Expression profile of high yielding rice introgression line
Ontology highlight
ABSTRACT:
ORGANISM(S): Oryza sativa
PROVIDER: GSE30487 | GEO | 2011/12/31
SECONDARY ACCESSION(S): PRJNA143481
REPOSITORIES: GEO
Similar Datasets
Project description:Leaves and panicles from recurrent parent KMR3 and a high yielding KMR3-O.rufipogon introgression line were used Microarray analysis was carried out to reveal up- and down-regulated DEGs in leaves and panicles of control and experimental line for identifying key genes that help improve yield Leaves and fully emerged young panicles from both lines were used for RNA extraction and hybridization on Affymetrix microarrays
2011-12-31 | E-GEOD-30487 | biostudies-arrayexpress
Project description:Transcriptional profiling of sweet corn plant density (crowding stress) tolerance influencing yield. Tolerance to crowding stress has played a crucial role in improving agronomic productivity in field corn; however, commercial sweet corn hybrids vary greatly in crowding stress tolerance. The experiment was conducted to 1) explore transcriptional changes among sweet corn hybrids with differential yield under crowding stress, 2) identify relationships between phenotypic responses and gene expression patterns, and 3) identify groups of genes associated with yield and crowding stress tolerance. Under conditions of crowding stress, three high-yielding and three low-yielding sweet corn hybrids were grouped for transcriptional and phenotypic analyses. Transcriptional analyses identified from 372 to 859 common differentially expressed genes (DEGs) for each hybrid. Large gene expression pattern variation among hybrids and only 26 common DEGs across all hybrid comparisons were identified, suggesting each hybrid has a unique response to crowding stress. Over-represented biological functions of DEGs also differed among hybrids. Strong correlation was observed between: 1) modules with up-regulation in high-yielding hybrids and yield traits, and 2) modules with up-regulation in low-yielding hybrids and plant/ear traits. Modules linked with yield traits may be important crowding stress response mechanisms influencing crop yield. Functional analysis of the modules and common DEGs identified candidate crowding stress tolerant processes in photosynthesis, glycolysis, cell wall, carbohydrate/nitrogen metabolic process, chromatin, and transcription regulation. Moreover, these biological functions were greatly inter-connected, indicating the importance of improving the mechanisms as a network.
2016-01-05 | GSE73435 | GEO
Project description:Transcriptional profiling of sweet corn plant density (crowding stress) tolerance influencing yield. Tolerance to crowding stress has played a crucial role in improving agronomic productivity in field corn; however, commercial sweet corn hybrids vary greatly in crowding stress tolerance. The experiment was conducted to 1) explore transcriptional changes among sweet corn hybrids with differential yield under crowding stress, 2) identify relationships between phenotypic responses and gene expression patterns, and 3) identify groups of genes associated with yield and crowding stress tolerance. Under conditions of crowding stress, three high-yielding and three low-yielding sweet corn hybrids were grouped for transcriptional and phenotypic analyses. Transcriptional analyses identified from 372 to 859 common differentially expressed genes (DEGs) for each hybrid. Large gene expression pattern variation among hybrids and only 26 common DEGs across all hybrid comparisons were identified, suggesting each hybrid has a unique response to crowding stress. Over-represented biological functions of DEGs also differed among hybrids. Strong correlation was observed between: 1) modules with up-regulation in high-yielding hybrids and yield traits, and 2) modules with up-regulation in low-yielding hybrids and plant/ear traits. Modules linked with yield traits may be important crowding stress response mechanisms influencing crop yield. Functional analysis of the modules and common DEGs identified candidate crowding stress tolerant processes in photosynthesis, glycolysis, cell wall, carbohydrate/nitrogen metabolic process, chromatin, and transcription regulation. Moreover, these biological functions were greatly inter-connected, indicating the importance of improving the mechanisms as a network. 3 high-and 3 low-yielding hybrids with 2-3 biological replications grown under high population density (crowding stress)
2016-01-05 | E-GEOD-73435 | biostudies-arrayexpress
Project description:Rice is the most salt sensitive cereal crop and its cultivation is particularly threatened by salt stress. This study reports the development of salt tolerant introgressed lines (ILs) derived from crosses between the salt tolerant indica rice variety FL478, which harbors the Saltol QTL, and the salt-sensitive japonica elite cultivar PL12. Although the introgression of the Saltol QTL has been widely used to improve salinity tolerance, the molecular basis underlying the salinity tolerance conferred by Saltol remains poorly understood. Equally, the impact of introgressions from a Saltol donor parent on the global transcriptome of ILs is largely unknown. Here, genotyping-by-sequencing (GBS) and Kompetitive allele specific PCR (KASP) genotyping, in combination with step-wise phenotypic selection in hydroponic culture, were used for the identification of salt-tolerant ILs. Transcriptome-based genotyping allowed the fine mapping of indica genetic introgressions in the best performing IL line (IL22). A total of 1,595 genes were identified in indica regions in IL22, which mainly located in large introgressions at Chromosomes 1 and 3. In addition to OsHKT1;5, an important number of genes potentially contributing to salt stress tolerance were identified in indica segments of IL22. Comparative transcript profiling also revealed important transcriptional reprograming in IL22 plants both under non-stress and salt-stress conditions, indicating an impact on the transcriptome of the japonica background by the indica introgressed genes and vice versa. Interactions among indica and japonica genes would provide novel regulatory networks contributing to salt stress tolerance in introgression rice lines.
