Development of a target capture sequencing SNP genotyping platform for genetic analysis and genomic breeding in rapeseed

Rapeseed(Brassica napus) is an oil crop grown worldwide, making it a key plant species in molecular breeding research. However, the complexity of its polyploid genome increases sequencing costs and reduces sequencing accuracy. Target capture coupled with high-throughput sequencing is an efficient approach for detecting genetic variation at genomic regions or loci of interest. In this study, 588 resequenced accessions of rapeseed were used to develop a target capture sequencing SNP genotyping platform named BnaPan50T. The platform comprised 54,765, with 54,058 resequenced markers from the pan-genome, and 855 variant trait-associated markers for 12 agronomic traits. The capture quality of BnaPan50T was demonstrated well in 12 typical accessions. Compared with a conventional genotyping array, BnaPan50T has a high SNP density and a high proportion of SNPs in unique physical positions and in annotated functional genes, promising wide application. Target capture sequencing and wholegenome resequencing in 90 doubled-haploid lines yielded 60% specificity, 78% uniformity within tenfold coverage range, and 93% genotyping accuracy for the platform. BnaPan50T was used to construct a genetic map for quantitative trait loci(QTL) mapping, identify 21 unique QTL, and predict several candidate genes for yield-related traits in multiple environments. A set of 132 core SNP loci was selected from BnaPan50T to construct DNA fingerprints and germplasm identification resources. This study provides genomics resources to support target capture sequencing, genetic analysis and genomic breeding of rapeseed.