Dissection of expression‐quantitative trait locus and allele specificity using a haploid/diploid plant system – insights into compensatory evolution of transcriptional regulation within populations

SummaryRegulation of gene expression plays a central role in translating genotypic variation into phenotypic variation. Dissection of the genetic basis of expression variation is key to understanding how expression regulation evolves. Such analyses remain challenging in contexts where organisms are outbreeding, highly heterozygous and long‐lived such as in the case of conifer trees. We developed an RNA sequencing ( RNA ‐seq)‐based approach for both expression‐quantitative trait locus ( eQTL ) mapping and the detection of cis‐ acting (allele‐specific) vs trans‐ acting (non‐allele‐specific) eQTL s. This method can be potentially applied to many conifers. We used haploid and diploid meiotic seed tissues of a single self‐fertilized white spruce ( Picea glauca ) individual to dissect eQTL s according to linkage and allele specificity. The genetic architecture of local eQTL s linked to the expressed genes was particularly complex, consisting of cis‐ acting, trans‐ acting and, surprisingly, compensatory cis‐trans effects. These compensatory effects influence expression in opposite directions and are neutral when combined in homozygotes. Nearly half of local eQTL s were under compensation, indicating that close linkage between compensatory cis‐trans factors is common in spruce. Compensated genes were overrepresented in developmental and cell organization functions. Our haploid–diploid eQTL analysis in spruce revealed that compensatory cis‐trans eQTL s segregate within populations and evolve in close genetic linkage.