2021-12-20 | GSE167342 | GEO
Project description:To dissect the molecular mechanisms underlying drought tolerance (DT) in rice, transcriptome differences of a DT introgression line H471, the DT donor P28 and the drought sensitive recurrent parent HHZ under drought stress were investigated using deep transcriptome sequencing. Results revealed a differential constitutive gene expression prior to stress and distinct global transcriptome reprogramming among three genotypes under time-series drought stress, consistent with their differential genotypes and DT phenotypes. DT introgression line H471, the DT donor P28 and the drought sensitive recurrent parent HHZ under drought stress were investigated using deep transcriptome sequencing.The drought stress treatment was started by withholding water at the tillering stage. The days were counted after the AWC in the soil reached 20% to allow drought measurements at precisely determined intervals, and the soil water content reached 15%, 10% and 7.5% after 1d, 3d and 4d drought treatment, respectively.Three top leaves for each sample were harvested for each genotype under 1d and 3d drought stress and control conditions. All samples were immediately frozen in liquid nitrogen and stored at -80C and then for transcriptome sequencing.
2014-12-30 | E-GEOD-57950 | biostudies-arrayexpress
Project description:Purpose: The goal of the study is to compare the transcriptomic differences of the panicle tissue at the reproductive-stage of the Introgression Line (IR 96321-1447-165-B-3-1-2), which is drought-tolerant, to Swarna (recipient parent), which is drought-sensitive.
2020-02-25 | GSE145869 | GEO
Project description:Purpose: The goal of the study is to compare the transcriptomic differences of the flag-leaf tissue at the reproductive-stage of the Introgression Line (IR 96321-1447-165-B-3-1-2), which is drought-tolerant, to Swarna (recipient parent), which is drought-sensitive.
2020-02-25 | GSE145868 | GEO
Project description:Here, we first reported the construction of a phosphoproteomic landscape of 6 tissues, including callus, leaves, roots, shoot meristem (SM), young panicles (YP) and mature panicles (MP), from Nipponbare (Oryza sativa ssp. japonica). By employing a non-gel, quantitative phosphoproteomic approach, a total of 4792 phosphopeptides from 2657 phosphoproteins were identified, which were found to be differentially phosphorylated among tissues.
2018-04-11 | PXD005241 | Pride
Project description:One-step and two-step pathways are proposed to synthesize cytokinin. One-step pathway is mediated by LONELY GUY (LOG) proteins. However, the enzyme for two-step pathway has not been identified yet. Here, we show that a QTL GY3 boosts grain yield by more than 20% via manipulating two-step pathway. GY3 encodes a LOG protein that acts as a 5’-ribonucleotide phosphohydrolase by excessive consuming the cytokinin precursors, which contrasts with the activity of canonical LOG members as phosphoribohydrolases in a one-step pathway. The residue S41 of GY3 is crucial for the dephosphorylation of iPRMP. A solo-LTR insertion within the promoter of GY3 suppressed its expression and resulted in a higher content of active cytokinins in young panicles. Introgression of GY302428 increased grain yield per plot by 7.4% to 16.3% in all investigated indica backgrounds both under long-day and short-day conditions, which demonstrates the great value of GY302428 in indica rice production.
2023-05-05 | GSE231360 | GEO
Project description:To dissect the molecular mechanisms underlying drought tolerance (DT) in rice, transcriptome differences of a DT introgression line H471, the DT donor P28 and the drought sensitive recurrent parent HHZ under drought stress were investigated using deep transcriptome sequencing. Results revealed a differential constitutive gene expression prior to stress and distinct global transcriptome reprogramming among three genotypes under time-series drought stress, consistent with their differential genotypes and DT phenotypes.
2014-12-30 | GSE57950 | GEO