Effector genomics accelerates discovery and functional profiling of potato disease resistance and phytophthora infestans avirulence genes.

Vivianne G A A Vleeshouwers,Richard G F Visser,Sophien Kamoun,Pavel Krenek,Francine Govers,Klaas Bouwmeester,Evert Jacobsen,Edwin A G Van Der Vossen,Miqia Wang,Nicolas Champouret,Hendrik Rietman,Sang-Keun Oh,Ben Vosman,Carolyn Young,Hany A El-Shemy

doi:10.1371/journal.pone.0002875

Vivianne G A A Vleeshouwers, Richard G F Visser + Show 13 more

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https://doi.org/10.1371/journal.pone.0002875

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Abstract

Potato is the world's fourth largest food crop yet it continues to endure late blight, a devastating disease caused by the Irish famine pathogen Phytophthora infestans. Breeding broad-spectrum disease resistance (R) genes into potato (Solanum tuberosum) is the best strategy for genetically managing late blight but current approaches are slow and inefficient. We used a repertoire of effector genes predicted computationally from the P. infestans genome to accelerate the identification, functional characterization, and cloning of potentially broad-spectrum R genes. An initial set of 54 effectors containing a signal peptide and a RXLR motif was profiled for activation of innate immunity (avirulence or Avr activity) on wild Solanum species and tentative Avr candidates were identified. The RXLR effector family IpiO induced hypersensitive responses (HR) in S. stoloniferum, S. papita and the more distantly related S. bulbocastanum, the source of the R gene Rpi-blb1. Genetic studies with S. stoloniferum showed cosegregation of resistance to P. infestans and response to IpiO. Transient co-expression of IpiO with Rpi-blb1 in a heterologous Nicotiana benthamiana system identified IpiO as Avr-blb1. A candidate gene approach led to the rapid cloning of S. stoloniferum Rpi-sto1 and S. papita Rpi-pta1, which are functionally equivalent to Rpi-blb1. Our findings indicate that effector genomics enables discovery and functional profiling of late blight R genes and Avr genes at an unprecedented rate and promises to accelerate the engineering of late blight resistant potato varieties.

Highlights

Despite more than a century of resistance breeding [1], late blight remains a major constraint for potato cultivation resulting in multibillion dollar annual losses in most regions of the world
As part of a wide-ranging potato improvement program, we selected ten Solanum genotypes belonging to eight wild species representing a wide taxonomic and phylogenetic diversity [16,17,18], that exhibited late blight resistance to various P. infestans isolates in multi-year laboratory and field trials (Table 1, Table S1)
To clarify the specificity spectra of these resistant plants, we assayed them with 54 putative effector genes predicted computationally from the P. infestans transcriptome to belong to the RXLR family of cytoplasmic effectors [19]

Summary

Introduction

Despite more than a century of resistance breeding [1], late blight remains a major constraint for potato cultivation resulting in multibillion dollar annual losses in most regions of the world. The recent cloning of the R genes Rpi-blb ( known as RB) [3,4] and Rpi–blb2 [5] from the sexually incompatible species S. bulbocastanum enabled transgenic engineering of resistant potatoes. Plants carrying these genes have entered the commercialization pipeline and are expected to be the first GM potatoes to be cultivated in Europe for consumption purposes [6]. In contrast to the S. demissum-derived race-specific R genes which were singly introduced and quickly overcome in the field [1], the combination of Rpi-blb and –blb is expected to remain effective to a broader spectrum of P. infestans isolates [4,5]. Knowledge of the pathogen targets of these R genes is essential for classifying them into functional and spectral categories, evaluating the likelihood of resistance durability, and devising scientifically sound stacking strategies

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