Journal of Dairy Science

Feed efficiency in dairy cattle has gained much attention recently. Due to the cost-prohibitive measurement of individual feed intakes, combining data from multiple countries is often necessary to ensure an adequate reference population. It may then be essential to model genetic heterogeneity when making inferences about feed efficiency or selecting efficient cattle using genomic information. In this study, we constructed a marker x environment interaction model that decomposed marker effects into main effects and interaction components that were specific to each environment. We compared environment-specific variance component estimates and prediction accuracies from the interaction model analyses, an across-environment analyses ignoring population stratification, and a within-environment analyses using an international feed efficiency data set. Phenotypes included residual feed intake, dry matter intake, net energy in milk, and metabolic body weight from 3,656 cows measured in 3 broadly defined environments: North America (NAM), the Netherlands (NLD), and Scotland (SAC). Genotypic data included 57,574 single nucleotide polymorphisms per animal. The interaction model gave the highest prediction accuracy for metabolic body weight, which had the largest estimated heritabilities ranging from 0.37 to 0.55. The within environment model performed the best when predicting residual feed intake, which had the lowest estimated heritabilities ranging from 0.13 to 0.41. For traits (dry matter intake and net energy in milk) with intermediate estimated heritabilities (0.21 to 0.50 and 0.17 to 0.53, respectively), performance of the 3 models was comparable. Genomic correlations between environments also were computed using variance component estimates from the interaction model. Averaged across all traits, genomic correlations were highest between NAM and NLD, and lowest between NAM and SAC. In conclusion, the interaction model provided a novel way to evaluate traits measured in multiple environments in which genetic heterogeneity may exist. This model allowed estimation of environment-specific parameters and provided genomic predictions that approached or exceeded the accuracy of competing within- or across environment models. Agriculture and Food Research Initiative Competitive Grants from the USDA National Institute of Food and Agriculture (Washington, DC) [2008-35205-18711, 2011-68004-30340]; Hatch grant from the Wisconsin Agricultural Experiment Station (Madison, WI) [MSN139239]; National Association of Animal Breeders (Columbia, MO) This project was supported by Agriculture and Food Research Initiative Competitive Grants no. 2008-35205-18711 and 2011-68004-30340 from the USDA National Institute of Food and Agriculture (Washington, DC). Support from Hatch grant no. MSN139239 from the Wisconsin Agricultural Experiment Station (Madison, WI) is acknowledged, and K. A. Weigel acknowledges partial financial support from the National Association of Animal Breeders (Columbia, MO). Public domain – authored by a U.S. government employee