Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Wheat expression level polymorphism study 39 genotypes 2 biological reps

ABSTRACT: The use of statistical tools established for the genetic analysis of quantitative traits can be applied to gene expression data. Quantitative trait loci (QTL) analysis can associate expression of genes or groups of genes with particular genomic regions and thereby identify regions that play a role in the regulation of gene expression. A segregating population of 41 doubled haploid (DH) lines from the hard red spring wheat cross RL4452 x AC Domain was used. This population had previously been mapped with microsatellites and includes a full QTL analysis for agronomic and seed quality traits. Expression analysis from 5 day post anthesis developing seed was conducted on 39 of the 41 DH lines using the Affymetrix wheat array. Expression analysis of developing seeds from field grown material identified 1,327 sequences represented by Affymetrix probe sets whose expression varied significantly between genotypes of the population. A sub-set of 378 transcripts were identified that each mapped to a single chromosome interval illustrating that major expression QTLs can be found in wheat. Genomic regions corresponding to multiple expression QTLs were identified that were coincident with previous identified seed quality trait QTL. These regions may be important regulatory regions governing economically important traits. Comparison of expression mapping data with physical mapping for a sub-set of sequences showed that both cis and trans acting expression QTLs were present. Keywords: genetic differences, expression QTL

ORGANISM(S): Triticum aestivum

PROVIDER: GSE4935 | GEO | 2007/03/25

SECONDARY ACCESSION(S): PRJNA95889

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

wheat expression level polymorphism study parental genotypes 2 biological reps

Project description:The use of statistical tools established for the genetic analysis of quantitative traits can be applied to gene expression data. Quantitative trait loci (QTL) analysis can associate expression of genes or groups of genes with particular genomic regions and thereby identify regions that play a role in the regulation of gene expression. A segregating population of 41 doubled haploid (DH) lines from the hard red spring wheat cross RL4452 x AC Domain was used. This population had previously been mapped with microsatellites and includes a full QTL analysis for agronomic and seed quality traits. Expression analysis from 5 day post anthesis developing seed was conducted on 39 of the 41 DH lines using the Affymetrix wheat array. Expression analysis of developing seeds from field grown material identified 1,327 sequences represented by Affymetrix probe sets whose expression varied significantly between genotypes of the population. A sub-set of 378 transcripts were identified that each mapped to a single chromosome interval illustrating that major expression QTLs can be found in wheat. Genomic regions corresponding to multiple expression QTLs were identified that were coincident with previous identified seed quality trait QTL. These regions may be important regulatory regions governing economically important traits. Comparison of expression mapping data with physical mapping for a sub-set of sequences showed that both cis and trans acting expression QTLs were present. Keywords: genetic differences, expression QTL

2007-03-25 | GSE4929 | GEO

Transcription profiling of wheat expression level polymorphism study parental genotypes 2 biological reps from SB location

Project description:The use of statistical tools established for the genetic analysis of quantitative traits can be applied to gene expression data. Quantitative trait loci (QTL) analysis can associate expression of genes or groups of genes with particular genomic regions and thereby identify regions that play a role in the regulation of gene expression. A segregating population of 41 doubled haploid (DH) lines from the hard red spring wheat cross RL4452 x AC Domain was used. This population had previously been mapped with microsatellites and includes a full QTL analysis for agronomic and seed quality traits. Expression analysis from 5 day post anthesis developing seed was conducted on 36 of the 41 DH lines using the Affymetrix wheat array. Expression analysis of developing seeds from field grown material in location 2 identified 10,280 sequences represented by Affymetrix probe sets whose expression varied significantly between genotypes of the population. Of these 1,455 were identified in the point location as well. A sub-set of 542 transcripts were identified that each mapped to a single chromosome interval illustrating that major expression QTLs can be found in wheat. Genomic regions corresponding to multiple expression QTLs were identified that were coincident with previous identified seed quality trait QTL. These regions may be important regulatory regions governing economically important traits. Comparison of expression mapping data with physical mapping for a sub-set of sequences showed that both cis and trans acting expression QTLs were present. Experiment Overall Design: Parental genotypes of mapping population RL4452 x AC Domain with 2 biological replicates per genotype. Grown in the field in a lattice design at SB location with the 41 DH progeny lines.

