title: Genome-wide investigation of genetic changes during modern breeding of Brassica napus.
abstract: Considerable genome variation had been incorporated within rapeseed breeding programs over past decades. In past decades, there have been substantial changes in phenotypic properties of rapeseed as a result of extensive breeding effort. Uncovering the underlying patterns of allelic variation in the context of genome organisation would provide knowledge to guide future genetic improvement. We assessed genome-wide genetic changes, including population structure, genetic relatedness, the extent of linkage disequilibrium, nucleotide diversity and genetic differentiation based on F ST outlier detection, for a panel of 472 Brassica napus inbred accessions using a 60 k Brassica Infinium® SNP array. We found genetic diversity varied in different sub-groups. Moreover, the genetic diversity increased from 1950 to 1980 and then remained at a similar level in China and Europe. We also found ~6-10 % genomic regions revealed high F ST values. Some QTLs previously associated with important agronomic traits overlapped with these regions. Overall, the B. napus C genome was found to have more high F ST signals than the A genome, and we concluded that the C genome may contribute more valuable alleles to generate elite traits. The results of this study indicate that considerable genome variation had been incorporated within rapeseed breeding programs over past decades. These results also contribute to understanding the impact of rapeseed improvement on available genome variation and the potential for dissecting complex agronomic traits.
authors.affiliation: Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, China, nian.wang1982@gmail.com.
authors.forename: Nian
authors.initials: N
authors.lastname: Wang
authors.forename: Feng
authors.initials: F
authors.lastname: Li
authors.forename: Biyun
authors.initials: B
authors.lastname: Chen
authors.forename: Kun
authors.initials: K
authors.lastname: Xu
authors.forename: Guixin
authors.initials: G
authors.lastname: Yan
authors.forename: Jiangwei
authors.initials: J
authors.lastname: Qiao
authors.forename: Jun
authors.initials: J
authors.lastname: Li
authors.forename: Guizhen
authors.initials: G
authors.lastname: Gao
authors.forename: Ian
authors.initials: I
authors.lastname: Bancroft
authors.forename: Jingling
authors.initials: J
authors.lastname: Meng
authors.forename: Graham J
authors.initials: GJ
authors.lastname: King
authors.forename: Xiaoming
authors.initials: X
authors.lastname: Wu
mesh_terms: D029688:Brassica napus / Q000235:genetics*; D001947:Breeding; D032461:Chromosomes, Plant / Q000235:genetics; D060146:Ecotype; D005787:Gene Frequency / Q000235:genetics; D014644:Genetic Variation; D018745:Genome, Plant / Q000235:genetics*; D015810:Linkage Disequilibrium; D058977:Molecular Sequence Annotation; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D011157:Population Dynamics; D025341:Principal Component Analysis; D012641:Selection, Genetic