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United States Department of Agriculture

Agricultural Research Service

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

Location: Animal Genomics and Improvement Laboratory

Title: Assessing signatures of selection through variation in linkage disequilibrium between taurine and indicine cattle

Authors
item Perez O'Brien, Ana -
item Utsunomiya, Yuri -
item Meszaros, Gabor -
item Bickhart, Derek
item Liu, Ge
item Garcia, J. Fernando -
item Van Tassell, Curtis
item Sonstegard, Tad
item Solkner, Johann -

Submitted to: Genetics Selection Evolution
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: January 9, 2014
Publication Date: March 4, 2014
Citation: Perez O'Brien, A.M., Utsunomiya, Y.T., Meszaros, G., Bickhart, D.M., Liu, G., Garcia, J., Van Tassell, C.P., Sonstegard, T.S., Solkner, J. 2014. Assessing signatures of selection through variation in linkage disequilibrium between taurine and indicine cattle. Genetics Selection Evolution. 46:19.

Interpretive Summary: It is possible to analyze high density DNA marker (single nucleotide polymorphism or SNP-based data) to find regions of the genome that have undergone natural selection or human-directed selection for important production traits (signatures of selection). This paper describes a previously untested analysis method for cattle, which identifies signatures of selection based upon genome regions that have undergone lower than normal rates of recombination. The contrasts to find these regions were based on comparisons between beef and dairy breeds and between temperate and tropically adapted cattle. Some of the genes found in the indicine versus taurine comparisons indicate potential adaptive gene variants for climate change, while the dairy and beef comparisons identify genetic variation related to production of milk and beef. The information from this research will be used to identify the actual gene variants, which will in turn be used to breed more efficient animals for production in sub-tropical regions, where global food security concerns are prevalent.

Technical Abstract: Signatures of selection are regions in the genome that have been preferentially maintained because of their functional importance in specific processes. These regions can be detected because of their lower genetic variability and specific regional linkage disequilibrium patterns. The varLD methodology was applied to compare the linkage disequilibrium patterns between breeds including Angus and Brown Swiss, representing Taurine breeds and Nelore and Gir, representing Indicine breeds. The regions containing the top 0.01 and 0.1 27 percentile of signals were characterized using the UMD3.1 Bos Taurus genome assembly to identify genes in those regions. For all comparison groups 26 signals in the top 0.01 and 165 in the top 0.1 percentile were found, and 17 and 125 genes respectively were identified underlying the signals, including TECRL, FPPS_BOVIN, CAST, MYOM1, UVRAG and DNAJA1. VarLD is a powerful tool to identify differences in linkage disequilibrium between cattle populations and putative signatures of selection with potential adaptive and productive importance. VarLD signals typically point to very narrow regions, located in regions of 37 individual genes.

Last Modified: 12/18/2014
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