Major histocompatibility complex B variability in Korean native chicken breeds

Abstract

Adaptive genetic variations have direct influences on the fitness traits of the animal. The major histocompatibility complex B ( MHC-B ) region is responsible for adaptive and innate immune responses in chickens. In native Korean chicken breeds, no information on serologically defined B haplotypes is available. We investigated the MHC-B diversity in 5 restored lines of Korean native chicken and Ogye chicken breeds using a recently described MHC-B single-nucleotide polymorphism ( SNP ) panel and the MHC-linked LEI0258 variable number of tandem repeat marker. High SNP haplotype diversity was observed in Korean native chicken breeds with an average of 9.7 MHC-B SNP haplotypes per line. The total number of haplotypes ranged from 6 to 12 per line, and population-specific haplotypes ranged from 3 to 4. A total of 41 BSNP haplotypes, including 26 novel population-specific haplotypes and 15 common haplotypes, were reported over all populations. The 15 common haplotypes included 7 novel and 8 previously reported standard haplotypes. Selection and breeding evidence supports the observation of common haplotypes between the Korean native chicken and exotic breeds. Similarly, the LEI0258 marker showed allele variation, between 193 bp and 474 bp having 5 to 8 alleles per population. Some of these alleles (193, 249, 309, and 443 bp) were shared and more frequently observed. Comparison between SNP haplotypes and LEI0258 allele sizes for the same samples showed that some LEI0258 allele sizes correspond to more than one BSNP haplotype. The use of the MHC-B SNP panel greatly enhances the identification of MHC diversity compared with the sole use of the LEI0258 marker in native chicken populations.

High Levels of Genetic Variation in MHC-Linked Microsatellite Markers from Native Chicken Breeds

“…Korean populations had consistent allele diversity, which is in agreement with our previous studies and explained the MHC diversity in Korean chicken breeds using the MHC- B SNP panel [ 30 , 49 ]. Compared to the YOG populations and Korean commercial hybrid populations, the six conserved populations had low diversity.…”

“…Nigerian local chicken samples (NIG) used in this study were collected from Umuobasi village (Osisioma Ngwa area, Abia State, Nigeria). We used 12 South Korean native chicken breeds: the six native lines used by Manjula et al [ 30 ], a Korean native black chicken population called “Ogye” sampled from Yeonsan Ogye Jisan farm in Nonsan city (YOG), four Korean native commercial hybrid lines from the Hanhyup private breeding company (CC1, CC2, CC3, and CC4), and a hybrid population from the National Institute of Animal Science (NIAS; YCC). Two imported and adapted standard breeds, Rhode Island rock (RIR) and white leghorn (WL), were sampled at NIAS.…”

Population structure analysis of Yeonsan Ogye using microsatellite markers

“…In an environment where pedigrees are not recorded, the influence of phenotypic selections can have a great influence on the gene pool, and there is a possibility that the appearance selection of a certain standard may cause inbreeding by selecting only a single ancestry group. Our recent study of Major Histocompatibility Complex B region variation showed that YO population maintain in National Institute of Animal Science (NIAS) has unique genetic variation compare to other chicken populations [15]. MHC-B linked microsatellite marker LEI0258 diversity in the present study population showed that they have 9 alleles with varied frequencies (unpublished data).…”

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

“…These selective sweeps in KNCs are presumably adaptations to rearing under non-standardized backyard conditions. Based on findings in previous studies, we presume that KNCs have stronger immune responses because they exhibit higher genetic diversity, compared with commercial chickens, in the major histocompatibility complex B region, which plays major roles in adaptive and innate immune responses [33,34].…”