Introduction

Late blight is a common and potentially devastating disease of potatoes (Solanum tuberosum L.) caused by the fungal-like pathogen Phytophthora infestans (Mont.) de Bary. Endemic to Central and possibly South America, its introduction into North America and Europe has led to pathogen population explosions which have caused a series of crop failures over the past two centuries (Bourke 1964; Fry 2008; Goodwin et al. 1994b; Yoshida et al. 2013). Late blight is infamous for its role in the Irish potato famine of the 1840s and the disease remains a major cause of significant, worldwide potato crop losses. The pathogen also infects tomato (Solanum lycopersicon L.) and other crop, weedy, and ornamental members of the Solanaceae (Platt 1999). Although worldwide crop losses have more recently been averted through disease management strategies and preventative fungicide treatments, economic losses are still estimated at several billion dollars per annum (Haverkort et al. 2008).

P. infestans belongs to the oomycetes, a destructive group of non-photosynthetic eukaryotes that are closely related to the brown algae and diatoms (Sogin and Silberman 1998). P. infestans may infect all parts of the plant, including stems, leaves, fruits, and tubers (Fig. 1). The pathogen is capable of penetrating a healthy tuber periderm which reduces yield and quality and diminishes storability by facilitating secondary infections (Smart and Fry 2001). The pathogen reproduces predominantly by asexual means in the United States and Canada via sporangia formation on infected host tissues which are readily dispersed by wind and rain (Goodwin et al. 1998; Hu et al. 2012; Kalischuk et al. 2012). These sporangia then directly initiate infection or form motile zoospores. The near-obligate pathogen often survives from season to season in infected volunteers and culled potato tubers. P. infestans is a heterothallic species with two compatible mating types, A1 and A2 (Cohen et al. 1997). Coexistence of both mating types in close proximity is usually required for sexual reproduction to occur and to allow for the formation of thick-walled resting oospores that may remain viable in the soil for many years in the absence of host tissues (Mayton et al. 2000). The presence of sexual recombination increases both the genetic variation in P. infestans populations and the survivability of the pathogen.

Fig. 1
figure 1

Late blight symptoms associated with the infection of potato and tomato by Phytophthora infestans. a A P. infestans infected potato leaf exhibiting necrosis and mycelial growth producing sporangia from the leading edge of the diseased tissue. b Tomato fruit from a backyard garden infected by the P. infestans US-23 genotype that is more aggressive on tomato than potato. This P. infestans genotype is often observed infecting potato and tomato fruit in field samples. c Late blight on a potato tuber produces necrotic brown tissue initially located close to the periderm. d A tomato stem from the field showing necrotic lesions from a P. infestans US-23 genotype infection, a characteristic usually associated with this clonal lineage. e An example of a potato field infected with the P. infestans US-23 genotype showing early symptoms of late blight infection with necrotic tissue on plants radiating out from the initial infection foci

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Late Blight Population Genetic Diversity

The late blight epidemic that has occurred over the past 5 years in the United States and Canada represents a population explosion resulting from rapid asexual reproduction of P. infestans on susceptible host tissues under favorable conditions that include high humidity and cool temperatures (Fry and Goodwin 1997b). Because these initial infections may be difficult to detect, and given the short latency period under favorable conditions, the total devastation of infected plants may occur within a few days. However, there are effective management strategies for preventing late blight, which include the timely detection of early symptoms, knowledge of weather conditions, effective fungicide spray programs, removal of possible primary inoculum sources, and the introduction of host resistance (Fry 2008).

