Skip navigation
Skip navigation

Genetic architecture of regulatory variation in Arabidopsis thaliana

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.authorZhang, Xu
dc.contributor.authorCal, Andrew
dc.contributor.authorBorevitz, Justin
dc.date.accessioned2015-12-13T22:41:41Z
dc.identifier.issn1088-9051
dc.identifier.urihttp://hdl.handle.net/1885/78613
dc.description.abstractStudying 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.publisherCold Spring Harbor Laboratory Press
dc.rightsAuthor/s retain copyright
dc.sourceGenome Research
dc.subjectKeywords: 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.titleGenetic architecture of regulatory variation in Arabidopsis thaliana
dc.typeJournal article
local.description.notesImported from ARIES
local.identifier.citationvolume21
dc.date.issued2011
local.identifier.absfor060411 - Population, Ecological and Evolutionary Genetics
local.identifier.ariespublicationf5625xPUB7227
local.type.statusPublished Version
local.contributor.affiliationZhang, Xu, University of Chicago
local.contributor.affiliationCal, Andrew, University of Chicago
local.contributor.affiliationBorevitz, Justin, College of Medicine, Biology and Environment, ANU
local.bibliographicCitation.issue5
local.bibliographicCitation.startpage725
local.bibliographicCitation.lastpage733
local.identifier.doi10.1101/gr.115337.110
local.identifier.absseo970106 - Expanding Knowledge in the Biological Sciences
dc.date.updated2016-02-24T09:33:37Z
local.identifier.scopusID2-s2.0-79955556526
local.identifier.thomsonID000290088000010
dcterms.accessRightsOpen Access
CollectionsANU Research Publications

Download

File Description SizeFormat Image
01_Zhang_Genetic_architecture_of_2011.pdf855.59 kBAdobe PDF


Items in Open Research are protected by copyright, with all rights reserved, unless otherwise indicated.

Updated:  20 July 2017/ Responsible Officer:  University Librarian/ Page Contact:  Library Systems & Web Coordinator