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Dwarfism in crops is a useful breeding trait. In this study, we aimed to identify a candidate gene controlling semi-dwarfism in watermelon (Citrullus lanatus) using a combination of genetic mapping and quantitative trait loci (QTL)-seq. We evaluated phenotypes using an F2and F2:3population derived from a cross between a “Bush Sugar Baby” (BSB, semi-dwarf type) and a PCL-J1 (normal type) cultivar. Results indicated that a single recessive gene confers semi-dwarfism in BSB. We constructed a genetic map using 180 F2plants and 336 single-nucleotide polymorphisms (SNPs), detected using genotyping-by-sequencing, and mapped the semi-dwarfism locus, sdw-1, between the SNP markers linked by 9.6 cM (0.99 Mb) on Chr. 9. QTL analysis pointed to the same genomic location for sdw-1using single-marker analysis. Further, based on the QTL-seq, we identified a significant genomic region for sdw-1that matched with the sdw-1-flanking region in the genetic linkage map. This 1-Mb region was narrowed down by mapping three SNP markers developed from the QTL-seq data. The sdw-1locus was mapped to the 0.44-Mb genomic region, which harbored 13 genes. One of the 13 genes, ClCG09G018320 (ATP-binding cassette (ABC) transporter B family member 19), showed the SNPs in its coding sequence, and cleaved amplified APS markers developed from those SNPs co-segregated with sdw-1in fine mapping using 620 F2plants. Our results implied that a frameshift mutation in the ABC transporter gene and the resulting alteration in auxin transportation are the most likely to be responsible for semi-dwarfism in BSB.

Current nomenclature for the taxonomic classification of melon cultivars (Cucumis meloL.) at the horticultural group level relies on morphological variation in certain key characters. However, the reliability of current infraspecific classification scheme in considering horticultural groups as botanical taxa was not fully understood. In the present study, the information of horticultural group classification in melon was assessed at the molecular level using genome-wide single nucleotide polymorphisms (SNPs). A total of 143 melon accessions of 15 horticultural groups in two subspecies, subsp. meloand subsp. agrestiwere collected and genotyped by using Genotyping-By-Sequencing (GBS). From the filtering of resultant sequence variants, 10,949 SNPs were selected and used for downstream genetic analysis including population structure, principle component analysis, and hierarchical clustering of 143 melon accessions. Our genetic analyses indicated that the distribution of accessions at the molecular level generally matched the subspecies classification and no substantial contradictions existed between the division of accessions based on horticultural group information and genetic relatedness revealed by the GBS. However, the distinction between horticultural groups was not clear-cut, implying the limitation of considering horticultural groups as botanical taxa. To improve the resolution of horticultural group classification in melon, our SNP data may be useful as supporting information in conjunction with morphological characters.