MHC class IIa haplotypes derived by high-throughput SNP screening in an isolated sheep population

Abstract

Investigating the current evolutionary processes acting on a highly polymorphic gene region, such as the major histocompatibility complex (MHC), requires extensive population data for both genotypes and phenotypes. The MHC consists of several tightly linked loci with both allelic and gene content variation, making it challenging to genotype. Eight class IIa haplotypes have previously been identified in the Soay sheep (Ovis aries) of St. Kilda using Sanger sequencing and cloning, but no single locus is representative of all haplotypes. Here, we exploit the closed nature of the island population of Soay sheep and its limited haplotypic variation to identify a panel of SNPs that enable imputation of MHC haplotypes. We compared MHC class IIa haplotypes determined by Sanger sequence-based genotyping of 135 individuals to their SNP profiles generated using the Ovine Infinium HD BeadChip. A panel of 11 SNPs could reliably determine MHC diplotypes, and two additional SNPs within the DQA1 gene enabled detection of a recombinant haplotype affecting only the SNPs downstream of the expressed genes. The panel of 13 SNPs was genotyped in 5951 Soay sheep, of which 5349 passed quality control. Using the Soay sheep pedigree, we were able to trace the origin and inheritance of the recombinant SNP haplotype. This SNP-based method has enabled the rapid generation of locus-specific MHC genotypes for large numbers of Soay sheep. This volume of high-quality genotypes in a well-characterized population of free-living sheep will be valuable for investigating the mechanisms maintaining diversity at the MHC.

Associations between MHC class II variation and phenotypic traits in a free‐living sheep population

“…The genetic data used in this study was obtained through two previous studies (Dicks et al, 2019, 2021). Seven expressed loci ( DRB1 , DQA1 , DQA2 , DQA2 ‐ like , DQB1 , DQB2 and DQB2 ‐ like ) within the MHC class IIa region were characterised in 118 Soay sheep using Sanger sequencing, including 94 sheep genotyped on the Ovine Infinium HD chip.…”

“…The genetic data used in this study was obtained through two previous studies (Dicks et al, 2019(Dicks et al, , 2021. Seven expressed loci (DRB1, were identified (Dicks et al, 2021).…”

“…The genetic data used in this study was obtained through two previous studies (Dicks et al, 2019(Dicks et al, , 2021. Seven expressed loci (DRB1, were identified (Dicks et al, 2021). For each individual successfully diplotyped, the functional divergence between an individual's two haplotypes (MHC divergence) was calculated by hand as the proportion of the amino acid sequence that differed between the two MHC haplotypes (p-distance) (Henikoff, 1996;Huang et al, 2020).…”

“…We were able to identify a total of eight MHC class II haplotypes (named A‐H) through sequence‐based genotyping of a subset of the population (Dicks et al, 2019) and imputed diplotypes successfully for 5349 sheep sampled from 1985 to 2012 using 13 SNPs (Dicks et al, 2021). We found haplotypes C and D are associated with decreased and increased male total fitness (measured as the number of offspring that an individual had throughout its life span) respectively.…”

Patterns of MHC‐dependent sexual selection in a free‐living population of sheep

“…First, seven expressed loci (DRB1, DQA1, DQA2, DQA2-like, DQB1, DQB2 and DQB2-like) within the MHC class IIa region were characterized in 118 Soay sheep using genotyping-by-sequencing which identified eight haplotypes named A to H (Dicks et al, 2019). Second, a panel of 13 SNPs located in the MHC class IIa region haplotypes including 11 SNPs from the Ovine Infinium high density SNP array (Illumina) and two other SNPs located within DQA1 gene were selected to impute eight haplotypes using Kompetitive Allele-specific PCR (KASP) in 5951 Soay sheep(Dicks, Pemberton et al 2020). After genotyping quality control and pedigree checking, 5349 individuals were successfully diplotyped.…”