Effector evolution analysis for late blight pathogen resistance durability

Overview

This research program investigates the rapid evolutionary adaptation of effectors in Phytophthora infestans, the pathogen responsible for late blight in tomato and potato. The work focuses on understanding how the pathogen overcomes resistance (R) genes through gene duplication and differentiation of its effector repertoire. Recent resistance breakdowns in pyramided tomato R genes (Ph-2+Ph-3) in North Carolina underscore the urgency of this research. Findings are expected to inform strategies for designing durable host resistance, with potential extension to other pathogens including those affecting soybean.

Technical specifications

Research approach:

• Whole-genome sequencing of historic and modern P. infestans isolates to compare effector content over time
• Gene prediction and effectome analysis to identify expansion or contraction of effector families
• Allele-specific detection of known virulence determinants (e.g., Avr3a)
• In vitro evolution experiments passaging isolates across tomato genotypes carrying Ph-2, Ph-3, Ph-2+Ph-3, and Ph-5 resistance genes
• Targeted effectome sequencing (PenSeq) before and after experimental evolution to track effector changes driven by host genotype

Key findings to date:

• A large proportion of reference genes missing in historic isolates are effectors, indicating effector expansion over time
• No novel effectors unique to historical isolates were identified through gene prediction
• The virulence allele for Avr3a was detected only in modern samples
• Differential absence of homologous effectors observed among modern isolates

Technology readiness level

The research is at an early-to-mid stage of validation. Genome sequencing and gene content analysis have been completed on a foundational set of isolates (n=5 historic, n=3 modern). Isolates with differential resistance backgrounds have been collected, and in vitro evolution experiments are planned. The next critical step is targeted effectome sequencing (PenSeq) of isolates before and after the evolutionary period to evaluate host genotype-driven changes. Support is sought to advance this validation phase toward actionable insights for resistance breeding and pathogen management.