Effector-based biomarkers for monitoring phytophthora infestans host adaptation in potato and tomato

Overview

This research addresses one of the most persistent challenges in potato and tomato production: late blight disease caused by Phytophthora infestans. The work focuses on understanding how this pathogen adapts to different hosts at the molecular level and translating that knowledge into practical diagnostic tools. By identifying effector genes that change depending on which host the pathogen infects, the project aims to deliver biomarker-based monitoring systems that help growers and crop protection professionals track pathogen populations with greater precision. The ultimate goal is to enable earlier detection of host-adapted strains and more targeted disease management strategies.

Technical specifications

• Pathogen system: Phytophthora infestans, the causal agent of late blight in potato and tomato, with focus on persistent US-1 genotypes and displacing 2_A1 genotypes
• Effector profiling: RNA-sequencing approaches to compare differentially expressed effectors when isolates from tomato or potato origins are inoculated on their original versus alternative hosts
• Key effectors studied: ipiO, Avrblb2, and Avrvnt1, with ipiO showing distinct variant profiles between tomato-adapted US-1 and 2_A1 genotypes not found in potato-adapted US-1
• Biomarker platform: Kompetitive Allele Specific PCR (KASP) technology for designing and validating host-adaptation biomarkers
• Validation approach: Allele-specific PCR comparing 20 tomato-adapted US-1, 20 potato-adapted US-1, and 20 potato 2_A1 DNA samples for effector variation
• Future scope: Genome-wide identification of effectors underlying host specialization across the P. infestans pathosystem

Technology readiness level

The research is currently at an early-to-mid stage of development. Preliminary allele-specific PCR validation has been completed on a defined sample set and identified ipiO as a candidate effector with host-associated variant patterns. RNA-sequencing data already exists and is awaiting detailed analysis. The next phase involves expanding to genome-wide effector discovery, validating differentially expressed effector genes, and designing and testing KASP-based biomarkers. A one-year partnership is sought to support data analysis, biomarker validation, and funding of key personnel to advance the technology toward field-ready diagnostic application.