수박에서 덩굴마름병 감수성 및 저항성 양친에 대한 차세대 염기서열 재분석으로 탐색된 SNP 기반 HRM 분자표지 개발
Development of HRM Markers Based on SNPs Identified from Next Generation Resequencing of Susceptible and Resistant Parents to Gummy Stem Blight in Watermelon
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초록
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 F1 and F2 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.
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 F1 and F2 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.
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