Population Structure of Ten US Beef Cattle Revealed By Principal Components Analysis on Genomic Data

Analysis of whole genome haplotype diversity can characterize the genetic population structure and selection signals. Prior to commencing studies of haplotypes from breed-distinct populations, however, it is important to consider the purity of breeds, which will influence the accuracies of conclusions about haplotype sharing. Here we studied a dataset comprising over 30,000 animals genotyped for 50k SNPs and representing 10 beef cattle breeds (including some cross-bred offspring), seeking to distinguish purebred from crossbred animals. Taking advantage of the Principal Components Analysis implemented in R packages gdsfmt and SNPRelate, we presented a comprehensive examination of genetic population structure in these breeds. The results demonstrated that on average, 7% of genotyped cattle were not pure bred. This is not surprising since some breeds record crossbred and composite cattle.  Among pure-bred populations, Charolais and Maine-Anjou showed the closest relationships. Distinguishing outbred animals from purebred ones provides crucial information for haplotype diversity analysis on different breeds. It can be used to inform the design of studies of the genetic structure analysis on outbred populations.

Keywords: haplotype diversity, principle components analysis, US beef cattle, population genetic structure