Genome-wide association study identifies candidate genes and favorable haplotypes for seed yield in Brassica napus

Haijiang Liu; Maoyan Zou; Bingbing Zhang; Xinyu Yang; Pan Yuan; Guangda Ding; Fangsen Xu; Lei Shi

doi:10.1007/s11032-022-01332-6

Genome-wide association study identifies candidate genes and favorable haplotypes for seed yield in Brassica napus

Mol Breed. 2022 Sep 27;42(10):61. doi: 10.1007/s11032-022-01332-6. eCollection 2022 Oct.

Authors

Haijiang Liu^#^{1

2}, Maoyan Zou^#^{1

2}, Bingbing Zhang^{1

2}, Xinyu Yang^{1

2}, Pan Yuan^{1

2}, Guangda Ding^{1

2}, Fangsen Xu^{1

2}, Lei Shi^{1

2}

Affiliations

¹ National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 Hubei Province China.
² Key Lab of Cultivated Land Conservation, Ministry of Agriculture and Rural Affairs/Microelement Research Centre, Huazhong Agricultural University, Wuhan, 430070 Hubei Province China.

^# Contributed equally.

Abstract

Oilseed rape (Brassica napus L.) is one of the most essential oil crops. Genetic improvement of seed yield (SY) is a major aim of B. napus breeding. Several studies have been reported on the genetic mechanisms of SY of B. napus. Here, a genome-wide association study (GWAS) of SY was conducted using a panel of 403 natural accessions of B. napus, with more than five million high-quality single-nucleotide polymorphisms (SNPs). A total of 1773 significant SNPs were detected associated with SY, and 783 significant SNPs were co-located with previously reported QTLs. The lead SNPs chrA01__8920351 and chrA02__4555979 were jointly detected in Trial 2_2 and Trial 2_mean value, and in Trial 1_2 and Trial 1_mean value, respectively. Subsequently, two candidate genes of BnaA01g17200D and BnaA02g08680D were identified through combining transcriptome, candidate gene association analysis, and haplotype analysis. BnaA09g10430D detected through lead SNP chrA09__5160639 was associated with SY of B. napus. Our results provide valuable information for studying the genetic control of seed yield in B. napus and valuable genes, haplotypes, and cultivars resources for the breeding of high seed yield B. napus cultivars.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-022-01332-6.

Keywords: Candidate genes association analysis; Genome-wide association study; Haplotype analysis; Oilseed rape; Seed yield.

© The Author(s), under exclusive licence to Springer Nature B.V. 2022. Springer Nature or its licensor holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.