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

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

doi:10.3389/fgene.2021.710770

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.

Highlights

China has the most abundant resources of domestic chickens, which possess highly genetic polymorphisms
Chicken major histocompatibility complex (MHC)-B and MHC-Y regions reside on the micro-chromosome 16, which are located on the same side of nucleolar organizing region (NOR) (Miller and Taylor, 2016)
We comprehensively evaluated the polymorphisms of BF/BL region among 16 Chinese domestic populations, as well as White Leghorns (WLs), Cornish (CS), Red Jungle Fowl (RJF), and two high inbred lines (Waters, 1945; Stone, 1975; Bacon et al, 2000) using the WaferGen platform, which is a more costeffective method for identifying variations in targeted regions (De Wilde et al, 2014)

Summary

Introduction

China has the most abundant resources of domestic chickens, which possess highly genetic polymorphisms. As a highly polymorphic region across the genome, major histocompatibility complex (MHC) is a group of tightly linked genes, encoding major histocompatibility antigens, which discriminate between self and non-self cells and regulate immune responses. Chicken MHC-B and MHC-Y regions reside on the micro-chromosome 16, which are located on the same side of nucleolar organizing region (NOR) (Miller and Taylor, 2016). 46 genes within a 2,41,833 bp in MHC-B were identified (Shiina et al, 2007), including three highly polymorphic gene groups: BF, BL, and BG, which encode class I, class II, and class IV glycoproteins on cell surface, respectively (Lamont et al, 1987). The encoded proteins play important roles in rapid allograft rejection, immune response and determining susceptibility/resistance to pathogen infections (Pazderka et al, 1975; Plachy et al, 1992; Kaufman, 2018)

Methods

Results

Discussion

Conclusion