title: Uncovering genomic features and maternal origin of korean native chicken by whole genome sequencing.
abstract: The Korean Native Chicken (KNC) is an important endemic biological resource in Korea. While numerous studies have been conducted exploring this breed, none have used next-generation sequencing to identify its specific genomic features. We sequenced five strains of KNC and identified 10.9 million SNVs and 1.3 million InDels. Through the analysis, we found that the highly variable region common to all 5 strains had genes like PCHD15, CISD1, PIK3C2A, and NUCB2 that might be related to the phenotypic traits of the chicken such as auditory sense, growth rate and egg traits. In addition, we assembled unaligned reads that could not be mapped to the reference genome. By assembling the unaligned reads, we were able to present genomic sequences characteristic to the KNC. Based on this, we also identified genes related to the olfactory receptors and antigen that are common to all 5 strains. Finally, through the reconstructed mitochondrial genome sequences, we performed phylogenomic analysis and elucidated the maternal origin of the artificially restored KNC. Our results revealed that the KNC has multiple maternal origins which are in agreement with Korea's history of chicken breed imports. The results presented here provide a valuable basis for future research on genomic features of KNC and further understanding of KNC's origin.
authors.affiliation: C & K genomics, Seoul, Republic of Korea; Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea.
authors.forename: Woori
authors.initials: W
authors.lastname: Kwak
authors.affiliation: Genomic Informatics Center, Hankyong National University, Anseong, Republic of Korea.
authors.forename: Ki-Duk
authors.initials: KD
authors.lastname: Song
authors.affiliation: Genomic Informatics Center, Hankyong National University, Anseong, Republic of Korea.
authors.forename: Jae-Don
authors.initials: JD
authors.lastname: Oh
authors.affiliation: Poultry Science Division, National Institute of Animal Science, Cheonan, Republic of Korea.
authors.forename: Kang-Nyeong
authors.initials: KN
authors.lastname: Heo
authors.affiliation: Department of Animal Science and Biotechnology, Chungnam National University, Daejeon, Republic of Korea.
authors.forename: Jun-Heon
authors.initials: JH
authors.lastname: Lee
authors.affiliation: Inha Research Institute for Medical Sciences, Inha University School of Medicine, Inchon, Republic of Korea.
authors.forename: Woon Kyu
authors.initials: WK
authors.lastname: Lee
authors.affiliation: Department of Agricultural Biotechnology and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea.
authors.forename: Sook Hee
authors.initials: SH
authors.lastname: Yoon
authors.affiliation: Department of Agricultural Biotechnology and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea.
authors.forename: Heebal
authors.initials: H
authors.lastname: Kim
authors.affiliation: C & K genomics, Seoul, Republic of Korea.
authors.forename: Seoae
authors.initials: S
authors.lastname: Cho
authors.affiliation: Genomic Informatics Center, Hankyong National University, Anseong, Republic of Korea.
authors.forename: Hak-Kyo
authors.initials: HK
authors.lastname: Lee
mesh_terms: D000818:Animals; D001483:Base Sequence / Q000235:genetics*; D001947:Breeding; D002645:Chickens / Q000235:genetics*; D016678:Genome; D054643:INDEL Mutation / Q000235:genetics; D058977:Molecular Sequence Annotation; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D056910:Republic of Korea; D017422:Sequence Analysis, DNA