Development and Validation of Conventional and Quantitative Polymerase Chain Reaction Assays for the Detection of Storage Rot Potato Pathogens, Phytophthora erythroseptica, Pythium ultimum and Phoma foveata

The diseases pink rot, watery wound rot and gangrene are important storage rot diseases of potato associated predominantly with Phytophthora erythroseptica (P.), Pythium ultimum (Py.) and Phoma exigua (Phoma) var. foveata respectively. Reliable molecular‐based diagnostic tests are required that will not only allow unequivocal identification of symptoms but will further advance epidemiological studies of these potato diseases to increase our understanding and contribute to more effective management and control strategies to the potato industry. Primers and probes were designed in specific regions of the internal transcribed spacer (ITS) regions to develop conventional and real‐time quantitative polymerase chain reaction (PCR) assays able to detect all possible fungal and oomycete pathogens causing pink rot, watery wound rot and gangrene. The specificity of each diagnostic assay was rigorously tested with over 500 fungal/oomycete plant pathogen isolates from potato and reference culture collections, and both conventional and real‐time PCR methods produced similar results. In terms of sensitivity, the detection limits for real‐time PCR went below ag DNA levels compared with pg DNA levels with conventional PCR. The real‐time PCR assays developed to detect Phoma foveata and Py. ultimum on tubers were suitable for the comparative C_t method (ΔΔCt) of quantification using the cytochrome oxidase gene of potato as a normalizer assay; an advantage as the need for a standard curve is eliminated. Each assay detected Phoma species (var. foveata or exigua) from naturally infected tubers showing symptoms of gangrene, and P. erythroseptica or Py. ultimum were also detected following inoculation of Russet Burbank tubers. Each diagnostic assay developed could reliably detect and distinguish between the pink rot, watery wound rot and gangrene‐causing potato pathogens.     

The effect of soil- and tuber-borne inoculum on the incidence of potato gangrene

Under optimum growing conditions neither tuber- nor soil-borne Phoma exigua var. foveata inoculum appreciably affected stand or yield of the subsequent potato crop. Seed tubers with gangrene rots caused high levels of stem and tuber symptoms when planted in var. foveata contaminated or uncontaminated land; contaminated seed tubers with no rots also produced progeny with a high gangrene potential. Sufficient soil-borne inoculum was carried over in land that produced a gangrene affected crop in the previous year to override the effect of tuber disinfection. Effective gangrene control was achieved by a combination of tuber disinfection shortly after harvest over successive years with a 1 in 5 yr potato crop rotation. Gangrene rots usually developed through injuries to the tuber periderm, rots in other tubers being associated with pustules of powdery scab (Spon-gospora subterranea).     

Development of a Genotyping Method for Potato Scab Pathogens Based on Multiplex PCR

Scab disease significantly damages potato and other root crops. Streptomyces scabiei, S. acidiscabiei, and S. turgidiscabiei are the best-known causal agents of this disease. We have developed a novel genotyping method for these potato scab pathogens using multiplex PCR, whose benefits include rapid and easy detection of multiple species. We designed a species-specific primer set (6 primers, 3 pairs) for the 16S rRNA genes and 16S–23S ITS regions of these potato scab pathogens. The specificity of the primer set was confirmed by testing 18 strains containing potato scab pathogens, other Streptomyces species, and strains of other genera. The application of the developed method to potato field soil and potato tissue samples resulted in the clear detection and identification of pathogens. Since this method is applicable to a large number of environmental samples, it is expected to be useful for a high-throughput analysis of soil and plant tissues of scab disease.     

The behaviour of potato mop-top virus in soil, and evidence for its transmission by Spongospora subterranea (Wallr.) Lagerh.

