Comparison of Selection Signatures between Korean Native and Commercial Chickens Using 600K SNP Array Data

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.

Keywords: Korean native chicken; quantitative trait locus; signature of selection.

Figure 1

Principal component analysis results for commercial (broilers and layers) chicken breeds (Ab, Arbor Acre broiler; CB, Cobb broiler; RS, Ross broiler; HL, Hy-line Brown layer; and LO, Lohmann Brown layer) and five Korean native chicken (KNC) lines (NG, grey–brown; NL, black; NR, red–brown; NW, white; and NY, yellow–brown). (A) Plot with principal component (PC) 1 and PC2. (B) Plot with PC1 and PC3. (C) Plot with PC1 and PC4.

Figure 2

Phylogenetic tree including commercial (broilers and layers) chicken breeds (Ab, Arbor Acre broiler; CB, Cobb broiler; RS, Ross broiler; HL, Hy-line Brown layer; and LO, Lohmann Brown layer) and five KNC lines (NG, grey–brown; NL, black; NR, red–brown; NW, white; and NY, yellow–brown).

Figure 3

Results of admixture analysis of commercial (broilers and layers) chicken breeds (Ab, Arbor Acre broiler; CB, Cobb broiler; RS, Ross broiler; HL, Hy-line Brown layer; and LO, Lohmann Brown layer) and five KNC lines (NG, grey–brown; NL, black; NR, red–brown; NW, white; and NY, yellow–brown).

Figure 4

Results of comparative selection signal analysis between commercial chickens (broilers and layers) and KNCs based on the extended haplotype homozygosity ratio between populations (Rsb) and the integrated haplotype homozygosity score (iHS). (A) Regions in the KNC population exhibiting selection signals based on the iHS. (B) Pairwise Rsb indicating selection signals in the KNC population vs. the broiler population. (C) Pairwise Rsb indicating selection signals in the KNC population vs. the layer population. Black lines indicate threshold at p < 0.01.

Figure 5

Heatmap of linkage disequilibrium blocks including the myocyte-specific enhancer-binding factor 2D (MEF2D) gene (Chr 25: 1,557,867–1,620,174 bp) in broilers and five KNC lines.

Figure 6

Selective sweep regions shared between commercial chickens and KNCs. (A) Commercial broilers and the KNC NW line. (B) Commercial layers and the KNC NL line. Black lines indicate shared selective sweep regions.