"Genome-Wide Association Study (GWAS) Uncovers Candidate Genes Linked to the Germination Performance of Bread Wheat (Triticum aestivum L.) under Salt Stress"
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PROVIDER: PRJEB81451 | ENA |
REPOSITORIES: ENA
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Project description:Wheat seed germination is highly related to seedling survival rate and subsequent vegetative growth,and therefore directly affects the conformation of wheat yield and quality. So wheat seed germination is not only important to itself, but the whole human society. However, due to the large genome size, many studies related to wheat seed are very complex and uncompleted. Transcriptome analysis of elite Chinese bread wheat cultivar Jimai 20 may provides a comprehensive understanding of wheat seed germination. Seed germination involves in the regulation of large number of genes, whether these genes are normal activated or not is very important to seed germination. We performed microarray analysis using the Affymetrix Gene Chip to reveal the gene expression profiles in five phases of wheat cultivar Jimai 20 seed germination. Our results provide a new insights into the thoroughly metabolic changes of seed germination as well as the relationship between some significant genes.
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Project description:An investigation into the Candidate Genes Linked to the Germination Performance of Bread Wheat under Salt Stress
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Project description:Wheat seed germination is highly related to seedling survival rate and subsequent vegetative growth,and therefore directly affects the conformation of wheat yield and quality. So wheat seed germination is not only important to itself, but the whole human society. However, due to the large genome size, many studies related to wheat seed are very complex and uncompleted. Transcriptome analysis of elite Chinese bread wheat cultivar Jimai 20 may provides a comprehensive understanding of wheat seed germination. Seed germination involves in the regulation of large number of genes, whether these genes are normal activated or not is very important to seed germination. We performed microarray analysis using the Affymetrix Gene Chip to reveal the gene expression profiles in five phases of wheat cultivar Jimai 20 seed germination. Our results provide a new insights into the thoroughly metabolic changes of seed germination as well as the relationship between some significant genes. The five groups including germinating seeds were harvest at five successive phases, which were 0 (P0), 12 (P1), 24 (P2), 36 (P3), 48 (P4) hour after imbibition respectively. Three independent experiments were performed for each group.
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Project description:Purpose: To identify the potential genes that regulate seed germination speed in maize, we performed a time-series transcriptome analysis with two inbred maize lines (72-3 fast germination, F9721 slow germination) during the seed germination and compared the differentially expressed genes (DEGs) in transcriptome with genes identified by GWAS Methods: Methods: mRNA profiles of two maize inbred lines 72-3 and F9721 showing divergent seed germination at six stages during germination were generated by deep sequencing, in triplicate, using Illumina Hiseq2500. The sequence reads that passed quality filters were analyzed at the gene level. Hisat2 was used to align clean reads to maize B73 reference genome, and HTSeq was used to count transcript abundance. DESeq2 models were used to compare DEGs at each germination stage within or between samples Results: Comparative transcriptome study identified 12 hours after imbibition (HAI) as the critical stage responsible for the variation of germination speed. The DEGs between 72-3 and F9721 were mainly enriched in metabolic pathways, biosynthesis of secondary metabolites, oxidoreductase activity pathways, hormone signal transduction, and amino acid transporter activity pathways Conclusions: Combined with evidence from gene expression data, GWAS, and gene synteny with other model species, we finally anchored three genes as the likely candidate genes regulating germination speed in maize
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Project description:Wheat seed germination directly affects wheat yield and quality. The wheat grains mainly include embryo and endosperm, and both play important roles in seed germination, seedling survival and subsequent vegetative growth. ABA can positively regulate dormancy induction and then negatively regulates seed germination at low concentrations. H2O2 treatment with low concentration can promote seed germination of cereal plants. Although various transcriptomics and proteomics approaches have been used to investigate the seed germination mechanisms and response to various abiotic stresses in different plant species, an integrative transcriptome analysis of wheat embryo and endosperm response to ABA and H2O2 stresses has not reported so far. We used the elite Chinese bread wheat cultivar Zhenmai 9023 as material and performed the first comparative transcriptome microarray analysis between embryo and endosperm response to ABA and H2O2 treatments during seed germination using the GeneChip® Wheat Genome Array Wheat seed germination includes a great amount of regulated genes which belong to many functional groups. ABA/H2O2 can repress/promote seed germination through coordinated regulating related genes expression. Our results provide new insights into the transcriptional regulation mechanisms of embryo and endosperm response to ABA and H2O2 treatments during seed germination
