Estimation of linkage disequilibrium and analysis of genetic diversity in Korean chicken lines

Abstract

The development of genetic markers for animal breeding is an effective strategy to reduce the time and cost required to improve economically important traits. To implement genomic selection in the multibreed chicken population of Korea, an understanding of the linkage disequilibrium (LD) status of the target population is essential. In this study, we performed population genetic analyses to investigate LD decay, the effective population size, and breed diversity using 600K high-density single nucleotide polymorphism genotypes of 189 native chickens in 14 lines (including Korean native chicken, imported and adapted purebred and commercial chickens). The results indicated that commercial native chickens have less calculated LD (average, r2 = 0.13–0.26) and purebred native chickens have more calculated LD (average, r2 = 0.24–0.37) across the entire genome. The effective population sizes of the examined lines showed patterns opposite to those of population LD. The phylogeny and admixture analyses showed that commercial and purebred chickens were well distinguished, except for Rhode Island Red (RIR) purebred lines of NC (NIAS_RIR_C) and ND (NIAS_RIR_D). These lines are difficult to distinguish clearly because they originated from the same respective breeds. The results of this study may provide important information for the development of genetic markers that can be used in breeding to improve the economic traits of native chickens.

Major histocompatibility complex B variability in Korean native chicken breeds

“…Several studies, using DNA fingerprinting, polymorphic microsatellite markers, and 600k SNP chip data, found evidence of such genetic introgressions into the KNC since 1960. Based on the previous results, KNC lines are closely related to Cornish, New Hampshire, and RIR breeds and genetically more distant from the white Leghorn breed ( Lee et al., 1996a , b ; Kong et al., 2006 ; Oh et al., 2008 ; Suh et al., 2014 ; Seo et al., 2017 ; Seo et al., 2018 ). Seo et al.…”

“…Sharing of the novel BSNP haplotypes across the KNC lines is in agreement with previous studies that found KNC lines have a close genetic relationship by sharing common ancestors at the origin ( Seo et al., 2013 ; Shu et al., 2014 ; Choi et al., 2015 ). In the early backyard breeding system, the KNC lines may have interbred despite being separated based on the feather color and body conformation traits ( Seo et al., 2013 , 2018 ).…”

“…To improve these remaining KNC and to supply the rising demand for quality native chicken meat, a nationwide native chicken breed restoration and establishment project was developed from 1992 to 2007, mainly by the National Institute of Animal Science ( NIAS ) in South Korea. Fifteen years later, 5 distinct KNC lines with distinctive feather color (white [ KNCW ], black [ KNCL ], gray–brown [ KNCG ], red–brown [ KNCR ], and yellow–brown [ KNCY ]) were established ( Kwak et al., 2014 ; Seo et al., 2018 ). Previous genetic analyses using microsatellite markers have shown that these lines are genetically distinct ( Suh et al., 2014 ).…”

“…Currently, these breeds have been maintained as separate stocks by the NIAS and a private breeding company. More detailed descriptions of these breeds can be found in the study by Seo et al. (2018) .…”

On the Extent of Linkage Disequilibrium in the Genome of Farm Animals

“…In comparison, Indicine breeds have a lower LD than Taurine, suggestive of a larger ancestral population (e.g., Porto-Neto et al, 2014). The involvement of human in shaping genetic makeup of livestock is also evident in domestic chickens, where local breeds mostly exhibit shorter extent of LD (Khanyile et al, 2015) and among the commercials, the broilers presents faster decay of LD than layer populations (Pengelly et al, 2016;Seo et al, 2018 andHérault et al, 2018). This is attributed to a more intensive selection scheme running over many generations during past several decades in layers resulting in a lower population haplotype diversity and a smaller Ne.…”