Genetic analysis and gene mapping of the orange flower trait in Chinese cabbage (Brassica rapa L.)

Flower color is considered an important appealing signal to pollinators and also a marker trait in Brassica crop breeding. However, the genetic basis of orange flower trait remains poorly understood in Brassica rapa. In this study, we conducted a genetic analysis of orange flower trait and fine mapped the underlying gene in B. rapa. Two populations, BC1F1 and BC1F2 with 478 and 443 individuals, respectively, were constructed from a cross between 94C9 (orange flower) and 92S105 (yellow flower). Genetic analysis showed that a single recessive gene, BrOF, controlled the orange flower trait. Using Indel and dCAPS markers developed from whole-genome resequencing data of 94C9 and 92S105, BrOF was mapped to a 41.5-kb region on chromosome A09 delimited by InDel409 and dCAPS425 containing six putative genes. Among them, only Bra037124 and Bra037125, which encode an AP2 domain-containing transcription factor and an SEC-C motif-containing protein/OTU-like cysteine protease family protein, respectively, were successfully cloned. The sequence analysis revealed two SNPs resulting in amino acid residue changes in the coding region of Bra037124, as well as seven SNPs and one insertion leading to amino acid residue mutations in the coding region of Bra037125, between 94C9 and 92S105. The reliability of a co-segregating marker InDel314 in marker-assisted selection (MAS) was confirmed by testing different yellow/orange flower Chinese cabbage lines. These results provide a good foundation to identify BrOF and facilitate our understanding of the genetic basis underlying the development of orange flowers in Chinese cabbage.