Fine mapping and candidate gene analysis of a seed glucosinolate content QTL, qGSL-C2, in rapeseed (Brassica napus L.).

key messageQTL mapping and candidate gene analysis indicate that allelic variations in BnaC2.MYB28 resulted from homeologous exchange and determine difference in seed glucosinolate content. A low seed glucosinolate content has long been an important breeding objective in rapeseed improvement. However, the molecular mechanisms underlying seed GSL content variations remain to be elucidated in allotetraploid Brassica napus. Here, we developed a double haploid population from a cross between two B. napus accessions that possess relatively low, but significantly different seed GSL contents and identified a major QTL, qGSL-C2, on chromosome C02 that explains 30.88-72.87% of the phenotypic variation observed in five environments. Using near-isogenic lines, we further delimited qGSL-C2 to a physical region of 49 kb on the B. rapa chromosome A02 which is highly homologous to the target C02 interval. Among five candidate genes, BnaC2.MYB28, a homologue of the Arabidopsis MYB28 encoding a putative R2R3-MYB-type transcription factor functioning in aliphatic methionine-derived GSL synthesis, was most likely to be the target gene underlying the QTL. Sequence analysis revealed multiple insertion/deletion and SNP variations in the genomic region between the alleles of the NILs. Furthermore, the allelic variations in BnaC2.MYB28 in the natural B. napus population were significantly associated with seed GSL content. Remarkably, the phylogenetic analysis and sequence comparison suggested that while the BnaC2.MYB28 allele from the parental line G120 was inherited from B. oleracea BolC2.MYB28, its counterpart from the other parent, 9172, most likely evolved from B. rapa BraA2.MYB28 via possible homeologous exchange. Our study promotes greater understanding of the molecular regulation of seed GSL content and provides useful molecular markers for seed GSL improvement in B. napus.