Construction of a high-density genetic map for watermelon (Citrullus lanatus L.) based on large-scale SNP discovery by specific length amplified fragment sequencing (SLAF-seq)

- The high-density genetic map presented herein is the densest map based on two elite watermelon cultivars.
- The genetic map and markers will facilitate the mapping of quantitative trait loci, map-based cloning, molecular breeding and marker-assisted selection in cultivated watermelon breeding programs.
- Several unassembled scaffolds were anchored to different linkage groups, which considerably improved the assembly of the watermelon genome.

Watermelon (Citrullus lanatus L.) is an important vegetable crop worldwide, but a high-density genetic map of elite watermelon cultivars has not yet been reported. The present study reported the large-scale discovery of single nucleotide polymorphisms (SNPs) by specific length amplified fragment sequencing (SLAF-seq) for high-density genetic map construction using two elite watermelon cultivars. The map contained 2634 SNPs distributed on 11 linkage groups (LGs) corresponding to the number of chromosome pairs in watermelon. The total length of the linkage map was 1,906.31 cM, with an average distance of 0.72 cM between adjacent markers. Notably, 35 unmapped scaffolds, which contained 91 SNPs and covered 4.56 Mb, were dispersedly anchored to LG1, LG2, LG4, LG7, LG8, LG9 and LG11. Although disagreements were observed on LG1 and LG11, the local collinearity between the genetic and physical distances, haplotype map and heat map indicated that the genetic map herein is of high quality. The present study reports the first high-density linkage map of two watermelon elite parents.