Mapping and validation of a new quantitative trait locus (QTL) for fruit size in watermelon (Citrullus lanatus)

Watermelon (Citrullus lanatus) is one of the top ten fruit-bearing species in the world and is mainly grown for its edible fruit. However, the understanding of watermelon fruit size is still incomplete, with relatively few studies on the genetic and molecular mechanisms of this trait. In the present study, three segregation populations from one novel germplasm with small fruit and different inbred lines with medium fruit, big fruit and giant fruit, respectively, were constructed to locate and fine map one new quantitative trait locus (QTL) on chromosome 8 for fruit size in watermelon. Inheritance analysis of these three populations suggested that small fruit was controlled by a single recessive gene in watermelon. We located a new QTL for fruit size on chromosome 8, and developed markers to conduct fine mapping of the genomic region and to identify candidate genes. Specifically, we constructed a high-density genetic linkage map using restriction-site associated DNA (RAD)-based high-throughput genotyping data from a second-filial generation (F2) mapping family derived from novel germplasms with small fruit and big fruit. The total genetic map length was 1315.53 cM with an average inter-locus distance of 0.18 cM, which contained 7,272 high-quality single nucleotide polymorphism (SNP) markers distributed on 11 linkage groups corresponding to the number of chromosome pairs in watermelon. Genome wide QTL mapping revealed one significant QTL (fs-chr8) on chromosome 8 associated with fruit size. One major QTL (fs-B171) on chromosome 8 was also identified in another BC1 population derived from giant watermelon and small watermelon, which overlapped with fs-chr8. Moreover, based on the markers obtained from next-generation sequencing of the parental lines, we conducted fine mapping of the interval to a 304 kb region (from 26.83 to 27.14 Mb) on chromosome 8 using 7 polymerase chain reaction (PCR) based markers. The PCR based markers confirmed the accuracy of our mapping results for watermelon fruit size. Finally, candidate genes underlying fruit size were identified from the reference genome 97103v2, including genes related to cytochrome P450 family enzymes, gibberellin-regulated proteins, transcription factor and basic leucine zipper (bZIP) transcription factor family proteins. Our study provides fine mapping results for watermelon fruit size and will lay the foundation for the identification of candidate genes to elucidate the molecular mechanism underlying fruit size in this species.