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

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.

A New Chicken Genome Assembly Provides Insight into Avian Genome Structure

“…In one example, we found a 61-kb insertion in Gallus_gallus-4.0 compared with MHC AB268588.1, which we believe represents misplaced contigs since Gallus_gallus-5.0 and MHC AB268588.1 agree at this location. Utilizing this new MHC region of Gallus_gallus-5.0, we confirm significant SNP variability across MHC- B , supporting findings from an earlier extensive study of MHC haplotypes (Fulton et al 2016). Gallus_gallus-5.0 also contains 1.5-fold more sequence identifiable as representative of the second MHC region on GGA16, called MHC- Y .…”

“…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. Assembly of GGA16 has advanced in Gallus_gallus-5.0 and is now supporting the emerging picture that some segments of GGA16 are subject to gene copy number variation (Afanassieff et al 2001; Salomonsen et al 2014; Fulton et al 2016). However, more complete MHC and other immune system genes sequence representation are needed to further advance our knowledge of immune response.…”

Peer Review #1 of "Effective population sizes and adaptive genetic variation in a captive bird population (v0.1)"

“…Multiplex genotyping was performed on the ABI 3730 capillary analyzer at the DNA sequencing facility on Science Hill (Yale University, New Haven, CT) for fragment analysis. For SNP analyses, equimolar DNA isolates were submitted to the molecular genetics lab at Hy-Line International for genotyping using a custom SNP panel (Fulton et al, 2016b;Nguyen-Phuc, Fulton & Berres, 2016). The SNP panel was developed as an assay for the Major Histocompatibility Complex -B locus (MHC-B), based on the KASP TM chemistry (LGC group, UK) where each allele is identified by its fluorescent label (VIC or FAM).…”

Effective population sizes and adaptive genetic variation in a captive bird population

“…It is also worth noting that the genetic bottleneck and the resulting reduction in genetic diversity in only 50 years perhaps mirror the early genetic history during selection for domestication, except for periodic gene flow from wild individuals. It would appear that such immigration was necessary to maintain the high levels of genetic diversity that is found in domestic chickens today (Granevitze et al, 2007;Fulton et al, 2016) .…”