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Predicting MHC Haplotypes from High-Density SNP Genotypes in Pigs
The major histocompatibility complex (MHC) region in swine contains genes associated with disease resistance, many of which have haplotype-specific expression. The objective of this study was to determine whether SNP genotypes from a high-density SNP chip can be used to predict haplotypes within the MHC region of the swine genome. In total, 920 pigs were genotyped using the Illumina SNP60 BeadChip. SNPs located within the Swine Leukocyte Antigen (SLA) I and SLA II regions of chromosome 7 were used to define SNP haplotypes for MHC classes I and II, respectively, using BEAGLE phasing software. Each SNP haplotype corresponded uniquely to a MHC haplotype defined by a PCR-based method. In conclusion, high-density SNP genotypes from the Illumina Porcine SNP60 BeadChip can be used to predict MHC haplotypes with fairly high accuracy, as an alternative to PCR-based approaches.
Keywords:
Swine Major Histocompatibility Complex
Swine Leukocyte Antigen haplotypes
High-density SNP genotyping
