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ARS Home » Pacific West Area » Maricopa, Arizona » U.S. Arid Land Agricultural Research Center » Plant Physiology and Genetics Research » Research » Publications at this Location » Publication #324498

Research Project: Genetic Improvement and Phenotyping of Cotton, Bioenergy and Other Industrial Crops

Location: Plant Physiology and Genetics Research

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

Author
item GAZAVE, ELODIE - Cornell University - New York
item Tassone, Erica
item ILUT, DANIEL - Cornell University - New York
item WINGERSON, MEGAN - University Of Idaho
item DATEMA, M - Keygene, Inc
item WITSENBOER, H - Keygene, Inc
item DAVIS, JAMES - University Of Idaho
item Grant, David
item Dyer, John
item JENKS, MATTHEW - University Of West Virginia
item BROWN, JACK - University Of Idaho
item GORE, MICHAEL - Cornell University - New York

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/4/2016
Publication Date: 4/21/2016
Publication URL: https://handle.nal.usda.gov/10113/62493
Citation: Gazave, E., Tassone, E.E., Ilut, D.C., Wingerson, M., Datema, M., Witsenboer, H., Davis, J.B., Grant, D.M., Dyer, J.M., Jenks, M.A., Brown, J., Gore, M.A. 2016. Population genomic analysis reveals differential evolutionary histories and patterns of diversity across subgenomes and subpopulations of Brassica napus L. Frontiers in Plant Science. 7:525. doi: 10.3389/fpls.2016.00525.

Interpretive Summary: Brassica napus is a crop of major economic importance whose products are used for a diverse number of applications, including food, feed, and biofuel production. In order to increase the amount of feedstocks available for these purposes, there has been an effort to include B. napus as a rotation crop in the wheat belt of the US. While B. napus has been cultivated and grown around the world, little is known about the overall diversity of the species, which is important for further germplasm improvement and preservation. In this study, scientists from the ARS lab in Maricopa, AZ, in collaboration with scientists at Cornell University, the University of Idaho, West Virginia University, and the ARS lab in Ames, Iowa characterized the genetic diversity of B. napus in a population of 782 B. napus lines, representing worldwide diversity. From this analysis, the plant lines could be separated into three main groups, which were distinguished by growth habit (winter or spring types) and geographic point of origin. One group in particular, those with a winter growth habit and European background, were found to be a potential source of genetic variation that can be used to increase the genetic diversity of the overall B. napus population. Understanding this evolutionary history and genetic diversity is imperative for breeders who want to improve the yield and/or performance of the crop, and the results provide specific insight to the plant subpopulations that will be most useful for this purpose.

Technical Abstract: 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.