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Genomics and high throughput phenomics have the potential to revolutionize the field of wheat ( Triticum aestivum  L.) breeding. Genomic selection (GS) has been used for predicting various quantitative traits in wheat, especially grain yield. However, there are few GS studies for grain protein content (GPC), which is a crucial quality determinant. Incorporation of secondary correlated traits in GS models has been demonstrated to improve accuracy. The objectives of this research were to compare performance of single and multi-trait GS models for predicting GPC and grain yield in wheat and to identify optimal growth stages for collecting secondary traits. We used 650 recombinant inbred lines from a spring wheat nested association mapping (NAM) population. The population was phenotyped over 3 years (2014–2016), and spectral information was collected at heading and grain filling stages. The ability to predict GPC and grain yield was assessed using secondary traits, univariate, covariate, and multivariate GS models for within and across cycle predictions. Our results indicate that GS accuracy increased by an average of 12% for GPC and 20% for grain yield by including secondary traits in the models. Spectral information collected at heading was superior for predicting GPC, whereas grain yield was more accurately predicted during the grain filling stage. Green normalized difference vegetation index had the largest effect on the prediction of GPC either used individually or with multiple indices in the GS models. An increased prediction ability for GPC and grain yield with the inclusion of secondary traits demonstrates the potential to improve the genetic gain per unit time and cost in wheat breeding.

Combining Genomic and Phenomic Information for Predicting Grain Protein Content and Grain Yield in Spring Wheat