Potato mop-top virus (PMTV) was best detected in field soils by air-drying them for more than a week before remoistening and growing seedlings of Nicotiana tabacum or N. debneyi for a 6–10 week period. Infection of N. tabacum was assessed by inoculating sap from roots and shoots to Chenopodium amaranticolor. Similar inoculations from N. debneyi were far less convenient for detecting PMTV than recording leaf symptoms, but slightly more efficient. Air-dry soil retained PMTV infectivity for 9 months, when passed through a 50 μ sieve or when diluted with 10³ but not 10⁴ parts of steamed soil. Tobacco seedlings were not infected when their roots were steeped in PMTV-containing tobacco sap. Infective soils contained Spongospora subterranea, spore balls of which resisted air-drying for more than a year and passed a 50 μ sieve. Roots of susceptible seedlings were infected with PMTV when exposed to spore balls of S. subterranea taken from powdery scabs on PMTV-infected potato tubers, or to suspensions obtained by steeping, in nutrient solution, roots infected with virus-carrying cultures of S. subterranea. Plants in several families were hosts of S. subterranea, but probabilities of infection when exposed to spore balls differed greatly between families and only species of Solanaceae were good hosts. The ten species infected with PMTV when grown in infective soil or when exposed to spore balls of S. subterranea taken from PMTV-infected potato tubers are all members of this family. PMTV seems to be carried internally in S. subterranea spore balls and survived in them for at least a year. PMTV was transmitted by S. subterranea to Arran Pilot potato, causing yellow blotches in some leaves and spraing in many tubers. However, when newly infected with PMTV in the field, not all Arran Pilot tubers developed spraing. Also, although many spraing-affected or symptomless but PMTV-infected tubers carried PMTV-containing spore balls of S. subterranea, powdery scabs were rarely found near the centres of the rings of primary spraing. PMTV became established in virus-free soil when PMTV-infected tubers carrying S. subterranea were planted as ‘seed’ but not when virus-free tubers bearing powdery scabs were used. 5. subterranea seems the main, and possibly the only, vector of PMTV in the soils examined. S. subterranea did not transmit potato aucuba mosaic virus from potato to N. debneyi or Capsicum annuum.     

Detection,distribution and control of Potato mop-top virus,a soil-borne virus,in northern Europe

Potato mop-top virus (PMTV; genus Pomovirus; family Virgaviridae) is transmitted by the soil-borne Spongospora subterranea f.sp. subterranea, a protoctist that causes powdery scab on potato. PMTV is distributed widely in the potato growing areas in South and North America, Japan and northwestern Europe. This article reviews the current knowledge on detection, distribution and control of PMTV with focus on the Baltic Sea region. Since the 1980s, PMTV has caused great economic losses to potato production in the Nordic countries (Norway, Sweden, Denmark and Finland), but its occurrence in other countries of the Baltic Sea region remained unknown. To fill this knowledge gap, harmonised sampling and virus detection procedures including bioassays and serological and molecular methods were employed by 21 research institutions to detect PMTV in potato tubers and soil samples in 2005–2008. Potato growing areas were widely contaminated with PMTV in the Nordic countries. Only the main seed potato production area in northern Sweden and the High Grade seed potato production zone in Finland were negative for PMTV. Intensive and systematic surveys in Poland in 2004–2008 found no evidence of PMTV, except a single PMTV-infected tuber detected in 2008. Surveys in the Baltic countries (Lithuania, Latvia and Estonia) and northwestern Russia (Leningrad province) were negative for PMTV, except infection of minitubers in a screenhouse in Latvia in 2005. Varying percentages of tubers expressing spraing symptoms in Sweden, Norway, Denmark and Poland were infected with Tobacco rattle virus, and bioassays indicated similar results for Russia. Incidence of symptomless infections with PMTV was high in tubers of many potato cultivars. Here, we discuss the contrasting patterns of distribution of PMTV in the Baltic Sea region, factors playing a role in dispersal and establishment of PMTV in new fields and means for controlling PMTV and its spread to new areas. We emphasise the use of the current virus-specific methods for the detection of PMTV in symptomless potato tubers and the high risks of disseminating PMTV to new fields and areas in viruliferous resting spores of S. subterranea in the soil adhering to seed tubers. PMTV-resistant potato cultivars will provide the only sustainable means for preventing yield losses in the infested fields and the prospects of resistance breeding are summarised.     

