title: Population Genomic Analysis Reveals Differential Evolutionary Histories and Patterns of Diversity across Subgenomes and Subpopulations of Brassica napus L.
abstract: 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.
authors.affiliation: Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca NY, USA.
authors.forename: Elodie
authors.initials: E
authors.lastname: Gazave
authors.affiliation: Plant Physiology and Genetics Research Unit, U.S. Arid Land Agricultural Research Center, United States Department of Agriculture - Agricultural Research Service, Maricopa AZ, USA.
authors.forename: Erica E
authors.initials: EE
authors.lastname: Tassone
authors.affiliation: Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca NY, USA.
authors.forename: Daniel C
authors.initials: DC
authors.lastname: Ilut
authors.affiliation: Department of Plant, Soil and Entomological Sciences, University of Idaho, Moscow ID, USA.
authors.forename: Megan
authors.initials: M
authors.lastname: Wingerson
authors.affiliation: Keygene N.V. Wageningen, Netherlands.
authors.forename: Erwin
authors.initials: E
authors.lastname: Datema
authors.affiliation: Keygene N.V. Wageningen, Netherlands.
authors.forename: Hanneke M A
authors.initials: HM
authors.lastname: Witsenboer
authors.affiliation: Department of Plant, Soil and Entomological Sciences, University of Idaho, Moscow ID, USA.
authors.forename: James B
authors.initials: JB
authors.lastname: Davis
authors.affiliation: Corn Insects and Crop Genetics Research Unit, United States Department of Agriculture - Agricultural Research Service, Ames IA, USA.
authors.forename: David
authors.initials: D
authors.lastname: Grant
authors.affiliation: Plant Physiology and Genetics Research Unit, U.S. Arid Land Agricultural Research Center, United States Department of Agriculture - Agricultural Research Service, Maricopa AZ, USA.
authors.forename: John M
authors.initials: JM
authors.lastname: Dyer
authors.affiliation: Division of Plant and Soil Sciences, West Virginia University, Morgantown WV, USA.
authors.forename: Matthew A
authors.initials: MA
authors.lastname: Jenks
authors.affiliation: Department of Plant, Soil and Entomological Sciences, University of Idaho, Moscow ID, USA.
authors.forename: Jack
authors.initials: J
authors.lastname: Brown
authors.affiliation: Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca NY, USA.
authors.forename: Michael A
authors.initials: MA
authors.lastname: Gore
keywords: Brassica napus; diversity panel; inversion polymorphism; nucleotide diversity; phylogenetic tree; population differentiation; sequence-based genotyping; site frequency spectrum