Quantitative trait loci and candidate genes responsible for pale green flesh colour in watermelon (Citrullus lanatus)

Flesh colour is an important trait that affects the nutritional value, consumer preference, and breeder selection of fruits. In this study, we developed an F-2 population derived from crossing the parental lines ZXG1555 (pale green flesh) and Cream of Saskatchewan (short for 'COS'; pale yellow flesh) to identify quantitative trait loci (QTLs) and predict candidate genes that determine flesh colour and chlorophyll content. We found a major effective QTL (qfc10.1) region harbouring 22 annotated genes related to pale green flesh colour and chlorophyll content in the same region (similar to 519 kb) on chromosome 10. Two Kompetitive Allele-Specific PCR (KASP) markers were developed based on two single nucleotide polymorphisms (SNPs) in candidate gene Cla97C10G185970 annotated as plastid lipid-associated protein, which exhibited a high correlation of pale green and non-pale green flesh fruits according to the genotype results. The findings of this study provide a fundamental basis for further fine mapping and functional analyses of candidate genes associated with pale green flesh colour in watermelon.