The first single-nucleotide polymorphism (SNP) maps for watermelon [Citrullus lanatus (Thunb.) Matsum. et Nakai] were constructed and compared. Three populations were developed from crosses between two elite cultivars, Klondike Black Seeded × New Hampshire Midget (KBS × NHM), an elite cultivar and wild egusi accession, Strain II × PI 560023 (SII × Egusi) and an elite cultivar and a wild citron accession, ZWRM50 × PI 244019 (ZWRM × Citroides). The SII × Egusi and ZWRM × Citroides F(2) populations consisted of 187 and 182 individuals respectively while the KBS × NHM recombinant inbred line (RIL) population consisted of 164 lines. The length of the genetic maps were 1,438, 1,514 and 1,144 cM with average marker distances of 3.8, 4.2, and 3.4 cM for the KBS × NHM, SII × Egusi and ZWRM × Citroides populations, respectively. Shared markers were used to align the three maps so that the linkage groups (LGs) represented the 11 chromosomes of the species. Marker segregation distortion were observed in all three populations, but was highest (12.7 %) in the ZWRM × Citroides population, where Citroides alleles were favored. The three maps were used to construct a consensus map containing 378 SNP markers with an average distance of 5.1 cM between markers. Phenotypic data was collected for fruit weight (FWT), fruit length (FL), fruit width (FWD), fruit shape index (FSI), rind thickness (RTH) and Brix (BRX) and analyzed for quantitative trait loci (QTL) associated with these traits. A total of 40 QTL were identified in the three populations, including major QTL for fruit size and shape that were stable across genetic backgrounds and environments. The present study reports the first SNP maps for Citrullus and the first map constructed using two elite parents. We also report the first stable QTL associated with fruit size and shape in Citrullus lanatus. These maps, QTL and SNPs should be useful for the watermelon community and represent a significant step towards the potential use of molecular tools in watermelon breeding.

The egusi watermelon (Citrullus lanatus) is popular in West Africa for its oil and protein-rich seed, which is consumed in soups and stews. The egusi phenotypic trait is controlled by a single recessive gene (eg) and is characterized by large seed size and fleshy, thick pericarp. An F 2 mapping population was derived from Strain II (PI 279461) of the Japanese cultivar Yamato-cream with normal seed type and low seed oil percentage (SOP = 25.2%) and an egusi type from Nigeria [Egusi (PI 560023)] with high SOP (40.6%). Genetic analysis confirmed that the egusi seed trait is controlled by a single recessive gene (eg) and the location of the gene was mapped to 57.8 cM on linkage group (LG) 2, between markers NW0248325 and NW0250248. Four main quantitative trait loci (M-QTL) were identified for SOP in the population with the eg locus contributing 84% of the explained phenotypic variation (R 2 ). A significant epistatic interaction (E-QTL) was identified between, the eg locus and an M-QTL on LG 9B. The present study reports the location of the eg locus responsible for the egusi seed trait in watermelon on LG 2 as well as M-QTL and E-QTL associated with SOP.

Watermelon (Citrullus lanatus) is an important crop grown for both its edible flesh and seeds. Seed size is an important trait in watermelon breeding, with large seeds preferred for planting and edible seeds but small seeds preferred in fruit sold for consumption. Large, medium, and small seed sizes are thought to be controlled by two genes with epistatic interaction. A ‘Klondike Black Seeded’ × ‘New Hampshire Midget’ (KBS × NHM) recombinant inbred line population and a ZWRM 50 × PI 244019 (ZWRM × Citroides) F2 population were used to identify main effect quantitative trait loci (M-QTL) and epistatic QTL (E-QTL) associated with 100 seed weight (100SWT), seed length (SL), and seed width (SWD). Thirteen M-QTL were identified on four linkage groups (LGs) for the three traits in the two populations. Major M-QTL (R2 = 26.9% to 73.6%) were identified at the same location on LG 2 in both populations for all three traits. M-QTL for all three traits also colocalized on LG 9 in the ZWRM × Citroides population and on LG 4 for 100SWT and SL in the KBS × NHM population. Significant epistatic effects were found between the M-QTL on LG 2 and LG 4 in the KBS × NHM population and between LG 2 and LG 9 in the ZWRM × Citroides population. The phenotypic variance explained by the E-QTL was generally small. The stable, major M-QTL on LG 2 is a candidate for marker-assisted selection for seed size in watermelon.