All members of a clonal lineage are asexual descendants of a single individual and variation may occur through mutation or mitotic recombination (Anderson and Kohn 1995). A standardized framework has been developed to classify clonal lineages of P. infestans based on phenotypic and genotypic markers (Forbes et al. 1998; Cooke and Lees 2004). All members of a P. infestans genotype, that may include several different clonal lineages, exhibit many of the same characteristics. Thus, identification can assist in tracking movement of the pathogen and preventing disease losses. Genetic analysis of P. infestans populations has facilitated a proactive approach in the application of sustainable disease management practices that involve the elimination of specific pathogen genotypes and the selection of effective fungicides. Phenotypic markers available for characterizing P. infestans isolates include mating type (A1 or A2) (Gallegly and Galindo 1958), virulence (Malcolmson and Black 1966; Malcolmson 1969; Cooke et al. 2003), host preference (Kalischuk et al. 2012; Danies et al. 2013), and resistance or sensitivity to the fungicide metalaxyl (Dowley and O’Sullivan 1981; Fry et al. 1993).

Genotypic markers routinely used to characterize P. infestans isolates include the allozyme glucose-6-phosphate isomerase [Gpi] and peptidase [Pep] loci profiles (Tooley et al. 1985; Spielman et al. 1991; Goodwin et al. 1998), mitochondrial DNA (mtDNA) haplotype Ia, Ib, IIa and IIb markers (Carter et al. 1990; Griffith and Shaw 1998), and genomic DNA restriction fragment length polymorphism (RFLP) analysis with moderately repetitive nuclear DNA sequence RG57 (Goodwin et al. 1992) (Fig. 2). Although the allozyme assay may be applied to sporangia from a sporulating lesion, this technique has a relatively limited discriminatory ability. For example, the Gpi profiles of the P. infestans US-6 and US-23 or US-11 and US-24 genotypes are identical (Table 1). Analysis by RFLP provides greater resolution of P. infestans genotypes with well-characterized markers that are conserved and stringent but it also requires the isolation and propagation of the pathogen, a process that often takes weeks or months to complete (Goodwin et al. 1992; Hausner et al. 2000). Most recently, analysis of simple sequence repeats (SSRs) has been used to distinguish the P. infestans genotypes (Knapova and Gisi 2002; Lees et al. 2006). This PCR-based method may be used on small samples and sporangia from a lesion, and thereby facilitate the rapid identification of a P. infestans genotype (Cooke and Lee 2004; Lees et al. 2006; Danies et al. 2013). However, the SSR sequences are inherently hypervariable and a single P. infestans genotype often produces more than one allelic pattern (Danies et al. 2013). It is therefore often necessary to perform multiple analyses with several procedures to clearly determine the genotype of a specific P. infestans isolate.

Fig. 2
figure 2

Biochemical and molecular markers utilized to identify Phytophthora infestans genotypes. a Glucose-6-phosphate isomerase (Gpi) allozyme profile of P. infestans isolates from infected potato and tomato samples collected in 2011. Allozymes were separated on cellulose-acetate gels and stained for Gpi activity. The Gpi profiles of the P. infestans genotypes collected include US-8, Gpi 100/111/122 (lane 1); US-11, Gpi 100/100/111 (lanes 2, 7 and 8); US-23, Gpi 100/100 (Lanes 5 and 6); and US-24, Gpi 100/100/111 (lane 3). The Gpi genotype of US-11 is identical to that of US-24 (Gpi 100/100/111). b Restriction fragment length polymorphic (RFLP) profile of P. infestans isolates recovered from infected potato and tomato samples collected in 2011. P. infestans genotypes US-8 (lanes 2, 3, 4, 5 and 9), US-22 (lane 6), a variant clonal lineage US-22.l (lane 7), and US-24 (lanes 1 and 8) were determined using the RG57 probe to detect homologous EcoRI restricted genomic DNA products. c Amplified DNA products P2 (lanes 1 to 5) and P4 (lanes 8 to 12) containing variable sequences from the mitochondrial genome of P. infestans isolates. Amplicons are shown following restriction digestion with MspI (lanes 1 to 5) or EcoRI (lanes 8 to 12) and gel electrophoresis. Four mitochondrial DNA haplotypes of P. infestans designated as Ia, Ib, IIa or IIb have been previously identified through DNA amplification and restriction. All isolates of P. infestans US-8, US-22, US-23, US-24, CA-9, CA-10 and CA-11 genotypes produced the mtDNA haplotype Ia (lanes 2 to 5 and 9 to 12) and all US-11 isolates were mtDNA haplotype IIb (lanes 1 and 8). Lane 6 shows a 100 bp DNA ladder (Fermentas, ON). d) Microsatellite amplification products produced with 6-FAM-labelled oligonucleotides specific to Pi4B and analyzed with an ABI 3730xl capillary system. The P. infestans genotypes US-22 and US-23 may be distinguished by the microsatellite sequence Pi4B that gives dominant peaks with sizes of approximately 213 bp or 213 and 217 bp in size, respectively

