Abstract
Korean native chickens (KNCs) comprise an indigenous chicken breed of South Korea that was restored through a government project in the 1990s. The KNC population has not been developed well and has mostly been used to maintain purebred populations in the government research institution. We investigated the genetic features of the KNC population in a selection signal study for the efficient improvement of this breed. We used 600K single nucleotide polymorphism data sampled from 191 KNCs (NG, 38; NL, 29; NR, 52; NW, 39; and NY, 33) and 54 commercial chickens (Hy-line Brown, 10; Lohmann Brown, 10; Arbor Acres, 10; Cobb, 12; and Ross, 12). Haplotype phasing was performed using EAGLE software as the initial step for the primary data analysis. Pre-processed data were analyzed to detect selection signals using the ‘rehh’ package in R software. A few common signatures of selection were identified in KNCs. Most quantitative trait locus regions identified as candidate regions were associated with traits related to reproductive organs, eggshell characteristics, immunity, and organ development. Block patterns with high linkage disequilibrium values were observed for LPP, IGF11, LMNB2, ERBB4, GABRB2, NTM, APOO, PLOA1, CNTN1, NTSR1, DEF3, CELF1, and MEF2D genes, among regions with confirmed selection signals. NL and NW lines contained a considerable number of selective sweep regions related to broilers and layers, respectively. We recommend focusing on improving the egg and meat traits of KNC NL and NW lines, respectively, while improving multiple traits for the other lines.
Highlights
Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affiliations
The Korean native chickens (KNCs) lines and commercial chicken breeds could be distinguished based on PC1, which had the greatest explanatory power
There are many differences between KNCs and commercial chicken breeds, the greatest difference is related to artificial selection
Summary
Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affiliations. The study of selection signals can be used to identify a genomic region fixed within a population undergoing selection, or to search for genes or genomic regions associated with a specific trait through comparative analysis. The analysis of selection signals is free from some limitations associated with other methods It is considered an appropriate analytical method for fixed unknown traits or gene-tracking studies in populations without quantitative phenotype information. The Korean native chicken (KNC) nearly became extinct because of the Korean War and industrialization, but in 1992, five pure lines were restored through a restoration project implemented by the government These lines are categorized as follows, according to the colors of their feathers: red–brown (NR), yellow–brown (NY), grey–brown (NG), black (NL), and white (NW). This study was performed to identify genetic similarities and differences among the lines by comparing selection signatures of broiler and layer populations with the five KNC lines
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
