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ARS Home » Plains Area » Clay Center, Nebraska » U.S. Meat Animal Research Center » Genetics, Breeding, and Animal Health Research » Research » Publications at this Location » Publication #323645

Research Project: Genetic and Biological Determinants Of Respiratory Diseases Of Ruminants

Location: Genetics, Breeding, and Animal Health Research

Title: A searchable, whole genome resource designed for protein variant analysis in diverse lineages of U.S. beef cattle

Author
item Heaton, Michael - Mike
item Kalbfleisch, Theodore - University Of Louisville
item Carnahan, Jacky
item Smith, Timothy - Tim
item Harhay, Gregory
item Simpson, Barry - Geneseek Inc, A Neogen Company
item Qiu, Jiansheng - Geneseek Inc, A Neogen Company

Submitted to: Plant and Animal Genome Conference Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: 11/5/2015
Publication Date: 12/5/2015
Citation: Heaton, M.P., Kalbfleisch, T.S., Carnahan, J.K., Smith, T.P.L., Harhay, G.P., Simpson, B., Qiu, J. 2015. A searchable, whole genome resource designed for protein variant analysis in diverse lineages of U.S. beef cattle [abstract]. International Plant and Animal Genome XXIV Conference Proceedings, January 9-13, 2016, San Diego, CA. Poster #P0506.

Interpretive Summary:

Technical Abstract: A key feature of a gene's function is the variety of protein isoforms it encodes in a population. However, the genetic diversity in bovine whole genome databases tends to be underrepresented because these databases contain an abundance of sequence from the most influential sires. Our first aim was to create a unique set of 96 mapped genomes from 19 U.S. beef breeds, with bulls from distinct lineages. Our second aim was to illustrate the utility of this publicly viewable set of genomes for identifying rare protein variants encoded by a gene of interest. For each bull, the identity and quality of its mapped data set was tested by comparing more than 700k single nucleotide polymorphism (SNP) genotypes to those previously derived from other platforms. The average read depth at parentage SNPs was about 12.5, and the scoring rate and accuracy were approximately 99% each. The bovine beta-2 integrin gene (ITGB2) was used as an example of protein variant analysis and found to contain 14 missense SNPs affecting 12 codons. Rare codon mutations, not previously detected by PCR-Sanger sequencing, were observed in Simmental and Santa Gertrudis bulls. Eleven protein haplotypes were inferred by maximum parsimony, resulting in 66 possible paired combinations of ITGB2 protein variants. Thus, this searchable, diverse, whole genome resource facilitates accurate identification of protein variants in silico for U.S. beef cattle and provides a means of translating WGS data into a biological context.