Genome‐wide analysis of allele frequency change in sunflower crop–wild hybrid populations evolving under natural conditions

Abstract

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 9 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 favours wild alleles and phenotypes.However, crop alleles in certain genomic regions can be favoured, 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.

Does introgression of crop alleles into wild and weedy living populations create cryptic in situ germplasm banks?

“…The results are approximately the same for both sites and striking for so few generations (Corbi et al., ; Figure ). Only about 8% of the crop alleles significantly increased in frequency in at least one location (about 5% for each site).…”

“…What do Corbi et al. () and previous studies tell us about crop allele introgression into wild genomes under natural conditions, especially with regard to enhancing their germplasm value? Overall, alleles associated with domestication traits are strongly disadvantageous.…”

“…Corbi, Baack, Dechaine, Seiler, & Burke () take the next step, studying crop allele evolution in a highly outcrossing species. They started with 169 recombinant inbred lines (RILs) derived from a single hybrid individual from a cross between a wild sunflower and an oilseed cultivar (both Helianthus annuus ).…”

“…Corbi et al. () venture a few guesses. The first is that the contemporary cultivated sunflower has an improvement history that involves introgression from Helianthus species other than its progenitor.…”

“…Certain Nebraska alleles might be maladaptive in the other locations. Their final hypothesis is that “some increases in the crop allele are due to beneficial mutations that occurred following sunflower domestication” (Corbi et al., ). Note, “following sunflower domestication” could be as recent as a decade ago or as long as thousands of years ago.…”