Genotyping by sequencing for SNP discovery and genetic mapping of resistance to race 1 of Fusarium oxysporum in watermelon

Abstract

a b s t r a c t Management of fusarium wilt caused by Fusarium oxysporum f. sp. niveum (Fon) (E.F. Sm.) W.C. Snyder & H.N. Han. in watermelon [Citrullus lanatus (Thunb.) Matsum.& Nakai] is largely dependent on cultivation of resistant cultivars. Application of marker-assisted selection (MAS) in conventional breeding programs can accelerate the release of new watermelon cultivars resistant to fusarium wilt. Towards developing tools for MAS, physical (1024 SNPs) and genetic (389 SNPs) maps were developed in the current study for an F 2 population (n = 89; Calhoun Gray x Sugar Baby) segregating for resistance against Fon race 1 using the genotyping by sequencing platform. A modified tray-dip method was established for high-throughput phenotyping of the segregating F 3 population. A major quantitative trait locus (QTL) accounting for up to 38.4% of the phenotypic variation in the F 3 population was identified on chromosome 1 on both the physical and genetic maps in a region previously associated with Fon race 1 resistance. This resistance locus was consistently detected over five different time points and three different phenotypic screens, showing the reliability of the screening method in discriminating susceptible and resistant genotypes. Eight resistance genes were found within the confidence interval of the identified QTL. SNPs close to this QTL may be exploited in MAS for fusarium wilt resistance in breeding programs. This study confirms the resistance locus on chromosome 1 and demonstrates the use of a physical map for QTL detection in watermelon. The SNPs reported here will be useful for future genetic studies in watermelon.

A Genetic Locus Associated with Resistance to Fusarium oxysporum f. sp. niveum Race 2 in Citrullus lanatus-type Watermelon

“…Based on this criterion, 501 SNPs were placed on the physical map (Guo et al, 2013) and used for QTL mapping. Meru and McGregor (2016) previously showed that comparable results were obtained when using the physical (markers ordered according to their physical positions) or genetic map to identify QTL associated with FON 1 resistance in watermelon.…”

“…niveum race 2. Disease severity was visually rated on a scale of 0 to 5 where, 0 = asymptomatic plants, 1 = initial wilting on one leaf, 2 = continued wilting in more than one leaf, 3 = all leaves wilted, 4 = all leaves wilted and stem collapsing, and 5 = dead plants (Meru and McGregor, 2016).…”

“…In addition to the parental materials ('Charleston Gray' and UGA147), the F 1 and 178 F 2:3 lines, the following controls were included: 'Sugar Baby' (susceptible), 'Calhoun Gray' (susceptible), 'SP-6' [resistant (Syngenta, Basel, Switzerland)], and USVL252-FR2 [resistant (Wechter et al, 2012b)]. Disease screening experiments were performed as described previously for QTL mapping of FON 1 resistance (Meru and McGregor, 2016), but using a spore concentration of 5 • 10 5 spores/mL. The lower spore concentration was used to slow down disease development to improve discrimination among F 2:3 lines.…”

“…Plants were evaluated 26 d after inoculation for symptom severity on a scale of 0 to 5 with a score of 0 representing asymptomatic plants, a score of 1 for plants showing initial wilting on one leaf, a score of 2 for plants showing continued wilting in more than one leaf, a score of 3 for plants with all the leaves wilted, a score of 4 for plants with all leaves wilted and stem collapsing, and a score of 5 for dead plants (Meru and McGregor, 2016). Pearson pairwise correlations (r), Spearman rank order correlation (r s ), and the Shapiro and Wilk test for normality (Shapiro and Wilk, 1965) were calculated in JMP Ò Pro (version 12.1.0; SAS Institute, Cary, NC).…”

“…Several recent molecular studies have shown that Fo-1 is associated with a major QTL (Qfon1.1; R 2 = 23% to 60%) on chr. 1 (Lambel et al, 2014;Meru and McGregor, 2016;Ren et al, 2015) of the watermelon draft genome (Guo et al, 2013).…”