MHC variability in heritage breeds of chickens

Abstract

The chicken Major Histocompatibility Complex (MHC) is very strongly associated with disease resistance and thus is a very important region of the chicken genome. Historically, MHC (B locus) has been identified by the use of serology with haplotype specific alloantisera. These antisera can be difficult to produce and frequently cross-react with multiple haplotypes and hence their application is generally limited to inbred and MHC-defined lines. As a consequence, very little information about MHC variability in heritage chicken breeds is available. DNA-based methods are now available for examining MHC variability in these previously uncharacterized populations. A high density SNP panel consisting of 101 SNP that span a 230,000 bp region of the chicken MHC was used to examine MHC variability in 17 heritage populations of chickens from five universities from Canada and the United States. The breeds included 6 heritage broiler lines, 3 Barred Plymouth Rock, 2 New Hampshire and one each of Rhode Island Red, Light Sussex, White Leghorn, Dark Brown Leghorn, and 2 synthetic lines. These heritage breeds contained from one to 11 haplotypes per line. A total of 52 unique MHC haplotypes were found with only 10 of them identical to serologically defined haplotypes. Furthermore, nine MHC recombinants with their respective parental haplotypes were identified. This survey confirms the value of these non-commercially utilized lines in maintaining genetic diversity. The identification of multiple MHC haplotypes and novel MHC recombinants indicates that diversity is being generated and maintained within these heritage populations.

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

“…Close examination of the populations of heritage and commercial breeds in which MHC haplotypes were segregating revealed BSNP patterns that were consistent with recombination [ 70 ]. We found evidence for an additional 33 novel recombinant haplotypes, BSNP-Rec12 to BSNP-Rec44 (see Additional file 3 : Table S3).…”

“…Complete genotyping and LEI0258 typing information was obtained for over 5000 samples. An additional 1351 samples were obtained from 17 heritage chicken lines that are maintained at various universities in Canada and the USA [ 70 ]. DNA from the same RJF Line 256 individual used as the reference for the chicken genome sequence project (provided by H. Cheng, USDA) was also tested with this SNP panel.…”

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

“…The haplotype diversity and linkage patterns we observed in our captive population appear to be consistent with what might occur early during domestication, if a small number of individuals are selected. The high genetic diversity found in domestic chicken breeds and wild junglefowl populations, and also at the MHC-linked SNP loci (Fulton et al, 2016a(Fulton et al, , 2017Nguyen-Phuc, Fulton & Berres, 2016) would suggest that domestication of chicken would have included frequent immigration over several tens of generations. One glimpse at this is found in the estimates of Tajima's D from Wild Junglefowl (Nguyen-Phuc, Fulton & Berres, 2016) versus the captive junglefowl population (this study).…”

Genetic structure in Red Junglefowl (Gallus gallus) populations: Strong spatial patterns in the wild ancestors of domestic chickens in a core distribution range

“…Although genetic contributions from multiple Junglefowl species may have played a role in the domestication process (Eriksson et al., 2008; Nishibori, Shimogiri, Hayashi, & Yasue, 2005), archeological and genetic evidence (Fumihito et al., 1994, 1996; Gongora et al., 2008; Storey et al., 2012; Thomson et al., 2014) indicate that Red Junglefowl from Southeast Asia was the primary progenitor of all domestic breeds of modern chickens. In a previous study, we identified substantial haplotype variation in the major histocompatibility complex (MHC) B‐locus of wild Red Junglefowl (Fulton et al., 2016; Nguyen‐Phuc, Fulton, & Berres, 2016). Curiously, none of the Red Junglefowl haplotypes were found in a large sample of commercial and heritage chicken breeds (Fulton et al., 2016; Nguyen‐Phuc et al., 2016).…”

“…In a previous study, we identified substantial haplotype variation in the major histocompatibility complex (MHC) B‐locus of wild Red Junglefowl (Fulton et al., 2016; Nguyen‐Phuc, Fulton, & Berres, 2016). Curiously, none of the Red Junglefowl haplotypes were found in a large sample of commercial and heritage chicken breeds (Fulton et al., 2016; Nguyen‐Phuc et al., 2016). This result has many open interpretations including that Red Junglefowl in Vietnam may not be the direct ancestor of domestic chickens or that the MHC B‐locus in domestic chickens was altered radically by artificial selection.…”