Potato and Tomato Late Blight Caused by Phytophthora infestans: An Overview of Pathology and Resistance Breeding

Multiple QTL for horticultural traits and quantitative resistance to Phytophthora infestans linked on Solanum habrochaites chromosome 11

Previously, a Phytophthora infestans resistance QTL from Solanum habrochaites chromosome 11 was introgressed into cultivated tomato (S. lycopersicum). Fine mapping of this resistance QTL using near-isogenic lines (NILs) revealed some co-located QTL with undesirable effects on plant size, canopy density, and fruit size traits. Subsequently, higher-resolution mapping with sub-NILs detected multiple P. infestans resistance QTL within this 9.4-cM region of chromosome 11. In our present study, these same sub-NILs were also evaluated for 17 horticultural traits, including yield, maturity, fruit size and shape, fruit quality, and plant architecture traits in replicated field experiments over 2 years. The horticultural trait QTL originally detected by fine mapping each fractionated into two or more QTL at higher resolution. A total of 34 QTL were detected across all traits, with 14% exhibiting significant QTL × environment interactions (QTL × E). QTL for many traits were co-located, suggesting either pleiotropic effects or tight linkage among genes controlling these traits. Recombination in the pericentromeric region of the introgression between markers TG147 and At4g10050 was suppressed to approximately 29.7 Mbp per cM, relative to the genomewide average of 750 kbp per cM. The genetic architecture of many of the horticultural and P. infestans resistance traits that mapped within this chromosome 11 S. habrochaites region is complex. Complicating factors included fractionation of QTL, pleiotropy or tight linkage of QTL for multiple traits, pericentromeric chromosomal location(s), and/or QTL × E. High-resolution mapping of QTL in this region would be needed to determine which specific target QTL could be useful in breeding cultivated tomato.

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

During the summers of 2012 and 2013, 39 tomato (Solanum lycopersicum) lines or varieties were evaluated for resistance to late blight in three separate field trials. In each trial, late blight was caused by field isolates of Phytophthora infestans clonal lineage US-23. Varieties with the late blight resistance genes Ph-1, Ph-2, Ph-3, and Ph-2 + Ph-3 were included, along with several heirloom varieties with grower-reported resistance and varieties with no known resistance. All six varieties with Ph-2 + Ph-3, along with NC25P, which is homozygous for Ph-3 only, showed a high level of resistance. Plum Regal F1, which is heterozygous for Ph-3 only, showed moderate resistance. Legend, the only variety with Ph-2 alone, also showed moderate resistance. Three heirloom varieties, Matt's Wild Cherry, Lemon Drop, and Mr. Stripey, showed a high level of resistance comparable with that of varieties with Ph-2 + Ph-3. New Yorker, possessing Ph-1 only, showed no resistance. Indeterminate varieties had significantly less disease than determinate varieties in two of the three trials. Overall, this study suggests that tomato varieties with both Ph-2 and Ph-3 can be used to effectively manage late blight caused by P. infestans clonal lineage US-23. Varieties possessing only Ph-2, or heterozygous for Ph-3, were better protected than those without any late blight resistance but might still require supplemental fungicide applications, while the variety that was homozygous for Ph-3 was highly resistant. Several heirloom varieties were also highly resistant, and the unknown mechanism of their resistance warrants further research. Finally, the plasticity observed in United States P. infestans populations over the past several decades necessitates continued monitoring for genetic changes within P. infestans that could lead to the breakdown of resistance reported here.

The Effect of Open-Ended High Tunnels in Western Washington on Late Blight and Physiological Leaf Roll Among Five Tomato Cultivars

