Genome-Wide Survey of SNP Variation Uncovers the Genetic Structure of Cattle Breeds
From the main body of the paper:
To examine relatedness among breeds, we analyzed SNP genotype frequencies with InSTRUCT (11) and performed principal component analysis (PCA) using Eigenstrat (12) (Fig. 1 and fig. S27). Varying the number of presumed ancestral populations (K) within InSTRUCT revealed clusters consistent with the known history of cattle breeds (Fig. 1A). The first level of clustering (K = 2) reflects the primary, predomestication division of taurine from indicine cattle. Consequently, breeds derived from indicine and taurine crosses (Beefmaster, Santa Gertrudis, and Sheko) show signatures of admixture with both approaches. At K = 3, the African breeds N’Dama and Sheko separate from the European breeds—a division that reflects an early, possibly predomestication, divergence. PCA recapitulated these findings (Fig. 1B). At higher levels of K, we observed clusters that identify single breeds as closed endogamous breeding units. For example, at K = 9, Jersey, Hereford, Romagnola, and Guernsey each form unique clusters.
(A) Population structure assessed by InStruct. Bar plot, generated by DISTRUCT, depicts classifications with the highest probability under the model that assumes independent allele frequencies and inbreeding coefficients among assumed clusters. Each individual (more ...)
From the Supplemental Material:
Multidimensional scaling plots were also generated from the Fst distances and are presented in Fig. S24. In Fig. S24A in which all breeds are included in the analysis, the first dimension clearly represents an indicine division in cattle genomes. The two pure indicine breeds are to one extreme and both the European and African taurine cattle are to the other extreme for the first dimension. Again, the hybrid Sheko, Santa Gertrudis, and Beefmaster are intermediate on this axis. It is possible that there might be some indicine ancestry in the Italian Romagnola breed - previous microsatellite work has suggested that there may be traces of indicine in Mediterranean breeds (Romagnola is the most easterly of the European breeds represented in the sample.) In Fig. S24B, in which the indicine and hybrid breeds were excluded from the analysis, there is a clear separation of the West African N’Dama from the other breeds, supporting the tentative archaeological and mtDNA evidence that suggests that there may have been a separate African
site of cattle domestication.