Potato Root Exudation and Release of Spongospora subterranea Resting Spore Germination Stimulants are Affected by Plant and Environmental Conditions

Variation in plant and environmental conditions were studied to determine the effect thereof on the exudation of low‐molecular‐weight organic compounds by potato roots. The results of the phytochemical analyses showed that among the conditions investigated, root vigour, potato cultivar, nutrients in incubation solution and temperature influenced the number and the type of primary metabolites released. Moreover, these conditions influenced our detection of compounds known to stimulate germination of resting spores of the pathogen Spongospora subterranea, causal agent of powdery scab and root diseases of potato. We conclude that changes in plant and environmental conditions can affect the release of specific compounds that stimulate germination of S. subterranea resting spores. The impact of the factors affecting potato root exudation on subsequent disease development is discussed.     

Multiplex real‐time PCR assays for detection of four seedborne spinach pathogens

Aims

To develop multiplex TaqMan real‐time PCR assays for detection of spinach seedborne pathogens that cause economically important diseases on spinach.

Methods and Results

Primers and probes were designed from conserved sequences of the internal transcribed spacer (for Peronospora farinosa f. sp. spinaciae and Stemphylium botryosum), the intergenic spacer (for Verticillium dahliae) and the elongation factor 1 alpha (for Cladosporium variabile) regions of DNA. The TaqMan assays were tested on DNA extracted from numerous isolates of the four target pathogens, as well as a wide range of nontarget, related fungi or oomycetes and numerous saprophytes commonly found on spinach seed. Multiplex real‐time PCR assays were evaluated by detecting two or three target pathogens simultaneously. Singular and multiplex real‐time PCR assays were also applied to DNA extracted from bulked seed and single spinach seed.

Conclusions

The real‐time PCR assays were species‐specific and sensitive. Singular or multiplex real‐time PCR assays could detect target pathogens from both bulked seed samples as well as single spinach seed.

Significance and Impact of the Study

The freeze‐blotter assay that is currently routinely used in the spinach seed industry to detect and quantify three fungal seedborne pathogens of spinach (C. variabile, S. botryosum and V. dahliae) is quite laborious and takes several weeks to process. The real‐time PCR assays developed in this study are more sensitive and can be completed in a single day. As the assays can be applied easily for routine seed inspections, these tools could be very useful to the spinach seed industry.     

Susceptibility of opium poppy and pyrethrum to root infection by Spongospora subterranea

Spongospora subterranea, which causes powdery scab of potato, infects a diverse range of plant species. Crop rotation as a powdery scab management tool will be compromised if pathogen hosts exist between potato crops. Opium poppy (Papaver somniferum) and pyrethrum (Tanacetum cinerariifolium) are important crops within intensive vegetable production rotations in NW Tasmania. Measurements of S. subterranea soil inoculum within a commercial field showed pathogen amounts were substantially elevated following an opium poppy crop, which suggested host status. In glasshouse testing, opium poppy and pyrethrum were confirmed as hosts of S. subterranea, with opium poppy the more susceptible of the two. Both species were less susceptible than tomato, a known host. Observations of early growth suggested inoculation impacts on all three plant species, although at 16 (tomato and opium poppy) or 26 (pyrethrum) weeks postinoculation, only tomato had significantly reduced shoot and root development. The role of rotation crops in inoculum persistence and the possible role of S. subterranea as a minor pathogen of nonpotato crops are discussed.     