A 3-year study in western Washington from 2010 to 2012 evaluated five tomato cultivars for tomato disease development and yield in open-ended high-tunnel versus open-field settings. Findings in 2010 revealed that severity of late blight, caused by Phytophthora infestans (US-11), was significantly (P = 0.002) lower in high-tunnel compared with open-field experimental plots based on area under disease progress curve (AUDPC) values of 0.02 versus 321, respectively. In spite of rescue foliar fungicide applications to open-field plots in 2011 and 2012, the mean number of late blight infections across cultivars was 1.8 to 30.8 compared with only 0 to 6.5 in high tunnels for these years. Furthermore, accumulated hours of leaf wetness were fewer in high tunnels than the open field each year (857 versus 1,060 in 2010, 598 versus 998 in 2011, and 885 versus 923 in 2012). Cultivar susceptibility to late blight could not be differentiated in high tunnels due to low disease pressure. However, all five cultivars proved susceptible in the open field, with 'Oregon Spring' consistently having the most lesions. In contrast, high-tunnel production contributed to an increased severity of physiological leaf roll compared with open-field production each year, and these values differed significantly (P = 0.0335 and 0.0252) in 2011 and 2012, respectively. AUDPC values for physiological leaf roll showed that Oregon Spring was significantly (P = <0.0001) less susceptible than other cultivars each year. Physiological leaf roll correlated positively (r values of 0.758 to 0. 960) and significantly (P < 0.05) with leaf wetness and air temperature in all years in both high-tunnel and open-field settings but the same was not true for relative humidity. Even with severe physiological leaf roll, high-tunnel production in 2010 resulted in significantly (P < 0.0001) greater total tomato yield than open-field production (35.0 versus 10.6 t ha^-1). Although a significant interaction between production system and cultivar occurred in 2011 and 2012, tomato yield always was greater in high-tunnel than open-field plots. Open-ended high tunnels offer tomato growers a potential tool for managing late blight in western Washington while also increasing yield, and could be especially useful in organic production.

N-acyl-homoserine lactones-producing bacteria protect plants against plant and human pathogens

The implementation of beneficial microorganisms for plant protection has a long history. Many rhizobia bacteria are able to influence the immune system of host plants by inducing resistance towards pathogenic microorganisms. In this report, we present a translational approach in which we demonstrate the resistance-inducing effect of Ensifer meliloti (Sinorhizobium meliloti) on crop plants that have a significant impact on the worldwide economy and on human nutrition. Ensifer meliloti is usually associated with root nodulation in legumes and nitrogen fixation. Here, we suggest that the ability of S. meliloti to induce resistance depends on the production of the quorum-sensing molecule, oxo-C14-HSL. The capacity to enhanced resistance provides a possibility to the use these beneficial bacteria in agriculture. Using the Arabidopsis-Salmonella model, we also demonstrate that the application of N-acyl-homoserine lactones-producing bacteria could be a successful strategy to prevent plant-originated infections with human pathogens.

Appraisal of artificial screening techniques of tomato to accurately reflect field performance of the late blight resistance

Late blight (LB) caused by the oomycete Phytophthora infestans continues to thwart global tomato production, while only few resistant cultivars have been introduced locally. In order to gain from the released tomato germplasm with LB resistance, we compared the 5-year field performance of LB resistance in several tomato cultigens, with the results of controlled conditions testing (i.e., detached leaflet/leaf, whole plant). In case of these artificial screening techniques, the effects of plant age and inoculum concentration were additionally considered. In the field trials, LA 1033, L 3707, L 3708 displayed the highest LB resistance, and could be used for cultivar development under Polish conditions. Of the three methods using controlled conditions, the detached leaf and the whole plant tests had the highest correlation with the field experiments. The plant age effect on LB resistance in tomato reported here, irrespective of the cultigen tested or inoculum concentration used, makes it important to standardize the test parameters when screening for resistance. Our results help show why other reports disagree on LB resistance in tomato.

Phosphite-induced changes of the transcriptome and secretome in Solanum tuberosum leading to resistance against Phytophthora infestans

BACKGROUND

Potato late blight caused by the oomycete pathogen Phytophthora infestans can lead to immense yield loss. We investigated the transcriptome of Solanum tubersoum (cv. Desiree) and characterized the secretome by quantitative proteomics after foliar application of the protective agent phosphite. We also studied the distribution of phosphite in planta after application and tested transgenic potato lines with impaired in salicylic and jasmonic acid signaling.

