QTL mapping identifies novel loci and putative candidate genes for rind traits in watermelon.

Unlabelled: Rind color and pattern are important external fruit quality traits of watermelon influencing the consumer attention and market acceptance. Varying degrees of green and yellow colors in different combinations forming distinct patterns have been observed on watermelon rind. In the current experiment, an attempt has been made to map the QTLs/genes for four important rind traits, namely, stripe color, stripe pattern, interstripe color, and interstripe pattern. The experiment consisted of two mapping populations namely F (Pop I) and BCF (Pop II) derived from two parental lines, viz., BIL-53 (characterized by medium green marbled rind pattern and yellowish white blotchy interstripe pattern) and IIHR-140-152 (characterized by dark green solid stripes and greenish wavy interstripe pattern). Linkage mapping identified consistent QTLs across populations on chromosome 9. Comparative genomic analysis of these regions revealed two genes, namely, and as potential candidates for stripe and interstripe color. Sequence analysis of gene in parents along with reference genotypes, viz., 97,103 and Charleston gray suggests a 3 bp deletion on 11th exon to be associated with stripe color polymorphism in watermelon.

Supplementary Information: The online version contains supplementary material available at 10.1007/s13205-022-03112-7.