Korean Journal of Breeding Science (한국육종학회지)

The Korean Society of Breeding Science (한국육종학회)
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Construction of a Genetic Map using the SSR Markers Derived from "Wonwhang" of Pyrus pyrifolia

배 '원황'(Pyrus pyrifolia) 유전체 해독에 기반한 SSR 마커 개발 및 유전자 지도 작성

  • Lee, Ji Yun (Genomics Division, Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, RDA) ;
  • Seo, Mi-Suk (Genomics Division, Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, RDA) ;
  • Won, So Youn (Genomics Division, Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, RDA) ;
  • Lim, Kyoung Ah (Genomics Division, Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, RDA) ;
  • Shin, Il Sheob (Postharvest Research Division, National Institute of Horticultural and Herbal Science, RDA) ;
  • Choi, Dongsu (Departments of Biology, Kunsan National University) ;
  • Kim, Jung Sun (Genomics Division, Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, RDA)
  • 이지윤 (농촌진흥청 국립농업과학원 농업생명자원부 유전체과) ;
  • 서미숙 (농촌진흥청 국립농업과학원 농업생명자원부 유전체과) ;
  • 원소윤 (농촌진흥청 국립농업과학원 농업생명자원부 유전체과) ;
  • 임경아 (농촌진흥청 국립농업과학원 농업생명자원부 유전체과) ;
  • 신일섭 (농촌진흥청 국립원예특작과학원) ;
  • 최동수 (군산대학교 생물학과) ;
  • 김정선 (농촌진흥청 국립농업과학원 농업생명자원부 유전체과)
  • Received : 2018.09.12
  • Accepted : 2018.11.09
  • Published : 2018.12.01
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Abstract

High-density genetic linkage mapping is critical for undertaking marker-assisted selection and confirming quantitative trait loci, as well as helping to build pseudomolecules of genomes. We constructed a genetic map using 94 $F_1$ populations generated from the interspecific cross between Korean cultivar "Wonwhang" (Pyrus pyrifolia, NCBI BioSample SAMN05196235) and European cultivar "Bartlett" (Pyrus communis). We designed a total of 24,267 SSR markers based on the genome sequences of "Wonwhang" for this. To select the markers that are linked to the traits important in pear breeding programs, SSR-containing genomic sequences were subjected to nucleotide sequence homology searches, which resulted in 510 SSR markers with high similarity to genes encoding proteins with putative functions such as transcription factors, resistance proteins, flowering time, and regulatory genes. Of these, 70 markers showed polymorphisms in parents and segregating populations and were used to construct a genetic linkage map, together with the unpublished 579 SNPs obtained from genotyping by sequencing analysis. The genetic linkage map covered 3,784.2 cM and the average distance between adjacent markers was 5.8 cM. Seventy SSR markers were distributed across 17 chromosomes with more than one locus.

본 연구에서는 배 '원황'(Pyrus pyrifolia)의 유전체 정보를 바탕으로, 유용 유전자 관련 SSR 마커를 선발하였고, 선발된 SSR과 SNP 마커를 이용하여 '원황' ${\times}$ 'Bartlett' $F_1$ 교배집단에 대한 유전자 지도를 작성하였다. '원황'의 scaffold에서 제작된 SSR 마커 유래 염기서열들과 NCBI nucleotide DB와 BLASTn 분석하여, 유용한 유전자들과 높은 상동성을 보이는 510개 SSR 마커를 선발하였다. 이들 마커를 사용하여 양친과 F1 집단 94개체의 대립 단편의 증폭 양상을 확인한 결과, 88개 마커들이 헤테로 집단에 맞는 분리비를 보였다. 선발된 88개의 SSR 마커는 GBS 분석을 통해 획득한 579개 SNP 마커와 함께 '원황'의 유전자지도를 작성하였다. 70개의SSR 마커들은 배 염색체 수와 같은 17개의 염색체에 잘 위치하였고, 모든 염색체에 한 개 이상의 마커로 위치하였다. 유전자지도의 총 유전거리는 3784.2cM이고 마커간 평균거리는 5.8cM이었다. 본 연구에서 개발된 SSR 분자마커 및 이를 기반으로 만들어진 유전자지도는 배의 육종 및 유전 연구에 유용한 정보를 제공할 것으로 기대한다.

Keywords

Acknowledgement

Supported by : 국립농업과학원

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