RGB image-based method for phenotyping rust disease progress in pea leaves using R

• Published in: Plant methods 2023-08, Vol.19 (1), p.1-86, Article 86
• Main Authors: Osuna-Caballero, Salvador, Olivoto, Tiago, Jiménez-Vaquero, Manuel A, Rubiales, Diego, Rispail, Nicolas
• Format: Article
• Language: English
• Subjects: Analysis; Controlled conditions; Correlation coefficient; Correlation coefficients; Cultivars; Data collection; Development and progression; Disease control; Disease resistance; Diseases and pests; Drug resistance in microorganisms; Equipment and supplies; Error analysis; Evaluation; Evolution; Genotypes; Germplasm; Health aspects; Image analysis; Image processing; Image segmentation; Infection; Infections; Latency; Leaf area; Leaves; Mathematical analysis; Medical research; Medicine, Experimental; Methodology; Methods; Monitoring methods; Multiprocessing; Optimization; Parallel processing; Parameters; Pathogens; Pea; Peas; Phenotyping; Phytopathometry; Pipelining (computers); Plant breeding; Plant diseases; Rust; Rust diseases; Rust fungi; Signs and symptoms; Unmanned aerial vehicles; Visual observation; Wheat
• ISSN: 1746-4811; 1746-4811
• DOI: 10.1186/s13007-023-01069-z

Rust is a damaging disease affecting vital crops, including pea, and identifying highly resistant genotypes remains a challenge. Accurate measurement of infection levels in large germplasm collections is crucial for finding new resistance sources. Current evaluation methods rely on visual estimation of disease severity and infection type under field or controlled conditions. While they identify some resistance sources, they are error-prone and time-consuming. An image analysis system proves useful, providing an easy-to-use and affordable way to quickly count and measure rust-induced pustules on pea samples. This study aimed to develop an automated image analysis pipeline for accurately calculating rust disease progression parameters under controlled conditions, ensuring reliable data collection. A highly efficient and automatic image-based method for assessing rust disease in pea leaves was developed using R. The method's optimization and validation involved testing different segmentation indices and image resolutions on 600 pea leaflets with rust symptoms. The approach allows automatic estimation of parameters like pustule number, pustule size, leaf area, and percentage of pustule coverage. It reconstructs time series data for each leaf and integrates daily estimates into disease progression parameters, including latency period and area under the disease progression curve. Significant variation in disease responses was observed between genotypes using both visual ratings and image-based analysis. Among assessed segmentation indices, the Normalized Green Red Difference Index (NGRDI) proved fastest, analysing 600 leaflets at 60% resolution in 62 s with parallel processing. Lin's concordance correlation coefficient between image-based and visual pustule counting showed over 0.98 accuracy at full resolution. While lower resolution slightly reduced accuracy, differences were statistically insignificant for most disease progression parameters, significantly reducing processing time and storage space. NGRDI was optimal at all time points, providing highly accurate estimations with minimal accumulated error. A new image-based method for monitoring pea rust disease in detached leaves, using RGB spectral indices segmentation and pixel value thresholding, improves resolution and precision. It rapidly analyses hundreds of images with accuracy comparable to visual methods and higher than other image-based approaches. This method evaluates rust progression in pea, elim