Fine-mapping and candidate gene analysis of the Brassica juncea white-flowered mutant Bjpc2 using the whole-genome resequencing

Flower color in Brassica spp. is an important trait and considered a major visual signal for insect-pollinated plants. In previous study, we isolated and identified two genes (BjPC1 and BjPC2) that control the flower color in B. juncea, and mapped BjPC1 to a 0.13-cM region. In this study, we report the fine-mapping and candidate analysis of BjPC2. We conducted whole-genome resequencing, using bulked segregant analysis (BSA) to determine the BjPC2 candidate intervals. Crossing, allelism testing, and repeated full-sib mating were used to generate XG3, a near isogenic line (NIL) population that segregated on the BjPC2 locus. Through a genome-wide comparison of single nucleotide polymorphism (SNP) profiles between the yellow- and white-flowered bulks, a candidate interval for BjPC2 was identified on chromosome B04 (2.45 Mb). The BjPC2 linkage map was constructed with the newly developed simple sequence repeat (SSR) markers in the candidate interval to narrow the candidate BjPC2 region to 31-kb. Expression profiling and RNA-seq analysis partially confirmed that the AtPES2 homolog, BjuB027334 is the most promising candidate gene for BjPC2. Furthermore, analyses with high pressure liquid chromatography and transmission electron microscopy demonstrated that BjPC2 might be important in xanthophyll esterification, a process that limits xanthophyll degradation and increases sequestration. Overall, we mapped the BjPC2 to a 31-kb region on the B04 in B. juncea and identified BjuB027334 as a valuable candidate gene. Our results provide a basis for understanding the molecular mechanisms underlying the white-flowered trait and for molecular marker-assisted selection of flower color in B. juncea breeding.