Spatial distribution of Aphanomyces euteiches inoculum in a naturally infested pea field

The main objective of the study was to describe the horizontal and vertical distribution of Aphanomyces root rot in a naturally infested pea field. Measurements of inoculum potential clearly indicated a horizontal distribution of inoculum among several foci in the field, these foci differing in size and disease intensity. A highly significant relationship was observed between disease severity on plants during the cropping season and soil inoculum potential. In terms of the vertical distribution of inoculum in the soil, detection was maximal at a depth of 10 to 40 cm, but inoculum was detected down to a depth of 60 cm. Generally, inoculum potential was lowest for the layers at depths of 0 to 10 and 50 to 60 cm. Inoculum distribution and the value of the methodologies used are discussed in terms of possible use for epidemiology and disease forecasting.     

Successive legumes tested in a greenhouse crop rotation experiment modify the inoculum potential of soils naturally infested by Aphanomyces euteiches

The consequence of 10 successive monocultural cycles involving different legume species/cultivars on the inoculum potential (IP) of soils naturally infested by Aphanomyces euteiches was investigated under greenhouse conditions. The results showed that the IP of a soil naturally infested by A. euteiches can be significantly modified not only by the non‐host or host status of crop species but also by the level of resistance of the cultivar. Susceptible species/cultivars (pea, lentil and susceptible cultivars of vetch and faba bean) are very favourable to pathogen multiplication, and continuous cultivation of each of these increased the IP values of a soil with a moderate initial IP (from 1·9 to 3·5 after 10 cycles). Conversely, non‐host species and resistant cultivars of vetch or faba bean contributed to reducing the IP values of soils irrespective of the initial IP (from 1·9 to 0·5 and from 4 to 2, respectively, after 10 cycles). Aphanomyces root rot severity values on the resistant legume species/cultivars were not affected by the successive cultural cycles. This study, which showed that the IP of A. euteiches in soil can be reduced by planting appropriate legume species and cultivars in greenhouse conditions, will be useful for defining better crop successions for legumes.     

Aphanomyces euteiches as a component of the complex of foot and root pathogens of peas in Dutch soils

The occurrence ofAphanomyces euteiches Drechs. in Dutch soils is reported for the first time. Isolates of the pathogen were obtained from peas (Pisum sativum L.). A bioassay was used that baited the pathogen from soil into the cortex of stem and root of seedlings of a highly susceptible pea cultivar. The pathogen could subsequently be isolated on a semi-selective medium. Screening of soil samples from 13 fields known to be infested with fungi causing foot and root rot demonstrated the presence ofA. euteiches in 10 cases. In a second screening on soil samples from 43 fields, the pathogen was present in 16 cases. A positive correlation was found between the disease severity caused byA. euteiches in the seedling bioassay and the disease severity caused by the complex of foot and root pathogens in the same soils as evidenced by a mature plant bioassay. It is considered probable thatA. euteiches has since long been a common component of the foot and root rot complex in Dutch soils but has not been detected previously due to inadequate sampling and isolation techniques.Samenvatting De aanwezigheid vanAphanomyces euteiches Drechs. in Nederlandse gronden is voor het eerst aangetoond. Isolaten van het pathogeen werden verkregen van erwten (Pisum sativum L.). De pathogene schimmel werd in petrischalen uit grond in het schorsweefsel van wortel en stengel van een zeer vatbaar erwteras gelokt. Met behulp van een semiselectief medium konden vervolgens isolaten van de schimmel worden verkregen. Toetsing van grondmonsters afkomstig van 13 percelen, waarvan bekend was dat ze besmet waren met schimmels die voetziekten in erwten veroorzaken, toonde de aanwezigheid vanA. euteiches aan in 10 gevallen. In een tweede biotoets op grondmonsters van 43 percelen bleken 16 monsters het pathogeen te herbergen. Er werd een positieve correlatie gevonden tussen de ernst van de aantasting doorA. euteiches van kiemplanten en de aantasting van volwassen planten in een biotoets in de kas. Het is waarschijnlijk dat de schimmel reeds lang in Nederlandse akkers voorkomt, maar door inadequate bemonsterings- en isolatietechnieken over het hoofd is gezien.     

