Comparative Transcriptomics Provides Insight into Rind Color Polymorphism in Watermelon

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Background: As an important agronomic trait affecting breeding and consumption choice, the rind color of watermelon [Citrullus lanatus (Thunb.) Matsum. and Nakai] receives considerable attention from breeders. Although rind color occupies an important place in watermelon breeding work, the underlying molecular mechanism governing this complex trait has still not been determined. Results: In the present study, chlorophyll and carotenoid contents were hypothesized to be the main factors determining rind color. Clearly different structures and numbers of chloroplasts and grana lamellae were found among materials with different rind colors. To study the genes involved in the coloration process of the yellow, dark green, light green, and light green-gray rinds, 84,516 unigenes were obtained from the rind transcriptome. Through DEGs screening and pathway analysis of chlorophyll and carotenoid mechanism, the genes with abnormal expression levels were identified. Then, the nucleotide sequences and expression levels of the putative genes responsible for different rind colors were studied.Conclusions: This study provides a comprehensive insight on the factors affecting rind coloration and investigated expression levels of the critical genes concerning pigment metabolism in watermelon. These results would help to analyze the molecular mechanisms of rind coloration regulation and development of the related organelles.