Differential Susceptibility of 39 Tomato Varieties to Phytophthora infestans Clonal Lineage US-23

Transcriptome-Assisted SNP Marker Discovery for Phytophthora infestans Resistance in Solanum lycopersicum L

Late blight, caused by oomycetes Phytophthora infestans is one of the most challenging fungal diseases to manage in tomato plants (Solanum lycopersicum L.). Toward managing the disease, conventional breeding has successfully introgressed genetic loci conferring disease resistance from various wild relatives of tomato into commercial varieties. The cataloging of disease-associated SNP markers and a deeper understanding of disease-resistance mechanisms are needed to keep up with the demand for commercial varieties resistant against emerging pathogen strains. To this end, we performed transcriptome sequencing to evaluate the gene expression dynamics of tomato varieties, resistant and susceptible to Phytophthora infection. Further integrating the transcriptome dataset with large-scale public genomic data of varieties with known disease phenotypes, a panel of single nucleotide polymorphism (SNP) markers correlated with disease resistance was identified. These SNPs were then validated on 31 lines with contrasting phenotypes for late blight. The identified SNPs are located on genes coding for a putative cysteine-rich transmembrane module (CYSTM), Solyc09g098310, and a nucleotide-binding site-leucine-rich repeat protein, Solyc09g098100, close to the well-studied Ph-3 resistance locus known to have a role in plant immunity against fungal infections. The panel of SNPs generated by this study using transcriptome sequencing showing correlation with disease resistance across a broad set of plant material can be used as markers for molecular screening in tomato breeding.

Contact Reflectance Spectroscopy for Rapid, Accurate, and Nondestructive Phytophthora infestans Clonal Lineage Discrimination

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.

Genetic Structure and Subclonal Variation of Extant and Recent U.S. Lineages of Phytophthora infestans

The oomycete Phytophthora infestans is an important plant pathogen on potato and tomato crops. We examined the genetic structure of extant 20th and 21st century U.S. lineages of P. infestans and compared them with populations from South America and Mexico to examine genetic relationships and potential sources of lineages. US-23, currently the most prevalent lineage detected in the United States, shared genetic similarity primarily with the BR-1 lineage identified in the 1990s from Bolivia and Brazil. Lineages US-8, US-14, and US-24, predominantly virulent on potato, formed a cluster distinct from other U.S. lineages. Many of the other U.S. lineages shared significant genetic similarity with Mexican populations. The US-1 lineage, dominant in the mid-20th century, clustered with US-1 lineages from Peru. A survey of the presence of RXLR effector PiAVR2 revealed that some lineages carried PiAVR2, its resistance-breaking variant PiAVR2-like, or both. Minimum spanning networks developed from simple sequence repeat genotype datasets from USABlight outbreaks clearly showed the expansion of US-23 over a 6-year time period and geographic substructuring of some lineages in the western United States. Many clonal lineages of P. infestans in the United States have come from introductions from Mexico, but the US-23 and US-1 lineages were most likely introduced from other sources.

Five Reasons to Consider Phytophthora infestans a Reemerging Pathogen

Phytophthora infestans has been a named pathogen for well over 150 years and yet it continues to "emerge", with thousands of articles published each year on it and the late blight disease that it causes. This review explores five attributes of this oomycete pathogen that maintain this constant attention. First, the historical tragedy associated with this disease (Irish potato famine) causes many people to be fascinated with the pathogen. Current technology now enables investigators to answer some questions of historical significance. Second, the devastation caused by the pathogen continues to appear in surprising new locations or with surprising new intensity. Third, populations of P. infestans worldwide are in flux, with changes that have major implications to disease management. Fourth, the genomics revolution has enabled investigators to make tremendous progress in terms of understanding the molecular biology (especially the pathogenicity) of P. infestans. Fifth, there remain many compelling unanswered questions.