Journal of Plant Biotechnology

  • 제44권4호
  • /
  • Pages.372-378
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  • 2017
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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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RNA-Seq data를 이용한 사과 과육색 판별 SNP 분자표지 개발

Development of SNP markers for the identification of apple flesh color based on RNA-Seq data

  • 김세희 (농촌진흥청 국립원예특작과학원 과수과) ;
  • 박서준 (농촌진흥청 국립원예특작과학원 과수과) ;
  • 조강희 (농촌진흥청 국립원예특작과학원 과수과) ;
  • 이한찬 (농촌진흥청 국립원예특작과학원 과수과) ;
  • 이정우 (농촌진흥청 국립원예특작과학원 인삼과) ;
  • 최인명 (농촌진흥청 국립원예특작과학원 과수과)
  • Kim, Se Hee (Fruit Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration) ;
  • Park, Seo Jun (Fruit Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration) ;
  • Cho, Kang Hee (Fruit Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration) ;
  • Lee, Han Chan (Fruit Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration) ;
  • Lee, Jung Woo (Ginseng Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration) ;
  • Choi, In Myung (Fruit Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration)
  • 투고 : 2017.10.21
  • 심사 : 2017.11.01
  • 발행 : 2017.12.31
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초록

과육색이 다르게 발현되는 사과(Malus domestica L.) 품종의 유전자 발현을 비교하기 위해 2개의 cDNA library를 제작하였다. 붉은 색 과육 품종인 'Redfield'와 백색 과육 품종인 'Granny Smith'의 유전자 발현 차이를 보기 위해 차세대 염기서열 분석(NGS) 기술을 사용하였고 두 품종으로부터 얻은 EST의 염기서열을 결정하고 기존에 보고된 유전자와의 상동성을 분석하였다. HRM 기술은 붉은 색 과육 품종 사과와 백색 과육 품종 사과의 짧은 PCR 증폭산물에서 한 개의 서로 다른 염기서열을 구분하여 분리해낼 수 있다. 'Redfield'와 'Granny Smith'의 EST database로부터 103쌍의 단일염기다형성(SNP) 분자표지를 선발하였고, 붉은 색 과육 품종 10개와 백색 과육 품종 11개를 구분할 수 있는 SNP 분자표지를 HRM 방법으로 분석하였다. 본 연구에서는 사과 EST database를 기반으로 HRM 분석 방법을 이용하여 사과 품종의 적육계와 백육계를 구분할 수 있는 효율적인 SNP 분자표지를 개발하였다. 이러한 SNP 분자표지는 사과육종에 유용하게 사용할 수 있으며 사과 품종의 다양한 색 변화에 관한 분자 기작 연구에 좋은 참고자료가 될 수 있을 것이다.

For comparison of the transcription profiles in apple (Malus domestica L.) cultivars differing in flesh color expression, two cDNA libraries were constructed. Differences in gene expression between red flesh apple cultivar, 'Redfield' and white flesh apple cultivar, 'Granny Smith' were investigated by next-generation sequencing (NGS). Expressed sequence tag (EST) of clones from the red flesh apple cultivar and white flesh apple cultivar were selected for nucleotide sequence determination and homology searches. High resolution melting (HRM) technique measures temperature induced strand separation of short PCR amplicons, and is able to detect variation as small as one base difference between red flesh apple cultivars and white flesh apple cultivars. We applied high resolution melting (HRM) analysis to discover single nucleotide polymorphisms (SNP) based on the predicted SNP information derived from the apple EST database. All 103 pairs of SNPs were discriminated, and the HRM profiles of amplicons were established. Putative SNPs were screened from the apple EST contigs by HRM analysis displayed specific difference between 10 red flesh apple cultivars and 11 white flesh apple cultivars. In this study, we report an efficient method to develop SNP markers from an EST database with HRM analysis in apple. These SNP markers could be useful for apple marker assisted breeding and provide a good reference for relevant research on molecular mechanisms of color variation in apple cultivars.

키워드

참고문헌

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