Genomic prediction of seasonal forage yield in perennial ryegrass

Abstract

Background

Genomic selection has the potential to accelerate genetic gain in perennial ryegrass breeding, provided complex traits such as forage yield can be predicted with sufficient accuracy.

Methods

In this study, we compared modelling approaches and feature selection strategies to evaluate the accuracy of genomic prediction models for seasonal forage yield production.

Results

Overall, model selection had limited impact on predictive ability when using the full data set. For a baseline genomic best linear unbiased prediction model, the highest mean predictive accuracy was obtained for spring grazing (0.78), summer grazing (0.62) and second cut silage (0.56). In terms of feature selection strategies, using uncorrelated single-nucleotide polymorphisms (SNPs) had no impact on predictive ability, allowing for a potential decrease of the data set dimensions. With a genome-wide association study, we found a significant SNP marker for spring grazing, located in the genic region annotated as coding for an enzyme responsible for fucosylation of xyloglucans—major components of the plant cell wall. We also presented an approach to increase interpretability of genomic prediction models with the use of Gene Ontology enrichment analysis.

Conclusions

Approaches for feature selection will be relevant in development of low-cost genotyping platforms in support of routine and cost-effective implementation of genomic selection.