
Project description:The hypothesis whether CaCl2 seed treatment prior to sowing (osmopriming) can enhance drought stress tolerance, and/or alleviate the effect on plant growth was tested. Here we elucidate whether seed treatment prior to sowing (osmopriming) with CaCl2 can improve the drought stress tolerance, as it was previously reported for salt stress on wheat. Thus the effect of 50 mM CaCl2, previously chosen based on pilot experiment, versus water-treated control exposed to drought stress was investigated.
2015-09-30 | GSE56437 | GEO
Project description:It is not known to what degree aquaporin-facilitated water uptake differs between root developmental regions and types of root. The aim of this study was to measure aquaporin-dependent water flow in the main types of root and root developmental regions of 14- to 17-d-old barley plants and to identify candidate aquaporins which mediate this flow. Water flow at root level was related to flow at cell and plant level. Plants were grown hydroponically. Hydraulic conductivity of cells and roots was determined with a pressure probe and through exudation, respectively, and whole-plant water flow (transpiration) determined gravimetrically in response to the commonly used aquaporin inhibitor HgCl(2). Expression of aquaporins was analysed by real-time PCR and in situ hybridization. Hydraulic conductivity of cortical cells in seminal roots was largest in lateral roots; it was smallest in the fully mature zone and intermediate in the not fully mature 'transition' zone along the main root axis. Adventitious roots displayed an even higher (3- to 4-fold) cortical cell hydraulic conductivity in the transition zone. This coincided with 3- to 4-fold higher expression of three aquaporins (HvPIP2;2, HvPIP2;5, HvTIP1:1). These were expressed (also) in cortical tissue. The largest inhibition of water flow (83-95%) in response to HgCl(2) was observed in cortical cells. Water flow through roots and plants was reduced less (40-74%). It is concluded that aquaporins contribute substantially to root water uptake in 14- to 17-d-old barley plants. Most water uptake occurs through lateral roots. HvPIP2;5, HvPIP2;2, and HvTIP1;1 are prime candidates to mediate water flow in cortical tissue.
| S-EPMC3153672 | biostudies-literature