Comparative genomics and selection analysis of Yeonsan Ogye black chicken with whole-genome sequencing = 전장 유전체를 이용한 연산오계의 비교 유전체 분석

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Title
Comparative genomics and selection analysis of Yeonsan Ogye black chicken with whole-genome sequencing = 전장 유전체를 이용한 연산오계의 비교 유전체 분석
Author(s)
Youngbum Cho; Jae-Yoon Kim; Namshin Kim
Bibliographic Citation
Genomics, vol. 114, no. 2, pp. 110298-110298
Publication Year
2022
Abstract
Yeonsan Ogye (OGYE; Gallus gallus domesticus) is a rare indigenous chicken breed that inhabits the Korean Peninsula. This breed has completely black coloring, including plumage, skin, eyes, beak, and internal organs. Despite these unique morphological characteristics, the population of OGYE has declined without in-depth research into their genome research. Therefore, this study aimed to compare the whole genome of OGYE to 12 other chicken populations, including ancestral breed, commercial breeds, Chinese indigenous breeds, and Korean native chickens. We focused on revealing the selection signature of OGYE, which has occurred through environmental pressures in the Korean Peninsula. Genome-wide selection analysis has identified local adaptation traits, such as egg development, that contribute to fetal viability and innate immune response to prevent viral and microbes infection in OGYE. In particular, SPP1 (Secreted Phosphoprotein 1), HSP90AA1 (Heat Shock Protein 90 Alpha Family Class A Member 1), and P2RX4 (Purinergic Receptor P2X 4) could have considerable involvement in egg development and RNASEL (Ribonuclease L), BRIP1 (BRCA1 Interacting Protein C-terminal Helicase 1), and TLR4 (Toll-Like Receptor 4) are crucial for the determination of the innate immune response. This study revealed the unique genetic diversity of OGYE at the genome-wide level. Furthermore, we emphasized the sustainable management of genetic resources and formulated breeding strategies for livestock on the Korean Peninsula.
Keyword
ChickenPopulation geneticsSelection signatureWhole-genome sequencingGenomic characteristicsYeonsan Ogye
ISSN
0888-7543
Publisher
Elsevier
DOI
http://dx.doi.org/10.1016/j.ygeno.2022.110298
Type
Article
Appears in Collections:
Division of Biomedical Research > Personalized Genomic Medicine Research Center > 1. Journal Articles
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