Abstract
BackgroundAnalyses 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.ResultsTwo 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.ConclusionThe 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.
Highlights
Analyses of population structure and breed diversity have provided insight into the origin and evolution of cattle
We first explored the appropriate number of iterations for the initial burn-in and estimation phases of the analysis. These preliminary analyses indicated that the probability of the number of ancestral populations being greater than five was very small and we restricted our analyses of all datasets to K ≤ 5 to limit computation time
Several domestication events have been suggested for cattle involving different strains of aurochs, including an independent taurine domestication event in Asia [12,13]. These results suggest that the Japanese Black breed is genetically distinct from the European taurine breeds and because the divergence greatly exceeds the variation between the beef and dairy breeds (Figure 2b), we believe that an independent Asian domestication event is more likely to explain the divergence than does selection or drift following domestication
Summary
Analyses of population structure and breed diversity have provided insight into the origin and evolution of cattle These studies have used a low density of microsatellite markers, with the large number of single nucleotide polymorphism markers that are available, it is possible to perform genome wide population genetic analyses in cattle. 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. MacHugh et al [2] used 20 microsatellites to help clarify the genetic relationships between cattle populations from Africa, Europe and Asia and provided support for a separate origin of domestication for Bos taurus and Bos indicus cattle. We examine population substructure and interbreed diversity among eight breeds of cattle using 2,641 autosomal genome-wide SNPs
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