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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 #323611

Research Project: ENHANCING GENETIC MERIT OF RUMINANTS THROUGH GENOME SELECTION AND ANALYSIS

Location: Animal Genomics and Improvement Laboratory

Title: Diversity and population-genetic properties of copy number variations and multicopy genes in cattle

Author
item Bickhart, Derek
item Xu, Lingyang - University Of Maryland
item Hutchison, Jana - Edwards
item Cole, John
item Null, Daniel
item Schroeder, Steven - Steve
item Song, Jiuzhou - University Of Maryland
item Garcia, Jose Fernando - Universidade Estadual Paulista (UNESP)
item Van Tassell, Curtis - Curt
item Sonstegard, Tad - Former Ars Employee
item Schnabel, Robert - University Of Missouri
item Taylor, Jeremy - University Of Missouri
item Lewin, Harris - University Of California
item Liu, Ge - George

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 1/9/2016
Publication Date: 1/9/2016
Citation: Bickhart, D.M., Xu, L., Hutchison, J.L., Cole, J.B., Null, D.J., Schroeder, S.G., Song, J., Garcia, J., Van Tassell, C.P., Sonstegard, T.S., Schnabel, R.D., Taylor, J.F., Lewin, H.A., Liu, G. 2016. Diversity and population-genetic properties of copy number variations and multicopy genes in cattle [abstract]. USDA NIFA Animal Genome Program PD Meeting, January 8, 2016, San Diego, California.

Interpretive Summary:

Technical Abstract: The diversity and population-genetics of copy number variation (CNV) in domesticated animals are not well understood. In this study, we analyzed 75 genomes of major taurine and indicine cattle breeds (including Angus, Brahman, Gir, Holstein, Jersey, Limousin, Nelore, Romagnola), sequenced to 11-fold coverage to identify 1,853 nonredundant CNV regions. With high validation rates by array comparative genomic hybridization (CGH) and qPCR, this CNV dataset covers 3.1% (87.5 Mb) of the cattle genome, representing a dramatic increase over previous estimates (~2%). Further population genetics and evolutionary genomics analyses based on these CNVs revealed the population structures of the cattle taurine and indicine breeds and uncovered potential diversely selected CNVs near important functional genes, including AOX1, ASZ1, GAT, GLYAT, and KRTAP9-1. Additionally, hundreds of CNVs were found to be either breed specific or differentially variable across breeds, such as RICTOR in dairy breeds and PNPLA3 in beef breeds. In contrast, clusters of the PRP and PAG genes were found to be duplicated in all sequenced animals, suggesting that subfunctionalization, neofunctionalization or overdominance play roles in diversifying those fertility related genes. These CNV results provide a new glimpse into the diverse selection histories of cattle breeds and a basis for correlating structural variation with complex traits in the future.