Pest and pathogen losses jeopardise global food security and ever since the 19th century Irish famine, potato late blight has exemplified this threat. The causal oomycete pathogen, Phytophthora infestans, undergoes major population shifts in agricultural systems via the successive emergence and migration of asexual lineages. The phenotypic and genotypic bases of these selective sweeps are largely unknown but management strategies need to adapt to reflect the changing pathogen population. Here, we used molecular markers to document the emergence of a lineage, termed 13_A2, in the European P. infestans population, and its rapid displacement of other lineages to exceed 75% of the pathogen population across Great Britain in less than three years. We show that isolates of the 13_A2 lineage are among the most aggressive on cultivated potatoes, outcompete other aggressive lineages in the field, and overcome previously effective forms of plant host resistance. Genome analyses of a 13_A2 isolate revealed extensive genetic and expression polymorphisms particularly in effector genes. Copy number variations, gene gains and losses, amino-acid replacements and changes in expression patterns of disease effector genes within the 13_A2 isolate likely contribute to enhanced virulence and aggressiveness to drive this population displacement. Importantly, 13_A2 isolates carry intact and in planta induced Avrblb1, Avrblb2 and Avrvnt1 effector genes that trigger resistance in potato lines carrying the corresponding R immune receptor genes Rpi-blb1, Rpi-blb2, and Rpi-vnt1.1. These findings point towards a strategy for deploying genetic resistance to mitigate the impact of the 13_A2 lineage and illustrate how pathogen population monitoring, combined with genome analysis, informs the management of devastating disease epidemics.

The Irish potato famine pathogen Phytophthora infestans is predicted to secrete hundreds of effector proteins. To address the challenge of assigning biological functions to computationally predicted effector genes, we combined allele mining with high-throughput in planta expression. We developed a library of 62 infection-ready P. infestans RXLR effector clones, obtained using primer pairs corresponding to 32 genes and assigned activities to several of these genes. This approach revealed that 16 of the 62 examined effectors cause phenotypes when expressed inside plant cells. Besides the well-studied AVR3a effector, two additional effectors, PexRD8 and PexRD36 45-1 , suppressed the hypersensitive cell death triggered by the elicitin INF1, another secreted protein of P. infestans. One effector, PexRD2, promoted cell death in Nicotiana benthamiana and other solanaceous plants. Finally, two families of effectors induced hypersensitive cell death specifically in the presence of the Solanum bulbocastanum late blight resistance genes Rpi-blb1 and Rpi-blb2, thereby exhibiting the activities expected for Avrblb1 and Avrblb2. The AVRblb2 family was then studied in more detail and found to be highly variable and under diversifying selection in P. infestans. Structure-function experiments indicated that a 34-amino acid region in the C-terminal half of AVRblb2 is sufficient for triggering Rpi-blb2 hypersensitivity and that a single positively selected AVRblb2 residue is critical for recognition by Rpi-blb2.

Potato (Solanum tuberosum) is the world's third-largest food crop. It severely suffers from late blight, a devastating disease caused by Phytophthora infestans. This oomycete pathogen secretes host-translocated RXLR effectors that include avirulence (AVR) proteins, which are targeted by resistance (R) proteins from wild Solanum species. Most Solanum R genes appear to have coevolved with P. infestans at its center of origin in central Mexico. Various R and Avr genes were recently cloned, and here we catalog characterized R-AVR pairs. We describe the mechanisms that P. infestans employs for evading R protein recognition and discuss partial resistance and partial virulence phenotypes in the context of our knowledge of effector diversity and activity. Genome-wide catalogs of P. infestans effectors are available, enabling effectoromics approaches that accelerate R gene cloning and specificity profiling. Engineering R genes with expanded pathogen recognition has also become possible. Importantly, monitoring effector allelic diversity in pathogen populations can assist in R gene deployment in agriculture.

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.

