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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.

As an important commodity trait in melons, the rind is the most direct standard of evaluation for consumers. In this study, we obtained an F2 melon population derived from self-crossing an F1 generation from a cross between X010 (green rind with stripes) and M1-113 (white rind without stripes) and performed genetic analysis and mapping. Genetic analysis revealed that a single dominant gene (st3) controlled the striped rind trait in melons. According to bulked segregant analysis, two DNA bulks were constructed (20 striped and 20 solid-colored rind plants). Next-generation sequencing was used on two parental lines (X010 and M1-113) and two DNA bulks. The st3 gene was identified on chromosome 4 within 2.7 Mbp region. Fourty cleaved amplified polymorphic sequences (CAPS) markers were developed, and sixteen CAPS markers with polymorphisms on chromosome 4 were used for constructing a genetic linkage map, and identifying recombinants in a large F2 population with six new CAPS markers. The location of the st3 gene was narrowed to 172.8 kbp on chromosome 4 between markers M-4-28 (825,401 bp) and M-4-27 (998,261 bp). This study provides a theoretical basis for the fine mapping, cloning and functional characterization of st3.

Lycopene content is an important factor for determining watermelon fruit quality. However, the low DNA polymorphism among cultivated watermelon (Citrullus lanatus) has hindered the ability to establish high quality genetic maps and study the quantitative trait loci (QTL) controlling the lycopene content trait. In this study, we successfully constructed a genetic map of watermelon to determine lycopene content and other horticultural fruit traits using a F2 population developed from a cross between the two lines of watermelon LSW-177 and Cream of Saskatchewan. The genetic map contained 16 linkage groups covering a total length of 2,039.5 cM, which included 37 SSRs (Simple Sequence Repeat) and 107 CAPSs (Cleaved Amplified Polymorphic Sequences), with all of the CAPS markers developed from high-throughput re-sequencing of data from this study. Three CAPS markers (WII04E07-33,WII04E07-37,WII04E07-40) caused the F2 population to perfectly co-segregate for each F2 population plants. We also obtained 12 QTLs for all of the traits measured. Only one QTL (LCYB4.1) was detected with a high value of trait variation (83.50 %) that related to lycopene content and mapped on Chromosome 4 between CAPS markers WII04E07-33 and WII04E07-40, which could nearly account for all of the differences in lycopene content between the two parental strains. In this study, we highlighted 2,458 CAPS loci that were suitable for primer design with a polymorphism of 48.9 %, which is approximately a 12-fold increase from previous studies. The present map and QTLs will facilitate future studies on determining lycopene content related genes and cloning watermelon genes, while also providing for useful markers for breeding for lycopene content.