Development of a gene-based marker set for orange-colored watermelon flesh with high b-carotene content

Watermelons exhibit various fruit flesh colors due to the accumulation of distinct carotenoid composition. Specifically, orange-colored flesh is attributed to the accumulation of b-carotene, which plays a vital role in promoting human health. To determine the genetic mechanism behind orange watermelon flesh, canary-yellow-fleshed OTO-DAH and orange-b-fleshed (orange-fleshed with high b-carotene) NB-DAH near-isogenic lines (NILs) were used in this study. For genetic mapping, an F2 population was developed by crossing the two NILs. The segregation ratio of flesh color in the F2 population indicated that the orange-b flesh of NB-DAH NIL is controlled by a single incompletely dominant gene. A major introgression region unique to the NB-DAH NIL was detected on chromosome 1 by the comparative analysis of whole-genome sequences of the parent lines and NILs. This introgression region was considered a candidate region harboring genes that distinguish orange from canary-yellow and red flesh. Among the 13 genes involved in the carotenoid metabolic pathway in watermelons, only ClPSY1 (ClCG01G008470), which encodes phytoene synthase 1, was located within the introgression region. The genotyping of the F2 plants using a cleaved amplified polymorphic sequence marker developed from a non-synonymous SNP in ClPSY1 revealed its relationship with orange-b flesh. This study offers valuable insights into the molecular mechanisms underlying the expression of orange-b flesh and its application in marker-assisted breeding for this desirable trait.