Journal of Plant Biotechnology

  • 제45권3호
  • /
  • Pages.242-249
  • /
  • 2018
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  • 1229-2818(pISSN)
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  • 2384-1397(eISSN)
한국식물생명공학회 (The Korean Society of Plant Biotechnology)
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수박 엘리트 계통의 GBS를 통한 마커이용 육종용 SNP 마커 개발

Development of an SNP set for marker-assisted breeding based on the genotyping-by-sequencing of elite inbred lines in watermelon

  • 이준우 (부산대학교 생명자원과학대학 원예생명과학과) ;
  • 손병구 (부산대학교 생명자원과학대학 원예생명과학과) ;
  • 최영환 (부산대학교 생명자원과학대학 원예생명과학과) ;
  • 강점순 (부산대학교 생명자원과학대학 원예생명과학과) ;
  • 이용재 (부산대학교 생명자원과학대학 원예생명과학과) ;
  • 제병일 (부산대학교 생명자원과학대학 원예생명과학과) ;
  • 박영훈 (부산대학교 생명자원과학대학 원예생명과학과)
  • Lee, Junewoo (Department of Horticultural Bioscience, Pusan National University (PNU)) ;
  • Son, Beunggu (Department of Horticultural Bioscience, Pusan National University (PNU)) ;
  • Choi, Youngwhan (Department of Horticultural Bioscience, Pusan National University (PNU)) ;
  • Kang, Jumsoon (Department of Horticultural Bioscience, Pusan National University (PNU)) ;
  • Lee, Youngjae (Department of Horticultural Bioscience, Pusan National University (PNU)) ;
  • Je, Byoung Il (Department of Horticultural Bioscience, Pusan National University (PNU)) ;
  • Park, Younghoon (Department of Horticultural Bioscience, Pusan National University (PNU))
  • 투고 : 2018.08.17
  • 심사 : 2018.08.17
  • 발행 : 2018.09.30
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초록

본 연구는 국내 육종 회사에서 개발된 수박(Citrullus lanatus L.) 우량 육성계통 20종을 대상으로 Genotyping-by-sequencing(GBS) 분석을 통해 품종식별, 순도검정, 그리고 마커이용여교잡(Marker-assisted backcross, MABC)용 SNP 세트를 개발하고자 수행되었다. GBS 분석 결과 총 1,100,000천개 raw read 중 77%가 수박 유전체에 mapping되었으며 평균 mapping region은 약 4,000 Kb로 2.3%의 genome coverage를 보였다. Filtering을 통해 평균 depth 31.57의 SNP 총 2,670개를 얻었으며, 20개 계통에 대한 이들의 Polymorphic information content(PIC) 값의 범위는 0.1 ~ 0.38 였다. 이 중 PIC 값이0.3이상이며 각 염색체 별로 5개씩 균등히 분포된 SNP 총 55개를 최종 선발하였다. 사용된 20개 계통의 유연관계분석을 위해 선발된 55개 SNP를 기반으로 한 주성분 분석(Principle component analysis, PCA) 결과 주성분 1 (52%)과 주성분 2 (11%)를 기준으로 4개의 그룹으로 분류 되었으며 각 계통 간 유전자형에 따른 뚜렷한 식별이 가능하였다. 계층적 군집화(Hierarchical clustering) 분석에서도PCA에서와 유사한 분류양상을 관찰할 수 있었다. 따라서 본 연구에서 개발된 SNP 세트는 적용 가능성이 검증된 20개 계통뿐 만 아니라 향후 다양한 수박 육종소재 및 품종에 대한 품종식별, F1 순도검정 및 MABC에 활용될 수 있으리라 기대된다.

This study was conducted to develop an SNP set that can be useful for marker-assisted breeding (MAB) in watermelon (Citrullus. lanatus L) using Genotyping-by-sequencing (GBS) analysis of 20 commercial elite watermelon inbreds. The result of GBS showed that 77% of approximately 1.1 billion raw reads were mapped on the watermelon genome with an average mapping region of about 4,000 Kb, which indicated genome coverage of 2.3%. After the filtering process, a total of 2,670 SNPs with an average depth of 31.57 and the PIC (Polymorphic Information Content) value of 0.1~0.38 for 20 elite inbreds were obtained. Among those SNPs, 55 SNPs (5 SNPs per chromosome that are equally distributed on each chromosome) were selected. For the understanding genetic relationship of 20 elite inbreds, PCA (Principal Component Analysis) was carried out with 55 SNPs, which resulted in the classification of inbreds into 4 groups based on PC1 (52%) and PC2 (11%), thus causing differentiation between the inbreds. A similar classification pattern for PCA was observed from hierarchical clustering analysis. The SNP set developed in this study has the potential for application to cultivar identification, F1 seed purity test, and marker-assisted backcross (MABC) not only for 20 elite inbreds but also for diverse resources for watermelon breeding.

키워드

참고문헌

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