Enhancing Predictive Ability of Agronomic and Quality Traits in Ethiopian Malting Barley ( Hordeum vulgare L.) Using Spectral Variable Selection Methods
Abstract
Phenomic selection (PS) offers a cost‐effective , breeder‐friendly approach for public breeding programmes with limited access to genotyping or restricted financial resources for laboratory infrastructure. Since PS relies on high‐throughput phenotyping data, which is often derived from near‐infrared spectroscopy (NIRS) of harvested seeds, prediction is challenged by the high dimensionality and strong intercorrelation of NIRS data, which means that only a subset of wavelengths is informative. This study evaluates spectral variable selection models for predicting key morpho‐agronomic and quality traits in malt barley ( Hordeum vulgare L.) and assesses their performance under realistic breeding scenarios. Four NIRS‐based regularized regression models (Lasso, Enet, Ridge and a heritability‐filtered Ridge model) were tested to predict 10 morphological, agronomic and quality traits measured in two malt barley trials conducted during the 2022 and 2024 cropping seasons at three locations in Ethiopia using 100 genotypes in each trial. Model performance was evaluated across four practical breeding scenarios: within‐location unseen genotype prediction (WL‐uG), leave‐one‐location‐out prediction (LOLO), target environment unseen genotype prediction (TargetEnv) and across‐location wide adaptability (RuG). Accordingly, Cross‐validation identified stable, informative spectral predictors for each trait, scenario and trial. Among the models tested, Lasso and Enet consistently outperformed Ridge regression, with Enet showing the best predictive performance across scenarios. Prediction ability (r) ranged from 0.15 to 0.85 for quality traits, 0.16 to 0.79 for agronomic traits and 0.07 to 0.89 for morphological traits across scenarios. Thus, these findings underscore the importance of spectral predictor selection in improving predictive ability and demonstrate the transferability of PS in barley breeding.