title: Dissection of expression-quantitative trait locus and allele specificity using a haploid/diploid plant system - insights into compensatory evolution of transcriptional regulation within populations.
abstract: Regulation 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) eQTLs. 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 eQTLs according to linkage and allele specificity. The genetic architecture of local eQTLs 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 eQTLs 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 eQTLs segregate within populations and evolve in close genetic linkage.
authors.affiliation: Centre d'étude de la forêt, Département des sciences du bois et de la forêt, Université Laval, Québec, QC, Canada G1V 0A6.|Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada G1V 0A6.
authors.forename: Jukka-Pekka
authors.initials: JP
authors.lastname: Verta
authors.affiliation: Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada G1V 0A6.|Département de Biologie, Université Laval, Québec, QC, Canada G1V 0A6.
authors.forename: Christian R
authors.initials: CR
authors.lastname: Landry
authors.affiliation: Centre d'étude de la forêt, Département des sciences du bois et de la forêt, Université Laval, Québec, QC, Canada G1V 0A6.|Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada G1V 0A6.|Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK.
authors.forename: John
authors.initials: J
authors.lastname: MacKay
mesh_terms: D000483:Alleles; D004171:Diploidy; D018506:Gene Expression Regulation, Plant; D008040:Genetic Linkage; D005828:Genetics, Population; D006238:Haploidy; D028222:Picea / Q000235:genetics*; D040641:Quantitative Trait Loci; D057945:Self-Fertilization; D017423:Sequence Analysis, RNA
keywords: Picea glauca; allele-specific gene expression; cis-trans compensation; evolution of gene expression; expression-quantitative trait locus (eQTL); gymnosperms; stabilizing selection