2008-06-14 | E-GEOD-5937 | biostudies-arrayexpress

Transcription profiling of wheat expression level polymorphism study parental genotypes 2 biological reps

2008-06-13 | E-GEOD-4929 | biostudies-arrayexpress

Wheat expression level polymorphism study 36 genotypes 2 biological reps from SB location

Project description:The use of statistical tools established for the genetic analysis of quantitative traits can be applied to gene expression data. Quantitative trait loci (QTL) analysis can associate expression of genes or groups of genes with particular genomic regions and thereby identify regions that play a role in the regulation of gene expression. A segregating population of 41 doubled haploid (DH) lines from the hard red spring wheat cross RL4452 x AC Domain was used. This population had previously been mapped with microsatellites and includes a full QTL analysis for agronomic and seed quality traits. Expression analysis from 5 day post anthesis developing seed was conducted on 36 of the 41 DH lines using the Affymetrix wheat array. Expression analysis of developing seeds from field grown material in location 2 identified 10,280 sequences represented by Affymetrix probe sets whose expression varied significantly between genotypes of the population. Of these 1,455 were identified in the point location as well. A sub-set of 542 transcripts were identified that each mapped to a single chromosome interval illustrating that major expression QTLs can be found in wheat. Genomic regions corresponding to multiple expression QTLs were identified that were coincident with previous identified seed quality trait QTL. These regions may be important regulatory regions governing economically important traits. Comparison of expression mapping data with physical mapping for a sub-set of sequences showed that both cis and trans acting expression QTLs were present. Keywords: genetic differences, expression QTL

2007-03-25 | GSE5939 | GEO

Wheat expression level polymorphism study parental genotypes 2 biological reps from SB location

Project description:The use of statistical tools established for the genetic analysis of quantitative traits can be applied to gene expression data. Quantitative trait loci (QTL) analysis can associate expression of genes or groups of genes with particular genomic regions and thereby identify regions that play a role in the regulation of gene expression. A segregating population of 41 doubled haploid (DH) lines from the hard red spring wheat cross RL4452 x AC Domain was used. This population had previously been mapped with microsatellites and includes a full QTL analysis for agronomic and seed quality traits. Expression analysis from 5 day post anthesis developing seed was conducted on 36 of the 41 DH lines using the Affymetrix wheat array. Expression analysis of developing seeds from field grown material in location 2 identified 10,280 sequences represented by Affymetrix probe sets whose expression varied significantly between genotypes of the population. Of these 1,455 were identified in the point location as well. A sub-set of 542 transcripts were identified that each mapped to a single chromosome interval illustrating that major expression QTLs can be found in wheat. Genomic regions corresponding to multiple expression QTLs were identified that were coincident with previous identified seed quality trait QTL. These regions may be important regulatory regions governing economically important traits. Comparison of expression mapping data with physical mapping for a sub-set of sequences showed that both cis and trans acting expression QTLs were present. Keywords: genetic differences, expression QTL

2007-03-25 | GSE5937 | GEO

Transcription profiling of wheat expression level polymorphism study 39 genotypes 2 biological replicates

2008-06-13 | E-GEOD-4935 | biostudies-arrayexpress

Transcription profiling of wheat - expression level polymorphism study 36 genotypes 2 biological replicates from SB location

Project description:The use of statistical tools established for the genetic analysis of quantitative traits can be applied to gene expression data. Quantitative trait loci (QTL) analysis can associate expression of genes or groups of genes with particular genomic regions and thereby identify regions that play a role in the regulation of gene expression. A segregating population of 41 doubled haploid (DH) lines from the hard red spring wheat cross RL4452 x AC Domain was used. This population had previously been mapped with microsatellites and includes a full QTL analysis for agronomic and seed quality traits. Expression analysis from 5 day post anthesis developing seed was conducted on 36 of the 41 DH lines using the Affymetrix wheat array. Expression analysis of developing seeds from field grown material in location 2 identified 10,280 sequences represented by Affymetrix probe sets whose expression varied significantly between genotypes of the population. Of these 1,455 were identified in the point location as well. A sub-set of 542 transcripts were identified that each mapped to a single chromosome interval illustrating that major expression QTLs can be found in wheat. Genomic regions corresponding to multiple expression QTLs were identified that were coincident with previous identified seed quality trait QTL. These regions may be important regulatory regions governing economically important traits. Comparison of expression mapping data with physical mapping for a sub-set of sequences showed that both cis and trans acting expression QTLs were present. Experiment Overall Design: 36 genotypes of mapping population RL4452 x AC Domain with 2 biological replicates per genotype. Grown in the field in a lattice design at SB location

