Dr. Lina Quesada, NC State University

Applied genomics for disease management in vegetable crops

Lina Quesada, Ph.D., Professor and University Faculty Scholar at NC State University

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Abstract

Pseudoperonospora cubensis, an obligate oomycete pathogen, causes cucurbit downy mildew (CDM) on a broad range of host plants including cucumber, cantaloupe, watermelon, pumpkin, and squash. In 2004, CDM re-emerged in the United States (US) by overcoming host resistance in cucumber and fungicides used for disease control in other cucurbits. Population genetics analysis revealed two host-adapted clades in P. cubensis with clade 1 preferentially infecting squash, pumpkin, and watermelon, and clade 2 infecting cucumber and cantaloupe. Using Next Generation Sequencing (NGS), species-specific and host-preference diagnostic markers were identified in the nuclear genome and developed into qPCR assays. Clade-specific assays were able to detect low amounts of P. cubensis sporangia sampled using spore traps as a first step to develop a biosurveillance system for CDM. Assays to detect resistance to Carboxylic Acid Amide (CAA) and Quinone Outside Inhibitor (QoI) fungicides were also developed and indicated widespread fungicide resistance in both clades for QoIs but showed that clade 2 isolates are less sensitive to CAAs than clade 1. Similarly, effector repertoire analyses in clade 1 and clade 2 isolates revealed effectors with clade specific occurrence or expression during host colonization. Overall, findings indicate that understanding population clade composition is critical for effective management of P. cubensis using crop-specific cultural practices, chemical control, and host resistance.

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