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Table 1 Summary of the mating type, mitochondrial haplotype, Gpi allozymes, RG57 RFLP profiles, and metalaxyl sensitivity for Phytophtophora infestans isolates identified in the United States and Canada
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Evolution of Late Blight Populations in United States and Canada

Several lines of evidence indicate that P. infestans originated in the central highlands of Toluca Mexico (Goodwin et al. 1994b; Grünwald et al. 2001). The genotypic diversity of pathogen populations from this region is much greater than pathogen populations elsewhere in the world. This variation is evident from virulence differences producing races, allozyme allelic polymorphism, mating types, mtDNA haplotypes and genomic profiles with the RG57 probe and microsatellite markers (Grünwald and Flier 2005). The genetic variation observed in P. infestans populations in the highlands of central Mexico provides strong genetic evidence that the pathogen was the progeny of sexual recombination. Consistent with this observation is that both mating types of P. infestans isolates were found in the same geographic area, thereby increasing the opportunities for sexual reproduction (Gallegly and Galindo 1958; Grünwald and Flier 2005).

The spread of P. infestans from central Mexico into the United States and then to Europe had contributed to the Irish potato famine in the 1840s (Goodwin et al. 1994b). The continued spread of the P. infestans US-1 genotype in the nineteenth century subsequently led to the worldwide distribution of late blight (Fry et al. 1993). Prior to the 1980s, the only clonal lineage detected in potato-growing areas outside of Mexico consisted exclusively of the US-1 genotype or “old population”, which had the A1 mating type (Hohl and Iselin 1984; Goodwin et al. 1994b). Therefore, in most parts of the world, P. infestans populations were limited to asexual reproduction (Fry and Goodwin 1997a). Since then, a second migration that included mating type A2 from Mexico had produced dramatic changes in the pathogen populations that had previously consisted exclusively of the A1 mating type in Europe (Hohl and Iselin 1984; Spielman et al. 1991), Asia (Mosa et al. 1993), and North America (Fry et al. 1993).

In contrast to parts of Europe and Mexico where pathogen populations are genetically very diverse, the genetic structures of P. infestans in the United States and Canada remain mostly composed of clonal lineages with mating types A1 or A2 separated geographically with few opportunities for sexual reproduction (Goodwin et al. 1995, 1998). However, evidence of possible sexual reproduction has been reported in British Columbia and the Columbia Basin of Washington and Oregon (Gavino et al. 2000; Goodwin 1997; Goodwin et al. 1996) and the opportunity for sexual recombination has increased considerably since 2009 in the United States and Canada with both mating types of P. infestans having been discovered in close proximity (Fig. 3). Moreover, we have recently observed multiple recombination events in several P. infestans isolates from Ontario, in addition to the A1 and A2 mating types, found in relatively close proximity on tomatoes (Kalischuk et al. 2012; Peters et al. 2014). Perhaps tomato is a preferred host for increased P. infestans recombination and the generation of new genotypes with challenging characteristics.