RESULTS

Phosphite had a rapid and transient effect on the transcriptome, with a clear response 3 h after treatment. Strikingly this effect lasted less than 24 h, whereas protection was observed throughout all time points tested. In contrast, 67 secretome proteins predominantly associated with cell-wall processes and defense changed in abundance at 48 h after treatment. Transcripts associated with defense, wounding, and oxidative stress constituted the core of the phosphite response. We also observed changes in primary metabolism and cell wall-related processes. These changes were shown not to be due to phosphate depletion or acidification caused by phosphite treatment. Of the phosphite-regulated transcripts 40% also changed with β-aminobutyric acid (BABA) as an elicitor, while the defence gene PR1 was only up-regulated by BABA. Although phosphite was shown to be distributed in planta to parts not directly exposed to phosphite, no protection in leaves without direct foliar application was observed. Furthermore, the analysis of transgenic potato lines indicated that the phosphite-mediated resistance was independent of the plant hormones salicylic and jasmonic acid.

CONCLUSIONS

Our study suggests that a rapid phosphite-triggered response is important to confer long-lasting resistance against P. infestans and gives molecular understanding of its successful field applications.

Novel Resistance in Heirloom Tomatoes and Effectiveness of Resistance in Hybrids to Phytophthora infestans US-22, US-23, and US-24 Clonal Lineages

Late blight, caused by the oomycete Phytophthora infestans, causes serious losses in tomato production worldwide. Application of fungicides is the primary means of management but cultivar resistance, primarily through Ph resistance genes from Solanum pimpinellifolium, can provide a cost-effective and environmentally sound approach to an overall disease management program. Due to highly adaptable pathogen populations, cultivar resistance against late blight is often short lived and continual assessment of disease response to new pathogen types is necessary. We evaluated the disease response of 11 tomato cultivars to one isolate from each of three clonal lineages (US-22, US-23, and US-24) of P. infestans novel to the United States to determine the efficacy of currently deployed Ph genes in hybrid cultivars and the validity of claims of resistance in heirloom cultivars. Lesion length and pathogen growth were reduced on tomato genotypes 'Plum Regal' (Ph-3) and 'Legend' (Ph-2) compared with the susceptible control 'Brandywine Red' following inoculation with one isolate (US-23) but were not significantly different from the control with an isolate of US-22. 'Mountain Magic' (Ph-2 and Ph-3) and three heirloom cultivars ('Wapsipinicon Peach', 'Matt's Wild Cherry,' and 'Pruden's Purple') had reduced lesion length and pathogen growth to all three isolates. Although the genetics of resistance are not fully understood for many of these, the heirloom cultivars may be useful for future tomato late blight breeding efforts. All of the cultivars investigated in this work are currently available and use of cultivars exhibiting reduced disease development may limit losses to late blight and reduce reliance on fungicides. Resistant cultivars also limit the production of inoculum, reducing overall late blight risk and spread in tomato and potato crops.

The Ph-3 gene from Solanum pimpinellifolium encodes CC-NBS-LRR protein conferring resistance to Phytophthora infestans

KEY MESSAGE

Ph-3 is the first cloned tomato gene for resistance to late blight and encodes a CC-NBS-LRR protein. Late blight, caused by Phytophthora infestans, is one of the most destructive diseases in tomato. The resistance (R) gene Ph-3, derived from Solanum pimpinellifolium L3708, provides resistance to multiple P. infestans isolates and has been widely used in tomato breeding programmes. In our previous study, Ph-3 was mapped into a region harbouring R gene analogues (RGA) at the distal part of long arm of chromosome 9. To further narrow down the Ph-3 interval, more recombinants were identified using the flanking markers G2-4 and M8-2, which defined the Ph-3 gene to a 26 kb region according to the Heinz1706 reference genome. To clone the Ph-3 gene, a bacterial artificial chromosome (BAC) library was constructed using L3708 and one BAC clone B25E21 containing the Ph-3 region was identified. The sequence of the BAC clone B25E21 showed that only one RGA was present in the target region. A subsequent complementation analysis demonstrated that this RGA, encoding a CC-NBS-LRR protein, was able to complement the susceptible phenotype in cultivar Moneymaker. Thus this RGA was considered the Ph-3 gene. The predicted Ph-3 protein shares high amino acid identity with the chromosome-9-derived potato resistance proteins against P. infestans (Rpi proteins).

