Abstract
SummaryYears of selection for desirable fruit quality traits in dessert watermelon (Citrullus lanatus) has resulted in a narrow genetic base in modern cultivars. Development of novel genomic and genetic resources offers great potential to expand genetic diversity and improve important traits in watermelon. Here, we report a high‐quality genome sequence of watermelon cultivar ‘Charleston Gray’, a principal American dessert watermelon, to complement the existing reference genome from ‘97103’, an East Asian cultivar. Comparative analyses between genomes of ‘Charleston Gray’ and ‘97103’ revealed genomic variants that may underlie phenotypic differences between the two cultivars. We then genotyped 1365 watermelon plant introduction (PI) lines maintained at the U.S. National Plant Germplasm System using genotyping‐by‐sequencing (GBS). These PI lines were collected throughout the world and belong to three Citrullus species, C. lanatus, C. mucosospermus and C. amarus. Approximately 25 000 high‐quality single nucleotide polymorphisms (SNPs) were derived from the GBS data using the ‘Charleston Gray’ genome as the reference. Population genomic analyses using these SNPs discovered a close relationship between C. lanatus and C. mucosospermus and identified four major groups in these two species correlated to their geographic locations. Citrullus amarus was found to have a distinct genetic makeup compared to C. lanatus and C. mucosospermus. The SNPs also enabled identification of genomic regions associated with important fruit quality and disease resistance traits through genome‐wide association studies. The high‐quality ‘Charleston Gray’ genome and the genotyping data of this large collection of watermelon accessions provide valuable resources for facilitating watermelon research, breeding and improvement.
Highlights
Watermelon (Citrullus lanatus) is an important crop consumed throughout the world and is a rich source of lycopene, citrulline and other human health-promoting compounds (Perkins-Veazie et al, 2007)
The ‘Charleston Gray’ genome was sequenced using the Illumina technology, which produced a total of 95.5 Gb of high-quality cleaned sequences from paired-end and mate-pair libraries with insert sizes ranging from 400 bp to 20 kb (Table S1)
The assembly consisted of 21 498 contigs and 2034 scaffolds (>500 bp), with N50 sizes of 36.7 kb and 7.47 Mb, respectively, and 90% of the genome draft was assembled into only 60 scaffolds (Table 1)
Summary
Watermelon (Citrullus lanatus) is an important crop consumed throughout the world and is a rich source of lycopene, citrulline and other human health-promoting compounds (Perkins-Veazie et al, 2007). China is the largest producer and consumer of watermelon with 70 million tonnes produced per year. Cultivars of East Asian ancestry mainly produce small to mid-sized globular fruits with a thin rind, while American cultivars tend to produce large, oblong fruits with a thick rind. Differential selection pressures in the two regions have led to distinct East Asian and American watermelon ecotypes (Guo et al, 2013; Sheng et al, 2012). The only published watermelon reference genome was constructed using the Chinese elite line ‘97103’, representing the East Asian type (Guo et al, 2013). Quantitative trait locus (QTL) and association mapping studies with American germplasm using the ‘97103’ genome as the reference would be limited to the genetic makeup of a single East Asian cultivar, potentially missing causal variants
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