Linkage disequilibrium in the genome of synthetic Brassica napus populations

Abstract

New technologies as high-density single-nucleotide polymorphism (SNP) genotyping arrays are a powerful tool that can give valuable insight into patterns of linkage disequilibrium (LD) in the recent domesticated Brassica napus genome. This study used the Brassica 60k SNP Illumina consortium genotyping array to assess the distribution of LD and haplotype structure in a diverse panel of 200 synthetic lines of winter oilseed rape (Brassica napus). Pairwise LD analysis was conducted within the A- and C-subgenomes of oilseed rape. Results revealed that LD decayed, on average, more rapidly in the A-subgenome (0.15 Mb) than in the C-subgenome (2.00 Mb). Our findings suggest the presence of a strong selection of large genomic regions associated with important agronomical traits, especially on the Csubgenome. These results imply that during oilseed rape artificial and natural selection, the C-subgenome was of particular interest for breeders. Increasing the genetic diversity and recombination rate on the whole genome level is of crucial importance for future breeding efforts.