Fig. 3
figure 3

Population composition of Phytophthora infestans causing late blight in Canada and the United States between 2010 and 2012 shows the ability for complete state or province genotype changes in a single year. Potato samples are indicated by circles and tomato samples are shown as squares. a Locations of P. infestans populations and mating type distribution in major potato production areas of Canada in 2010 (left) and 2011 (right), determined from samples exhibiting symptoms of late blight (Kalischuk et al. 2012; Peters et al. 2014). Distribution of the P. infestans isolates shows annual changes and in Ontario the proximity of the genotypes US-11 A1 mating type and US-22 A2 mating type relative to the recombinant genotypes CA-9 A1, CA-10 A1 and CA-11 A2. b Areas show annual changes in the general distribution and diversity of P. infestans genotypes in the United States during 2011 (left) and 2012 (right) (http://usablight.org/map; Hu et al. 2012; Danies et al. 2013; Seidl and Gevens 2013; http://edis.ifas.ufl.edu/pp301). In 2012, the P. infestans US-23 genotype emerged as the dominant clonal lineage in the United States. Continued surveillance will help determine the changing P. infestans population composition, frequency of recombination, and characteristics of any new genotypes that threaten potato and tomato production in Canada and the United States

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The P. infestans US-1 genotype (pathogenic to potato) of mating type A1 remained the predominant genotype in the United States and Canada until late 1987 when other lineages began to emerge (Goodwin et al. 1995). Genotypes US-3 and CA-1 appeared to be closely related to US-1 and might have been introduced together from the same source population in Mexico (Goodwin et al. 1994a). Analyses of variants within the clonal lineage of US-1 genotypes revealed that they were identical to the most common genotype, except for the changes in the allozyme alleles and DNA fingerprints that arose from mutation or mitotic recombination (Goodwin 1997). For example, US-1.2, US-1.3 US-1.5, and US-1.6 variants within the US-1 clonal lineage of P. infestans might have originated from mutations at DNA fingerprint loci, while US-1.1 and US-1.4 variants might have originated from mitotic recombination at DNA fingerprint loci that were heterozygous (Goodwin 1997; Goodwin et al. 1994a). The variations within a clonal lineage resulted in characteristic changes such as aggressiveness, growth rate, and colony morphology which allowed for selection by evolutionary processes, such that the selected lines proliferated while the other variants eventually disappeared (Goodwin 1997; Kalischuk et al. 2012). The US-6 genotype was introduced into the United States and Canada in the late 1980s from northwestern Mexico near Los Mochis, Sinaloa (Fry and Goodwin 1997b; Smart and Fry 2001). The US-6 genotype (A1 mating type) was the predominant genotype affecting tomato and potato populations in the United States and Canada from 1987 through 1991, however it was displaced and may now be extinct in the United States. The US-6 genotype infects both the tomato and the potato, but it seems to be particularly virulent on tomato (Goodwin et al. 1994a; Goodwin 1997; Fry and Goodwin 1997a). Thus, it has a survival advantage over the US-1 genotype because it infects both tomato and potato populations.

Prior to 1994, the phenylamide fungicide metalaxyl had been shown to be an effective systemic fungicide providing protection against late blight (Bruck et al. 1980; Fry et al. 1979). However, applications of metalaxyl created selection pressure on the pathogen, leading to the establishment of individuals in the population with increased insensitivity to the fungicide (Daggett et al. 1993). This was evident from the appearance, in the late 1970s, of metalaxyl-resistant isolates of P. infestans in European populations after only a few seasons of fungicide application (Dowley and O’Sullivan 1981). By 1993, the metalaxyl-resistant isolates of the US-7 and US-8 genotypes had displaced the metalaxyl-sensitive isolate of the US-6 genotype (Fraser et al. 1999). The P. infestans US-7 genotype was the predominant in the Columbia Basin of Washington and Oregon during 1993, and was highly pathogenic on tomatoes in addition to potatoes (Goodwin et al. 1998). The P. infestans US-8 genotype was predominant in most other potato-growing areas of Canada and the United States since the mid-1990s and displaced all other genotypes (Fraser et al. 1999; Fry and Goodwin 1997a). The P. infestans US-8 genotype was reported to have greater pathogenic fitness on the potato, with higher infection efficiency, sporulation capacity, and shorter latent period on potato foliage and tubers than other genotypes (Lambert and Currier 1997; Miller et al. 1998). The rapid spread of the US-8 genotype (A2 mating type) was most likely caused by the importation of infected seed tubers (Fraser et al. 1999; Goodwin et al. 1995, 1998).

