Deviation Patterns of Observed and Expected Haplotype Blocks Associated with Potential Recessive Disorders in Tyrol Grey Cattle

Abstract

Confirmed by phenotypic records, several studies across different breeds in different locations have linked missing homozygous pattern with several defects in the functional system and recessive genetic disorders. Recessive genetic diseases are expressed when the recessive alleles appear in a homozygous state for an individual. One of the indicators to detect the recessive allele is through haplotypes, which have a normal frequency in the population, but never occur in the homozygous state. In this study, we used SNP genotypes of 220 Austrian Tyrol Grey cattle and 80 Italian Tyrol Grey cattle to identify the haplotype blocks (Hapblocks) that possibly carry genes causing recessive disorders. Hapblocks with missing homozygous state in the population were statistically tested as to whether this is very unlikely in Hardy-Weinberg equilibrium. Eight out of all hapblocks passing the threshold had functional genes which are crucial in maintaining the metabolism, production, reproduction, and health of the individuals. These hapblocks had a high frequency of above 13% but never appear in homozygous state. Thus, these are foreseen as potential source of genetic defects. Our finding in this analysis can be used as a reference for further study in haplotype analyses of inherited recessive disease for other cattle breeds.

Identification of lethal recessive genetic variants in Holstein cattle

“…Nevertheless, for some animal populations, it is not possible to study large samples due to the small number of breeds. Naji and co-authors [24] performed a search for haploblocks in cattle of the Tyrolean Grey breed (n=276). Haploblocks were identified using the GHap package (Utsunomiya and Milanesi, 2017) in the R software, a scan window of 500 KB in size and a sliding step of 100 kb.…”