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A global analysis of QTLs for expression variations in rice flag leaf at heading date

ABSTRACT: Analyses of QTLs for expression levels (eQTLs) of the genes reveal genetic relationship between expression variation and the regulator, thus unlocking the information for identifying the regulatory network. In this study, we used Affymetrix GeneChip Rice Genome Array to analyze eQTLs in rice flag leaf at heading date from 210 recombinant inbred lines (RILs) derived from a cross between Zhenshan 97 and Minghui 63. In the study, we attempted to construct the regulatory network by identifying putative regulators and the respective targets using an eQTL guided co-expression analysis with a recombinant inbred line population of rice.

ORGANISM(S): Oryza sativa

PROVIDER: GSE49020 | GEO | 2014/02/05

SECONDARY ACCESSION(S): PRJNA212700

REPOSITORIES: GEO

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Project description:Analyses of QTLs for expression levels (eQTLs) of the genes reveal genetic relationship between expression variation and the regulator, thus unlocking the information for identifying the regulatory network. Oligo-nucleotide expression microarrays hybridized with RNA can simultaneously provide data for molecular markers and transcript abundance. In this study, we used Affymetrix GeneChip Rice Genome Array to analyze eQTLs in rice shoots at 72 h after germination from 110 recombinant inbred lines (RILs) derived from a cross between Zhenshan 97 and Minghui 63. Totally 1,632 single feature polymorphisms (SFPs) plus 23 PCR markers were identified and placed into 601 recombinant bins, spanning 1,459 cM in length, which were used as markers to genotype the RILs. We obtained 16,372 expression traits (e-traits) each with at least one eQTL, resulting in 26,051 eQTLs in total, including both cis- and trans-eQTLs. We also identified 171 eQTL hotspots among rice genome, each of which controls transcript variations of many e-traits. Gene Ontology analysis revealed enrichment of certain functional categories of genes in some of the eQTL hotspots. In particular, eQTLs for e-traits involving DNA metabolic process was significantly enriched in several eQTL hotspots on chromosomes 3, 5 and 10. Several transcription factors colocalizing with cis-eQTLs showed significant correlations with hundreds of e-traits, indicating possible co-regulation. We also detected correlations between the QTLs for shoot dry weight and eQTLs, revealing possible candidate genes for the trait. These results provided the clues for identification and characterization of regulatory network in the whole genome at the transcriptional level. To dissect the genetic variation between the two rice indica varieties Minghui 63 and Zhenshan 97, a total of 110 RILs from Minghui 63 and Zhenshan 97 and parents were sampled. And the Affymetrix Genechip rice Genome Array was used to investigate their dynamic transcript levels. Two independent biological replicates were sampled from each RIL, and three replicates for each parent.resulting in a dataset of 226 microarrays.

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A global analysis of QTLs for expression variations in rice flag leaf at heading date

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