Effect of population structure on the accuracy of genomic prediction for carcass traits in Hanwoo cattle: a simulation study

Abstract

Improvement of quantitative traits in livestock is an essential goal of animal breeding. For the achievement of this goal, an accurate breeding value estimation is needed. The genetic relationship between reference and test groups is a key factor in determining the accuracy of genomic estimated breeding value (GEBV) thus, the structure of the reference population is crucial for efficient genomic selection. By the number of sharing parents, the population structure can be divided into half-sibling and full-sibling families. Also, the population structure of Hanwoo cattle primarily consists of half-sibling families because of the production system. Therefore, comparing half-sibling and full-sibling families is challenging in the Hanwoo cattle population, yet an important issue in the direction of breeding strategy in Korea. The objective of this study was to compare the accuracy of GEBV between different family structures and investigate efficient family size in the reference population using simulated data. 6 different populations were simulated using QMSim software, and the individuals in the last generations were separated into reference and test groups. The GEBV was calculated using BLUPF90 software. Practical accuracy was between 0.36-0.52 in half-sibling families and 0.55-0.77 in full-sibling families. The increase rate of accuracy was highest at the sibling size of 20, with practical accuracy of 0.52 in half-sibling families and 0.77 in full-sibling families. As a result, the most efficient population structure for genomic prediction was a sibling size of 20 in a full-sibling family.