Biparental genetic mapping reveals that CmCLAVATA3 (CmCLV3) is responsible for the variation in carpel number in melon (Cucumis melo L.).

KEY MESSAGES: Genetic analysis revealed that CmCLV3 is a candidate gene for the variation in melon carpel number. Carpel number (CN) is an important trait in melon. Three-CN melon fruit is oval, while 5-CN melon fruit has a round or flat shape. Herein, a genetic analysis of a population in which the CN locus was segregated indicated that 3-CN is controlled by a major dominant effective gene. Bulked segregant analysis and initial linkage mapping placed the CN locus in a 6.67 Mb region on chromosome 12, and it was narrowed to 882.19 kb with molecular markers and recombinant plants. Fine mapping with a large F2 population containing 1026 individuals further narrowed the locus to an 83.98 kb region harboring five annotated genes. Gene structure alignment between the parental lines revealed MELO3C035640.2 (annotated as CLAVATA3, CmCLV3) as the best candidate gene for the CN trait. CmCLV3 was more highly expressed in 3- than 5-CN lines and specifically expressed in terminal buds rather than in young leaves, hypocotyls, and roots. The CmCLV3 coding region was cloned from eight 3- or 5-CN melon accessions, and a nonsynonymous SNP site was highly correlated with CN variation. This SNP site was also related to CN variations among 40 melon lines according to their resequencing data, causing a helix alteration in the CmCLV3 protein. Promoter region sequence alignment and activity analysis showed that, unlike in cucumber and tomato, CmCLV3 promoter variation and activity were not the main reasons for CN alteration. Overall, this study provides a genetic resource for melon fruit development research and molecular breeding tools for melon CN improvement.