Phytophthora infestans , the agent of potato and tomato late blight disease, produces a 10-kD extracellular protein, INF1 elicitin. INF1 induces a hypersensitive response in a restricted number of plants, particularly those of the genus Nicotiana. In virulence assays with different P. infestans isolates, five Nicotiana species displayed resistance responses. In all of the interactions, after inoculation with P. infestans zoospores, penetration of an epidermal cell was observed, followed by localized necrosis typical of a hypersensitive response. To determine whether INF1 functions as an avirulence factor in these interactions, we adopted a gene-silencing strategy to inhibit INF1 production. Several transformants deficient in inf1 mRNA and INF1 protein were obtained. These strains remained pathogenic on host plants. However, in contrast to the wild-type and control transformant strains, INF1-deficient strains induced disease lesions when inoculated on N. benthamiana . These results demonstrate that the elicitin INF1 functions as an avirulence factor in the interaction between N. benthamiana and P. infestans . INTRODUCTIONMicrobial plant pathogens often exhibit high degrees of specialization and can only infect a limited number of plant species (Agrios, 1988). Pathogen specialization results when a complex set of preformed and induced mechanisms is put into motion to defend a plant against invading pathogens. In some interactions, preformed physical barriers and antimicrobial compounds in the plant help to ward off pathogens (Osbourn, 1996a(Osbourn, , 1996b. In other interactions, perception by the plant of signal molecules, namely, elicitors, produced by the avirulent pathogen leads to the induction of effective defense responses, including a programmed cell death response termed the hypersensitive response (HR) (Lamb et al., 1989; Dixon and Harrison, 1990; Ebel and Scheel, 1992; Baker et al., 1997;Morel and Dangl, 1997). This model has been genetically defined by Flor's gene-for-gene hypothesis (Flor, 1956(Flor, , 1971. According to this hypothesis, a resistance reaction is determined by the simultaneous expression of a pathogen avirulence ( Avr ) gene with the corresponding plant resistance ( R ) gene (Staskawicz et al., 1995).In recent years, the gene-for-gene hypothesis has received tremendous experimental support through the identification and functional characterization of both Avr and R genes. A number of Avr genes from fungi, bacteria, and viruses were shown to encode specific elicitor proteins. This was demonstrated directly by infiltration of Avr proteins into plant leaves or indirectly by expression of Avr genes in plant cells containing the corresponding R gene (Culver and Dawson, 1991; de Wit, 1995; Alfano and Collmer, 1996;Knogge, 1996; Bonas and van den Ackerveken, 1997; van den Ackerveken and Bonas, 1997). Elicitor treatment or Avr gene expression triggers the HR and related defense responses in plants that mimic the response induced by avirulent pathogens (Hahlbrock et al., 1995; Hammond-Kosa...

SummaryComparative genomics provides a tool to utilize the exponentially increasing sequence information from model plants to clone agronomically important genes from less studied crop species. Plant disease resistance (R) loci frequently lack synteny between related species of cereals and crucifers but appear to be positionally well conserved in the Solanaceae. In this report, we adopted a local RGA approach using genomic information from the model Solanaceous plant tomato to isolate R3a, a potato gene that confers race-specific resistance to the late blight pathogen Phytophthora infestans. R3a is a member of the R3 complex locus on chromosome 11. Comparative analyses of the R3 complex locus with the corresponding I2 complex locus in tomato suggest that this is an ancient locus involved in plant innate immunity against oomycete and fungal pathogens. However, the R3 complex locus has evolved after divergence from tomato and the locus has experienced a significant expansion in potato without disruption of the flanking colinearity. This expansion has resulted in an increase in the number of R genes and in functional diversification, which has probably been driven by the co-evolutionary history between P. infestans and its host potato. Constitutive expression was observed for the R3a gene, as well as some of its paralogues whose functions remain unknown.

Potato late blight, caused by the destructive Irish famine pathogen Phytophthora infestans, is a major threat to global food security(1,2). All late blight resistance genes identified to date belong to the coiled-coil, nucleotide-binding, leucine-rich repeat class of intracellular immune receptors(3). However, virulent races of the pathogen quickly evolved to evade recognition by these cytoplasmic immune receptors(4). Here we demonstrate that the receptor-like protein ELR (elicitin response) from the wild potato Solanum microdontum mediates extracellular recognition of the elicitin domain, a molecular pattern that is conserved in Phytophthora species. ELR associates with the immune co-receptor BAK1/SERK3 and mediates broad-spectrum recognition of elicitin proteins from several Phytophthora species, including four diverse elicitins from P. infestans. Transfer of ELR into cultivated potato resulted in enhanced resistance to P. infestans. Pyramiding cell surface pattern recognition receptors with intracellular immune receptors could maximize the potential of generating a broader and potentially more durable resistance to this devastating plant pathogen.

Analysis of electrically recorded feeding behaviour of aphids was combined with colony‐development tests to search for sources of resistance to Myzus persicae (Sulzer) (Homoptera: Aphididae) in tuber‐bearing Solanum species (Solanaceae), aiming at a reduction of potato leaf roll virus (PLRV) transmission. Twenty genotypes, originating from 14 gene bank accessions, representing 13 wild tuber‐bearing Solanum spp., three Solanum tuberosum L. (potato) cultivars, and one S. tuberosum breeding line, were selected. Colony‐development tests were carried out in no‐choice experiments by placing adult aphids on plants of each genotype and counting numbers of nymphs and adults on young plants after 8 and 15 days, and on flowering plants after 14 and 30 days. Large differences were observed among genotypes: some developed small colonies and others developed large ones. Also, in a few genotypes, resistance in mature plants was different for leaves of different ages; young leaves were resistant to aphids whereas old senescent leaves were susceptible. The electrical penetration graph (DC‐EPG system) technique was used to study aphid feeding behaviour on each Solanum genotype for 6 h. Electrical penetration graph (EPG) results also showed large differences among the genotypes, indicating resistance at the leaf surface and at three different levels of plant tissue (epidermis, mesophyll, and phloem). Therefore, it was concluded that different mechanisms of resistance to M. persicae exist among the genotypes analysed. EPGs recorded from aphids on Solanum berthaultii Hawkes and Solanum tarijense Hawkes with and without glandular trichomes showed that strong surface resistance can bias EPG parameters associated with resistance located in deeper tissues. Experimental evidence is presented that the resistance to aphids in the genotypes with glandular trichomes strongly depends on these morphological structures.