GPS Coordinates for Modelling Correlated Herd Effects in Genomic Prediction Models Applied to Hanwoo Beef Cattle

SIMPLE SUMMARY: It is widely known that the environment influences phenotypic expression and that its effects must be accounted for in genetic evaluation programs. The most used method to account for environmental effects is to add herd and the contemporary group to the model. Although generally informative, the herd effect treats different farms as independent units. However, if two farms are located physically close to each other, they potentially share correlated environmental factors. We introduce a method to model herd effects using physical distances between farms based on GPS coordinates as a proxy for the correlation matrix of these effects, aiming to account for similarities and differences between farms due to environmental factors. A population of beef cattle was used to evaluate the impact on the variance components and on the genomic prediction, of modelling herd effects as correlated, in comparison to assuming the farms as completely independent units. The main result was an increase in the reliabilities of the predicted genomic breeding values compared to reliabilities obtained with traditional models, a finding of practical relevance for genetic evaluation programs. ABSTRACT: It is widely known that the environment influences phenotypic expression and that its effects must be accounted for in genetic evaluation programs. The most used method to account for environmental effects is to add herd and contemporary group to the model. Although generally informative, the herd effect treats different farms as independent units. However, if two farms are located physically close to each other, they potentially share correlated environmental factors. We introduce a method to model herd effects that uses the physical distances between farms based on the Global Positioning System (GPS) coordinates as a proxy for the correlation matrix of these effects that aims to account for similarities and differences between farms due to environmental factors. A population of Hanwoo Korean cattle was used to evaluate the impact of modelling herd effects as correlated, in comparison to assuming the farms as completely independent units, on the variance components and genomic prediction. The main result was an increase in the reliabilities of the predicted genomic breeding values compared to reliabilities obtained with traditional models (across four traits evaluated, reliabilities of prediction presented increases that ranged from 0.05 ± 0.01 to 0.33 ± 0.03), suggesting that these models may overestimate heritabilities. Although little to no significant gain was obtained in phenotypic prediction, the increased reliability of the predicted genomic breeding values is of practical relevance for genetic evaluation programs.