Genome wide association study for feed efficiency traits in beef cattle using CNV

The purpose of this study was: (i) to validate and detect copy number variations (CNV) in the cattle genome, and (ii) to find associations between CNV and feed efficiency traits. Average daily gain and dry matter intake were obtained from 3,884 beef cattle. Animals were genotyped with the panels of 50,000 single nucleotide polymorphisms (SNP) or 770,000 SNP. The log R ratio (LRR) was used as an indicator of CNV. Genetic correlations were used to find CNV in the genome (neighboring SNP with highly correlated LRR) and to find associations between CNV and traits. A spectral decomposition of the genomic relationship matrix was obtained to improve computational efficiency. We found 73 CNV regions, and 619 CNV correlated with traits. The results of this study will improve our understanding of structural variants in the cattle genome and help us in selecting more efficient animals.