Journal of Korean Society of Forest Science (한국산림과학회지)

Korean Society of Forest Science (한국산림과학회)
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Identification and Characterization of Polymorphic Microsatellite Loci using Next Generation Sequencing in Quercus variabilis

차세대 염기서열 분석을 이용한 굴참나무(Quercus variabilis)의 microsatellite 마커 개발 및 특성 분석

  • Baek, Seung-Hoon (Division of Forest Genetic Resources, National Institute of Forest Science) ;
  • Lee, Jei-Wan (Division of Forest Genetic Resources, National Institute of Forest Science) ;
  • Hong, Kyung-Nak (Division of Forest Genetic Resources, National Institute of Forest Science) ;
  • Lee, Seok-Woo (Division of Forest Genetic Resources, National Institute of Forest Science) ;
  • Ahn, Ji-Young (Division of Forest Genetic Resources, National Institute of Forest Science) ;
  • Lee, Min-Woo (Division of Forest Genetic Resources, National Institute of Forest Science)
  • 백승훈 (국립산림과학원 산림유전자원과) ;
  • 이제완 (국립산림과학원 산림유전자원과) ;
  • 홍경낙 (국립산림과학원 산림유전자원과) ;
  • 이석우 (국립산림과학원 산림유전자원과) ;
  • 안지영 (국립산림과학원 산림유전자원과) ;
  • 이민우 (국립산림과학원 산림유전자원과)
  • Received : 2016.02.29
  • Accepted : 2016.04.04
  • Published : 2016.06.30
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Abstract

This study was conducted to develop microsatellite markers in Quercus variabilis using next generation sequencing. A total of 305,771 reads (384 bp on average) were generated on a Roche GS-FLX system, yielding 117 Mbp of sequences. The de novo assembly resulted in 7,346 contigs. A total of 606 contigs (20.75%) including 911 microsatellite loci were derived from the 2,921 contigs longer than 500 bp. A total of 180 primer sets were designed from the 911 microsatellite loci and screened in eight Q. variabilis individual trees sampled from a natural stand to obtain polymorphic loci. As a result, a total of thirteen polymorphic microsatellite loci were selected and used for estimating population genetic parameters in the 54 individual trees. The mean number of effective alleles was 4.996 ranging from 2.439 to 7.515. The observed heterozygosity and the expected heterozygosity ranged between 0.731 and 1.000 with an average of 0.873 and from 0.590 to 0.867 with an average of 0.766, respectively. Null alleles were not detected in all loci. No significant linkage disequilibrium was detected after Bonferroni correction in all loci. In the near future, these novel polymorphic microsatellite markers will be used to study population and conservation genetics of Q. variabilis of Korea in more detail.

본 연구는 차세대 염기서열 분석방법을 이용하여 굴참나무의 microsatellite 마커를 개발하고 특성을 분석하기 위해 수행되었다. GS-FLX Titanium 차세대 염기서열 분석 장비를 이용하여 305,771개의 read를 얻었고, 117 Mbp의 데이터를 생산하였다. De novo assembly를 통하여 7,326개의 contig를 확보하였다. 크기가 500 bp 이상이 되는 contig는 2,921개로 나타났다. 그 중 microsatellite 영역을 포함하는 contig는 606개(20.75%)로 나타났으며, 총 microsatellite의 수는 911개로 확인되었다. 그 중 13개의 microsatellite 유전자좌에서 굴참나무 개체 간 다형성이 관찰되었다. 이들 microsatellite 유전자좌에 대하여 주왕산 집단에서 관찰된 유효 대립유전자수($A_e$)는 평균 4.966(2.439~7.515)로 나타났다. 평균 이형접합도 관측치($H_o$)와 평균 이형접합도 기대치($H_e$)는 각각 0.873(0.731~1.000)과 0.766(0.590~0.867)으로 나타났다. 다형성이 관찰된 모든 microsatellite 유전자좌에서 null 대립유전자는 관찰되지 않았으며, 마커 간 연관불평형은 나타나지 않았다. 따라서 본 연구에서 개발된 13개의 microsatellite 마커는 굴참나무 집단의 유전변이 분석에 유용할 것으로 사료된다.

Keywords

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