Fine-mapping and candidate gene analysis of the <italic>Brassica juncea</italic> white-flowered mutant <italic>Bjpc2</italic> using the whole-genome resequencing.

Flower color in <italic>Brassica</italic> spp. is an important trait and considered a major visual signal for insect-pollinated plants. In previous study, we isolated and identified two genes (<italic>BjPC1</italic> and <italic>BjPC2</italic>) that control the flower color in <italic>B. juncea</italic>, and mapped <italic>BjPC1</italic> to a 0.13-cM region. In this study, we report the fine-mapping and candidate analysis of <italic>BjPC2</italic>. We conducted whole-genome resequencing, using bulked segregant analysis (BSA) to determine the <italic>BjPC2</italic> 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 <italic>BjPC2</italic> locus. Through a genome-wide comparison of single nucleotide polymorphism (SNP) profiles between the yellow- and white-flowered bulks, a candidate interval for <italic>BjPC2</italic> was identified on chromosome B04 (2.45 Mb). The <italic>BjPC2</italic> linkage map was constructed with the newly developed simple sequence repeat (SSR) markers in the candidate interval to narrow the candidate <italic>BjPC2</italic> region to 31-kb. Expression profiling and RNA-seq analysis partially confirmed that the <italic>AtPES2</italic> homolog, <italic>BjuB027334</italic> is the most promising candidate gene for <italic>BjPC2</italic>. Furthermore, analyses with high pressure liquid chromatography and transmission electron microscopy demonstrated that <italic>BjPC2</italic> might be important in xanthophyll esterification, a process that limits xanthophyll degradation and increases sequestration. Overall, we mapped the <italic>BjPC2</italic> to a 31-kb region on the B04 in <italic>B. juncea</italic> and identified <italic>BjuB027334</italic> 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 <italic>B. juncea</italic> breeding. [ABSTRACT FROM AUTHOR]