Whole-Genome Resequencing of a Worldwide Collection of Rapeseed Accessions Reveals the Genetic Basis of Ecotype Divergence

Abstract

Rapeseed (Brassica napus), an important oilseed crop, has adapted to diverse climate zones and latitudes by forming three main ecotype groups, namely winter, semi-winter, and spring types. However, genetic variations underlying the divergence of these ecotypes are largely unknown. Here, we report the global pattern of genetic polymorphisms in rapeseed determined by resequencing a worldwide collection of 991 germplasm accessions. A total of 5.56 and 5.53 million singlenucleotide polymorphisms (SNPs) as well as 1.86 and 1.92 million InDels were identified by mapping reads to the reference genomes of ''Darmor-bzh'' and ''Tapidor,'' respectively. We generated a map of allelic drift paths that shows splits and mixtures of the main populations, and revealed an asymmetric evolution of the two subgenomes of B. napus by calculating the genetic diversity and linkage disequilibrium parameters. Selective-sweep analysis revealed genetic changes in genes orthologous to those regulating various aspects of plant development and response to stresses. A genome-wide association study identified SNPs in the promoter regions of FLOWERING LOCUS T and FLOWERING LOCUS C orthologs that corresponded to the different rapeseed ecotype groups. Our study provides important insights into the genomic footprints of rapeseed evolution and flowering-time divergence among three ecotype groups, and will facilitate screening of molecular markers for accelerating rapeseed breeding.

Genome‐wide association study reveals new genes involved in leaf trichome formation in polyploid oilseed rape (Brassica napus L.)

“…The 290 red dots represent the core accessions amid the background of 991 Gy dots (Figure a). When based on the resequencing data of either the 290 core accessions or the 991 total accessions, the calculations of SNP distribution on the 19 chromosomes showed negligible differences (Figure b; Wu et al, ). Only minor differences in the percentages of SNPs that fall in different regions of the genome, namely, CDS, splice site donors, intergenic regions, splice site acceptors, upstream regions, splice site regions, downstream regions, introns, and intragenic regions, were observed between the two calculations (Figure c; Wu et al, ).…”

“…The SNPs among the 290 accessions were extracted from the total SNPs of the 991 accessions, which was identified in our previous study (Wu et al, ). A total of 2,705,480 high‐quality SNPs (MAF > 0.05, missing rates <0.5) were used for the GWAS.…”

“…RT‐qPCR experiments were conducted following our previous description (Wu et al, ). BnACTIN7 was used as the internal control.…”

“…rapa (AA) (2n = 2X = 20) and B . oleracea (CC) (2n = 2X = 18) less than 7,500 years ago (Chalhoub et al, ; Wu et al, ). Thus, in parallel to a single Arabidopsis gene, there normally exist 2–10 orthologous copies, which are by no means all functional.…”

“…We identified the worldwide pattern of genetic polymorphisms in B . napus and unveiled the genetic basis of ecotype divergence in this crop species (Wu et al, ). In this study, we established a core germplasm collection including 290 accessions, representing 97.3% of the SNPs and 97.9% of the indels of the 991‐accession collection, for GWAS on leaf trichome initiation in oilseed rape.…”