Gene expression quantitative trait locus analysis of 16 000 barley genes reveals a complex pattern of genome‐wide transcriptional regulation

Abstract

SummaryTranscript abundance from cRNA hybridizations to Affymetrix microarrays can be used for simultaneous marker development and genome-wide gene expression quantitative trait locus (eQTL) analysis of crops. We have previously shown that it is easily possible to use Affymetrix expression arrays to profile individuals from a segregating population to accurately identify robust polymorphic molecular genetic markers. We applied the method to identify more than 2000 genetic polymorphisms (transcript derived markers, TDMs) from an experiment involving two commercial varieties of barley (Hordeum vulgare; Steptoe and Morex) and their doubled-haploid progeny. With this set of TDMs, we constructed a genetic map and used it for the genomewide eQTL analysis of about 16 000 genes in a relatively large population (n = 139). We identified 23 738 significant eQTLs at a genome-wide significance (P £ 0.05), affecting the expression of 12 987 genes. Over a third of these genes with expression variation have only one identified eQTL while the rest have two to six. A large proportion of the quantitatively controlled transcripts appear to be regulated by both cis and trans effects. More than half of the quantitatively controlled transcripts appear to be primarily regulated by cis eQTLs in this population. We show that although there appear to be eQTL hotspots many of these are in chromosomal regions of low recombination, such as genetic centromeres, and so have a high gene density per centimorgan. Some chromosomal regions have a significant excess of eQTL over the number expected from gene density, and many of these are biased towards eQTL for which the allele from one particular parent increases the expression level.

Array-based high-throughput DNA markers for crop improvement

“…The false positives are believed to result due to alternative splicing or polyadenylation, gene duplications, chance alignments with RNA from another region, gene expression markers (resulting from polymorphism(s) at trans-acting regulators and secondary structures in target DNA) or SNPs that occur immediately adjacent to the position of a 25mer probe (cf. Luo et al, 2007;Zhu and Salmeron, 2007;Potokina et al, 2008). The number of these false positives can be reduced by (i) sampling more than one tissues per genotype (Rostoks et al, 2005;Luo et al, 2007); (ii) excluding sequence duplications during array design, (iii) studying segregation pattern in the progeny of the cross made from genotypes under question (Luo et al, 2007), (iv) adjusting stringency parameters (Luo et al, 2007) and through (v) the use of replication arrays.…”

Genetic Dissection of Barley Morphology and Development

“…The total number of unique rice hits was 17,868. Transcript-derived markers (TDMs; Potokina et al, 2008) were integrated in the SNP-based map as described previously . The map distances in the integrated map were adjusted by taking into account TDM mapping data (A. Druka, unpublished data).…”

Expression Quantitative Trait Loci Analysis of Carotenoid Metabolism-related Genes in Citrus

“…The eQTLs investigated in a population provide the necessary information required for identifying genes or loci that control quantitative traits. In plants, global eQTL analyses of gene expression have been applied to detect cis-polymorphisms controlling individual genes as well as to identify transeQTLs that regulate individual genes from remote loci (DeCook et al, 2006;Keurentjes et al, 2007;Potokina et al, 2008;West et al, 2007). Initial observations from ysis was performed with the backcross (BC1) model set independently for the female parent, 'Okitsu-46' (A255) and male parent, .…”