Whole-Genome Analysis of Taurine and Indicine Cattle

A comprehensive catalog of genetic variants in the bovine genome is needed to facilitate the identification of genes and genetic elements underlying phenotypes of biological and economical interest.  In this study we identified single nucleotide polymorphisms (SNPs), insertion-deletion polymorphisms (INDELs) and unbalanced structural rearrangements (i.e., copy number variants [CNVs]) in the genomes of taurine and indicine cattle using massively parallel sequencing, array comparative genomic hybridization (CGH), and SNP genotyping. Whole-genome sequencing of an Angus (taurine) and Nellore (indicine) cow identified over 11 million SNPs, 300 thousand INDELs and 900 CNVs. Analysis of a cohort of taurine (Angus and Holstein) and indicine (Nellore and Brahman) cattle identified over 1,000 CNV regions. Approximately 30-50% of the CNVs were not tagged by SNPs, suggesting that unbalanced genomic rearrangements have occurred since the formation of the breeds and continue to evolve in the bovine genome.  Functional clustering analysis of genetic variants revealed that taurine and indicine cattle diverged in processes regulating immunity and defense, signal transduction, and sensory perception.  Collectively, we have increased the catalog of genetic variants for use in bovine genomics by the addition of novel SNPs, INDELs, and CNVs. Furthermore, we show extensive genetic variation between taurine and indicine cattle and provide insights into the evolution and function of genetic variants in the bovine genome.