Identification of putative genetic regions for watermelon rind hardness and related traits by BSA-seq and QTL mapping

Textural quality of watermelon fruit is mainly determined by rind hardness/firmness and its related traits. The determination of genetic regions harboring QTLs/gene(s) has a primary worth in genetic breeding studies. In this study, whole genome BSA-seq and QTL mapping through newly developed CAPS markers were successfully performed, respectively. Total 133-F2 mapping individuals were derived from crossing of P1 ‘1061’ and P2 ‘812’ and slefing of F1 offspring. Whole genome BSA-seq revealed major genetic region controlling rind hardness trait on chromosome 10. The genetic linkage map was assembled by genotyping of 133 pairs of codominant CAPS markers which spanned total 2606.38 cM length with averaged 19.60 cM distance among whole genome flanking markers. Moreover, CAPS markers based QTL analysis revealed total 5 putative QTLs [2 rind-hardness (RH), 1 rind toughness (RTO), 1 rind thickness (RTH) and 1 fruit weight (FW)] on three distinct chromosomes (2, 9, and 10), which mainly contributed 5.44–49.11% PVE. Interestingly, the combined molecular techniques expressed putative genetic region controlling rind hardness at chromosome 10. According to the BSA-seq result, major genetic region was detected between 1792001 and 4036000 bp on chromosome 10 with 2.24 Mb range, while from QTLs analysis, two co-localized focal QTLs “RH10 and RTO10” revealed 20 and 39 predicted genes at shortened genetic distances of 292.76 kbp and 405.31 kbp, respectively. A significant correlation and normal distribution frequencies for rind-phenotypes were also noticed. In crux, our combined techniques proved as an effective mapping strategies for identification of QTLs/gene(s) and provided a strong theoretical basis for future breeding studies in watermelon.