Data from: Genome-wide analysis of allele frequency change in sunflower crop-wild hybrid populations evolving under natural conditions

Crop-wild hybridization occurs in numerous plant species, and could alter
the genetic structure and evolutionary dynamics of wild populations.
Studying crop-derived alleles in wild populations is also relevant to
assessing/mitigating the risks associated with transgene escape. To date,
crop-wild hybridization has generally been examined via short-term
studies, typically within a single generation, focusing on few traits or
genetic markers. Little is known about patterns of selection on
crop-derived alleles over multiple generations, particularly at a
genome-wide scale. Here, we documented patterns of natural selection in an
experimental crop × wild sunflower population that was allowed to evolve
under natural conditions for two generations at two locations. Allele
frequencies at a genome-wide collection of SNPs were tracked across
generations, and a common garden experiment was conducted to compare trait
means between generations. These data allowed us to identify instances of
selection on crop-derived alleles/traits and, in concert with QTL mapping
results, test for congruence between our genotypic and phenotypic results.
We found that natural selection overwhelmingly favors wild alleles and
phenotypes. However, crop alleles in certain genomic regions can be
favored, and these changes often occurred in parallel across locations. We
did not, however, consistently observe close agreement between our
genotypic and phenotypic results. For example, when a trait evolved
towards the wild phenotype, wild QTL alleles associated with that trait
did not consistently increase in frequency. We discuss these results in
the context of crop allele introgression into wild populations and
implications for the management of GM crops.