Migration has introduced P. infestans A2 mating types from northwestern Mexico into the United States and Canada and has probably contributed to the occurrence of several new genotypes (Goodwin et al. 1998; Danies et al. 2013; Peters et al. 2014; Table 1). The increased complexity of P. infestans populations has coincided with the emergence of aggressive genotypes with fungicide resistance (Goodwin et al. 1995, 1996). For example, the metalaxyl resistant US-11 genotype (A1 mating type) devastated both tomato and potato crops in the United States in 1996 and 1997 (Gavino et al. 2000; Derie and Inglis 2001; Wangsomboondee et al. 2002). The US-11 genotype originated as an especially fit recombinant of the US-6 and US-8 genotypes and displaced both the US-1 and US-6 genotypes. By 1997, US-8 and US-11 were the predominant P. infestans genotypes affecting potato and tomato crops (Dorrance et al. 1999; Gavino et al. 2000). Between 1995 and 1998, the P. infestans US-18 and US-19 genotypes (both sensitive to metalaxyl) were affecting tomatoes in North Carolina, while the US-17 genotype was the predominant genotype affecting tomatoes elsewhere in the United States (Fraser et al. 1999; Wangsomnoondee et al. 2002). Recently, the dominant P. infestans genotypes on tomato have been US-22 and US-23 which were initially sensitive to metalaxyl but developed insensitivity within a few years (Kalischuk et al 2012; Peters et al. 2014).

Conducive weather conditions and widespread inoculum from infected tomato transplants and seed tubers has contributed to a recent late blight epidemic, causing considerable crop losses in the United States and Canada (Fry et al. 2013). For example, from 2002 to 2007, the P. infestans genotypes US-20 and US-21 were the predominant genotypes affecting tomatoes in North Carolina and Florida (Hu et al. 2012). However, inoculum distribution enabled the US-22 genotype (mating type A2) to rapidly displace the other genotypes and cause significant damage to tomato and potato growing areas in the northeastern United States and central Canada (Hu et al. 2012; Kalischuk et al. 2012). In addition, the new A1 mating type P. infestans genotypes US-23 and US-24 were found in tomato and potato-growing areas, respectively, in the northwestern United States and Canada (Kawchuk et al. 2011; Hu et al. 2012; Kalischuk et al. 2012). These genotypes showed evidence of host specialization. For example, isolates of the P. infestans US-23 genotype have been shown to produce considerably more sporangia on tomatoes as compared to potatoes (Danies et al. 2013). Genotypes US-22 and US-23 are pathogenic to both potatoes and tomatoes, although they show a preference for tomatoes, while genotype US-24 is particularly pathogenic on potatoes and less aggressive towards tomatoes (Fry et al. 2013; Rojas et al. 2014). Moreover, recent results indicate a transcontinental distribution of the US-23 P. infestans genotype on infected tomato transplants being sold commercially (Kalischuk et al. 2012). The global movement of new P. infestans genotypes, such as US-23 on tomatoes destined for backyard gardens, is a concern as shipments of infected potato seed and tomato transplants increase the genetic diversity in a region beyond the traditional north–south and east–west corridors of movement (Fry et al. 2013). As a result, the P. infestans US-23 genotype is becoming the dominant lineage in both the United States and Canada (Fig. 3).

