Comparison of Genomic Selection Models for Exploring Predictive Ability of Complex Traits in Breeding Programs

Abstract

Traits with a complex unknown genetic architecture are common in breeding programs. However, they pose a challenge for selection due to a combination of complex environmental and pleiotropic effects that impede the ability to create mapping populations to characterize the traits genetic basis. One such trait, seedling emergence of wheat (Triticum aestivum L.) from deep planting, presents a unique opportunity to explore the best method to use and implement GS models to predict a complex trait. 17 GS models were compared using two training populations, consisting of 473 genotypes from a diverse association mapping panel (DP) phenotyped from 2015-2019 and the other training population consisting of 643 breeding lines phenotyped in 2015 and 2020 in Lind, WA with 40,368 markers. There were only a few significant differences between GS models, with support vector machines reaching the highest accuracy of 0.56 in a single breeding line trial using cross-validations. However, the consistent moderate accuracy of cBLUP and other parametric models indicates no need to implement computationally demanding non-parametric models for complex traits. There was an increase in accuracy using cross-validations from 0.40 to 0.41 and independent validations from 0.10 to 0.17 using diversity panels lines to breeding lines. The environmental effects of complex traits can be overcome by combining years of the same populations. Overall, our study showed that breeders can accurately predict and implement GS for a complex trait by using parametric models within their own breeding programs with increased accuracy as they combine training populations over the years.