Genetic Diversity of MHC B-F/B-L Region in 21 Chicken Populations

Yiming Yuan; Huanmin Zhang; Guoqiang Yi; Zhen You; Chunfang Zhao; Haixu Yuan; Kejun Wang; Junying Li; Ning Yang; Ling Lian

doi:10.3389/fgene.2021.710770

Genetic Diversity of MHC B-F/B-L Region in 21 Chicken Populations

Front Genet. 2021 Aug 13:12:710770. doi: 10.3389/fgene.2021.710770. eCollection 2021.

Authors

Yiming Yuan¹, Huanmin Zhang², Guoqiang Yi³, Zhen You¹, Chunfang Zhao¹, Haixu Yuan¹, Kejun Wang⁴, Junying Li¹, Ning Yang¹, Ling Lian¹

Affiliations

¹ National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China.
² United States Department of Agriculture, Agricultural Research Service, Avian Disease and Oncology Laboratory, East Lansing, MI, United States.
³ Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
⁴ College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China.

Abstract

The chicken major histocompatibility complex (MHC) on chromosome 16 is the most polymorphic region across the whole genome, and also an ideal model for genetic diversity investigation. The MHC B-F/B-L region is 92 kb in length with high GC content consisting of 18 genes and one pseudogene (Blec4), which plays important roles in immune response. To evaluate polymorphism of the Chinese indigenous chickens as well as to analyze the effect of selection to genetic diversity, we used WaferGen platform to identify sequence variants of the B-F/B-L region in 21 chicken populations, including the Red Jungle Fowl (RJF), Cornish (CS), White Leghorns (WLs), 16 Chinese domestic breeds, and two well-known inbred lines 6₃ and 7₂. A total of 3,319 single nucleotide polymorphism (SNPs) and 181 INDELs in the B-F/B-L region were identified among 21 populations, of which 2,057 SNPs (62%) and 159 INDELs (88%) were novel. Most of the variants were within the intron and the flanking regions. The average variation density was 36 SNPs and 2 INDELs per kb, indicating dramatical high diversity of this region. Furthermore, BF2 was identified as the hypervariable genes with 67 SNPs per kb. Chinese domestic populations showed higher diversity than the WLs and CS. The indigenous breeds, Nandan Yao (NY), Xishuangbanna Game (XG), Gushi (GS), and Xiayan (XY) chickens, were the top four with the highest density of SNPs and INDELs. The highly inbred lines 6₃ and 7₂ have the lowest diversity, which might be resulted from a long-term intense selection for decades. Collectively, we refined the genetic map of chicken MHC B-F/B-L region, and illustrated genetic diversity of 21 chicken populations. Abundant genetic variants were identified, which not only strikingly expanded the current Ensembl SNP database, but also provided comprehensive data for researchers to further investigate association between variants in MHC and immune traits.

Keywords: B-F/B-L region; MHC; chicken; genetic diversity; target enrichment sequencing.