A high-density SNP panel reveals extensive diversity, frequent recombination and multiple recombination hotspots within the chicken major histocompatibility complex B region between BG2 and CD1A1.

Janet E Fulton,Olympe Chazara,Ashlee R Lund,Mark Berres,Amy M Mccarron,Anna Wolc,Marcia M Miller,Bertrand Bed’Hom,Kara N Pinegar

doi:10.1186/s12711-015-0181-x

Abstract

BackgroundThe major histocompatibility complex (MHC) is present within the genomes of all jawed vertebrates. MHC genes are especially important in regulating immune responses, but even after over 80 years of research on the MHC, much remains to be learned about how it influences adaptive and innate immune responses. In most species, the MHC is highly polymorphic and polygenic. Strong and highly reproducible associations are established for chicken MHC-B haplotypes in a number of infectious diseases. Here, we report (1) the development of a high-density SNP (single nucleotide polymorphism) panel for MHC-B typing that encompasses a 209,296 bp region in which 45 MHC-B genes are located, (2) how this panel was used to define chicken MHC-B haplotypes within a large number of lines/breeds and (3) the detection of recombinants which contributes to the observed diversity.MethodsA SNP panel was developed for the MHC-B region between the BG2 and CD1A1 genes. To construct this panel, each SNP was tested in end-point read assays on more than 7500 DNA samples obtained from inbred and commercially used egg-layer lines that carry known and novel MHC-B haplotypes. One hundred and one SNPs were selected for the panel. Additional breeds and experimentally-derived lines, including lines that carry MHC-B recombinant haplotypes, were then genotyped.ResultsMHC-B haplotypes based on SNP genotyping were consistent with the MHC-B haplotypes that were assigned previously in experimental lines that carry B2, B5, B12, B13, B15, B19, B21, and B24 haplotypes. SNP genotyping resulted in the identification of 122 MHC-B haplotypes including a number of recombinant haplotypes, which indicate that crossing-over events at multiple locations within the region lead to the production of new MHC-B haplotypes. Furthermore, evidence of gene duplication and deletion was found.ConclusionsThe chicken MHC-B region is highly polymorphic across the surveyed 209-kb region that contains 45 genes. Our results expand the number of identified haplotypes and provide insights into the contribution of recombination events to MHC-B diversity including the identification of recombination hotspots and an estimation of recombination frequency.Electronic supplementary materialThe online version of this article (doi:10.1186/s12711-015-0181-x) contains supplementary material, which is available to authorized users.

Highlights

The major histocompatibility complex (MHC) is present within the genomes of all jawed vertebrates
This is due in part to the difficulty in obtaining consistent information for multiple haplotypes with some of the primer pairs used
The remaining 90 single nucleotide polymorphism (SNP) that covered the majority of the MHC-B sequence (GenBank accession number: AB268588) between SNPs MHC0J6 (30,189 bp) and MHC178 (240,933 bp) are indicated by black bars in Fig. 1 and the first 11 SNPs that are located between MHCNew003 (9551 bp) and MHCNew0019 (27,791 bp) are indicated by red bars

Summary

Introduction

The major histocompatibility complex (MHC) is present within the genomes of all jawed vertebrates. Strong and highly reproducible associations are established for chicken MHC-B haplotypes in a number of infectious diseases. The major histocompatibility complex (MHC) is a polymorphic gene region that is conserved in all jawed vertebrates. MHC genes are divided into two large gene clusters, MHC-B and MHCY, which are located in separate haplotypes but on the same chromosome [1] Many of these genes contribute to immune responses with specific alleles at some loci that potentially play a major role in the genetic mechanisms of resistance to infectious diseases. Another study that showed that the BG1 locus had a highly significant influence on the occurrence of Marek’s disease [4] provided evidence that genes other than those involved in classical peptide antigen presentation contribute to MHC-B-linked disease resistance. To understand the genetic basis of disease resistance, more powerful methods are needed to investigate the genetic variability of the highly polymorphic genes within the chicken MHC

Methods

Results

Conclusion