Genomic prediction for yield and malting traits in barley using metabolomic and near-infrared spectra.

Abstract

Key message: Genetic variation for malting quality as well as metabolomic and near-infrared features was identified. However, metabolomic and near-infrared features as additional omics-information did not improve accuracy of predicted breeding values. Significant attention has recently been given to the potential benefits of metabolomics and near-infrared spectroscopy technologies for enhancing genetic evaluation in breeding programs. In this article, we used a commercial barley breeding population phenotyped for grain yield, grain protein content, and five malting quality traits: extract yield, wort viscosity, wort color, filtering speed, and β-glucan, and aimed to: (i) investigate genetic variation and heritability of metabolomic intensities and near-infrared wavelengths originating from leaf tissue and malted grain, respectively; (ii) investigate variance components and heritabilities for genomic models including metabolomics (GOBLUP-MI) or near-infrared wavelengths (GOBLUP-NIR); and (iii) evaluate the developed models for prediction of breeding values for traits of interest. In total, 639 barley lines were genotyped using an iSelect9K-Illumina barley chip and recorded with 30,468 metabolomic intensities and 141 near-infrared wavelengths. First, we found that a significant proportion of metabolomic intensities and near-infrared wavelengths had medium to high additive genetic variances and heritabilities. Second, we observed that both GOBLUP-MI and GOBLUP-NIR, increased the proportion of estimated genetic variance for grain yield, protein, malt extract, and β-glucan compared to a genomic model (GBLUP). Finally, we assessed these models to predict accurate breeding values in fivefold and leave-one-breeding-cycle-out cross-validations, and we generally observed a similar accuracy between GBLUP and GOBLUP-MI, and a worse accuracy for GOBLUP-NIR. Despite this trend, GOBLUP-MI and GOBLUP-NIR enhanced predictive ability compared to GBLUP by 4.6 and 2.4% for grain protein in leave-one-breeding-cycle-out and grain yield in fivefold cross-validations, respectively, but differences were not significant (P-value > 0.01).