Korean Journal of Poultry Science (한국가금학회지)

The Korean Society of Poultry Science (한국가금학회)
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Genome-wide Copy Number Variation in a Korean Native Chicken Breed

한국 토종닭의 전장 유전체 복제수변이(CNV) 발굴

  • Cho, Eun-Seok (National Institute of Animal Science, RDA) ;
  • Chung, Won-Hyong (Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology) ;
  • Choi, Jung-Woo (National Institute of Animal Science, RDA) ;
  • Jang, Hyun-Jun (College of Pharmacy, Dankook University) ;
  • Park, Mi-Na (National Institute of Animal Science, RDA) ;
  • Kim, Namshin (Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology) ;
  • Kim, Tae-Hun (National Institute of Animal Science, RDA) ;
  • Lee, Kyung-Tai (National Institute of Animal Science, RDA)
  • 조은석 (농촌진흥청 국립축산과학원) ;
  • 정원형 (한국생명공학연구원 국가생명연구자원정보센터) ;
  • 최정우 (농촌진흥청 국립축산과학원) ;
  • 장현준 (단국대학교 약학대학) ;
  • 박미나 (농촌진흥청 국립축산과학원) ;
  • 김남신 (한국생명공학연구원 국가생명연구자원정보센터) ;
  • 김태헌 (농촌진흥청 국립축산과학원) ;
  • 이경태 (농촌진흥청 국립축산과학원)
  • Received : 2014.11.04
  • Accepted : 2014.12.01
  • Published : 2014.12.31
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Abstract

Copy number variation (CNV) is a form of structural variation that shows various numbers of copies in segments of the DNA. It has been shown to account for phenotypic variations in human diseases and agricultural production traits. Currently, most of chicken breeds in the poultry industry are based on European-origin breeds that have been mostly provided from several international breeding companies. Therefore, National Institute of Animal Science, RDA has been trying to restore and improve Korean native chicken breeds (12 lines of 5 breeds) for about 20 years. Thanks to the recent advance of sequencing technologies, genome-wide CNV can be accessed in the higher resolution throughout the genome of species of interest. However, there is no systematic study available to dissect the CNV in the native chicken breed in Korea. Here, we report genome-wide copy number variations identified from a genome of Korean native chicken (Line L) by comparing between the chicken reference sequence assembly (Gallus gallus) and a de novo sequencing assembly of the Korean native chicken (Line L). Throughout all twenty eight chicken autosomes, we identified a total of 501 CNVs; defined as gain and loss of duplication and deletion respectively. Furthermore, we performed gene ontology (GO) analysis for the putative CNVs using DAVID, leading to 68 GO terms clustered independently. Of the clustered GO terms, genes related to transcription and gene regulation were mainly detected. This study provides useful genomic resource to investigate potential biological implications of CNVs with traits of interest in the Korean native chicken.

복제수변이(Copy number variation, CNV)는 DNA 다양한 구조적 변화의 한 형태이다. 복제수변이는 인간의 질병 및 농업의 생산성에 영향을 미치는 것으로 알려져 있다. 이전 우리나라의 닭의 품종은 유럽에서 유입되어진 품종을 기반으로 구축되어져 있었다. 따라서 농촌진흥청 국립축산과학원에서는 20년 동안 재래품종을 복원하려고 노력하였고, 5품종 12계통으로 복원하였다. 최근 염기서열분석 기술의 발달로, 해상도가 좋은 게놈 전체의 복제수변이를 발굴할 수 있게 되었다. 그러나 한국 재래닭 품종에 대해서는 체계적인 연구가 이루어지지 않고 있다. 본 연구에서는 한국 재래 닭(계통 L)에 대해서 게놈 전체의 염기서열을 분석하고 닭의 참고서열과 비교하여 재래닭에서 확인된 복제수 변이를 보고하였다. 닭의 28개 염색체에서 총 501개의 복제수 변이를 확인하였고, 이를 Gain과 Loss로 나누어서 표시하였다. 또한 우리는 501개의 복제수 변이를 포함하고 있는 유전자의 기능을 분류하였다. 그 결과, 전사 및 유전자 조절에 관련된 유전자들이 많이 분류되었다. 본 연구의 결과는 복제수 변이와 한국 재래닭의 경제형질 간의 연관성을 설명할 수 있는 기초자료로 활용될 것으로 사료된다.

Keywords

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