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United States Department of Agriculture

Agricultural Research Service


Location: Animal Genomics and Improvement Laboratory

Title: Population analysis of 60 worldwide cattle breeds using high-density (700k)SNP genotyping

item Huson, Heather
item Sonstegard, Tad
item Soelkner, Johann -
item Mustafa, Hamid -
item Mukasa, Christopher -
item Nash, Oyekan -
item Bradely, Dan -
item Van Tassell, Curtis

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: December 26, 2012
Publication Date: January 12, 2013
Citation: Huson, H.J., Sonstegard, T.S., Soelkner, J., Mustafa, H., Mukasa, C., Nash, O., Bradely, D., Van Tassell, C.P. 2013. Population analysis of 60 worldwide cattle breeds using high-density (700k)SNP genotyping. Plant Animal Genome XXI, paper PO524, pp. 237.

Technical Abstract: Genetic differences associated with speciation, breed formation, or local adaptation can help inform efforts to preserve and to effectively utilize individuals in selection programs as well as assist in accurately identifying genomic region’s importance through genome-wide association studies. To this end, individuals representing 60 cattle breeds, distributed worldwide, were genotyped using the Illumina BovineHD BeadChip. Two approaches, principle component analysis and model-based analysis, were utilized to cluster the high-density (700K) genome-wide single-nucleotide polymorphisms (SNPs). The clustering of individuals into populations based upon their genetic “barcode” was used to ascertain relatedness between breeds, including their phylogenetic relationship, as well as identify genetic associations linked to geographic origin, climate, physical appearance, etc. The major components of population structure correlated with sub-species and geographical origins with finer analysis comparing genetic population alignment with accepted breed populations. While the Tharparker, a Pakistan cattle, were identified as the most genetically distinct breed, other breeds were genetically indistinguishable with historical data suggesting individuals were characterized into those breeds based upon usage. Overall, population clustering was capable of differentiating between “pure” individuals of a breed and admixed individuals hence identifying suitable individuals for breed bio-conservation or admixture mapping. We also determined inbreeding estimates using identity by descent, degree of autozygosity, rate of LD decay, and inbreeding coefficients. This documentation builds upon current knowledge of the genomic structure of cattle and creates a more comprehensive account of the 60 breeds examined for more informed usage towards the discovery of new regions of the genome experiencing selection.

Last Modified: 8/26/2016
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