The success of genome-wide association (GWA) studies for the detection of sequence variation affecting complex traits in human has spurred interest in the use of large-scale high-density single nucleotide polymorphism (SNP) genotyping for the identification of quantitative trait loci (QTL) and for marker-assisted selection in model and agricultural species. A cost-effective and efficient approach for the development of a custom genotyping assay interrogating 54,001 SNP loci to support GWA applications in cattle is described. A novel algorithm for achieving a compressed inter-marker interval distribution proved remarkably successful, with median interval of 37 kb and maximum predicted gap of <350 kb. The assay was tested on a panel of 576 animals from 21 cattle breeds and six outgroup species and revealed that from 39,765 to 46,492 SNP are polymorphic within individual breeds (average minor allele frequency (MAF) ranging from 0.24 to 0.27). The assay also identified 79 putative copy number variants in cattle. Utility for GWA was demonstrated by localizing known variation for coat color and the presence/absence of horns to their correct genomic locations. The combination of SNP selection and the novel spacing algorithm allows an efficient approach for the development of high-density genotyping platforms in species having full or even moderate quality draft sequence. Aspects of the approach can be exploited in species which lack an available genome sequence. The BovineSNP50 assay described here is commercially available from Illumina and provides a robust platform for mapping disease genes and QTL in cattle.

Residual feed intake (RFI) is the difference between the actual and expected feed intake of an animal based on its BW and growth rate over a specified period. The biological mechanisms underlying the variation in feed efficiency in animals with similar BW and growth rate are not well understood. This study determined the relationship of feedlot feed efficiency, performance, and feeding behavior with digestion and energy partitioning of 27 steers. The steers were selected from a total of 306 animals based on their RFI following feedlot tests at the University of Alberta Kinsella Research Station. Selected steers were ranked into high RFI (RFI >0.5 SD above the mean, n = 11), medium RFI (RFI ± 0.5 SD above and below the mean, n = 8), and low RFI (RFI <−0.5 SD below the mean, n = 8). The respective BW ± SD for the RFI groups were 495.6 ± 12.7, 529.1 ± 18.6, and 501.2 ± 15.5 kg. Digestibility and calorimetry trials were performed on a corn-or barley-based concentrate diet in yr 1 and 2, respectively, at 2.5 × maintenance requirements. Mean DMI (g/kg of BW^0.75) during the measurements for high-, medium-, and low-RFI groups, respectively, were 82.7 ± 2.0, 78.8 ± 2.6, and 81.8 ± 2.5 and did not differ (P > 0.10). Residual feed intake was correlated with daily methane production and energy lost as methane (r = 0.44; P < 0.05). Methane production was 28 and 24% less in low-RFI animals compared with high- and medium-RFI animals, respectively. Residual feed intake tended to be associated (P < 0.10) with apparent digestibilities of DM (r = −0.33) and CP (r = −0.34). The RFI of steers was correlated with DE (r = −0.41; P < 0.05), ME (r = −0.44; P < 0.05), heat production (HP; r = 0.68; P < 0.001), and retained energy (RE; r = −0.67; P < 0.001; energy values are expressed in kcal/kg of BW^0.75). Feedlot partial efficiency of growth was correlated (P < 0.01) with methane production (r = −0.55), DE (r = 0.46), ME (r = 0.49), HP (r = −0.50), and RE (r = 0.62). With the exception of HP (r = 0.37; P < 0.05), feed conversion ratio was unrelated to the traits considered in the study. Feeding duration was correlated (P < 0.01) with apparent digestibility of DM (r = −0.55), CP (r = −0.47), methane production (r = 0.51), DE (r = −0.52), ME (r = −0.55), and RE (r = −0.60). These results have practical implications for the selection of animals that eat less at a similar BW and growth rate and for the environmental sustainability of beef production.

We describe the organization of a nascent international effort, the Functional Annotation of Animal Genomes (FAANG) project, whose aim is to produce comprehensive maps of functional elements in the genomes of domesticated animal species.