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United States Department of Agriculture

Agricultural Research Service

Research Project: GENETIC AND BIOLOGICAL DETERMINANTS OF RESPIRATORY DISEASE SUSCEPTIBILITY Title: Discovery, Validation and Characterization of 1039 Cattle Single Nucleotide Polymorphisms

Authors
item Donthu, Ravikiran -
item Larkin, Denis -
item Heaton, Michael
item Lewin, Harris -

Submitted to: Animal Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: October 29, 2009
Publication Date: August 1, 2010
Repository URL: http://hdl.handle.net/10113/48977
Citation: Donthu, R., Larkin, D.M., Heaton, M.P., Lewin, H.A. 2010. Discovery, Validation and Characterization of 1039 Cattle Single Nucleotide Polymorphisms. Animal Genetics. 41(4):421-423.

Interpretive Summary: Cattle DNA markers are significant for mapping important traits for health and production. Single nucleotide polymorphisms (SNPs) are the most abundant DNA markers in cattle and are commonly used for gene mapping. We identified 13,000 SNPs by sequencing cattle DNA and characterizing the marker properties for mapping. A subset of 1039 SNPs was further evaluated in a panel containing 186 DNA samples from 18 cattle breeds, including 43 triad families. Results showed that all 1039 markers were directly confirmed by genotyping on the multi-breed panel and it is likely that the original polymorphisms were correctly identified. The minor allele frequency for 998 markers was greater than or equal to 0.25 among unrelated individuals of at least one breed. Thus, these markers had useful properties and were readily mapped to cattle chromosomes. The validated SNPs identified in this study represent a new and useful resource for genome-wide association studies and applications in animal breeding.

Technical Abstract: We identified approximately 13000 putative single nucleotide polymorphisms (SNPs) by comparison of repeat-masked BAC-end sequences from the cattle RPCI-42 BAC library with whole-genome shotgun contigs of cattle genome assembly Btau 1.0. Genotyping of a subset of these SNPs was performed on a panel containing 186 DNA samples from 18 cattle breeds including 43 trios. Of 1039 SNPs confirmed as polymorphic in the panel, 998 had minor allele frequency greater than or equal to 0.25 among unrelated individuals of at least one breed. When Btau 4.0 became available, 974 of these validated SNPs were assigned in silico to known cattle chromosomes, while 41 SNPs were mapped to unassigned sequence scaffolds, yielding one SNP every approximate 3 Mbp on average. Twenty-four SNPs identified in Btau 1.0 were not mapped to Btau 4.0. Of the 1015 SNPs mapped to Btau 4.0, 959 SNPs had nucleotide bases identical in Btau 4.0 and Btau 1.0 contigs, whereas, 56 bases were changed, resulting in the loss of the in silico SNP in Btau 4.0. Because these 1039 SNPs were all directly confirmed by genotyping on the multi-breed panel, it is likely that the original polymorphisms were correctly identified. The 1039 validated SNPs identified in this study represent a new and useful resource for genome-wide association studies and applications in animal breeding.

Last Modified: 10/1/2014