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ARS Home » Plains Area » Clay Center, Nebraska » U.S. Meat Animal Research Center » Livestock Bio-Systems » Research » Publications at this Location » Publication #331310
Title: Evolutionary and functional features of copy number variation in the cattle genome

Author
item Keel, Brittney
item Lindholm-Perry, Amanda
item Snelling, Warren

Submitted to: Frontiers in Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/9/2016
Publication Date: 11/22/2016
Citation: Keel, B.N., Lindholm-Perry, A.K., Snelling, W.M. 2016. Evolutionary and functional features of copy number variation in the cattle genome. Frontiers in Genetics. 7:207. doi:10.3389/fgene.2016.00207.

Interpretive Summary: Genomic structural variations are an important source of genetic diversity. Copy number variations (CNVs) are gains and losses of large regions of genomic sequence between individuals of a species and are known to be associated with both diseases and phenotypic traits. In cattle, as well as many other species, relatively little is known about the demographic and evolutionary forces that shape this variation within and among populations. Such information is critical for identifying variation that affects important traits. To identify DNA sequence variation that affects beef cattle performance and to understand the evolutionary drivers and functional effects of these variations, we identified CNV from expressed genes of 175 influential bulls in the U.S. Meat Animal Research Center Germplasm Evaluation (GPE) project. These bulls included 122 purebred sires representing 10 diverse breeds (Angus, Hereford, Simmental, Limousin, Charolais, Gelbvieh, Red Angus, Shorthorn, Braunvieh, and Brahman), as well as 53 natural service sires representing 10 different crosses of 7 breeds (Angus, Hereford, Simmental, Limousin, Charolais, Gelbvieh, and Red Angus). 131 CNVs were detected, and these CNVs overlapped 202 protein-coding genes. We examined the role of selective pressure, abstract forces that shape the behavior and fitness of an organism, on CNV genes. Patterns of CNV in the Bos taurus genome reveal that CNV overlapped genes may affect fitness traits, such as growth, reproduction, metabolism, and resistance to disease. This accelerated evolution can cause phenotypic changes by altering the expression of the gene. This work is a first exploration of evolutionary patterns of copy number variable genes in the cattle genome. Further investigation is needed to understand the exact role that CNVs play in shaping phenotypic variation.

Technical Abstract: Genomic structural variations are an important source of genetic diversity. Copy number variations (CNVs), gains and losses of large regions of genomic sequence between individuals of a species, are known to be associated with both diseases and phenotypic traits. In cattle, as well as many other species, relatively little is known about the evolutionary and functional impact of CNVs. In this study, we identified 131 CNV regions using whole exome sequence from 175 sires of a heavily phenotyped experimental herd of cattle. CNVs overlapped 226 cattle genes, including 202 protein-coding genes. We examined selective constraint on CNV genes and utilized gene expression data and protein-protein interaction networks to investigate network centrality and tissue specificity of CNV genes. Patterns of CNV in the Bos taurus genome reveal that negative selection and mutational bias may play a prominent role in shaping genomic structural variation. This work is a first exploration of evolutionary features of CNV and CNV genes in the cattle genome. Further investigation is needed to understand the role that CNVs play in reshaping gene structure, modulating gene expression, and ultimately contributing to phenotypic variation.