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United States Department of Agriculture

Agricultural Research Service

Research Project: ENHANCING GENETIC MERIT OF DAIRY CATTLE THROUGH GENOME SELECTION AND ANALYSIS Title: An assessment of population structure in eight breeds of cattle using a whole genome SNP panel

Authors
item Mckay, Stephanie -
item Schnabel, Robert -
item Murdoch, Brenda -
item Matukumalli, Lakshmi -
item Aerts, Jan -
item Coppieters, Wouter -
item Crews, Denny -
item Neto, Emmanuel -
item Gill, Clare -
item Gao, Chuan -
item Mannen, Hideyuki -
item Wang, Zhiquan -
item Van Tassell, Curtis
item Williams, John -
item Taylor, Jeremy -
item Moore, Stephen -

Submitted to: Journal of Animal Breeding and Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: May 20, 2008
Publication Date: May 20, 2008
Citation: Mckay, S.E., Schnabel, R.D., Murdoch, B.M., Matukumalli, L.K., Aerts, J., Coppieters, W., Crews, D., Neto, E.D., Gill, C.A., Gao, C., Mannen, H., Wang, Z., Van Tassell, C.P., Williams, J.L., Taylor, J.F., Moore, S.S. 2008. An assessment of population structure in eight breeds of cattle using a whole genome SNP panel. Journal of Animal Breeding and Genetics. 20(9):37.

Interpretive Summary: For the purposes of extensive selection of specific functional characteristics or production traits such as milk/beef cattle are segregated into different breeds. Sequencing of the cattle genome, polymorphism discovery and advances in genotyping technology have allowed us to rapidly genotype thousands of markers in hundreds of animals. In this study we have identified 8 breeds of diverse cattle representing both Bos indicus and Bos Taurus genera. The breeds represented are from Angus, Brahman, Charolais, Dutch Black and White Dairy, Holstein, Japanese Black, Limousin and Nelore. This is the first study to use large-scale SNP data revealing the population substructure and relationships across the cattle breeds across the world.

Technical Abstract: 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. 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. 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.

Last Modified: 12/18/2014
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