Efficiency of Factor Analysis-Based Selection Indices Under Varying Heritability and Trait-Environment Correlations

The main approach for improving multiple traits simultaneously is the selection index. The most widely used selection indices are those based on factor analysis, which overcome statistical limitations such as multicollinearity and the reliance on arbitrary weights of the classical Smith–Hazel approach and support multi-environment trials. Nevertheless, the efficiency indices are affected by factors such as genotype number, environment and trait correlation, and heritability. In this study, we simulated different scenarios varying the mentioned factors to evaluate the performance of the Factor-Analysis and Ideotype-Design-Based Index (FAI-BLUP), Multi-trait Genotype–Ideotype Distance Index (MGIDI), and Multi-Trait Stability Index (MTSI). All correlations were positive and constant within each scenario, while the ideotype sought genetic gains for traits in opposite directions. Simulations were conducted using AlphaSimR and FieldSimR, and indices were implemented via the metan package. Results showed that index efficiency was higher in scenarios with larger numbers of genotypes, low-to-moderate trait correlations, and moderate-to-high inter-environment correlations. However, strong correlations among traits, particularly when combined with high heritability, compromise selection index efficiency in scenarios with antagonistic trait objectives. Despite that, the MGIDI consistently outperformed the other indices across most scenarios. Therefore, we emphasize accounting for trait genetic architectures, genotype–trait correlations, and target environment correlations.