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

作　　者：Xiaodong Li Xumei Liu Yonghai Fan Shengting Li Mengna Yu Mingchao Qian Yuling Chen Hongqiao Chen Xinchun Li Bei Liu Xinfu Xu Cunmin Qu Jiana Li Kun Lu 

机构地区：[1]Integrative Science Center of Germplasm Creation in Western China(CHONGQING)Science City and Southwest University,College of Agronomy and Biotechnology,Southwest University,Beibei,Chongqing 400715,China [2]Engineering Research Center of South Upland Agriculture,Ministry of Education,Chongqing 400715,China [3]Academy of Agricultural Sciences,Southwest University,Beibei,Chongqing 400715,China [4]China Golden Marker(Beijing)Biotech Co.,Ltd.,Beijing 102206,China

出　　处：《The Crop Journal》2023年第2期499-510,共12页作物学报（英文版）

基　　金：supported by the National Natural Science Foundation of China(31871653 to K.L.,31830067 to J.L.);the Talent Project of Chongqing Natural Science Foundation(cstc2021ycjhbgzxm0033 to K.L.);Germplasm Creation Special Program of Southwest University.

摘　　要：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.

关 键 词：RAPESEED Target capture SNP genotyping platform Genomic breeding 

分 类 号：S565.4[农业科学—作物学]