Fungicides have been critical in preventing late blight, but several prevalent P. infestans genotypes have shown a propensity for developing insensitivity to these products. Because widely used site-specific fungicides, such as mefenoxam (the active isomer in metalaxyl), inhibit sporulation and mycelial growth inside host tissues by specifically inhibiting RNA polymearase-1, a mutation that changes the affinity of target sites could easily lead to fungicide resistance (Davidse et al. 1983). Significant variations for mefenoxam sensitivity were identified among P. infestans isolates from the different genotypes (Hu et al. 2012; Danies et al. 2013; Fry et al. 2013; Kalischuk et al. 2012). Isolates of the US-8 and US-11 genotypes were resistant to mefenoxam, while isolates of the genotypes US-22, US-23 and US-24 were initially highly sensitive to sensitive to this fungicide. Recent evidence shows a range of mefenoxam resistance among P. infestans US-22 and US-23 genotypes (Wijekoon et al. 2014; unpublished data). Studies have shown that a reduced use of fungicides lowers the selection pressure for mefonaxam-resistant strains and mixture with a contact fungicide improves efficacy and may slow the development of resistance to mefonoxam (Dowley and O’Sullivan 1985; Grünwald et al. 2001; Samouch and Cohen 1986). Also, reduced fungicide usage was associated with the recurrence of mefenoxam-sensitive strains. These observations have significant practical implications for late blight management and the continued effectiveness of systemic fungicides to control this disease.

To anticipate possible damage and control actions, and to minimize fungicide applications, late blight prediction models and forecasts based on temperature and moisture have been developed and widely used in many nations, including the United States, Canada, China, New Zealand, Egypt, and India. These models and forecasts typically utilize growth, development, and survival rates determined from experimental studies, and may also use mainly statistical relationships such as logistic regression and discriminant functions (Johnson et al. 1996). BLITECAST and WISDOM are examples of models used for monitoring and forecasting. WISDOM is a widely tested, modified version of BLIGHTCAST developed at the University of Wisconsin (Stevenson 1993). It uses standard weather data such as rainfall, temperature, and relative humidity (RH), to estimate simple predictive parameters such as how long RH exceeds 90%. Other software programs exist that make use of weather data, particularly humidity (e.g., Simblight, Lateblight, NEGfry, Jhulsacast). Improvements to the models have been made by increasing the density and reliability of weather stations distributed for collection of weather data. As is the case with other pests, such as insects and weeds, some related forecasting methods are now GIS-based, and use mapped or geo-referenced weather data as inputs. The previous history of disease at locations of interest and more detailed information such as possible fungicide resistance are believed to enhance predictive capabilities. Availability of inoculum and aspects of the pathogen life cycle may be included in either statistical or process-based modeling approaches (Skelsey et al. 2007, 2009). Additional data on the presence and pressure of the late blight pathogen may be added through the deployment of Rotorod or Burkhard spore traps (Bashi et al. 1982).

Genomic Analysis of Phytophthora Infestans

The sequenced genome of P. infestans strain T30-4 provides the genome organization and gene complement of this pathogen as well as valuable insights into our understanding of the molecular basis of pathogenicity (Haas et al. 2009). The P. infestans genome consists of a 240 megabase pair (Mb) sequence with 18,155 protein-coding genes and 74% repetitive DNA rich in transposable elements (Haas et al. 2009; Raffaele and Kamoun 2012). Results show that the P. infestans genome is comprised of blocks of gene-dense and repeat-poor sequences and blocks of gene-poor and repeat-rich sequences separated by intergenic regions or transposon islands (Gijzen 2009; Haas et al. 2009; Raffaele and Kamoun 2012). It has been suggested that the spread of repetitive sequences and also transposon elements in P. infestans might contribute to sequence-exchange mechanisms that rely on homologous recombination. Homologous-recombination within the RLXR and Crinkler (CRN) effector domains would result in higher rates of gene gain and loss, producing variation among pathogen strains that are capable of overcoming plant resistance (Gijzen 2009; Haas et al. 2009). Studies have shown that pathogen genotypes with large and flexible genomes are more likely to adapt faster to produce virulent pathotypes capable of challenging new resistance genes in host plants and new genotypes adapted to new host populations or species (Raffaele and Kamoun 2012; Wulff et al. 2007).

Several genes occupy the gene-sparse, repeat-rich regions of P. infestans and are involved in epigenetic processes that result in transcriptional or post-transcriptional modification of gene expression without the alteration of DNA sequence (Haas et al. 2009; Jiang and Tyler 2012; Raffaele et al. 2010a; Slotkin and Martienssen 2007). Small RNA, DNA methylation, and histone modulation can limit gene expression at a target locus or promoter. This may contribute in part to genome plasticity in P. infestans by regulating transposon activity and rapid gene expression changes for various characteristics such as host adaptation in lineages (Haas et al. 2009; Jiang and Tyler 2012; Raffaele et al. 2010b).

