Submitted to: Functional and Integrative Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: September 3, 2012
Publication Date: September 19, 2012
Repository URL: http://handle.nal.usda.gov/10113/56783
Citation: Hou, Y., Bickhart, D.M., Chung, H., Hutchison, J.L., Norman, H.D., Connor, E.E., Liu, G. 2012. Analysis of copy number variations in Holstein cows identify potential mechanisms contributing to differences in residual feed intake. Functional and Integrative Genomics. 12(4):717-723. Interpretive Summary: Structural variations within the genome may contribute to variation observed among animals in production traits such as feed efficiency. Herein we evaluated the association between gene copy number variation and a measurement of feed efficiency called residual feed intake in lactating dairy cattle. Our results suggested that more efficient cows may have a reduction in their immune function relative to less efficient cows, whereas less efficient cows may have a greater capacity for organ and bone development. This work is important for identifying potential mechanisms contributing to differences in feed efficiency among dairy cattle and enable animal selection or management practices that optimize both production efficiency and animal health.
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 cows identified as having high or low feed efficiency as estimated by residual feed intake (RFI). We detected 443 candidate CNV regions (CNVRs) that 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) for RFI, and referred to these groups as low intake (LI; more efficient) or high intake (HI; less efficient), respectively. We identified 240 (~9.0 Mb) and 274 (~10.2 Mb) CNVRs from LI and HI groups, respectively. Approximately 30-40% of the CNVRs were specific to the LI group or HI group of animals. The 240 LI CNVRs 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 CNVRs 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.