Korean Journal of Breeding Science (한국육종학회지)

The Korean Society of Breeding Science (한국육종학회)
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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

  • 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)
  • 이은수 (농촌진흥청 국립원예특작과학원 채소과) ;
  • 김진희 (농촌진흥청 국립원예특작과학원 채소과) ;
  • 홍종필 (농촌진흥청 국립원예특작과학원 채소과) ;
  • 김도선 (농촌진흥청 국립원예특작과학원 채소과) ;
  • 김민경 (농촌진흥청 국립원예특작과학원 채소과) ;
  • 허윤찬 (농촌진흥청 국립원예특작과학원 기획조정과) ;
  • 백창기 (농촌진흥청 국립원예특작과학원 원예특작환경과) ;
  • 이준대 (전북대학교 농업생명과학대학 원예학과) ;
  • 이혜은 (농촌진흥청 국립원예특작과학원 채소과)
  • Received : 2018.10.05
  • Accepted : 2018.10.30
  • Published : 2018.12.01
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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.

수박(Citrullus lanatus)은 전세계에서 경제적으로 중요한 채소작물이며, 라이코펜과 시트룰린과 같은 기능성 물질을 함유하고 있다. Didymella bryoniae 병원균에 의해 발생하는 덩굴마름병은 수박 재배에서 가장 피해를 많이 주는 병해 중에 하나이다. 단일염기다형성(SNP)은 한 개 염기에 관해 개체 간에 발생하는 유전적 변이로서 유전자 연관 지도를 작성하는 것과 원예적 형질 및 병저항성에 연관된 분자표지를 개발하는 데 자주 사용된다. 본 연구에서는 수박에서 모친과 부친의 차세대 염기서열 재분석(next generation resequencing)을 통해 SNP 분자표지를 선발하였다. 식물재료는 C. lanatus '920533'(모친, 감수성)과 C. amarus 'PI 189225'(부친, 저항성) 및 이들의 $F_1$, $F_2$ 개체를 이용하였다. NGS 분석 결과, '920533'과 'PI 189225'에서 각각 13.6 Gbp와 13.1 Gbp의 염기서열을 얻었다. '920533'과 'PI 189225' 간의 SNP 수는 609만 개였고, 그 중 HRM 프라이머로 디자인이 가능한 SNP의 수는 354,860개였다. 그 중에 HRM 분석을 위한 330개 프라이머 쌍이 디자인되었다. 결과적으로 HRM 분석을 통해 총 61개의 HRM 분자표지를 개발하였다. 이번 연구의 결과는 SNP 기반의 유전자지도 작성에 이용될 수 있으며 덩굴마름병 저항성과 연관된 양적 형질 유전자좌(QTL) 분석에 활용될 수 있을 것이다.

Keywords

Acknowledgement

Supported by : 농촌진흥청

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