Reassessment of QTLs for late blight resistance in the tomato accession L3708 using a restriction site associated DNA (RAD) linkage map and highly aggressive isolates of Phytophthora infestans

Tomato late blight caused by the oomycete pathogen Phytophthora infestans (Mont.) de Bary is a major threat to tomato production in cool and wet environments. Intensified outbreaks of late blight have been observed globally from the 1980s, and are associated with migration of new and more aggressive populations of P. infestans in the field. The objective of this study was to reassess late blight resistance in the wild tomato accession L3708 (Solanum pimpinellifolium L.) against pathogens of different aggressiveness. An F2:3 genetic mapping population was developed using L3708 as the paternal parent. Two isolates of P. infestans, Pi39A and Pi733, were used for inoculation. Pi733 is a highly aggressive genotype that defeats three known late blight resistance genes, Ph-1, Ph-2, and Ph-5t in tomato. In contrast, Pi39A is a less aggressive genotype that defeats only Ph-1. Restriction site Associated DNA Sequencing (RAD-Seq) technology was used to massively sequence 90 bp nucleotides adjacent to both sides of PstI restriction enzyme cutting sites in the genome for all individuals in the genetic mapping population. The RAD-seq data were used to construct a genetic linkage map containing 440 single nucleotide polymorphism markers. Quantitative trait locus (QTL) analysis identified a new disease-resistant QTL specific to Pi733 on chromosome 2. The Ph-3 gene located on chromosome 9 could be detected whichever isolates were used. This study demonstrated the feasibility and efficiency of RAD-Seq technology for conducting a QTL mapping experiment using an F2:3 mapping population, which allowed the identification of a new late blight resistant QTL in tomato.

Short stereoselective synthesis of the Phytophthora universal mating hormone α1 using lithiation/borylation reactions

The universal mating hormone α 1 of the virulent plant pathogen Phytophthora has been synthesized in 12 steps and 28 % overall yield. Key CC bond-forming steps involved the use of two lithiation/borylation reactions to couple together enantioenriched building blocks, one of which also set up the stereochemistry of the tertiary alcohol at C11. Detailed analysis showed that the diastereomeric purity of the target molecule was >91 %, the highest obtained to date.

Solanum resistance genes against Phytophthora infestans and their corresponding avirulence genes

Resistance genes against Phytophthora infestans (Rpi genes), the most important potato pathogen, are still highly valued in the breeding of Solanum spp. for enhanced resistance. The Rpi genes hitherto explored are localized most often in clusters, which are similar between the diverse Solanum genomes. Their distribution is not independent of late maturity traits. This review provides a summary of the most recent important revelations on the genomic position and cloning of Rpi genes, and the structure, associations, mode of action and activity spectrum of Rpi and corresponding avirulence (Avr) proteins. Practical implications for research into and application of Rpi genes are deduced and combined with an outlook on approaches to address remaining issues and interesting questions. It is evident that the potential of Rpi genes has not been exploited fully.

Comparative next-generation mapping of the Phytophthora infestans resistance gene Rpi-dlc2 in a European accession of Solanum dulcamara

Phytophthora infestans, the causal agent of late blight, remains the main threat to potato production worldwide. Screening of 19 accessions of Solanum dulcamara with P. infestans isolate Ipo82001 in detached leaf assays revealed strong resistance in an individual belonging to accession A54750069-1. This plant was crossed with a susceptible genotype, and an F(1) population consisting of 63 individuals was obtained. This population segregated for resistance in 1:1 ratio, both in detached leaf assays and in an open-field experiment. Presence of the formerly mapped Rpi-dlc1 gene as the cause of the observed segregating resistance could be excluded. Subsequently, AFLP analyses using 128 primer combinations enabled identification of five markers linked to a novel resistance gene named Rpi-dlc2. AFLP markers did not show sequence similarity to the tomato and potato genomes, hampering comparative genetic positioning of the gene. For this reason we used next-generation mapping (NGM), an approach that exploits direct sequencing of DNA (in our case: cDNA) pools from bulked segregants to calculate the genetic distance between SNPs and the locus of interest. Plotting of these genetic distances on the tomato and potato genetic map and subsequent PCR-based marker analysis positioned the gene on chromosome 10, in a region overlapping with the Rpi-ber/ber1 and -ber2 loci from S. berthaultii. Pyramiding of Rpi-dlc2 and Rpi-dlc1 significantly increased resistance to P. infestans, compared with individuals containing only one of the genes, showing the usefulness of this strategy to enhance resistance against Phytophthora.