Genome-Wide Analysis of SNP Diversity in Experimental Crop-Wild Sunflower Populations

Cultivated sunflower (Helianthus annuus) is a major oilseed, food, and ornamental crop what was domesticated in eastern North America ca. 4000-4500 years BP. Domestication was accompanied by drastic phenotypic changes resulting in cultivated plants that are poorly adapted for growth under natural conditions. In sunflower, frequent gene flow is known to occur from cultivated to wild populations and represents a major mechanism by which the preservation of wild genetic diversity could be threatened. However, the extent to which cultivated alleles will persist or in the crop-wild hybrid population under natural conditions has not been well-studied at a genomic scale. In this study, we track allele frequency changes across the genome in experimental populations evolving under natural conditions. Starting with a crop x wild recombinant inbred line population natural selection was applied for 2 generations and allele frequencies at 384 SNP markers were monitored to detect significant variations across the sunflower genome. Our results show that, even though selection tends to favor wild alleles overall, crop alleles in in certain genomic regions exhibit significant increases in frequency and that these changes often occur in parallel across locations. Future work aimed at identifying the specific crop-derived traits experiencing positive selection in these hybrid populations will provide insight into the selective processes governing introgression in crop-wild hybrid zones.