Comparative mapping in watermelon [Citrullus lanatus (Thunb.) Matsum. et Nakai]

Abstract

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.

An integrated genetic map based on four mapping populations and quantitative trait loci associated with economically important traits in watermelon (Citrullus lanatus)

“…In order to make map integration possible, the 388 SNP markers described by Sandlin et al [21] were genotyped in the 97103 × PI 296341-FR RIL population [20] by mining genotyping by sequencing (GBS) data for the population. A total of 386 SNP loci were segregating in the latter population, allowing the integration of 244449 data points generated from four mapping populations representing eight watermelon parental accessions (Table 1).…”

“…The largest data sets were from the parental accession 97103 × PI 296341-FR RIL population. Based on the high density saturated genetic map [20] and SNP map [21], we integrated 698 SSR, 219 InDel, 36 SV and 386 SNP markers to construct the integrated map. The integrated map contains 1339 markers, spanning 798 cM with an average marker interval of 0.6 cM (Figure 1, Table 2).…”

“…We also report new QTL identified for fruit sugar traits and the location of previously reported QTL [21-23] on the integrated map. This made it possible to compare the genomic location of the QTL mapped in the different populations and suggest a common nomenclature to name these QTL.…”

“…These low density maps were mainly based on isozymes [15,16], RAPD (randomly amplified polymorphic DNA), RFLP (restriction fragment length polymorphism), AFLP (amplified fragment length polymorphism) and SRAP (sequence related amplified polymorphism) markers, and only a limited number of SSR (simple sequence repeat) markers [17-19]. More recently, a high density linkage map with 953 loci was constructed using simple sequence repeat (SSR), insertion-deletion (InDel) and structure variation (SV) markers [20] by the National Engineering Research Center for Vegetables, and the first single-nucleotide polymorphism (SNP) genetic maps were constructed through a collaboration between the University of Georgia (Athens, GA) and Monsanto (Woodland, CA), resulting in 388 public SNP markers [21]. Quantitative trait loci (QTL) associated with economically important seed and fruit traits in watermelon were also mapped in the three individual populations used to create the SNP maps [21-23].…”

“…More recently, a high density linkage map with 953 loci was constructed using simple sequence repeat (SSR), insertion-deletion (InDel) and structure variation (SV) markers [20] by the National Engineering Research Center for Vegetables, and the first single-nucleotide polymorphism (SNP) genetic maps were constructed through a collaboration between the University of Georgia (Athens, GA) and Monsanto (Woodland, CA), resulting in 388 public SNP markers [21]. Quantitative trait loci (QTL) associated with economically important seed and fruit traits in watermelon were also mapped in the three individual populations used to create the SNP maps [21-23]. Together, these maps represent all three subspecies of C. lanatus , however the maps produced by the two research groups don’t include any common markers and possess large numbers of individual-specific markers.…”