Identification and validation of a core set of microsatellite markers for genetic diversity analysis in watermelon, Citrullus lanatus Thunb. Matsum. & Nakai

Abstract

Watermelon, Citrullus lanatus Thunb. Matsum. & Nakai is an important vegetable crop worldwide. Due to its narrow genetic base, detection and utilization of the genetic variations, cultivar identification and increasing genetic diversity are some important tasks for watermelon breeders. Molecular markers, especially microsatellites or simple sequence repeats (SSRs) are playing increasingly important roles for these purposes. In the present study, a core set of 23 highly informative SSR markers was developed for watermelon genetic diversity analysis. Based on whole genome sequencing of 17 watermelon inbred lines, we identified 3.9 million single nucleotide polymorphisms (SNPs) which were used to construct a SNP-based dendrogram for the 17 lines. Meanwhile, from the sequenced genome, 13,744 SSRs were developed, of which 704 were placed on a high-resolution watermelon linkage map. To develop the core set SSR markers, 78 of the 704 mapped SSRs were selected as the candidate markers. Using the SNPbased dendrogram as calibration, 23 SSR markers evenly distributed across the genome were identified as the core marker set for watermelon genetic diversity analysis. Each marker was able to detect 2-7 alleles with polymorphism information content values ranging from 0.45 to 0.82. The dendrograms of 17 watermelon lines based on SNPs, the base set of 78 SSRs and the core set of 23 SSRs were highly consistent. The utility of this core set SSRs was demonstrated in 100 commercial watermelon cultivars and elite lines, which could be placed into six clusters that were largely consistent with previous classification based on morphology and parentage data. This core set of SSR markers should be very useful for genotyping and genetic variation analysis in watermelon.

Assessment of the genetic diversity of dessert watermelon (Citrullus lanatus var. lanatus) landrace collections of South Africa using SSR markers

“…In the current study the number of alleles per locus ranged from 2 to 19, with a mean of 9.4. This was higher than the range from 2 to 7 alleles (mean = 3.7) reported by Zhang et al (2012). Jarret et al (1997) reported an average of 4.7 alleles per locus in 32 watermelon accessions which was lower than those observed in the current study.…”

“…Dessert watermelon has a narrow genetic base (Levi et al, 2001;Hwang et al, 2011) probably due to many years of domestication and selection for desirable horticultural traits (Levi et al, 2001;Dane and Liu, 2007;Minsart et al, 2011). Therefore, continued search, identification and selection of unique genotypes is important for sustainable production of dessert watermelon (Sheng et al, 2012;Zhang et al, 2012;Yang et al, 2016).…”

“…SSR sequences were amplified through polymerase chain reaction (PCR) using SSR primers specific for watermelon. Ten SSR markers were used for the analysis (Table 2) and were selected based on their high polymorphic information content and being developed specifically for watermelon (Joobeur et al, 2006;Zhang et al, 2012). High polymorphic information content values suggest markers may have high discriminatory power to distinguish differences between genotypes.…”

Mapping of quantitative trait loci for lycopene content and fruit traits in Citrullus lanatus

“…SNP and CAPS markers have been routinely used in agricultural breeding programs, plants and animal variation studies, genome mapping and association mapping studies (Kole and Abbott 2008). CAPS markers were proven to be useful for increasing marker resolution in cucurbita crops to identify genes related to plant diseases, but little attention has focused on flesh color markers for watermelon (Femandez-Silva et al 2008;Ling et al 2009;Morales et al 2005;Tezuka et al 2009;Zhang et al 2011). Only one CAPS marker (Phe226) has been identified thus far (Bang et al 2010), which could perfectly co-segregate the flesh color phenotype to distinguish red and canary yellow flesh color.…”

Molecular Characterisation Reveals the Existence of a Hybridogenous Intermediary Form between Sweet Watermelon and Cow Melon Forms of Watermelon

“…ISSR [8], SSR [9]- [16], SRAP [11] [17], EST-PCR [18], and HFO-TAG markers [19] have been used to estimate the genetic relationship among cultivated watermelons and different Citrullus species. Studies by [13] and [19] revealed low levels of DNA polymorphism among cultivated watermelons but high genetic diversity among the Citrullus subspecies. [20] and [21] also revealed very low genetic diversity in cultivated watermelon.…”