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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Expression profile of high yielding rice introgression line

ABSTRACT: 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

ORGANISM(S): Oryza sativa

SUBMITTER: Sarla Neelamraju

PROVIDER: E-GEOD-30487 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Os11Gsk gene from a wild rice, Oryza rufipogon improves yield in rice.

Thalapati Sudhakar S Batchu Anil K AK Neelamraju Sarla S Ramanan Rajeshwari R

Functional & integrative genomics 20120225 2

Chromosomal segments from wild rice species Oryza rufipogon, introgressed into an elite indica rice restorer line (KMR3) using molecular markers, resulted in significant increase in yield. Here we report the transcriptome analysis of flag leaves and fully emerged young panicles of one of the high yielding introgression lines IL50-7 in comparison to KMR3. A 66-fold upregulated gene Os11Gsk, which showed no transcript in KMR3 was highly expressed in O. rufipogon and IL50-7. A 5-kb genomic region i ...[more]

PMID: 22367483

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Expression profile of high yielding rice introgression line

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

2011-12-31 | GSE30487 | GEO

Sweet corn: low- vs. high-yielding hybrids

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

Sweet corn: low- vs. high-yielding hybrids

2016-01-05 | GSE73435 | GEO

Oryza sativa

Project description:Expression profile of high yielding rice introgression line

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Expression data from panicle in heat tolerant and heat susceptible rice under high temperature stress

Project description:To better understand the mechanisms that regulate the heat stress response in rice, we conducted a comparative analysis of transcriptome profile in panicles from two rice lines, heat-tolerant line 252 (HTL252) and heat-susceptible line 082 (HSL082) using rice Affymetrix GeneChip. In HTL252 panicles, 1538 differentially expressed genes (DEGs) genes with at least four-fold expression changes compared with the control under heat treatment were considered heat-responsive (HR). Of these DEGs, 522 genes were up-regulated while 1016 genes were repressed. Among DEGs in HSL082, 496 genes were induced and 1707 genes were repressed. Out of the 370 common DEGs found between HTL252 and HSL082, 129 genes were induced and 241 genes were repressed.

2019-06-20 | GSE83542 | GEO

Expression data from testes and abdomen in fertile and sterile introgression males

Project description:Postmating reproductive isolation is often manifested as hybrid male sterility, for which X-linked genes are over-represented. In contrast, X-linked gene are significantly under-represented among testis-expressing gene.This seeming contradiction may be germane to the X:autosome imbalance hypothesis on hybrid sterility ,in which the X-linked effect is mediated mainly through the misexpression of autosomal genes. We compared gene expression in fertile and sterile males in the hybrids between two Drosophila species. These hybrid males differ only in a small region of the X chromosome containing the OdsH locus of hybrid sterility. Of genes expressed in the testis, autosomal genes were indeed more likely to be misexpressed than X-linked genes under the steriizing action of OdsH. We compared gene expression between D. simulans males that carried either a fertile or sterile introgression (referred to as F or S males, respectively) from D. mauritiana. The introgressions span approximately 1/10 of the X chromosome, but the difference between the two introgressions is only about 3 Kb which contains exons 3 – 4 of OdsH. In short, F and S males have the same genetic background with respect to species origin, except the source of a portion of the OdsH gene. Three separate extractions and hybridizations were carried out for the RNA samples derived from testes and abdomens in each of two introgression lines.

2010-05-19 | E-GEOD-21734 | biostudies-arrayexpress

British European polecat introgression

Project description:British European polecat introgression.

| PRJEB48359 | ENA

Triticum aestivum cultivar:Introgression line (IL pau16058)

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Global identification of genes specific for rice meiosis

Project description:The leptotene-zygotene transition is a major step in meiotic progression during which pairing between homologous chromosomes is initiated and double strand breaks occur. OsAM1, a homolog of maize AM1 and Arabidopsis SWI1, encodes a protein with a coiled-coil domain in its central region that is required for the leptotene-zygotene transition during rice meiosis. To gain more insight into the role of OsAM1 in rice meiosis and to identify additional meiosis-specific genes, we characterized the transcriptomes of young panicles of Osam1 mutant and wild-type rice plants using RNA-Seq, bioinformatic and statistical analyses. As a result, a total of 25,750 and 28,455 genes were expressed in young panicles of wild-type and Osam1 mutant plants, respectively, and 4,400 differentially expressed genes (DEGs; log2 Ratio ≥ 1, FDR ≤ 0.05) were identified. Of these DEGs, four known rice meiosis-specific genes were detected, and 22 new putative meiosis-related genes were found by mapping these DEGs to reference biological pathways in the KEGG database. We identified eight additional well-conserved OsAM1-responsive rice meiotic genes by comparing our RNA-Seq data with known meiotic genes in Arabidopsis and fission yeast. We sequenced the transcriptome of young panicles of Osam1 mutant and wild-type rice.

2015-07-01 | E-GEOD-66469 | biostudies-arrayexpress

A phosphoproteomic landscape of rice (Oryza sativa L.) tissues

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

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