Host resistances to Aphanomyces trifolii root rot of subterranean clover: first opportunity to successfully manage this severe pasture disease

Subterranean clover (Trifolium subterraneum) is an important pasture legume in Australia (29 million ha) and elsewhere. However, severe pasture decline occurs in association with several root pathogens, including Aphanomyces trifolii, that has been misidentified for decades as A. euteiches until recently confirmed as A. trifolii. A series of controlled environment experiments was undertaken to identify host resistance to A. trifolii in subterranean clover and to compare virulence and phylogeny of isolates. In experiment 1, Dalkeith, Bacchus Marsh, Riverina and Yarloop were the most resistant of 38 cultivars with a percentage disease index (PDI) ≤10 for both tap and lateral roots. Experiment 2 confirmed resistance of Yarloop, but a change in some relative varietal resistances suggested physiological specialization among A. trifolii isolates. Experiment 3 confirmed extensive variation in virulence and physiological specialization across 23 isolates of A. trifolii, with three distinct clades, two of which were distinct from isolates collected previously. Experiment 4 identified host resistance(s) effective against a mixture of 20 A. trifolii isolates, but the most resistant cultivars (Antas, Uniwager, Leura) still showed significant disease. This is the first study to show physiological specialization in A. trifolii and to identify host resistance. This study defines A. trifolii as a significant but largely unknown contributor to severe root disease of subterranean clover in southern Australia. Finally, development and calibration of a new soil commercial DNA test not only enables field quantification of the disease, but development of appropriate breeding, selection and farm management strategies to reduce its impact.     

Disease risk assessment of sugar beet root rot using quantitative real-time PCR analysis of <Emphasis Type="Italic">Aphanomyces cochlioides</Emphasis> in naturally infested soil samples

Sugar beet root rot, caused by the oomycete Aphanomyces cochlioides, is a serious and economically important disease of sugar beets world-wide. Today, disease risk assessment consists of a time-consuming greenhouse bioassay using bait plants. In the present study, a real-time quantitative PCR (qPCR) assay for determination of A. cochlioides DNA in field-infested soil samples was developed and validated using the standard bioassay. The qPCR assay proved to be species-specific and was optimized to give high amplification efficiency suitable for target copy quantification. A high correlation (R² > 0.98, p < 0.001) with pathogen inoculum density was shown, demonstrating the suitability for monitoring soil samples. The limit of detection (LOD) was evaluated in several different soil types and varied between 1 and 50 oospores/g soil, depending on clay content. Soils with a high LOD were characterised as having a low clay content and high content of sand. Varying levels of the A. cochlioides target sequence were detected in 20 of the 61 naturally infested soil samples. Discrepancies between the bioassay and the qPCR assay were found in soils from low- and medium-risk fields. However, the qPCR diagnostic assay provides a potentially valuable new tool in disease risk assessment, enabling sugar beet growers to identify high-risk fields.     

Detection and quantification of Ilyonectria spp. associated with black‐foot disease of grapevine in nursery soils using multiplex nested PCR and quantitative PCR

Three nursery fields and three rootstock mother fields from commercial nurseries located in Comunidad Valenciana region (central‐eastern Spain) were surveyed in July 2011 to detect the presence and to quantify Ilyonectria spp. in the soil. In each field, ten soil samples were taken randomly with a soil probe at a depth of 10–30 cm, and 10–20 cm from the base of the plant. Three replicate subsamples (10 g each) were taken from each soil sample. DNA was extracted and a multiplex nested PCR with species‐specific primer pairs (Mac1/MaPa2, Lir1/Lir2 and Pau1/MaPa2) was used to identify the species present. Among the 180 soil DNA samples analysed, Ilyonectria spp. were detected in 172 of them. Ilyonectria macrodidyma complex was the most frequently detected, being identified in 141 samples from all the fields evaluated. However, I. liriodendri was detected in only 16 samples, but was present in all open‐root field nurseries and in two rootstock mother fields. In addition, quantitative PCR (qPCR) assays were done to assess the levels of I. liriodendri and I. macrodidyma‐complex DNA in the soil samples. Detection of Ilyonectria spp. DNA using qPCR correlated with the fields found positive with the nested multiplex PCR. DNA concentrations of Ilyonectria spp. ranged from 0·004 to 1904·8 pg μL^?1. In general, samples from rootstock mother fields showed the highest DNA concentrations. The ability to detect and quantify Ilyonectria spp. genomic DNA in soil samples from nursery fields and rootstock mother fields confirms soils from both field types as important inoculum sources for black‐foot pathogens.     

