Gene expression evolution during sunflower (Helianthus annuus) domestication

Domestication is characterized by dramatic phenotypic evolution from a wild progenitor to a species adapted for human use. In crops, much research has been dedicated to identifying traits associated with domestication and identifying loci underlying these traits on an individual basis as part of breeding programs. However, identifying genes or loci contributing to domestication phenotypes which are also under selection at the genome/transcriptome-wide level has only been recently explored in a few crops. Further, little is understood about the genome-wide effects of domestication. In this study I used developmental and tissue-specific RNA sequencing in combination with existing selective-sweep data to characterize differentially expressed (DE) genes between wild and domesticated sunflowers, associate DE genes with domestication phenotypes, identify DE genes with a signature of selection, and characterize how domestication altered the transcriptional landscape. Domestication significantly altered the expression of between 16 and 48 percent of genes in a tissue-specific manner, with a majority (54-70%) of those DE genes being expressed at higher levels in domesticated plants. Of the 183 previously identified domestication candidates showing signatures of selection in their coding regions, 120 were differentially expressed in at least one tissue, with many (85/120) differentially expressed in multiple tissues. The sunflower transcriptome was also substantially altered by domestication, with an overall increase in gene co-expression network connectivity. However, some individual putative domestication genes also experienced a reduction in co-expression network connectivity. These results indicate that domestication had far reaching and dramatic impacts on the transcriptional landscape of sunflowers.