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Project description:Global climate changes on one aspect of extreme temperature records would suddenly reset environmental growth conditions for field-grown crops, which severely affects agronomic and commercial traits. Taking the cold-season preferable crop rapeseed Brassica napus L. for example, low-temperature shocks change endogenous regulatory networks and cause phenotypic damages during most lifespan. Here we screened out two genetic breeding elites with different temperature-dependent germination rates, core germplasms with good germination performance and genetic loci and candidate genes potentially involved in low-temperature tolerant functions for the pre-breeding purpose of cold-tolerant germination. By using the phenotype of the germination index of 273 core germplasms under normal temperature and 10 transcriptomic datasets of cold-tolerant Jia You (JY) 1621 and cold-sensitive JY1605 elite cultivars on three timepoints during germination process, we successfully identified clustered genes of early and late temperature response germination (ETRG and LTRG) genes and several cold-tolerant (CDT) and temperature-insensitive (TPI) candidate regulators. This study performed comprehensive multi-omics research on potential cold-responsive genes for the rapeseed improvement of cold tolerance germination.
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Project description:B1118-8-4 expresses five HMW subunits encoded by Glu-B1 (14, 15) and Glu D1 (5, 10) and transgene Glu-A1 (Ax1).Cadenza does not express Glu-A1 (Ax1. B111-8-8-4 (6)transgenic wheat line was produced by co-transformation with two plasmids: one of the plasmids carring the transgene HMW-GS 1Ax1 (Halford, N.G. et al. Analysis of HMW glutenin subunits encoded bychromosome 1A of bread wheat (Triticum aestivum L.) and the other plasmid harbour the marker genes bar and gus indicates quantitative effects on grain quality. Theor Appl Genet 83, 373-378 (1992).) and the other the bar gus gene sequences. We compared the transcriptome of transgenic B1118-8 4(6) wheat line with its background control-Cadenza bread wheat line. Transcriptomes analysis was performed in endosperm tissue (14 and 28 days post anthesis-dpa) and in leaf tissue (8 days post germination dpg). Each of the transcriptome comparisons was performed using three biological replicates (i.e. per line/tissue/developmental stage selected). Hybridisations were performed in reverse dye labelling.
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Project description:Wheat seed germination directly affects wheat yield and quality. The wheat grains mainly include embryo and endosperm, and both play important roles in seed germination, seedling survival and subsequent vegetative growth. ABA can positively regulate dormancy induction and then negatively regulates seed germination at low concentrations. H2O2 treatment with low concentration can promote seed germination of cereal plants. Although various transcriptomics and proteomics approaches have been used to investigate the seed germination mechanisms and response to various abiotic stresses in different plant species, an integrative transcriptome analysis of wheat embryo and endosperm response to ABA and H2O2 stresses has not reported so far. We used the elite Chinese bread wheat cultivar Zhenmai 9023 as material and performed the first comparative transcriptome microarray analysis between embryo and endosperm response to ABA and H2O2 treatments during seed germination using the GeneChip® Wheat Genome Array Wheat seed germination includes a great amount of regulated genes which belong to many functional groups. ABA/H2O2 can repress/promote seed germination through coordinated regulating related genes expression. Our results provide new insights into the transcriptional regulation mechanisms of embryo and endosperm response to ABA and H2O2 treatments during seed germination The six groups including embryo and endosperm response to pure water (CK), ABA and H2O2 were havested respectively, which were CK_embryo (CKem), CK_endosperm (CKe), ABA_embryo (ABAem), ABA_endosperm (ABAe), H2O2_embryo (H2O2em), H2O2_endosperm (H2O2e). Three independent experiments were performed for each group.
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Project description:Bread wheat (Triticum aestivum L., cv. Fielder) plants were grown under iron (Fe) deficient hydroponic conditions to analyise transcriptomic changes in leaf and root tissue.
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