The search for genetic markers and genes affecting feed efficiency in beef cattle

Feed provision is one of the highest costs of beef production and improvement in efficiency has the potential to not only increase profits for cattle producers but to decrease the environmental footprint of beef cattle production. Residual feed intake (RFI) has increasingly become the measure of choice when evaluating feed efficiency in beef cattle especially because it is independent of growth and mature size. RFI is a prime candidate for marker assisted selection (MAS) as the trait is moderately heritable and is expensive to measure. The main objective of this work is to identify the genetic component of feed efficiency, measured as RFI, by identifying genetic marker associations and quantitative trait loci (QTL) throughout the bovine genome. This work was done using ∼2,600 markers on the 29 autosomes in 460 beef cattle. The first objective was to fine map QTL for RFI in beef cattle. In total, 24 QTL for RFI were identified. No QTL were identified on BTA 8, 10, 15, 16, 27. The most significant QTL for RFI was located on BTA 3 at 82 cM (P = 7.60 x 10-5). A whole-genome association (WGA) study was also performed using the same SNPs and 150 were identified with P < 0.05. Two panels of SNPs that were maximally informative for RFI were created from these 150 SNPs using a multivariate backwards elimination model and a forward sequential molecular breeding value model (SMBV). The SMBV model contained 79 SNP which explained 49.7% of the phenotypic variance and the multivariate model contained 32 SNPs which explained 41.6%. Candidate genes based on biological function or proximity to RFI QTL were also analyzed and associations with RFI were found with SNPs in several bovine genes. In conclusion, this work has resulted in the identification of SNPs and QTL for RFI throughout the bovine genome and represents significant progress towards use for MAS for feed efficiency in beef cattle.