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 SNP haplotype. The panel of 13 SNPs was genotyped in 5951 sheep, of which 5349 passed quality control. Using the Soay sheep pedigree, we were able to trace the origin and inheritance of a recombinant SNP haplotype.

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

“…Few previous studies have reported specific MHC variants being favoured or disfavoured during mating as the high polymorphism of MHC genes requires a large sample size to detect sexual selection on specific MHC variants (Eizaguirre, Yeates et al 2009). In this study, our finding for haplotype C in male parents was consistent with a negative association between MHC haplotype C and male breeding success found in a recent study on MHC-fitness associations (Huang, Dicks et al 2020). The fact that haplotype C males are also less often observed in consort than expected indicates that the effect of haplotype C is expressed at the pre-copulatory rather than post-copulatory stage.…”

“…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, Pemberton 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.…”

“…However, a previous study using five MHC-linked microsatellite loci genotyped in between 887 and 1209 individuals born between 1985 and 1994 found no evidence for MHC-dependent assortative or disassortative mating in this population (Paterson and Pemberton 1997). Recently, using genotyping-by-sequencing, a total of eight MHC class II haplotypes have been identified in the study populations and a large number of individuals alive between 1989 and 2012 have been diplotyped (Dicks, Pemberton et al 2019, Dicks, Pemberton et al 2020). In addition, pairwise relatedness based on genome-wide SNPs is available between most individuals.…”

Age-dependent selection on MHC class 2 variation in a free-living ruminant

“…A panel of 13 SNPs located in the region of MHC class IIa haplotypes was then selected to impute the eight MHC class IIa haplotypes in 5951 Soay sheep genotyped using Kompetitive Allele-specific PCR (KASP). This panel included 11 SNPs known to be variable in Soays based on data from the Illumina Ovine infinium HD chip and two other SNPs identified within the DQA1 gene (52). After quality control, the diplotypes of 5349 individuals that lived in the study area between 1985 and 2012 were identified.…”

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

“…The genetic data used in this study was obtained from a previous study (Dicks, Pemberton et al 2019, Dicks, Pemberton et al 2020). 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 sequence-based genotyping.…”