2008-06-14 | E-GEOD-5939 | biostudies-arrayexpress

Development of high-density genetic map by transcriptome sequencing

Project description:Ramie is an important industrial fiber crop, and the fiber yield and its related traits are the most valuable traits in ramie production. However, the genetic basis for these traits is still poorly understood. Herein, a high-density genetic map with 1085 markers spanning 2,118.8 cM was constructed using a population derived from two parents, cultivated ramie Zhongsizhu 1 (ZSZ1) and its wild progenitor B. nivea var. tenacissima (BNT). The fiber yield (FY) and its four related traits—stem diameter (SD) and length (SL), stem bark weight (BW) and thickness (BT)—were performed for quantitative trait locus (QTL) analysis, resulting in eight, six, six, three, and ten QTLs for SD, SL, BW, BD and FY traits, respectively. These 33 QTLs were mapped into 11 genomic regions, thus forming 11 QTL clusters; there were 11 QTLs identified their beneficial alleles from the wild species BNT. Interestingly, all QTLs in Cluster 8 and Cluster 10 displayed overdominance, indicating that these two regions were likely heterotic loci. In addition, there were five fiber yield-related genes identified to undergo positive selection in previous study, and they were found to locate into the genomic region near to the QTLs of this study. The genetic dissection for FY and its related traits improved our understanding to the genetic basis of these traits, as well to their domestication in ramie. The identification of many QTLs and the discovery of beneficial alleles from wild species provided a basis for the improvement of yield traits in ramie breeding.

2019-01-31 | GSE125891 | GEO

Transcriptome profiling of reproductive stage flag leaves of wheat from drought susceptible parent WL711, drought tolerant parent C306 and drought susceptible and drought tolerant RIL bulks in irrigated and drought condition

Project description:The aim of the study was to identify candidate genes responsible for drought tolerance trait between a pair of wheat varieties ( WL711 and C306) and correspondng progeny bulks (10 drought susceptible RILs and 10 drought tolerant RILs) by combining QTLs analysis with expression analysis. Microarray analysis of RNA extracted from the flag leaves showed large number of differentially expressed genes. The number of differentially expressed genes was reduced to 37 on the basis of their occurance in a major QTL region (responcible for drought tolerance) detected in RIL population derived from WL711 and C306.

2012-04-30 | GSE30436 | GEO

Identification of candidate genes involved in salt stress response at germination and seedling stages by QTL mapping in upland cotton

Project description:Salinity is a major abiotic stress at critical stages of seed germination and seedling establishment. Germination rate (GR) and field emergence rate (FER) are the key traits that determine the basic number of plants stand under field conditions. To explore molecular mechanisms in upland cotton under salt stress, a population of 177 recombinant inbred lines (RILs) and their parents were evaluated for seed germination traits (GP, germination potential; GR; FW, fresh weight; DW, dry weight; GL, germinal length) and seedling traits (FER; SH, seedling height; NL, Number of main stem leaves) in 2016-2018. Based on the linkage map contained 2,859 single nucleotide polymorphism (SNP) and simple sequence repeats (SSR) markers, traits under salt stress (E1) and normal condition, (E2) and the converted relative index (R-value) of three years’ trials were used to map quantitative trait loci (QTL). A total of three QTL and two clusters were detected as salt-tolerant QTL. Three QTL (qGR-Chr4-3, qFER-Chr12-3, qFER-Chr15-1) were detected under salt stress and R-value, which explained phenotypic variance of 9.62%-13.67%, and 4.2%-4.72%, 4.75%-8.96%, respectively. Two clusters (Loci-Chr4-2 and Loci-Chr5-4) harboring the QTL for four germination traits (GR, FER, GL, NL) and six seedling traits (GR, FER, DW, FW, SH, NL) were detected related under salt stress. A total of 691 genes were found in the candidate QTL or clusters. Among them, four genes (Gh_A04G1106, Gh_A05G3246, Gh_A05G3177, Gh_A05G3266) showed expression changes between sensitive and tolerant lines under salt stress, and were assigned as candidate genes in response to salt stress. The consistent salt-tolerance QTL identified in both germination and seedling stages will facilitate new information for cotton breeding.

2022-06-23 | GSE186533 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data