Inoculum Density and Population Dynamics of Suppressive and PathogenicStreptomycesStrains and Their Relationship to Biological Control of Potato Scab

SeveralStreptomycesstrains are capable of suppressing potato scab caused byStreptomyces scabies.Although these strains have been successful in the biocontrol of potato scab in the field, little is known about how populations of pathogenicStreptomycesin the potato rhizosphere are influenced by inoculation of the suppressive strains. The effects of inoculum densities of pathogenic and suppressiveStreptomycesstrains on their respective populations on roots and in rhizosphere soil were examined during the growing season. The relationships between inoculum density or rhizosphere population densities and disease severity were also investigated. Populations of suppressiveStreptomycesstrain 93 increased significantly on roots with increasing inoculum dose. At its highest inoculum dose, the suppressive strain reached a population density greater than 10⁶CFU/g root 14 weeks after planting. The ability of the suppressive strain to increase its populations with increasing inoculum density was hindered at high inoculum doses of the pathogen, suggesting that density-dependent competitive interactions may be occurring between the two antagonists. Strain 93 was most effective at preventing scab early in the growing season (8 weeks after planting), when tubers were most susceptible to the scab disease. Population densities of the suppressive strain in soil were more highly negatively correlated with scab severity than were populations on roots, suggesting that rhizosphere soil rather than potato roots may be the primary source of inoculum of the suppressive strain for tubers.     

Rapid detection and differentiation of Erysipelothrix spp. by a novel multiplex real‐time PCR assay

Aim: The aim of this study was to develop a multiplex real‐time PCR assay for the identification and discrimination of Erysipelothrix rhusiopathiae, tonsillarum and Erysipelothrix sp. strain 2 for direct detection of Erysipelothrix spp. from animal specimens. Methods and Results: A primer set and three species‐specific probes with different end labelling were designed from the noncoding region downstream of the 5S rRNA coding region. The sensitivity, specificity and repeatability of the assay were validated by analysing 27 Erysipelothrix spp. reference serotype strains and ten septicemia‐associated non‐Erysipelothrix spp. bacterial isolates. Cross‐reactivity with Erysipelothrix sp. strain 1 was not observed with any of the primer probe combinations. The detection limit was determined to be <10 colony forming units and as low as one genome equivalent per PCR . Further evaluation of the Erysipelothrix spp. multiplex PCR was performed by comparing an enrichment isolation culture method and a conventional differential PCR on 15 samples from pigs experimentally inoculated with Erysipelothrix spp. and 22 samples from pigs with suspected natural infection. Conclusion: The multiplex real‐time PCR assay was found to be simple, rapid, reliable, specific and highly sensitive. Significance and Impact of the Study: The developed real‐time multiplex PCR assay does not require cumbersome and lengthy cultivation steps prior to DNA extraction, obtained comparable results to enrichment isolation, and will be useful in diagnostic laboratories for rapid detection of Erysipelothrix spp.     

Major Streptomyces species associated with fissure scab of potato in South Africa including description of Streptomyces solaniscabiei sp. nov

Streptomyces species are the causal agents of several scab diseases on potato tubers. A new type of scab symptom, caused by Streptomyces species, was observed in South Africa from 2010 onwards. The disease was initially thought to be caused by a single Streptomyces species, however, subsequent isolations from similar symptoms on other potato tubers revealed diversity of the Streptomyces isolates. The objective of this study was to characterise these isolates in order to determine what are the major species involved in the disease. This was done by sequencing and phylogenetic analyses of the 16S rDNA as well as five housekeeping genes, investigation of growth on different culture media, standard phenotypic tests and scanning electron microscopy of culture morphology. The presence of the pathogenicity island (PAI) present in plant pathogenic Streptomyces species was also investigated. The genomes of eight isolates, selected from the three main clades identified, were sequenced and annotated to further clarify species boundaries. Three isolates of each of the three main clades were also inoculated onto susceptible potato cultivars in order to establish the pathogenicity of the species. The results of the phylogenetic and genome analyses revealed that there are three main species involved, namely, Streptomyces werraensis, Streptomyces pseudogriseolus and a novel Streptomyces species that is described here as Streptomyces solaniscabiei sp. nov., with strain FS70^T (=?PPPPB BD 2226^T?=?LMG 32103^T) as the type strain. The glasshouse trial results showed that all three of the Streptomyces species are capable of producing fissure scab symptoms. None of the Streptomyces isolates from fissure scab contained the full PAI and the mechanism of disease initiation still needs to be determined. Genomic comparisons also indicated that S. gancidicus Suzuki 1957 (Approved Lists 1980) is a later heterotypic synonym of S. pseudogriseolus Okami and Umezawa 1955 (Approved Lists 1980).

