Contact reflectance spectroscopy for rapid, accurate, and nondestructive phytophthora infestans clonal lineage discrimination

Kaitlin M. Gold*, Philip A. Townsend, Eric R. Larson, Ittai Herrmann, Amanda J. Gevens

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

18 Scopus citations


Populations of Phytophthora infestans, the oomycete causal agent of potato late blight in the United States, are predominantly asexual, and isolates are characterized by clonal lineage or asexual descendants of a single genotype. Current tools for clonal lineage identification are time consuming and require laboratory equipment. We previously found that foliar spectroscopy can be used for high-accuracy pre- and postsymptomatic detection of P. infestans infections caused by clonal lineages US-08 and US-23. In this work, we found subtle but distinct differences in spectral responses of potato foliage infected by these clonal lineages in both growth-chamber time-course experiments (12- to 24-h intervals over 5 days) and naturally infected samples from commercial production fields. In both settings, we measured continuous visible to shortwave infrared reflectance (400 to 2,500 nm) on leaves using a portable spectrometer with contact probe. We consistently discriminated between infections caused by the two clonal lineages across all stages of disease progression using partial least squares (PLS) discriminant analysis, with total accuracies ranging from 88 to 98%. Three-class random forest differentiation between control, US-08, and US-23 yielded total discrimination accuracy ranging from 68 to 76%. Differences were greatest during presymptomatic infection stages and progressed toward uniformity as symptoms advanced. Using PLS-regression trait models, we found that total phenolics, sugar, and leaf mass per area were different between lineages. Shortwave infrared wavelengths (>1,100 nm) were important for clonal lineage differentiation. This work provides a foundation for future use of hyperspectral sensing as a nondestructive tool for pathovar differentiation.

Original languageAmerican English
Pages (from-to)851-862
Number of pages12
Issue number4
StatePublished - 2020

Bibliographical note

Publisher Copyright:
© 2020 The American Phytopathological Society.


  • Analytical and theoretical plant pathology
  • Ecology and epidemiology
  • Techniques


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