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United States Department of Agriculture

Agricultural Research Service

Research Project: ENHANCING GENETIC MERIT OF DAIRY CATTLE THROUGH GENOME SELECTION AND ANALYSIS Title: Initial analysis of copy number variations in Holstein cattle selected for high or low feed efficiency

Authors
item Hou, Yali -
item Connor, Erin
item Liu, Ge

Submitted to: Meeting Proceedings
Publication Type: Proceedings
Publication Acceptance Date: June 21, 2012
Publication Date: July 21, 2012
Citation: Hou, Y., Connor, E.E., Liu, G. 2012. Initial analysis of copy number variations in Holstein cattle selected for high or low feed efficiency. Meeting Proceedings. No. 2.

Interpretive Summary: Genomic structural variation, including copy number variation (CNV), is an important and abundant source of genetic and phenotypic variation. We performed an initial analysis of CNVs using 147 Holstein cattle selected for high or low feed efficiency and identified related genes and potential networks. Farmers, Scientist, and policy planners who need improve animal health and production based on genome-enable animal selection will benefit from this study.

Technical Abstract: Genomic structural variation is an important and abundant source of genetic and phenotypic variation. In this study, we performed an initial analysis of CNVs using BovineHD SNP genotyping data from 147 Holstein cattle selected for high or low feed efficiency. We detected 443 candidate CNV regions, which represent 18.4 Mb (0.6%) of the genome. To investigate the functional impacts of CNVs, we created two groups of 30 individual animals with extremely low or high estimated breeding values (EBVs) of residual feed intakes (RFI), and referred to these groups as low intakes (LI; more efficient) or high intakes (HI; less efficient), respectively. We identified 240 (~9.0 Mb) and 274 (~10.2 Mb) CNV regions from LI and HI groups respectively. Approximately 30-40% of the CNV regions were specific to the LI group or HI group of animals. A total of 240 LI CNV regions overlapped with 137 Ensembl genes. Network analyses indicated that the LI-specific genes were predominantly enriched for those functioning in the inflammatory response and immunity. By contrast, the 274 HI CNV regions contained 177 Ensembl genes. Network analyses indicated that the HI-specific genes were particularly involved in the cell cycle, and organ and bone development. These results provide valuable information for the future study of cattle CNVs related to feed efficiency and suggest that more efficient cattle may differ in their ability to elicit an immune response, whereas less efficient cattle may have a greater capacity for organ and bone development.

Last Modified: 8/21/2014