Evaluation of SNP Haplotypes for Regions of Missing Homozygosity in the Pig

New genomic tools like high density SNP chips allow researchers to investigate underlying phenomenon that are not readily obvious from previous genetic studies. In particular, it has been hypothesized that individuals may carry deleterious recessives which has been termed the “genetic load” and that these result in a decrease in fitness of the average individual in a population.  To investigate this we examined 3 pig populations using 60K SNP chip data.  The first population involved 830 commercial females of Large White and Landrace background.  The other 2 populations (n=350, 380) were used for validation and were from Large White closed populations.  Haplotype homozygosity was assessed using 10, 50 and 100 SNP windows, a segment size equivalent to approximately 0.3, 1.5, and 3 Mb, respectively and a minimum haplotype frequency of >.2.  Based on 10 SNP haplotypes, a total of 13 regions were found where no homozygotes of haplotypes were found.  Examination in the other 2 populations revealed a total of ~25 other regions that were missing homozygotes of which 4 regions were similar to those in the first pig sample. When the size of SNP windows was increased there were no homozygous individuals for fewer haplotypes but some consensus regions were found on chromosomes 7 (position 86 Mb) and 14 (position 112 Mb), which extended over 3-4 Mb.  Further examinations will be conducted to reveal the possible reasons for missing homozygotes in these regions and to find underlying causative recessive mutation.