Research Article | Open Access

Volume 2026 |Article ID 100124 | https://doi.org/10.1016/j.plaphe.2025.100124

High-throughput plant phenotyping identifies and discriminates biotic and abiotic stresses in tomato

Maria Isabella Prigigallo a,^1,4 Giovanni Bubici ,^1,4 Giorgia Batelli,² Antonello Costa,² Monica De Palma,² Maria Teresa Melillo,¹ Angelo Petrozza,³ Alessandra Ruggiero,² Giorgia Sportelli,¹ Stephan Summerer,³ Pasqua Veronico,¹ Francesco Cellini,³ Marina Tucci,^2,5 Livia Stavolone,¹ Stefania Grillo ,² and Fabrizio Cillo ¹

¹Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, via Amendola 165/A, 70126, Bari, Italy
²Institute of Biosciences and Bioresources, National Research Council of Italy, via Universita, � 133, Portici, 80055, Napoli, Italy
³Agenzia Lucana Sviluppo & Innovazione in Agricoltura (ALSIA), Centro di Ricerche Metapontum Agrobios, S.S. 106 Jonica, km 448.2, Bernalda, 75010, Matera, Italy
⁴Contributed equally to the article.
⁵Deceased author.

Abstract

In the context of precision agriculture, high-throughput phenotyping (HTP) aims to rapidly and effectively identify factors that affect crop yield, enabling timely and appropriate interventions. However, interpreting data from HTP remains challenging. We performed a proximal red-green-blue (RGB)-based HTP on several tomato genotypes exposed to abiotic stress (drought) or biotic stress induced by tomato spotted wilt virus (TSWV), Pseudopyrenochaeta lycopersici (corky root rot; CRR), or Meloidogyne incognita (root-knot nematode; RKN). We aimed to determine if RGB-based HTP is effectively able to: a) distinguish the effects of biotic from abiotic stress; b) differentiate resistant/tolerant from susceptible genotypes. Our HTP data analysis produced 12 morphometric and eight colorimetric indices. Principal Component Analysis (PCA; P < 0.0001; 83 % variation explained by three PCs) showed that factors such as shoot area solidity and certain color-based indices, including the senescence index and green area, effectively differentiated biotic from abiotic stress. Morphometric parameters, including plant height, projected shoot area, and convex hull area, proved to be applicable for identifying the stress status regardless of the type of stress. HTP effectively distinguished the genotype resistant to TSWV from the susceptible ones. This task was more challenging for below-ground stresses like CRR and RKN. Different profiles of HTP indices were observed among the genotypes assayed for drought tolerance, indicating variability in their ability to withstand drought conditions. In conclusion, our findings highlight the value of RGB-based HTP as a tool for precision farming of tomatoes, enabling the identification of both biotic and abiotic stressors.