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

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.

SUBMITTER: Liu H

PROVIDER: S-EPMC10248642 | biostudies-literature | 2022 Oct

REPOSITORIES: biostudies-literature

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

Liu Haijiang H Zou Maoyan M Zhang Bingbing B Yang Xinyu X Yuan Pan P Ding Guangda G Xu Fangsen F Shi Lei L

Molecular breeding : new strategies in plant improvement 20220927 10

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 detect ...[more]

PMID: 37313016

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Project description:Genetic improvement of seed yield per plant (SY) is one of the major objectives in Brassica napus breeding programme. SY, being a complex quantitative trait is directly and indirectly influenced by yield-component traits such as siliqua length (SL), number of seeds per siliqua (NSS), and thousand seed weight (TSW). Therefore, concurrent improvement in SL, NSS and TSW can lead to higher SY in B. napus. This study was conducted to identify significant SNPs and putative candidate genes governing SY and its component traits (SL, NSS, TSW). All these traits were evaluated in a diverse set of 200 genotypes representing diversity from wide geographical locations. Of these, a set of 125 genotypes were chosen based on pedigree diversity and multi-location trait variation for genotyping by sequencing (GBS). Best linear unbiased predictors (BLUPs) of all the traits were used for genome-wide association study (GWAS) with 85,126 SNPs obtained from GBS. A total of 16, 18, 27 and 18 SNPs were found to be significantly associated for SL, NSS, TSW and SY respectively. Based on linkage disequilibrium decay analysis, 150 kb genomic region flanking the SNP was used for the identification of underlying candidate genes for each test trait. Important candidate genes involved in phytohormone signaling (WAT1, OSR1, ARR8, CKX1, REM7, REM9, BG1) and seed storage proteins (Cruciferin) were found to have significant influence on seed weight and yield. Genes involved in sexual reproduction and fertilization (PERK7, PERK13, PRK3, GATA15, NFD6) were found to determine the number of seeds per siliqua. Several genes found in this study namely ATS3A, CKX1, SPL2, SPL6, SPL9, WAT1 showed pleiotropic effect with yield component traits. Significant SNPs and putative candidate genes identified for SL, NSS, TSW and SY could be used in marker-assisted breeding for improvement of crop yield in B. napus. Genotypes identified with high SL, NSS, TSW and SY could serve as donors in crop improvement programs in B. napus.Supplementary informationThe online version contains supplementary material available at 10.1007/s12298-021-01060-9.

Dataset Information

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

Supplementary information

Publications

Genome-wide association study identifies candidate genes and favorable haplotypes for seed yield in <i>Brassica napus</i>.

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