     

Detection of Ralstonia solanacearum Strains with a Quantitative, Multiplex, Real-Time, Fluorogenic PCR (TaqMan) Assay

A fluorogenic (TaqMan) PCR assay was developed to detect Ralstonia solanacearum strains. Two fluorogenic probes were utilized in a multiplex reaction; one broad-range probe (RS) detected all biovars of R. solanacearum, and a second more specific probe (B2) detected only biovar 2A. Amplification of the target was measured by the 5′ nuclease activity of Taq DNA polymerase on each probe, resulting in emission of fluorescence. TaqMan PCR was performed with DNA extracted from 42 R. solanacearum and genetically or serologically related strains to demonstrate the specificity of the assay. In pure cultures, detection of R. solanacearum to ≥10² cells ml⁻¹ was achieved. Sensitivity decreased when TaqMan PCR was performed with inoculated potato tissue extracts, prepared by currently recommended extraction procedures. A third fluorogenic probe (COX), designed with the potato cytochrome oxidase gene sequence, was also developed for use as an internal PCR control and was shown to detect potato DNA in an RS-COX multiplex TaqMan PCR with infected potato tissue. The specificity and sensitivity of the assay, combined with high speed, robustness, reliability, and the possibility of automating the technique, offer potential advantages in routine indexing of potato tubers and other plant material for the presence of R. solanacearum.     

Detection of the nec1 virulence gene and its correlation with pathogenicity in Streptomyces species on potato tubers and in soil using conventional and real-time PCR

AIMS: To evaluate the virulence gene nec1 as a reliable marker for the detection of pathogenic Streptomyces species on potato tubers and in soil samples using conventional and real-time quantitative PCR assays. Methods AND RESULTS: Two pairs of conventional primers (outer and nested) and one set of primers/probe for use in real-time PCR were designed to detect the necrogenic protein encoding nec1 gene of Streptomyces scabiei strain ATCC 49173(T). The conventional PCR primers were also incorporated into a multiplex PCR assay to simultaneously detect the nec1 gene in conjunction with the potato pathogens Helminthosporium solani and Colletotrichum coccodes. The specificity of each PCR assay was confirmed by testing 32 pathogenic and nonpathogenic reference strains of Streptomyces representing 12 different species and 74 uncharacterized streptomycete strains isolated from diseased tubers. A clear correlation between pathogenicity and the detection of nec1 by PCR was demonstrated. The sensitivity and specificity of both the conventional and real-time PCR assays allowed the detection of nec1 on potato tubers in the absence of visible symptoms of common scab, and in seeded soil down to a level equivalent to three S. scabiei spores per gram soil. CONCLUSIONS: Reliable and quantitative PCR techniques were developed in this study for the specific detection of the virulence gene nec1 of pathogenic Streptomyces species on potato tubers and in soil samples, and the data demonstrated a clear correlation between pathogenicity in Streptomyces species and the presence of the nec1 gene. SIGNIFICANCE AND IMPACT OF THE STUDY: Together with the DNA extraction protocols, these diagnostic methods will allow a rapid and accurate assessment of tuber and soil contamination by pathogenic Streptomyces species.     

