Genome‐wide identification of loci affecting seed glucosinolate contents in Brassica napus L.

Abstract

Glucosinolates are amino acid-derived secondary metabolites that act as chemical defense agents against pests. However, the presence of high levels of glucosinolates severely diminishes the nutritional value of seed meals made from rapeseed (Brassica napus L.). To identify the loci affecting seed glucosinolate content (SGC), we conducted genome-wide resequencing in a population of 307 diverse B. napus accessions from the three B. napus ecotype groups, namely, spring, winter, and semi-winter. These resequencing data were used for a genome-wide association study (GWAS) to identify the loci affecting SGC. In the three ecotype groups, four common and four ecotype-specific haplotype blocks (HBs) were significantly associated with SGC. To identify candidate genes controlling SGC, transcriptome analysis was carried out in 36 accessions showing extreme SGC values. Analyses of haplotypes, genomic variation, and candidate gene expression pointed to five and three candidate genes in the common and spring group-specific HBs, respectively. Our expression analyses demonstrated that additive effects of the three candidate genes in the spring group-specific HB play important roles in the SGC of B. napus.

Genetic Characterization of Russian Rapeseed Collection and Association Mapping of Novel Loci Affecting Glucosinolate Content

“…The significance level for the next five SNPs ranged according to the observed association significance that passed the soft significance threshold of 0.0005 (Table S3). Notably, our analysis revealed no significant association signals for the SNPs linked to glucosinolate concentration in the foreign rapeseed lines in the previous studies [24][25][26]42,43] (Figure 5). The total phenotypic variation of glucosinolate levels explained by the two most significant SNPs varied from 13.8 to 20.4% across three years (Table S3).…”

“…Previously, this approach yielded several candidate genes located in the vicinity of the glucosinolate-associated SNPs. The first group of the candidate genes included the ones encoding enzymes directly responsible for glucosinolate metabolism, namely, AOP3 enzymes involved in the final steps of glucosinolate biosynthesis [26], glucosinolate side chain biosynthetic enzymes MAM1 and MAM3 [43,54], and glucosinolate transporter GTR2 [24,25]. The second group includes genes encoding proteins involved in the regulation of glucosinolate content, namely, the HAG1 transcription factor controlling aliphatic glucosinolate biosynthesis [26,42] and MYB28 and MYB34 family transcription regulators.…”

“…In order to compare the newly identified loci (SNP positions) with the loci that were previously demonstrated to be significantly associated with glucosinolate content, first, the available information on the exact physical distance of loci associated with glucosinolate content was collected from the previously published papers [24][25][26]42,43]. Second, for each SNP in the present study, the corresponding positions in the Darmor bzh assembly version 4.1 [3] were found.…”

“…These studies identified a number of genetic loci associated with glucosinolate content located on the chromosomes A01, A04, A06, A09, C02, C03, and C09. Following the increasing popularity of GWAS several works have been published on implementing this method to diverse rapeseed lines from global collections [24][25][26]. These approaches facilitated the identification of new loci as well as new candidate genes potentially responsible for glucosinolate content in rapeseed plants.…”

High-throughput genotyping for association mapping of agronomically important traits in rapeseed: a brief review of the current status

“…In contrast, unsaturated fatty acids, namely oleic and linoleic as well as tocopherols possessing vitamin E activity, are considered as beneficial components of the oil. Several studies indicate that glucosinolate content is related to SNP adjacent genes that encode glucosinolate transporters and various transcription factors (Qu et al, 2015, Li et al, 2014, Wei et al, 2019. Loci associated with erucic acid content were present on chromosomes A8, A9, A10, C3, C8, C9 (Li et al, 2014;Havlickova et al, 2017;Qu et al, 2017).…”