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Seed coat color is one of the most intuitive phenotypes in bitter gourd ( Momordica  spp.). Although the inheritance of the seed coat color has been reported, the gene responsible for it is still unknown. This study used two sets of parents, representing, respectively, the intersubspecific and intraspecific materials of bitter gourd, and their respective F 1  and F 2  progenies for genetic analysis and primary mapping of the seed coat color. A large F 2:3  population comprising 2,975 seedlings from intraspecific hybridization was used to fine-map the seed coat color gene. The results inferred that a single gene, named  McSC1 , controlled the seed coat color and that the black color was dominant over the yellow color. The  McSC1  locus was mapped to a region with a physical length of ∼7.8 Mb and 42.7 kb on pseudochromosome 3  via  bulked segregant analysis with whole-genome resequencing (BSA-seq) and linkage analysis, respectively. Subsequently, the  McSC1  locus was further fine-mapped to a 13.2-kb region containing only one candidate gene,  MC03g0810 , encoding a polyphenol oxidase (PPO). Additionally, the variations of  MC03g0810  in the 89 bitter gourd germplasms showed a complete correlation with the seed coat color. Expression and PPO activity analyses showed a positive correlation between the expression level of  MC03g0810  and its product PPO and the seed coat color. Therefore,  MC03g0810  was proposed as the causal gene of  McSC1 . Our results provide an important reference for molecular marker-assisted breeding based on the seed coat color and uncover molecular mechanisms of the seed coat color formation in bitter gourd.

MC03g0810, an Important Candidate Gene Controlling Black Seed Coat Color in Bitter Gourd (Momordica spp.)