Enhancing estimation of cover crop biomass using field-based high-throughput phenotyping and machine learning models

Authors

Geng Bai, University of Nebraska-LincolnFollow
Katja Koehler-Cole, University of Nebraska-LincolnFollow
David Scoby, University of Nebraska-LincolnFollow
Vesh R. Thapa, University of Nebraska-LincolnFollow
Andrea D. Basche, University of Nebraska - LincolnFollow
Yufeng Ge, University of Nebraska-LincolnFollow

Document Type

Article

Date of this Version

1-8-2024

Citation

Bai G, Koehler-Cole K, Scoby D, Thapa VR, Basche A and Ge Y (2024) Enhancing estimation of cover crop biomass using field-based high-throughput phenotyping and machine learning models. Front. Plant Sci. 14:1277672. doi: 10.3389/fpls.2023.1277672

Comments

Open acces.

Abstract

Incorporating cover crops into cropping systems offers numerous potential benefits, including the reduction of soil erosion, suppression of weeds, decreased nitrogen requirements for subsequent crops, and increased carbon sequestration. The aboveground biomass (AGB) of cover crops strongly influences their performance in delivering these benefits. Despite the significance of AGB, a comprehensive field-based high-throughput phenotyping study to quantify AGB of multiple cover crops in the U.S. Midwest has not been found. This study presents a two-year field experiment carried out in Eastern Nebraska, USA, to estimate AGB of five different cover crop species [canola (Brassica napus L.), rye (Secale cereale L.), triticale (Triticale × Triticosecale L.), vetch (Vicia sativa L.), and wheat (Triticum aestivum L.)] using high-throughput phenotyping and Machine Learning (ML) models. Destructive AGB sampling was performed three times during each spring season in 2022 and 2023. An array of morphological, spectral, thermal, and environmental features from the sensors were utilized as feature inputs of ML models. Moderately strong linear correlations between AGB and the selected features were observed. Four ML models, namely Random Forests Regression (RFR), Support Vector Regression (SVR), Partial Least Squares Regression (PLSR), and Artificial Neural Network (ANN), were investigated. Among the four models, PLSR achieved the highest Coefficient of Determination (R²) of 0.84 and the lowest Root Mean Squared Error (RMSE) of 892 kg/ha (Normalized RMSE (NRMSE) = 8.87%), indicating that PLSR could be the most appropriate method for estimating AGB of multiple cover crop species. Feature importance analysis ranked spectral features like Normalized Difference Red Edge (NDRE), Solarinduced Fluorescence (SIF), Spectral Reflectance at 485 nm (R485), and Normalized Difference Vegetation Index (NDVI) as top model features using PLSR. When utilizing fewer feature inputs, ANN exhibited better prediction performance compared to other models. Using morphological and spectral parameters as input features alone led to a R2 of 0.80 and 0.77 for AGB prediction using ANN, respectively. This study demonstrated the feasibility of high-throughput phenotyping and ML techniques for accurately estimating AGB of multiple cover crop species. Further enhancement of model performance could be achieved through additional destructive sampling conducted across multiple locations and years.