Brief review of the chicken Major Histocompatibility Complex: the genes, their distribution on chromosome 16, and their contributions to disease resistance

Abstract

Nearly all genes presently mapped to chicken chromosome 16 (GGA 16) have either a demonstrated role in immune responses or are considered to serve in immunity by reason of sequence homology with immune system genes defined in other species. The genes are best described in regional units. Among these, the best known is the polymorphic major histocompatibility complex-B (MHC-B) region containing genes for classical peptide antigen presentation. Nearby MHC-B is a small region containing two CD1 genes, which encode molecules known to bind lipid antigens and which will likely be found in chickens to present lipids to specialized T cells, as occurs with CD1 molecules in other species. Another region is the MHC-Y region, separated from MHC-B by an intervening region of tandem repeats. Like MHC-B, MHC-Y is polymorphic. It contains specialized class I and class II genes and c-type lectin-like genes. Yet another region, separated from MHC-Y by the single nucleolar organizing region (NOR) in the chicken genome, contains olfactory receptor genes and scavenger receptor genes, which are also thought to contribute to immunity. The structure, distribution, linkages and patterns of polymorphism in these regions, suggest GGA 16 evolves as a microchromosome devoted to immune defense. Many GGA 16 genes are polymorphic and polygenic. At the moment most disease associations are at the haplotype level. Roles of individual MHC genes in disease resistance are documented in only a very few instances. Provided suitable experimental stocks persist, the availability of increasingly detailed maps of GGA 16 genes combined with new means for detecting genetic variability will lead to investigations defining the contributions of individual loci and more applications for immunogenetics in breeding healthy poultry.

A New Chicken Genome Assembly Provides Insight into Avian Genome Structure

“…Gallus_gallus-5.0 also contains 1.5-fold more sequence identifiable as representative of the second MHC region on GGA16, called MHC- Y . MHC- Y contains distinctive MHC-like class I genes, similar to MR1 and class II genes, along with a number of c-type lectin-like genes (Miller and Taylor 2016). Although located on GGA16, MHC- Y is separated from MHC- B by a high frequency of recombination region and, as a result, MHC- Y haplotypes assort independently of MHC- B haplotypes (Figure 3).…”

“…A variety of immunologically interesting genes have been mapped to GGA16, including genes in MHC- B , MHC- Y , SRCR , and OR (Miller and Taylor 2016). Given the highly polymorphic nature of the region (Fulton et al 2016) and the known immune function of many of the genes, accurate and complete genome assembly is important for continued studies of immunity in avian diseases.…”

Identifying the causes and consequences of assembly gaps using a multiplatform genome assembly of a bird-of-paradise

“…In particular, with the new library we were able to 417 identify 9.4 Mb of satellite DNA in the PacBio-based assemblies, while the standard Repbase avian 418 library identified only 1 Mb (Figure 3e-f, Supplementary Table S10). Relative to lycPyr6, most of 419 the satellites and unknown repeats remain unassembled in the short-read and linked-read assemblies 420 In birds, the multi-copy gene family of the major histocompatibility complex (MHC) is arranged as 442 a megabase long tandem repeat array (Miller and Taylor 2016). Since we expect it to be even more 443 difficult to correctly assemble than the aforementioned interspersed repeats (O'Connor et al 2019), 444 it represents a prime candidate region for measuring the quality of an assembly.…”

Vaccination and Host Marek's Disease-Resistance Genotype Significantly Reduce Oncogenic <b><i>Gallid alphaherpesvirus 2</i></b> Telomere Integration in Host Birds

“…The chicken major histocompatibility complex (MHC) has long been known to have a major influence on MD disease incidence [Briles et al, 1983;Bacon, 1987;Schat et al, 1994;Bacon et al, 2000;Sarson et al, 2008;Miller and Taylor, 2016]. Conveniently, blood group and DNA markers have enabled poultry breeding companies to select birds with superior MD resistance.…”