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http://dx.doi.org/10.9787/KJBS.2018.50.4.424

Development of HRM Markers Based on SNPs Identified from Next Generation Resequencing of Susceptible and Resistant Parents to Gummy Stem Blight in Watermelon  

Lee, Eun Su (Vegetable Research Division, NIHHS, RDA)
Kim, Jinhee (Vegetable Research Division, NIHHS, RDA)
Hong, Jong Pil (Vegetable Research Division, NIHHS, RDA)
Kim, Do-Sun (Vegetable Research Division, NIHHS, RDA)
Kim, Minkyong (Vegetable Research Division, NIHHS, RDA)
Huh, Yun-Chan (Planning and Coordination Division, NIHHS, RDA)
Back, Chang-Gi (Horticultural and Herbal Crop Environment Division, NIHHS, RDA)
Lee, Jundae (Department of Horticulture, Chonbuk National University)
Lee, Hye-Eun (Vegetable Research Division, NIHHS, RDA)
Publication Information
Korean Journal of Breeding Science / v.50, no.4, 2018 , pp. 424-433 More about this Journal
Abstract
Watermelon (Citrullus lanatus) is an economically important vegetable crop all over the world, which has functional compounds such as lycopene and citrulline. Gummy stem blight caused by Didymella bryoniae is one of the most devastative diseases in watermelon. Single nucleotide polymorphisms (SNPs), which are genetic variations occurring between individuals with respect to a single base, were often used to construct genetic linkage maps and develop molecular markers linked to a variety of horticultural traits and resistance to several diseases. In this study, we developed high-resolution melting (HRM) markers based on SNPs generated from NGS resequencing of two parents in watermelon. Plant materials were C. lanatus '920533' (female and susceptible parent), C. amarus 'PI 189225' (male and resistant parent), and their $F_1$ and $F_2$ progenies. A total of 13.6 Gbp ('920533') and 13.1 Gbp ('PI 189225') of genomic sequences were obtained using NGS analysis. A total of 6.09 million SNPs between '920533' and 'PI 189225' were detected, and 354,860 SNPs were identified as potential HRM primer sets. From these, a total of 330 primer sets for HRM analysis were designed. As a result, a total of 61 HRM markers that have polymorphic melting curves were developed. These HRM markers can be used for the construction of SNP-based linkage maps and for the analysis of quantitative trait loci (QTLs) related to gummy stem blight resistance.
Keywords
Gummy stem blight; Resistance; Genetic linkage map; Melting curve; Polymorphism;
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