 a library of RXLR effector genes predicted computationally from the P. infestans genome to screen wild Solanum species (related to potato and tomato) for induction of hypersensitive responses indicating the presence of a plant R gene. A set of 54 effectors were expressed in planta using a Potato virus × (PVX) agroinfection assay optimized for Solanum. This led to the identification of AVRblb1, the effector protein recognized by the Solanum bulbocastanum (wild potato species) resistance protein Rpi-blb1. In a similar study, the S. bulbocastanum resistance gene Rpi-blb2 was co-expressed with a PVX-based library of 62 P. infestans RXLR effector clones in N. benthamiana. This approach allowed the identification of the corresponding effector Avrblb2 [60]. Both Rpi-blb1 and Rpi-blb2 are considered broad-spectrum resistance genes, and the availability of the corresponding Avr genes could assist the use of these R genes in agriculture [29].
In addition, the use of effectors in large-scale screens of germplasm has facilitated the discovery of new resistance genes and their classification into discrete recognition specificities, accelerating the cloning of R genes while avoiding redundant cloning efforts [61, 62, 65]. Effectors can be used to identify R gene homologs in plant species that are more compatible for breeding. These strategies are nicely illustrated by the work of Vleeshouwers et al. [61], in which the screen of several wild Solanum species with a set of predicted P. infestans RXLR effectors led to the discovery and rapid cloning of Solanum stoloniferum Rpi-sto1 and Solanum papita Rpi-pta1, both functionally equivalent to S. bulbocastanum Rpi-blb1, with the additional advantage that S. stoloniferum and S. papita are sexually more compatible with potato, which would facilitate the introgression of this resistance specificity into commercial potato cultivars.
Recently, high-throughput effector screens have also proved useful for dissecting the complex genetic basis of the late blight resistance in the potato cultivar Sarpo Mira, which has both qualitative and quantitative ('field' resistance) components [66]. This analysis identified Rpi-Smira2, an R protein conferring partial resistance on recognition of the P. infestans RXLR effector AVRSmira2. AvrSmira2 is diagnostic of field resistance to late blight and can be used to accelerate the breeding and cloning of Rpi-Smira2, showing that effectors can be used to map linkage of quantitative traits, facilitating quantitative resistance breeding.
Another approach in which knowledge of effectors can assist the deployment of disease resistance against oomycetes is through the monitoring of effector allele diversity in pathogen populations [29, 67, 68]. This can provide valuable information to assess the potential of a given R gene regarding its spectrum and durability, and to design control strategies based on the dynamic distribution of virulence alleles in a given population, allowing the early detection of races that can overcome the deployed R genes. For example, the P. infestans avirulence gene Avrblb1 belongs to the highly ipiO RXLR effector family. The set of ipiO variants present in a given isolate determines the outcome of the interaction between this isolate and host plants carrying the Rpi-blb1 gene, with some combinations conferring avirulence and others overcoming this resistance gene [69, 70]. Therefore, monitoring ipiO diversity in P. infestans populations can tell us whether races are evolving in the field to overcome Rpi-blb1. In addition, genome and transcriptome analysis can be used to determine the set of effector genes present and expressed during infection by isolates of a given genotype, providing information on the R genes that can be deployed to control that particular genotype. This was illustrated by Cooke et al. [54], who showed that an isolate of the P. infestans 13_A2 genotype carries intact coding sequences of Avrblb1, Avrblb2 and Avrvnt1, and that these avirulence genes are induced during infection, suggesting that the cognate R genes (Rpi-blb1, Rpi-blb2 and Rpi-vnt1) could be used to control this aggressive genotype that is predominant in UK fields.
Finally, it is also possible to expand the effector recognition specificity of a given R gene to new virulent alleles by performing artificial evolution by random mutagenesis [29], an approach that has been previously successful when applied to the PVX resistance gene Rx [71].
Pathogenomics has had a substantial impact on both basic and applied plant biology. Effectors have turned out to be effective molecular probes for a variety of plant processes, and knowledge gained from studying effectors has already had an impact on our understanding of basic plant processes, such as immune processes and cellular dynamics [5, 7]. So far, research has focused on a handful of species (Figure 2). In the future, the investigation of effectors from a diverse range of oomycetes, particularly species that alter plant development (such as those causing the deformity called 'witches' brooms') or rely on vertical transmission via plant seeds, is likely to reveal effectors that act beyond plant immunity [72]. Oomycete pathogenomics has also had a great impact on approaches to plant disease resistance breeding, an activity that has been traditionally somewhat 'blind' to the pathogen [29]. Effectors have turned out to be useful tools for probing plant germplasm for new resistance traits and are poised to improve the breeding and deployment of disease resistance genes in agriculture.
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