Comparative Study of Single-Trait and Multi-Trait Genomic Prediction Models

Conventional genomic selection models trait individually, neglecting complex trait interactions. Multi-trait models address this by considering genetic correlations, thus improving breeding value accuracy. Despite their theoretical benefits, quantifying these models' breeding advantages across genetic backgrounds is essential. This study evaluates the benefits of multi-trait models under varying population sizes and three levels of genetic correlations (low, medium, high) using simulations based on 50 K chip data from 5000 individuals. In equal heritability scenarios, the multi-trait GBLUP model consistently outperforms single-trait models, with breeding advantages increasing with heritability. For example, with a reference population of 4500, improvements range from 0.3% to 4.1%. Notably, trait combinations with low heritability are insensitive to changes in genetic correlation, with gains remaining ≤ 0.1% across different genetic correlations under low heritability conditions. In differing heritability scenarios, the multi-trait model's benefits vary, particularly enhancing low-heritability traits when paired with high-heritability ones. Additionally, modeling time increases as genetic correlation decreases. The results of this study indicate that multi-trait models improve breeding accuracy but require more modeling time and place higher demands on algorithms and software. We recommend breeding strategies tailored to different phenotypes and genetic backgrounds to balance efficiency and accuracy.