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

Here, 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 aremore » 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.« less
Authors:
 [1] ;  [2] ;  [1] ;  [3] ;  [4] ;  [4] ;  [3] ;  [5] ;  [2] ;  [6] ;  [3] ;  [1]
  1. Cornell Univ., Ithaca, NY (United States). School of Intgrative Plant Science.
  2. U.S. Arid Land Agricultural Research Center, Maricopa, AZ (United States)
  3. Univ. of Idaho, Moscow, ID (United States). Dept. of Plant, Soil and Entomological Sciences
  4. Keygene N.V., Wageningen (Netherlands)
  5. United States Dept. of Agriculture - Agricultural Research Service, Ames, IA (United States)
  6. West Virginia Univ., Morgantown, WV (United States). Div. of Plant and Soil Sciences
Publication Date:
OSTI Identifier:
1261987
Grant/Contract Number:
Proposal No. 2011-06476
Type:
Accepted Manuscript
Journal Name:
Frontiers in Plant Science
Additional Journal Information:
Journal Volume: 7; Journal ID: ISSN 1664-462X
Publisher:
Frontiers Research Foundation
Research Org:
USDA-NIFA/DOE Biomass Research and Development Initiative (BRIM); USDA-ARS; Cornell Univ., Ithaca, NY (United States)
Sponsoring Org:
USDOE Office of Energy Efficiency and Renewable Energy (EERE)
Country of Publication:
United States
Language:
English
Subject:
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