Haplotype Diversity of Ten US Beef Cattle Breeds Captured by Different Definitions of Haplotypes Based on BovineSNP50K Chip

Abstract Text: Different ways of defining haplotypes from marker alleles fundamentally affects the size of haplotype blocks and the corresponding number of alleles. Here we studied a dataset comprising over 32,000 animals genotyped with BovineSNP50K and representing 10 beef cattle breeds, seeking to reveal the extent of genetic diversity captured by haplotypes constructed from adjacent marker alleles (1) of arbitrary number of SNPs and (2) within predefined Mb-based windows according to UMD3.1 map positions. The average numbers of common haplotype alleles, which we defined as those that were observed at a frequency of at least 0.01 in each breed, were investigated in relation to the width of haplotypes. The results suggested that 20 SNP haplotypes and/or 1-Mb haplotypes were preferred and these are typically characterized by 20 alleles.

Keywords: beef cattle, haplotype definition, BovineSNP50K