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Population genomic analysis reveals differential evolutionary histories and patterns of diversity across subgenomes and subpopulations of Brassica napus L.

Gazave, Elodie, Tassone, Erica E., Ilut, Daniel C., Wingerson, Megan, Datema, Erwin, Witsenboer, Hanneke M. A., Davis, James B., Grant, David, Dyer, John M., Jenks, Matthew A., Brown, Jack, Gore, Michael A.
Frontiers in plant science 2016 v.7 no.525 pp. 1-16
Brassica napus, allopolyploidy, biogeography, canola oil, ecotypes, forage, genetic variation, genome, genomics, genotyping, geographical distribution, germplasm, meat and bone meal, phylogeny, population structure, single nucleotide polymorphism, vegetables
Brassica napus (L.) is a crop of major economic importance that produces canola oil (seed), vegetables, fodder and animal meal. Characterizing the genetic diversity present in the extant germplasm pool of B. napus is fundamental to better conserve, manage and utilize the genetic resources of this species. We used sequence-based genotyping to detect and genotype 30,881 SNPs in a diversity panel of 782 B. napus samples representative of the major ecotypes and worldwide geographic distribution of the species. Given that B. napus is an allotetraploid, we focused our analysis on patterns of genetic variation that differ between the two subgenomes. Our results reveal a strong population structure, mainly splitting accessions of spring types (SP), winter Europeans (WE) and winter Asian (WA) types. The number of population-specific SNPs was the highest in WA and comparable between SP and WE. However, the SNPs in WE had on average a lower frequency than in SP. Phylogenetic inferences showed a different evolutionary history in the two subgenomes, placing WE and WA as basal clades for the other populations in the C and A subgenomes, respectively. Finally, we identified 16 genomic regions where the patterns of diversity differ markedly from the genome average, several of which are consistent with putative genomic inversions. The SNPs discovered in our analysis are publicly available, providing a valuable resource for the community.