Simultaneous detection of major blackleg and soft rot bacterial pathogens in potato by multiplex polymerase chain reaction

A multiplex polymerase chain reaction (PCR) assay for simultaneous, fast and reliable detection of the main soft rot and blackleg potato pathogens in Europe has been developed. It utilises three pairs of primers and enables detection of three groups of pectinolytic bacteria frequently found in potato, namely: Pectobacterium atrosepticum, Pectobacterium carotovorum subsp. carotovorum together with Pectobacterium wasabiae and Dickeya spp. in a multiplex PCR assay. In studies with axenic cultures of bacteria, the multiplex assay was specific as it gave positive results only with strains of the target species and negative results with 18 non‐target species of bacteria that can possibly coexist with pectinolytic bacteria in a potato ecosystem. The developed assay could detect as little as 0.01 ng µL^–1 of Dickeya sp. genomic DNA, and down to 0.1 ng µL^–1 of P. atrosepticum and P. carotovorum subsp. carotovorum genomic DNA in vitro. In the presence of competitor genomic DNA, isolated from Pseudomonas fluorescens cells, the sensitivity of the multiplex PCR decreased tenfold for P. atrosepticum and Dickeya sp., while no change was observed for P. carotovorum subsp. carotovorum and P. wasabiae. In spiked potato haulm and tuber samples, the threshold level for target bacteria was 10¹ cfu mL^–1 plant extract (10² cfu g^–1 plant tissue), 10² cfu mL^–1 plant extract (10³ cfu g^–1 plant tissue), 10³ cfu mL^–1 plant extract (10⁴ cfu g^–1 plant tissue), for Dickeya spp., P. atrosepticum and P. carotovorum subsp. carotovorum/P. wasabiae, respectively. Most of all, this assay allowed reliable detection and identification of soft rot and blackleg pathogens in naturally infected symptomatic and asymptomatic potato stem and progeny tuber samples collected from potato fields all over Poland.     

Field and glasshouse experiments on the control of potato mop-top virus

Field observations during 3 yr on a stock of potato cv. Red Craigs Royal partially infected with potato mop-top virus (PMTV) confirmed that the virus was passed by an infected mother plant to only a proportion of its progeny tubers, and showed that in this cultivar symptomless plants gave rise only to symptomless progeny. The elimination of PMTV from stocks can therefore be greatly accelerated by removing symptom-bearing plants. Infected potato tubers were not freed from PMTV by treating them at 37 °C for up to 8 wk. Treating ‘seed’ tubers bearing powdery scabs that contain PMTV-carrying resting spores of Spongospora subterranea with formaldehyde or organo-mercurial fungicide greatly decreased PMTV establishment when the tubers were planted in previously uninfective soil, but fumigation with 2-aminobutane was ineffective. Decreasing the pH of infective soil to 5-0 by applying sulphur greatly decreased the infection of potato cv. Arran Pilot with PMTV and S. subterranea in field experiments, but this treatment did not eliminate either; when the pH of treated soil was raised the transmission of PMTV resumed. Treating infective soil with a range of fungicides greatly decreased the infection of Nicotiana debneyi bait seedlings in glasshouse experiments but only calomel at 75 kg/ha controlled spread of PMTV and 5. subterranea to potato in field experiments. In other field experiments, applying zinc frit, zinc sulphate or zinc oxide to infective soil greatly decreased the spread of both to potato. The amount of zinc required increased with increase in clay content of the soil. However, treatment with zinc compounds did not eliminate PMTV-carrying vectors from soil, and when treated soil was diluted with autoclaved soil many of the bait seedlings planted in the mixture became infected. The zinc frit was phytotoxic because of its boron content but zinc sulphate and zinc oxide caused little or no decrease in tuber yield. The zinc content of potato tubers was increased but not doubled in zinc-treated plots, and during the first year after treatment the zinc content of topsoil decreased greatly. The zinc content of ryegrass grown after potatoes was greater than of potato tubers but did not reach a level considered dangerous to livestock. Treatment of soil with sulphur, zinc oxide or calomel may be useful for small plots used in the early stages of propagation of virus-tested potato clones where there is risk of infection with PMTV.     

