Prediction of late blight severity in a large panel of potato genotypes using low-altitude aerial images and machine learning methods

Abstract

Potato (Solanum tuberosum L.) is a staple crop crucial to global food security, yet its production is severely threatened by late blight (LB), caused by Phytophthora infestans, one of the most destructive plant diseases worldwide. Breeding programs for LB resistance have traditionally relied on labor-intensive and subjective visual assessments, which limit scalability and consistency, particularly in early-generation trials. Unmanned aerial vehicle (UAV)-based remote sensing combined with machine learning (ML) offers a promising alternative for objective, high-throughput disease phenotyping. This study evaluated the potential of UAV-derived multispectral imagery and ML techniques to estimate LB severity across large and genetically diverse potato breeding populations, comprising 2,745 clones in one trial and 492 accessions in another, conducted in Oxapampa, Pasco, Peru. We compared vegetation index-based approaches with a machine learning framework that integrates K-means clustering and Kernel Ridge Regression (KRR) and assessed their ability to capture genotypic variation and support selection decisions. NDVI consistently showed a strong correlation with visually assessed LB severity, particularly at advanced stages of disease development, enabling objective discrimination between healthy and diseased canopy tissues. However, the KRR-based approach outperformed linear NDVI-based models by capturing nonlinear relationships between spectral responses and disease progression. Estimates of LB severity derived from NDVI and KRR models, expressed as best linear unbiased estimates (BLUEs), showed strong and biologically consistent relationships with the area under the disease progress curve (AUDPC), particularly during later UAV acquisitions. Selection coincidence between UAV-derived estimates and AUDPC-based rankings was substantially higher at intermediate to advanced stages of disease progression, suggesting that UAV assessments at these stages may capture sufficient phenotypic variation to distinguish genotypes. These findings indicate that UAV-based multispectral phenotyping, especially when integrated with ML, provides a practical and scalable approach for assessing LB severity in potato breeding programs while reducing the need for time-consuming field evaluations.