MHC-B variability within the Finnish Landrace chicken conservation program

Abstract

The major histocompatibility complex (MHC) is a cluster of genes involved with immune responses. The chicken MHC has been shown to influence resistance to viruses, bacteria, and infections from both internal and external parasites. The highly variable chicken MHC haplotypes were initially identified by the use of haplotype-specific serological reagents. A novel SNP-based panel encompassing 210,000 bp of the MHC-B locus was developed to allow fine scale genetic analyses including rapid identification of novel haplotypes for which serological reagents are not available. The Finnish Landrace breed of chickens traces its origins to almost 1,000 years ago, with multiple lineages maintained as small populations in isolated villages. The breed is well adapted to the cooler Finnish climate and is considered to be an infrequent egg layer. Conservation efforts to protect this endangered breed were initiated by a hobby breeder in the 1960s. An official conservation program was established in 1998 and now 12 different populations are currently maintained by a network of volunteer hobbyist breeders. Variation in the MHC-B region in these populations was examined using a panel of 90 selected SNP. A total of 195 samples from 12 distinct populations (average of 15 individuals sampled per population) were genotyped with the 90 SNP panel specific for the MHC-B region, spanning 210,000 bp. There were 36 haplotypes found, 16 of which are a subset of 78 that had been previously identified in either commercially utilized or heritage breeds from North America with the remaining 20 haplotypes being novel. The average number of MHC-B haplotypes found within each Finnish Landrace population was 5.9, and ranged from one to 13. While haplotypes common to multiple populations were found, population-specific haplotypes were also identified. This study shows that substantial MHC-B region diversity exists in the Finnish Landrace breed and exemplifies the significance tied to conserving multiple populations of rare breeds.

Assessing the genetic diversity conserved in the Norwegian live poultry genebank

“…It may also be of interest to look at diversity in specific areas of the genome. A study on Finnish landrace chicken found substantial diversity in a cluster of genes involved in immune response (Fulton et al 2017). Retaining diversity at such loci could prove valuable in the future as disease and parasite pressures change over time, possibly due to climate change.…”

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

“…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, 2017 ; Nguyen-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).…”

Assessing MHC-B diversity in Silkie chickens

“…Haplotypes were identified following a two-step process as described in the study by Fulton et al. (2017) .…”

“…The SNP panel was initially validated using DNA of known serologically defined MHC haplotypes from multiple research lines, as well as standard breeds, heritage breeds, and elite commercial egg production lines from multiple sources. Subsequently, additional haplotypes have been identified in Finnish Landrace populations ( Fulton et al., 2017 ) and an Argentinian Campero population ( Iglesias et al., 2019 ).…”