Genetic diversity of MHC-B in 12 chicken populations in Korea revealed by single-nucleotide polymorphisms
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ORIGINAL ARTICLE
Genetic diversity of MHC-B in 12 chicken populations in Korea revealed by single-nucleotide polymorphisms Prabuddha Manjula 1 & Bertrand Bed’Hom 2,3 & Md Rashedul Hoque 4 & Sunghyun Cho 1 & Dongwon Seo 1 & Olympe Chazara 2,5 & Seung Hwan Lee 1 & Jun Heon Lee 1 Received: 19 May 2020 / Accepted: 17 August 2020 # Springer-Verlag GmbH Germany, part of Springer Nature 2020
Abstract This study used a single-nucleotide polymorphism (SNP) panel to characterise the diversity in the major histocompatibility complex B region (MHC-B) in 12 chicken populations in Korea. Samples were genotyped for 96 MHC-B SNPs using an Illumina GoldenGate genotyping assay. The MHC-B SNP haplotypes were predicted using 58 informative SNPs and a coalescence-based Bayesian algorithm implemented by the PHASE program and a manual curation process. In total, 117 haplotypes, including 24 shared and 93 unique haplotypes, were identified. The unique haplotype numbers ranged from 0 in Rhode Island Red to 32 in the Korean native commercial chicken population 2 (“Hanhyup-3ho”). Population and haplotype principal component analysis (PCA) indicated no clear population structure based on the MHC haplotypes. Three haplotype clusters (A, B, C) segregated in these populations highlighted the relationship between the haplotypes in each cluster. The sequences from two clusters (B and C) overlapped, whereas the sequences from the third cluster (A) were very different. Overall, native breeds had high genetic diversity in the MHC-B region compared with the commercial breeds. This highlights their immune capabilities and genetic potential for resistance to many different pathogens. Keywords MHC-B . Haplotype . SNP . Chicken
Introduction Characterising the genetic profiles of indigenous chicken breeds is an important strategy for long-term preservation Electronic supplementary material The online version of this article (https://doi.org/10.1007/s00251-020-01176-4) contains supplementary material, which is available to authorized users. * Jun Heon Lee [email protected] 1
Division of Animal and Dairy Science, College of Agriculture and Life Sciences, Chungnam National University, Daejeon 34134, Republic of Korea
2
GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
3
Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d’Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 75005 Paris, France
4
Genet Bio Inc., Daejeon 34025, Republic of Korea
5
Department of Pathology and Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
because they are locally adapted and thrive under different environmental conditions (Hartmann 1997; Bettridge et al. 2018). Natural selection pressure imposed by environmental change, climate change and pathogen load might be the driving forces of extensive adaptive genetic variation in local chicken and wild populations (Nguyen-Phuc et al. 2016; Bettridge et al. 2018). In addition, they may be genetically resistant to some dise
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