P. infestans has great potential to become virulent on resistant Solanaceous plants (Fry 2008). For P. infestans to successfully infect and colonize its host, it secretes effector proteins that alter host physiology and facilitate colonization by suppressing host defences (Haas et al. 2009; Kamoun and Smart 2005). The effectors secreted by P. infestans can be differentiated into two different types depending on their site of action. Apoplastic effectors act in the apoplast space, where they interfere with host defenses. They include inhibitors which act against plant-derived hydrolytic enzymes (protease, lipases, and glucanases) and necrotizing toxins (such as the NLPs proteins and PcF-like cysteine rich inhibitors EPI1 and EPI10 and cysteine protease inhibitors EPIC1 and EPIC2b) (Dong et al. 2014; Haas et al. 2009; Jiang and Tyler 2012; Schornack et al. 2009). Cytoplasmic effectors, namely the RXLR and CRN, are characterized by N-terminal signal peptides with conserved motifs that are required for host translocation followed by a highly diverse C-terminal domain that confers effector biochemical activity (Schornack et al. 2009; Win et al. 2007). The RXLR effectors are defined by the conserved N-terminal RXLR-dEER motif that facilitates transport of these effectors into host cells (Haas et al. 2009; Jiang et al. 2008; Whisson et al. 2007; Win et al. 2012). This domain is functionally equivalent to the conserved N-terminal LXLFLAK motif of CRN effectors (Haas et al. 2009; Schornack et al. 2010; Win et al. 2012). In total, 564 potential RXLR and 196 potential CRN effector genes from the P. infestans genome were identified based on the conserved domains and motifs within the N-termini of effectors and computational prediction of secreted signals (Haas et al. 2009; Rivas and Genin 2011; Whisson et al. 2007). Because most effectors lack similarity to known enzymes or proteins, it is challenging to elucidate the molecular mechanisms which underlie the role of effectors and the various host targets (Haas et al. 2009; Raffaele and Kamoun 2012; Schornack et al. 2010).

The disease-effector encoding genes, specifically RXRL and CRN, are most frequently located in the repeat-rich regions of the P. infestans genome that have been implicated in non-allelic-homologous-recombination (Haas et al. 2009; Raffaele et al. 2010b). This is consistent with the view that effector genes with rapidly evolving C-terminal domains encode for effector proteins which circumvent recognition by the nucleotide binding site leucine-rich repeats domain (NBS-LRR) of intracellular host receptor resistance (R) proteins, thereby evading plant defence and facilitating colonization (Haas et al. 2009; Morgan and Kamoun 2007; Kamoun and Smart 2005; Raffaele et al. 2010b). Recombination of the CRN effectors C-terminal domains occurs at the highly-conserved HVLVXXP motif that marks the junction of the CRN N-terminal and the diverse C-terminal domain, thereby increasing the diversity of effectors and their ability to overcome host resistance (Haas et al. 2009; Raffaele and Kamoun 2012; Schornack et al. 2010).

