Genetic studies of root architecture provide valuable insight into the overall yield potential of chile pepper (Capsicum annuum L.) under various biotic and abiotic conditions. Phytophthora root rot , caused by soil born pathogen Phytophthora capsici, is one of the most destructive diseases of chile pepper that incur huge losses under severe infection. Rotting of the roots and crown are the primary symptoms with lesions on stem, wilting, and necrosis leading to the plant death. RhizoVision Explorer is a high throughput phenotyping tool that facilitates precise and in-depth phenotyping of root architecture. In this study, four chile pepper cultivars were planted in three replications under greenhouse conditions. A virulent isolate ‘6347’ was used to inoculate the cultivars. At maturity, shoots were removed, and roots were thoroughly washed to prepare them for scanning. A flatbed scanner was used where a transparent plastic flat allowing roots to be submerged in the water was set up to proceed with scanning and analysis using the RhizoVision Explorer. Analysis of variance (ANOVA) demonstrated significant differences between the treated and control groups coupled with strong positive correlation (r > 0.90; P < 0.001) for maximum number of roots (MNR), number of root tips (NRT), total root length (TRL), depth (DPT), maximum width (MAXW), and width-to-depth ratio (WDR). Preliminary results provided insights into root architecture under P. capsici infection and the optimization of key procedures such as root washing and scanning. Overall, the efficiency of root phenotyping using the RhizoVision Explorer under pathogen infection could be improved by modifying specific steps related to the washing and processing of chile pepper samples. Keywords: High throughput phenotyping, Phytophthora blight, root architecture
