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.

doi:10.3389/fpls.2016.00525

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

Journal Article · Thu Apr 21 00:00:00 EDT 2016 · Frontiers in Plant Science

DOI:https://doi.org/10.3389/fpls.2016.00525· OSTI ID:1261987

Gazave, Elodie ^[1]; Tassone, Erica E. ^[2]; Ilut, Daniel C. ^[1]; Wingerson, Megan ^[3]; Datema, Erwin ^[4]; Witsenboer, Hanneke M. A. ^[4]; Davis, James B. ^[3]; Grant, David ^[5]; Dyer, John M. ^[2]; Jenks, Matthew A. ^[6]; Brown, Jack ^[3]; Gore, Michael A. ^[1]

Cornell Univ., Ithaca, NY (United States). School of Intgrative Plant Science
U.S. Arid Land Agricultural Research Center, Maricopa, AZ (United States)
Univ. of Idaho, Moscow, ID (United States). Dept. of Plant, Soil and Entomological Sciences
Keygene N.V., Wageningen (Netherlands)
United States Dept. of Agriculture - Agricultural Research Service, Ames, IA (United States)
West Virginia Univ., Morgantown, WV (United States). Div. of Plant and Soil Sciences

The allotetraploid species Brassica napus L. is a global crop of major economic importance, providing canola oil (seed) and vegetables for human consumption and fodder and meal for livestock feed. 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 identify and genotype 30,881 SNPs in a diversity panel of 782 B. napus accessions, representing samples of winter and spring growth habits originating from 33 countries across Europe, Asia, and America. We detected strong population structure broadly concordant with growth habit and geography, and identified three major genetic groups: spring (SP), winter Europe (WE), and winter Asia (WA). Subpopulation-specific polymorphism patterns suggest enriched genetic diversity within the WA group and a smaller effective breeding population for the SP group compared to WE. Interestingly, the two subgenomes of B. napus appear to have different geographic origins, with phylogenetic analysis placing WE and WA as basal clades for the other subpopulations in the C and A subgenomes, respectively. Finally, we identified 16 genomic regions where the patterns of diversity differed markedly from the genome-wide average, several of which are suggestive of genomic inversions. The results obtained in this study constitute a valuable resource for worldwide breeding efforts and the genetic dissection and prediction of complex B. napus traits.

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Research Organization:: Cornell Univ., Ithaca, NY (United States); US Dept. of Agriculture (USDA), Washington, DC (United States). Agricultural Research Service; US Dept. of Agriculture (USDA), Washington, DC (United States). DOE Biomass Research and Development Initiative (BRIM)

Sponsoring Organization:: USDOE Office of Energy Efficiency and Renewable Energy (EERE)

Grant/Contract Number:: Proposal No. 2011-06476

OSTI ID:: 1261987

Journal Information:: Frontiers in Plant Science, Vol. 7; ISSN 1664-462X

Publisher:: Frontiers Research FoundationCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 20 works

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Related Subjects

58 GEOSCIENCES
Brassica napus
sequence-based genotyping
diversity panel
population differentiation
nucleotide diversity
site frequency spectrum
phylogenetic tree
inversion polymorphism
dna-sequencing data
genetic diversity
local adaptation
rapeseed
canola
inversions
selection
variants
polymorphism
bottlenecks

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

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