Hypersensitive late blight resistance is under the control of the plant R genes triggered by a distinct pathogen race carrying Avr genes producing effectors or pathogen-associated molecular patterns (PAMPs) that directly or indirectly elicit resistance and typically follow the gene-for-gene model (Dangl and Jones 2001; Peirce 1971; Song et al. 2003). A zig-zag model has been proposed to explain the recognition and evasion that occurs between the plant-pathogen recognition and interaction that limits the durability of R genes (Jones and Dangl 2006; Hein et al. 2009). Both potatoes and tomatoes have major genes that confer resistance to P. infestans, namely the Rpi genes in potatoes and Ph genes in tomatoes (Black et al. 1953; Oyarzun et al. 1998; Vleeshouwers et al. 2011). Initially, a total of 11 R genes (R1-R11) from Solanum demissum were characterized for potatoes (Table 2). Most of these R genes, R3 through R11 were mapped to chromosome 11 (Bradshaw et al. 2006; El-Kharbotly et al. 1994; Huang et al. 2004, 2005), while R1 (El-Kharbotly et al. 1994), R2 (Li et al. 2008), and R8 (Jo et al. 2011) were mapped to chromosomes 5, 4, and 8, respectively. These R genes were introduced into cultivated varieties worldwide. However, virulent races of P. infestans rapidly evolved to overcome the resistance, as observed for many R genes. More than 30 R genes have been identified from wild Solanum species that confer differential resistance to various Solanum species (Vleeshouwers et al. 2011; Table 2). The Ph-1-Ph3 genes from Solanum pimpenellifolium have been characterized for tomatoes (Chen et al. 2008; Panthee and Chen 2010) and Ph-1, Ph-2, and Ph-3 were mapped to chromosomes 7, 10, and 9, respectively (Table 2).

Table 2 Mapped or cloned late blight disease resistance genes derived from Solanum species
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Isolation of the R1 gene from S. demissum revealed a NBS/LRR class of protein with a nucleotide binding domain and a leucine rich repeat (Ballvora et al. 2002). Introduction of additional late blight resistant genes such as RB derived from the wild potato relative Solanum bulbocastanum, represents a promising strategy for the development of durable late blight resistant varieties (Song et al. 2003; Fig. 4). However, results show that even recently identified R genes such as RB may be quickly broken and that the P. infestans effectors are essential for elicitation and potentially suppression of resistance (Chen et al. 2012). One strategy to increase the durability of disease resistance has been to combine genes into a single variety but incompatibility loci and linkage to undesirable characteristics limits the available combinations. Advances in our understanding of the resistance-avirulence protein interactions will help identify sequences that facilitate the isolation of additional late blight resistance alleles (Vleeshouwers et al. 2008). Ensuring the availability of late blight disease resistant varieties, such as Defender, is a priority for most breeding programs as their introduction will improve yield and quality while supporting sustainable disease management practices (Novy et al. 2006).

Fig. 4
figure 4

In planta complementation with the Solanum bulbocastanum RB gene transformed into Shepody. Plants inoculated with the Phytophthora infestans US-8 genotype were photgraphed 21 days following inoculation. The plants within the left two rows show the severe late blight reaction in the parental Shepody and those in the two rows on the right containing the RB gene developed very limited disease

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Incorporation of late blight resistance into existing varieties through the transformation and production of transgenic lines is critical to the complementation studies required for gene isolation. However, restrictions related to intellectual property protection and consumer acceptance limits these transgenic potatoes to research applications. Recent efforts to develop cisgenic potato varieties through genetic engineering without any foreign sequences should address some consumer concerns (Jacobsen and Schouten 2007). Future efforts will edit specific nucleotides within loci of existing potato varieties through site-directed mutagenesis with zinc finger nuclease (ZFN) and transcription activator-like effector nuclease (TALEN) mediated homologous recombination (Gaj et al. 2013). The resulting isogenic lines would resemble tomatoes developed for disease resistance through multiple backcrosses and clonal variants of potato selected through somatic embryogenesis (Kawchuk et al. 2001; Nassar et al. 2011). In addition to providing improved late blight resistance in existing and new varieties, sequence editing would facilitate the design of new late blight resistant alleles recognizing epitopes conserved in PAMPs to provide durable protection against emerging races of P. infestans.

Conclusions

The effective management of late blight will be improved by advances in our understanding of P. infestans characteristics and host responses. Devastating losses by a particular P. infestans population are often associated with the pathogen’s ability to overcome specific host resistance, the development of fungicide resistance, the pathogen’s adaptation to the changing environment, or some other competitive advantage. Development of new effective fungicides, such as the low environmental impact phosphites and late blight resistant potato varieties should help with sustainable management practices. However, the epidemiology of P. infestans continues to be vexing and the Irish potato famine disease still remains the greatest threat to sustainable, global potato production.