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http://dx.doi.org/10.5536/KJPS.2014.41.4.305

Genome-wide Copy Number Variation in a Korean Native Chicken Breed  

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)
Publication Information
Korean Journal of Poultry Science / v.41, no.4, 2014 , pp. 305-311 More about this Journal
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.
Keywords
copy number variation; Korean native chicken; de novo sequencing;
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