Factors Influencing Phenomic Prediction: A Case Study on a Large Sorghum BCNAM Population

Abstract

Plant breeding efficiency is crucial to develop varieties able to cope with climate change and support food and feed value chains. Genomic prediction (GP) has been a major step in increasing this efficiency and is now routinely used in breeding programs. Recently, phenomic prediction (PP) has gained attention as a promising complementary approach to GP, further increasing the breeding programs’ efficiency. Factors impacting the predictive ability (PA) of PP have been studied on many species but are not fully clarified. In this context, we studied the impacts of spectra pre-processing, prediction methods, population structure, training set size, NIRS acquisition environment and wavelength selection on a large multi-parental sorghum population including 2498 genotypes. Our results show that PP can compete with GP, that it is less affected by population structure, and can reach its maximal PA with smaller training sets than GP, but its performances are trait dependant. We also show that NIRS can be acquired in a reference environment to perform prediction in other environments and that it is possible to randomly select as little as 10 wavelengths to perform predictions. Finally, we show that spectra pre-processing, and statistical methods have a limited and unclear impact on PA. Our study confirms that PP is a relevant trait prediction method that deserves attention to optimize breeding schemes. The main challenges for the future will be to better understand the information contained in the spectra and disentangle their genetic and proxy components to optimize the use of PP in breeding programs. Key message Phenomic prediction is promising for sorghum breeding. Geneticists’ methods may not be suited to optimally extract spectral information.

Plant phenotyping relevance

NIRSスペクトルから植物形質を予測するフェノミック予測手法を、前処理・予測法・集団構造・学習セット規模・取得環境・波長選択の観点で比較検証しており、手法が研究の中心です。

Code and data availability

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