Genetic architecture of regulatory variation in Arabidopsis thaliana
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Zhang, Xu; Cal, Andrew; Borevitz, Justin
Description
Studying the genetic regulation of expression variation is a key method to dissect complex phenotypic traits. To examine the genetic architecture of regulatory variation in Arabidopsis thaliana, we performed genome-wide association (GWA) mapping of gene expression in an F1 hybrid diversity panel. At a genome-wide false discovery rate (FDR) of 0.2, an associated single nucleotide polymorphism (SNP) explains >38% of trait variation. In comparison with SNPs that are distant from the genes to which...[Show more]
dc.contributor.author | Zhang, Xu | |
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dc.contributor.author | Cal, Andrew | |
dc.contributor.author | Borevitz, Justin | |
dc.date.accessioned | 2015-12-13T22:41:41Z | |
dc.identifier.issn | 1088-9051 | |
dc.identifier.uri | http://hdl.handle.net/1885/78613 | |
dc.description.abstract | Studying the genetic regulation of expression variation is a key method to dissect complex phenotypic traits. To examine the genetic architecture of regulatory variation in Arabidopsis thaliana, we performed genome-wide association (GWA) mapping of gene expression in an F1 hybrid diversity panel. At a genome-wide false discovery rate (FDR) of 0.2, an associated single nucleotide polymorphism (SNP) explains >38% of trait variation. In comparison with SNPs that are distant from the genes to which they were associated, locally associated SNPs are preferentially found in regions with extended linkage disequilibrium (LD) and have distinct population frequencies of the derived alleles (where Arabidopsis lyrata has the ancestral allele), suggesting that different selective forces are acting. Locally associated SNPs tend to have additive inheritance, whereas distantly associated SNPs are primarily dominant. In contrast to results from mapping of expression quantitative trait loci (eQTL) in linkage studies, we observe extensive allelic heterogeneity for local regulatory loci in our diversity panel. By association mapping of allele-specific expression (ASE), we detect a significant enrichment for cis-acting variation in local regulatory variation. In addition to gene expression variation, association mapping of splicing variation reveals both local and distant genetic regulation for intron and exon level traits. Finally, we identify candidate genes for 59 diverse phenotypic traits that were mapped to eQTL. | |
dc.publisher | Cold Spring Harbor Laboratory Press | |
dc.rights | Author/s retain copyright | |
dc.source | Genome Research | |
dc.subject | Keywords: allele; Arabidopsis; article; gene expression; gene linkage disequilibrium; gene mapping; gene structure; genetic heterogeneity; genetic variability; nonhuman; nucleotide sequence; plant genetics; priority journal; quantitative trait locus; single nucleot | |
dc.title | Genetic architecture of regulatory variation in Arabidopsis thaliana | |
dc.type | Journal article | |
local.description.notes | Imported from ARIES | |
local.identifier.citationvolume | 21 | |
dc.date.issued | 2011 | |
local.identifier.absfor | 060411 - Population, Ecological and Evolutionary Genetics | |
local.identifier.ariespublication | f5625xPUB7227 | |
local.type.status | Published Version | |
local.contributor.affiliation | Zhang, Xu, University of Chicago | |
local.contributor.affiliation | Cal, Andrew, University of Chicago | |
local.contributor.affiliation | Borevitz, Justin, College of Medicine, Biology and Environment, ANU | |
local.bibliographicCitation.issue | 5 | |
local.bibliographicCitation.startpage | 725 | |
local.bibliographicCitation.lastpage | 733 | |
local.identifier.doi | 10.1101/gr.115337.110 | |
local.identifier.absseo | 970106 - Expanding Knowledge in the Biological Sciences | |
dc.date.updated | 2016-02-24T09:33:37Z | |
local.identifier.scopusID | 2-s2.0-79955556526 | |
local.identifier.thomsonID | 000290088000010 | |
dcterms.accessRights | Open Access | |
Collections | ANU Research Publications |
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