Genome-wide Association Mapping Of Seed Glucosinolate And Fatty Acid Composition In Brassica Napus

Brassica napus L. is an important oil crop in China. Rapeseed oil is an important source of edible oil for our human beings, and rapeseed meal is also a protein-rich meal for live-stock. With the continuous improvement of people’s living standard and the further development of rapeseed breeding work, people put forward higher requirements for rapeseed quality. Based on the existing rapeseed quality, rapeseed quality improvement according to people’s demand is an important objective for rapeseed breeding programs. In this study, we performed association mapping of seed glucosinolate content, erucic acid, oleic acid, linoleic acid, linolenic acid and palmitic acid using the 60 K Brassica Infinium single nucleotide polymorphism(SNP) array in 520 oilseed rape accessions. And the candidate genes were predicted with the flanking sequences between the adjacent peak SNPs analyzed. The main results are as followes:1. Phenotypic analysis of seed glucisinolate content and fatty acid composition in Brassica napus L.: wide variation for six quality traits was observed, indicating a sign of abundant genetic diversity in this panel. Approximately 70% of the accessions had a seed glucosinolate content of 20.00 to 50.00 μmol·g-1,suggesting that the artificial selection have played an important role in breeding new accessions with low seed glucosinolate content in rapeseed globally. More than 60% of the accessions had a oleic acid content of 60% to 70%, indicating the high oleic acid breeding trend in rapeseed. Meanwhile, significant correlations were observed between fatty acid composition.2. Population structure, relative kinship and linkage disequilibrium analysis: 520 oilseed rape accessions were classified into two subpopulations. Of which 463(accounting for 89%) accessions were clssified into P1, mainly composed of those varieties and inbred lines from China, the remaining 57 accessions were clssified into P2, mainly from foreign accessions. Kinship analysis indicated that 50.55% of the kinship coefficients between lines were equal to 0, and 23.98% ranged from 0 to 0.2, indicating that most lines have no kinship or have a relatively weak kinship, and that spurious associations had been controlled. Linkage disequilibrium(LD) of A+C, Asubgenome and C-subgenome declined rapidly while the physical distance increased, and a considerably faster LD decay was obseved in A-subgenome compared with the C-subgenome. When the threshold of r2 was set to 0.2, we found that the LD decay in A-subgenome was about 200 kb, 750 kb of C-subgenome, and 700 kb of A+C.3. Association mapping of seed glucosinolate content and fatty acid composition: Using the Q+K model, association mapping of seed glucosinolate content and fatty acid composition were conducted based on 34,103 SNP makers(P < 0.05/34,103).(1) 15 SNPs associated with seed glucosinolate content were detected, meanwhile, 11 of these were simultaneously detected on chromosomes A8, A9, C3, and C9 in two years, and could explain 16.01 % to 33.50% of the phenotypic variation.(2) fatty acid composition : 469 SNPs associated with oleic acid content were detected, meanwhile, 204 of these were simultaneously detected on chromosomes A6、A8、A9 and on C-subgenome(C1 and C6 excluded) in two years, and could explain 3.64% to 30.82% of the phenotypic variation. 90 SNPs associated with linoleic acid content were detected, meanwhile, 27 of these were simultaneously detected on chromosomes A8 and C3 in two years, and could explain 5.03% to 14.27% of the phenotypic variation. 13 SNPs associated with linolenic acid content were detected on chromosomes A2、A9、C2 and C4 in 2013, and could explain 5.13% to 9.66% of the phenotypic variation, zero SNPs wre detected in 2014. 113 SNPs associated with palmitic acid content were detected, meanwhile, 15 of these were simultaneously detected on chromosomes A8 and C3 in two years, and could explain 5.70 % to 11.76% of the phenotypic variation. 24 SNPs associated with erucic acid content were detected on chromosomes A8、A9、C2、C3 in 2013, one on chromosome C2 in 2014, and could explain 10.14% to 26.09% of the phenotypic variation. no SNPs were simultaneously detected in two years. And 20 SNPs were associated with two or more fatty acid traits simultaneously.4. Candidate genes identification: To identify the candidate genes, the B. napus genomic sequences between the adjacent SNPs linked to seed glucosinolate content and fatty acid composition were extracted(about 200 kb). As a result, 3 genes involved in the glucosinolate metabolic pathway, and 15 genes involved in the lipid metabolic pathway were found.5. Expression analysis of the candidate genes related to seed glucosinolate content: Using qRT-PCR strategy, the relative expressions of BnGTR2,BnMYB28 and BnMYB34 genes were analyzed in different tissue of B. napus. The results showed that BnGTR2 and BnMYB28 genes had higher expression levels in relative high glucosinolate content than in relative low glucosinolate content asccessions, which confirms strong association of BnGTR2 and BnMYB28 with glucosinolate content in B. napus, indicating that they could play important roles in glucosinolate biosynthesis pathway in B. napus.