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

Transcript 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 genome-wide 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