An assessment of population structure in eight breeds of cattle using a whole genome SNP panel

Abstract

Background: Analyses of population structure and breed diversity have provided insight into the origin and evolution of cattle. Previously, these studies have used a low density of microsatellite markers, however, with the large number of single nucleotide polymorphism markers that are now available, it is possible to perform genome wide population genetic analyses in cattle. In this study, we used a high-density panel of SNP markers to examine population structure and diversity among eight cattle breeds sampled from Bos indicus and Bos taurus.

Results: Two thousand six hundred and forty one single nucleotide polymorphisms (SNPs) spanning all of the bovine autosomal genome were genotyped in Angus, Brahman, Charolais, Dutch Black and White Dairy, Holstein, Japanese Black, Limousin and Nelore cattle. Population structure was examined using the linkage model in the program STRUCTURE and Fst estimates were used to construct a neighbor-joining tree to represent the phylogenetic relationship among these breeds.

Conclusion: The whole-genome SNP panel identified several levels of population substructure in the set of examined cattle breeds. The greatest level of genetic differentiation was detected between the Bos taurus and Bos indicus breeds. When the Bos indicus breeds were excluded from the analysis, genetic differences among beef versus dairy and European versus Asian breeds were detected among the Bos taurus breeds. Exploration of the number of SNP loci required to differentiate between breeds showed that for 100 SNP loci, individuals could only be correctly clustered into breeds 50% of the time, thus a large number of SNP markers are required to replace the 30 microsatellite markers that are currently commonly used in genetic diversity studies.

Figure 1

(A-C). ΔK (-○-) and the mean log P(X|K) (-□-) based on the 5 replicate STRUCTURE runs indicate that K = 2 is optimal for each dataset. The highest point on the blue line depicts the optimal K value. The red line depcits the mean log P(X|K) (-□-) for each K value. (A) All eight breeds included, (B) Only Bos taurus and (C) Bos taurus without Japanese Black.

Figure 2

(A-C). Box plot of mean individual admixture coefficients for the 5 replicate STRUCTURE runs using K = 2 for each dataset. The boxes show the interquartile range of the mean individual admixture coefficients and contain 50% of the values. The black line shows the median value and the whiskers extend to the highest and lowest values. (A) All eight breeds included, (B) Only Bos taurus and (C) Bos taurus without Japanese Black. Breed abbreviations are defined in the text.

Figure 3

(A-C). Estimation of the number of ancestral populations based on samples of 25, 50, 100 or 150 loci randomly sampled from the complete dataset. In each panel, the solid bars represent the number of times each K was found to be optimal and the colored lines represent the ΔK values for each of the 10 replicate runs. (A) All eight breeds included, (B) All Bos taurus breeds and (C) Bos taurus without Japanese Black.

Figure 4

Neighbor-Joining Tree based on pairwise Fst values calculated using 2,641 SNP loci showing phylogenetic relationships between cattle breeds. Breed abbreviations are defined in the text.