Development and preliminary application of a triplex real‐time polymerase chain reaction assay for evaluating predation on three planthoppers in a rice ecosystem

A multiplex real‐time quantitative polymerase chain reaction (PCR) assay was developed to simultaneously detect the DNA of three rice planthoppers, that is, Sogatella furcifera (Horváth) (white‐backed planthopper), Nilaparvata lugens (Stål) (brown planthopper) and Laodelphax striatellus (Fallén) (small brown planthopper), in the gut of their predators. The sets of primers and ALLGlo probes were targeted to the regions of internal transcribed spacer 2 (ITS2) genes in nuclear ribosomal DNA (rDNA). The sensitivity, specificity and interference test for the multiplex real‐time quantitative PCR assay were analysed. The assay's detection limits were 100, 1000 and 100 copies for the white‐backed planthopper, the brown planthopper and the small brown planthopper, respectively. The specificity tests showed no cross‐reactivity with genomic DNA from 30 other dominant herbivores, saprophagous insects and predators from rice ecosystem for each planthopper species. The assay was used in a preliminary study of predation events on the three planthoppers by three major spiders viz., Pardosa pseudoannulata (Bösenberg et Strand), Ummeliata insecticeps (Bösenberg et Strand) and Tetragnatha maxillosa Thorell which each differ in their preferred microhabitat as well as their predatory habits in rice field, and the results showed their predation on each planthopper species could be well evaluated using this method. Therefore, the multiplex real‐time quantitative PCR assay provides a new tool to study the mechanisms of prey shifting and natural regulation of the three rice planthoppers by generalist predators in rice ecosystem.     

Establishment of an efficient multiplex real‐time PCR assay for human papillomavirus genotyping in cervical cytology specimens: comparison with hybrid capture II

J.‐H. Lee, N.‐W. Lee, S.‐W. Hong, Y.‐S. Nam, J.‐W. Choi and Y.‐S. Kim Establishment of an efficient multiplex real‐time PCR assay for human papillomavirus genotyping in cervical cytology specimens: comparison with hybrid capture II Objective: To establish an efficient multiplex real‐time PCR assay for 15 human papillomavirus (HPV) genotypes, we designed multiplexing parameters and compared our PCR system with the hybrid capture (HC) II test using cervical cytology samples. Methods: For preventing cross‐reactive amplifications, variable HPV genes (E1, E2, E6, E7 and L1) were targeted. The melting temperatures of all primers and probes, and the size of the PCR product were optimized for the multiplex PCR. Our PCR system was compared with the HC II assays in the detection and genotyping of HPV infection using 173 cytology smears. Discordant cases between the two assays were verified by direct HPV DNA sequencing. Results: Of 173 women, 93 (53.8%) were HPV‐positive by the HC II assay and/or the multiplex real‐time PCR assay. The HPV genotypes were determined in 92 (98.9%) of 93 cases by the multiplex real‐time PCR and/or DNA sequencing. The agreement rate between multiplex PCR and HC II methods was 91.9% (kappa = 0.84). Although the sample size of this study needs to be increased to have epidemiological significance, multiple infections and HPV 16 were the predominant type. HPV 58, 52 and 18 accounted for 25% of HPV infections. HPV 52, 58 and 31 constituted 30% of CIN 2/3. Conclusion: The multiplex real‐time PCR system shows a good and reliable clinical performance. This in house PCR assay is fast and cost‐effective for HPV genotyping and the detection of HPV co‐infection in the post‐HPV vaccination era.     

