SHORT COMMUNICATION Analysis of copy number variations in Holstein cows identify potential mechanisms contributing to differences in residual feed intake Yali Hou & Derek M. Bickhart & Hoyoung Chung & Jana L. Hutchison & H. Duane Norman & Erin E. Connor & George E. Liu Received: 8 July 2012 / Revised: 27 August 2012 / Accepted: 3 September 2012 / Published online: 19 September 2012 # Springer-Verlag (outside the USA) 2012 Abstract Genomic structural variation is an important and abundant source of genetic and phenotypic variation. In this study, we performed an initial analysis of copy number varia- tions (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 relate CNVs to two key variables, namely immune response and organ and bone development. The data indicate that greater feed efficiency relates more closely to immune response, whereas cattle with reduced feed efficiency may have a greater capacity for organ and bone development. Keywords Cattle genome . Copy number variation (CNV) . Feed efficiency . Residual feed intake (RFI) . Single nucleotide polymorphism (SNP) Introduction Feed efficiency is a measure of how well an animal converts nutrients into product. Residual feed intake (RFI) is defined as the difference between actual feed intake and that pre- dicted on the basis of mean requirements for body weight maintenance and levels of production (Koch et al. 1963). It is a corrected measure of live weight and production often referred to as net feed efficiency. To date, RFI has been used primarily by the beef, swine, and poultry industries to iden- tify superior animals for efficient growth as a means to reduce feed costs while maintaining desirable meat produc- tion. The application of RFI to estimate feed efficiency for milk production in lactating dairy cows, however, has been Electronic supplementary material The online version of this article (doi:10.1007/s10142-012-0295-y) contains supplementary material, which is available to authorized users. Y. Hou : D. M. Bickhart : H. Chung : E. E. Connor (*) : G. E. Liu (*) Bovine Functional Genomics Laboratory, ANRI, USDA-ARS, Beltsville, MD 20705, USA e-mail: erin.connor@ars.usda.gov e-mail: george.liu@ars.usda.gov Y. Hou Laboratory of Disease Genomics and Individualized Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China H. Chung Rural Development Administration, National Institute of Animal Science, Suwon, South Korea J. L. Hutchison : H. D. Norman Animal Improvement Programs Laboratory, ANRI, USDA-ARS, Beltsville, MD 20705, USA Funct Integr Genomics (2012) 12:717–723 DOI 10.1007/s10142-012-0295-y