Identification of a candidate gene controlling semi-dwarfism in watermelon, Citrullus lanatus, using a combination of genetic linkage mapping and QTL-seq

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 F-2 and F-2:3 population 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 F-2 plants 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-1 using single-marker analysis. Further, based on the QTL-seq, we identified a significant genomic region for sdw-1 that 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-1 locus 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-1 in fine mapping using 620 F-2 plants. 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.