Genetic mapping and meta-analysis identifies several candidate genes for watermelon (Citrullus lanatus) fruit quality traits

Abstract

Citron (Citrullus amarus), a wild relative of watermelon possesses white flesh with coarse texture and bland/bitter taste; this may cause undesirable effect on quality in watermelon breeding. It is therefore important to understand the genomic regions/genes governing fruit quality, while using this species in introgressive breeding to avoid linkage drag. Hence, in the current experiment an attempt has been made to understand genes/QTLs governing important fruit quality traits in an inbred line derived from C. amarus. BIL-53 (P1) characterized by creamish white flesh, low TSS, red colored seeds and flat fruit shape; and ice box type inbred line, IIHR-140–152 (P2) characterized by dark red colored flesh, high TSS, black colored seeds and oblong fruit shape were used as parents for this QTLs study. Among 693 markers screened, 202 (29.14%) markers were found to be polymorphic and were used for linkage map construction and QTL mapping. QTL mapping identified eleven major QTLs for fruit shape on chromosome 3, 4 and 11. Candidate gene analysis in these regions validated Cla011257 gene on chromosome 3 and predicted Cla016683 gene in a novel QTL region on chromosome 11 as a putative candidate for fruit shape. Similarly, one novel QTL was identified for total soluble solids on chromosome 11, candidate gene analysis in this region predicted Cla016890 and Cla016891 genes as putative candidates. For flesh color, this is the first attempt to map the genes/QTLs governing flesh color at the different regions of fruit through visual and colorimetric analysis. Results revealed fifteen major QTLs on chromosome 2, 4, 5, 6, 7 and 10 for flesh color at different regions. Candidate gene analysis predicted Cla020214 and Cla020121 on chromosome 2; Cla005011 on chromosome 4; Cla018767, Cla018768, Cla018769, Cla018770, Cla018771 on chromosome 6; Cla017416 and Cla017593 on chromosome 10 as a probable candidates genes governing flesh color at different regions. The results presented here provide valuable information for future studies on functional validation of putative candidate genes and breeding of important fruit quality traits in watermelon.