Real-time PCR assay detection of Hemileia vastatrix, causative agent of coffee leaf rust (CLR)

Authors: Heller, Wade; Kissinger, Karma; Brill, Eva; TORRES-CRUZ, TERRY - Purdue University; AIME, CATHERINE - Purdue University; Keith, Lisa

Submitted to: Journal of Plant Pathology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/21/2025
Publication Date: 8/11/2025
Citation: Heller, W.P., Kissinger, K.R., Brill, E., Torres-Cruz, T.J., Aime, M.C., Keith, L.M. 2025. Real-time PCR assay detection of Hemileia vastatrix, causative agent of coffee leaf rust (CLR). Journal of Plant Pathology. https://doi.org/10.1007/s42161-025-01991-2.
DOI: https://doi.org/10.1007/s42161-025-01991-2

Interpretive Summary: Hawaii is the only U.S. state to commercially grow coffee, which is the second most economically valuable specialty crop grown in the state. Up until late 2020, Hawaii’s geographic isolation and strict quarantine regulations helped distinguish the archipelago as one of the last major coffee growing regions in the world to be free of coffee leaf rust (CLR), the most devastating disease of coffee worldwide. However, in late October 2020, Hemileia vastatrix spores were detected on coffee plants on the island of Maui, and CLR quickly spread throughout the state. Early and accurate detection is a critical first step to manage this pathogen, particularly when incidence levels are low, and disease symptoms are in its early stages. For this reason, a molecular diagnostic tool was developed for rapid detection of H. vastatrix from DNA isolated directly from infected coffee leaves and excised spores.

Technical Abstract: The discovery of coffee leaf rust (CLR) on Maui and Hawaii Island in late 2020 brought the most devastating coffee disease in the world to the Hawaiian Archipelago. Its rapid spread throughout the state now threatens the survival of commercial coffee production in Hawaii. Coffee is one of the most economically important agricultural crops grown in Hawaii and is produced commercially on six islands across 7,300 acres with a raw value of more than $42.5M USD. Hemileia vastatrix, the obligate parasitic fungus that causes CLR, attacks the leaves of coffee trees, leading to severe defoliation, reduction in photosynthesis, and consequent loss of vigor and yield. High spore load and ease of dispersal make this disease extremely difficult to control and will require early and accurate detection as a critical first step to manage this pathogen when incidence levels are low and symptoms are in the early stages of development. Therefore, a molecular diagnostic real-time PCR protocol using TaqMan probe chemistry to detect targets based on simple sequence repeats (SSR) was developed. The assay provides rapid detection of H. vastatrix using DNA isolated directly from infected coffee leaves and excised spores.