The Genetics of Domestication and Improvement in Sunflowers (Helianthus annuus)

The globally important oil seed, sunflower, is highly differentiated from its wild progenitor. This transition included two main phases; the initial domestication event which created landraces from wild sunflowers, and the subsequent improvement of those land races into elite lines. Here we explore the underlying genetic changes associated with these transitions using transcriptome data from a panal of wild Helianthus annuus, native American landraces and elite lines. A set of >200,000 SNPs reveal the expected relationships of these different H. annuus groups and the decreases in genetic diversity associated with continued selection. Using Fst outliers to identify highly differentiated sites, we identified likely candidates of selection during domestication and improvement. During domestication, selection acted on several oil-synthesis genes, a variety of auxin related genes, and a gene which may be involved in flowering time. Improvement genes are highly enriched for ribosomal genes. Bayescan results suggest that selection during improvement may be more subtle, or harder to detect, compared to selection during domestication, possibly due to the derivation of independent elite gene pools lines. Selection appears to be wide spread across the genome during both phases. The locations of these selected sites in the genome do not differ from one another or from randomly selected sites in terms of gene density, recombination rates or size of divergent areas. A large number of the alleles favoured during domestication have decreased in frequency during improvement, possibly reflecting changes in selection.