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Development of HRM Markers Based on SNPs Identified from Next Generation Resequencing of Susceptible and Resistant Parents to Gummy Stem Blight in Watermelon
수박에서 덩굴마름병 감수성 및 저항성 양친에 대한 차세대 염기서열 재분석으로 탐색된 SNP 기반 HRM 분자표지 개발
Korean. J. Breed. Sci. 2018;50(4):424-433
Published online December 1, 2018
© 2018 Korean Society of Breeding Science.

Eun Su Lee1, Jinhee Kim1, Jong Pil Hong1, Do-Sun Kim1, Minkyong Kim1, Yun-Chan Huh2, Chang-Gi Back3, Jundae Lee4, and Hye-Eun Lee1*
이은수1, 김진희1, 홍종필1, 김도선1, 김민경1, 허윤찬2, 백창기3, 이준대4, 이혜은1*

1Vegetable Research Division, NIHHS, RDA, Wanju, 55365, Republic of Korea
2Planning and Coordination Division, NIHHS, RDA, Wanju, 55365, Republic of Korea
3Horticultural and Herbal Crop Environment Division, NIHHS, RDA, Wanju, 55365, Republic of Korea
4Department of Horticulture, Chonbuk National University, Jeonju, 54896, Republic of Korea
1농촌진흥청 국립원예특작과학원 채소과, 2농촌진흥청 국립원예특작과학원 기획조정과
3농촌진흥청 국립원예특작과학원 원예특작환경과, 4전북대학교 농업생명과학대학 원예학과
Correspondence to: E-mail: helee72@korea.kr, Tel: +82-63-238-6674, Fax: +82-63-238-6605
Received October 5, 2018; Revised October 9, 2018; Accepted October 30, 2018.
This is an Open-Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
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.
Keywords : Gummy stem blight, Resistance, Genetic linkage map, Melting curve, Polymorphism


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