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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Animal Genomics and Improvement Laboratory » Research » Publications at this Location » Publication #301093

Title: Population sequencing reveals breed and sub-species specific CNVs in cattle

item Liu, Ge - George
item Bickhart, Derek
item XU, LINGYANG - University Of Maryland
item Hutchison, Jana
item Sonstegard, Tad
item Van Tassell, Curtis - Curt
item Schroeder, Steven - Steve
item GARCIA, JOSE FERNANDO - Universidade Estadual Paulista (UNESP)
item TAYLOR, JEREMY - University Of Missouri
item SCHNABEL, ROBERT - University Of Missouri
item LEWIN, HARRIS - University Of California

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 12/4/2013
Publication Date: 2/12/2014
Citation: Liu, G., Bickhart, D.M., Xu, L., Hutchison, J.L., Sonstegard, T.S., Van Tassell, C.P., Schroeder, S.G., Garcia, J., Taylor, J.F., Schnabel, R.D., Lewin, H.A. 2014. Population sequencing reveals breed and sub-species specific CNVs in cattle. Meeting Abstract. Advances in Genome Biology & Technology Conference Meeting Abstract. p.58.

Interpretive Summary:

Technical Abstract: Individualized copy number variation (CNV) maps have highlighted the need for population surveys of cattle to detect the rare and common variants. While SNP and comparative genomic hybridization (CGH) arrays have provided preliminary data, next-generation sequence (NGS) data analysis offers an increased resolution and sensitivity for CNV detection. This study analyzed NGS sequence data derived from 67 taurine (consisting of the Angus, Holstein, Jersey, Limousin and Romagnola breeds) and 20 indicine cattle (consisting of the Brahman, Gir and Nelore breeds). Individual genome sequence coverage ranged from 4X to 30X, with an average coverage of 11.8X across animals. To identify CNVs, a customized read-depth CNV was used, calling algorithm that utilizes population-scale data to derive a smoothing coefficient for lowess normalization. We identified 2,947 unique CNV regions that account for approximately 4% (117 Mbp) of the cattle genome. Several dairy-breeds and beef-breeds specific variants were found, including a duplication of the cell growth-related RICTOR gene in dairy breeds and a duplication of the Patatin-like phospholipase 3 (PNPLA3) gene in beef breeds. Identification of low frequency and breed-specific CNVs within cattle will enable a better understanding of functional variants influenced by domestication and selection for performance traits.