Enhancing genomic-based forward prediction accuracy in wheat by integrating UAV-derived hyperspectral and environmental data with machine learning under heat-stressed environments.

Abstract

Integrating genomic, hyperspectral imaging (HSI), and environmental data enhances wheat yield predictions, with HSI providing detailed spectral insights for predicting complex grain yield (GY) traits. Incorporating HSI data with single nucleotide polymorphic markers (SNPs) resulted in a substantial improvement in predictive ability compared to the conventional genomic prediction models. Over the course of several years, the prediction ability varied due to diverse weather conditions. The most comprehensive parametric model tested, which included SNPs, HSI, and environmental covariates data, consistently achieved the best results, closely followed by machine learning (ML) approaches when considering the same omics data. For example, the most comprehensive model (M9), under the forward prediction cross-validation scheme, predicted the GY of the 2023 growing season using data from 2021 and 2022 for a correlation between predicted and observed values of 0.53. This model demonstrated superior performance compared to less complex models, emphasizing the advantage of integrating numerous data sources and their interactive effects. Furthermore, when comparing the top 25% of the predicted lines versus the corresponding observed lines with the highest GY, the M9 model returned a coincide index (CI) of 55% (i.e., in both sets, 55% of the top 25% values were common), whereas for the highest performing ML model (gradient boosting regression), the CI was of 46%. This study highlights the potential of multi-data source approaches to accelerate the selection of heat-tolerant wheat genotypes.

Plant phenotyping relevance

UAVハイパースペクトル画像を用いた小麦収量形質の推定を、ゲノム・環境データとの統合モデルで検証しており、形質予測性能の比較が研究の中心である。

Code and data availability

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