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.

Genome-wide mapping of signatures of selection using a high-density array identified candidate genes for growth traits and local adaptation in chickens

“…These local breeds have been mainly raised as backyard chickens and are, thus, more resistant to diseases and viruses than commercial chickens, for which selective breeding has reduced resistance to infectious diseases [ 34 ]. In fact, to adapt to these backyard conditions, selective sweeps might have occurred in genomic regions that are related to immune responses and disease sensitivity [ 35 ]. Effects of the geographical area of origin on genomic regions that have been subjected to selection have also been reported in local Italian goats [ 36 ] and sheep [ 37 ].…”

“…Numerous genomic studies of local chicken populations worldwide have allowed the identification of signatures of selection in local breeds, using methods based either on an excess of haplotype homozygosity or deformation of the allele frequency spectrum e.g., [ 8 , 9 , 11 , 35 , 41 ]. One observation that has emerged from this study is that, in most cases, the signatures of selection detected in local chicken breeds do not overlap across studies and even between lines from the same geographical location within the same study e.g., [ 35 ]. This is mainly explained by the fact that, following their expansion through human migrations, founder populations of present-day local chicken breeds have experienced drastic bottlenecks [ 47 ].…”

Genomics of Dwarfism in Italian Local Chicken Breeds

“…The most interesting gene related to the development of tissues in this region is double PHD fingers 3 ( DPF3 ), which has a role in heart development. The DPF3 gene is specifically expressed during heart development in mice, chickens, and zebrafish, and the knockdown of DPF3 in zebrafish resulted in myocardial contractility and incomplete heart formation; thus, DPF3 was categorized as a major gene for heart development, but it is also involved in skeletal muscle [ 68 , 75 ]. Another important gene related to dwarfism and growth is IGF1R , which was annotated with upstream genetic variation in the MM and MUG analyses.…”

Recent Progress of the Poultry Genome Research Based on the Experience in CNU, Korea

“…Advances in Biological Sciences Research, volume 19600K SNP chip data, determined the haplotypes, and directed the selection signals. The conclusion of the study suggested improving the traits related to egg and meat production in NL (KNC black line) and NW (KNC white line) lines respectively and multiple traits in other lines[13].…”