Fungus diseases on potato seed tubers planted in England and Wales, 1963-76

During 1963-76 samples of potato tubers from commercial seed stocks of cvs King Edward (14 yr), Pentland Crown (9 yr), Majestic (7 yr), Pentland Dell (3 yr), Record and Arran Pilot (2 yr) were received from farms in England and Wales. Fifty tubers from each sample were examined macroscopically for fungus diseases and eyes were excised from a 20-tuber sub-sample, incubated and examined for pathogenic fungi; 50 tubers were stored on trays to sprout and examined for diseases and sprouting in May and in most years samples of 50 tubers were wounded by dropping onto expanded metal, stored at 5° C and examined for gangrene and dry rot after 12 wk. Amounts of disease varied between years and during 14 yr black scurf and powdery scab on King Edward tended to increase and skin spot and late blight decrease. On average 44% of King Edward tubers were affected with skin spot, 25% with black scurf and 16% with powdery scab. Gangrene affected 5% of tubers and 97% of the isolates from rots were identified as Phoma exigua var. foveata. Wounding tubers increased the incidence of gangrene three-fold. During 1963-69 late blight affected 2% of King Edward tubers but fewer in later years and in other cultivars. Majestic had most common scab (44% tubers) and Arran Pilot most dry rot (9% tubers) and this disease was increased by wounding tubers. Conidiophores of Helminthosporium solani (silver scurf) were more common on excised eyes of Pentland Crown, Record and Arran Pilot than of other cultivars, and isolations from verticillate conidiophores that developed on the side of incubated eye plugs of King Edward and Majestic stocks gave pure cultures of Verticillium tricorpus (78%), V. nigrescens (9%) and V. nubilum (3%). Proportions of tubers with different diseases were affected by their country of origin; Scottish seed had most skin spot and gangrene, Irish seed most powdery scab and English seed most common scab, late blight and H. solani. There was also evidence of differing disease incidence in seed from different geographical areas in Scotland and England. Up to half the King Edward and Pentland Crown stocks examined in 1975 and 1976 were derived from stem cuttings and average amounts of diseased tubers were similar to those in stocks not derived from stem cuttings. Annual and cultivar differences in disease incidence and effects of date of receipt of seed on farms are discussed.     

Effect of Streptomyces melanosporofaciens strain EF-76 and of chitosan on common scab of potato

The efficiency of Streptomyces melanosporofaciens strain EF-76, a geldanamycin producer, and of chitosan, a polymer derived from chitin that elicits plant defense mechanisms, to protect potato tubers against common scab was evaluated under both controlled and field conditions (years 2000 and 2001). S. melanosporofaciens EF-76 reduced disease incidence in the greenhouse assay and in the 2001 field assay. EF-76 also reduced symptom severity on potato tubers grown under field conditions. Chitosan provided a protective effect against S. scabies,the causal agent of potato common scab during the 2000 field assay by reducing both disease incidence and symptom severity. Combination of S. melanosporofaciensEF-76 and chitosan ensures a level of protection that was at least equivalent to the protection conferred by one of the two products used alone. In some instances, an additive effect of protection was observed when both products were used in combination. Combination of S. melanosporofaciensEF-76 and of chitosan thus represents a promising method of biocontrol against common scab.     

A Real‐time PCR Assay to Identify Meloidogyne minor

Meloidogyne minor is a small root‐knot nematode that causes yellow patch disease in golf courses and severe quality damage in potatoes. It was described in 2004 and has been detected in The Netherlands, England, Wales, Northern Ireland, Ireland and Belgium. The nematode often appears together with M. naasi on grasses. It causes similar symptoms on potato tubers as M. chitwoodi and M. fallax, which are both quarantine organisms in Europe. An accurate identification method therefore is required. This study describes a real‐time PCR assay that enables the identification of M. minor after extraction of nematodes from soil or plant samples. Alignments of sequences of rDNA‐ITS fragments of M. minor and five other Meloidogyne species were used to design a forward primer Mminor_f299, a specific primer Mminor_r362 and the specific MGB TaqMan probe P_Mm_MGB321. PCR with this primers and probe results in an amplicon of 64 bp. The analytical specificity of the real‐time PCR assay was assessed by assaying it on six populations of M. minor and on 10 populations of six other Meloidogyne species. Only DNA from M. minor gave positive results in this assay. The assay was able to identify M. minor using DNA from a single juvenile independent from the DNA extraction method used.