Fusarium ear blight of wheat: the use of quantitative PCR and visual disease assessment in studies of disease control

Quantitative PCR analysis and visual disease assessment (VDA) were used to study Fusarium culmorum and F. poae ear blight of wheat and its fungicidal control in three glasshouse trials (1994–5 and 1996–7). VDA indicated high levels of both diseases in the trials, while PCR analysis showed that the amounts of F. poae detected in infected plants were low relative to the amounts detected for F. culmorum . PCR and VDA analysis both indicated that the demethylase-inhibiting (DMI) fungicides prochloraz and tebuconazole significantly decreased F. culmorum and F. poae ear blight. The PCR results, however, revealed levels of disease control by fungicide treatments that were consistently higher than those suggested by VDA. Overall, both fungicides appeared equally effective in controlling the two pathogens. PCR and VDA analysis indicated that the anilino-pyrimidine fungicide pyrimethanil had no significant effect on F. culmorum ear blight. Correlations between VDA at cereal growth stage 80 and PCR analysis were similar for F. culmorum and F. poae . Yield analysis, as measured by 1000 grain weight, indicated that DNA content more accurately predicted yield loss than did VDA scores. Inoculation with F. culmorum significantly reduced yield and significant relationships were observed between F. culmorum disease (as assessed visually or by PCR) and yield, with yield decreasing as disease increased. In contrast, inoculation with F. poae had no significant effect on yield and no significant relationships were observed between F. poae disease and yield. These results have important implications for field studies of Fusarium ear blight of wheat because they highlight the importance of identification of the causal organisms to the species level.     

The use of digital image analysis and real‐time PCR fine‐tunes bioassays for quantification of Cercospora leaf spot disease in sugar beet breeding

Cercospora leaf spot, caused by the fungus Cercospora beticola, is a major fungal sugar beet disease worldwide and the cause of significant yield losses. The disease is most successfully countered by the introduction of genetic tolerance into elite sugar beet hybrids. To this end, breeding programmes require high quality biological assays allowing discrimination of minor differences between plants within a segregating population. This study describes the successful implementation of image analysis software in the bioassays for quantification of necrotic lesions at different stages of C. beticola infection, allowing selection on minor phenotypic differences during the sugar beet breeding process for C. beticola resistance. In addition, a real‐time PCR assay was developed for the quantification of C. beticola pathogen biomass in infected beet canopy. The use of both techniques, even in an early stage of infection, fine‐tunes current bioassays, allowing more accurate and efficient selection of resistant breeding material.     

Occurrence of Grapevine Pinot gris virus in Friuli Venezia Giulia (Italy): field monitoring and virus quantification by real‐time RT‐PCR

Since 2003 the presence of a new syndrome characterized by symptoms of stunting, chlorotic mottling, leaf deformation, reduced yields and quality has been reported in some white berry varieties of Vitis vinifera in Trentino‐Alto Adige and Friuli Venezia Giulia vineyards. The identification of a new virus, provisionally called Grapevine Pinot gris virus (GPGV), in a cv. Pinot gris vine suggested an association between this new syndrome and the virus presence (Giampetruzzi et al., 2012), however the contemporary presence of GPGV in both symptomatic and asymptomatic plants has still to be explained. In this work, a large‐scale monitoring over a 3‐year period (2012–14) of Friuli Venezia Giulia vineyards and nurseries has shown a widespread presence of GPGV in symptomatic plants and also in asymptomatic vines, even if at a slightly lower percentage. Quantitative analyses of the virus titer revealed a great variability in the viral content of both symptomatic and asymptomatic plants but the mean GPGV quantity in symptomatic vines was significantly higher than in asymptomatic plants.     

Detection of Dickeya spp. latent infection in potato seed tubers using PCR or ELISA and correlation with disease incidence in commercial field crops under hot‐climate conditions

Over a 5‐year period (2006–2010), 277 certified, visually healthy potato seed lots, imported from Europe to Israel for commercial use, were tested for Dickeya spp. latent infection by PCR analysis (277 seed lots) and ELISA (154 seed lots). Seeds from these lots were grown in commercial potato fields which were inspected twice a season by Plant Protection and Inspection Services (PPIS). Stem samples were tested for the presence of Dickeya spp. by PCR analysis. PCR and ELISA results from seed lot testing correlated with disease expression in 74 and 83·8% of the cases, respectively. Positive laboratory results with no disease symptoms in the field (‘+lab/?field’ results) comprised 24·7 and 9·7% of the PCR and ELISA analyses, respectively, whereas negative laboratory results with disease symptoms in the field results (‘?lab/+field’) were obtained in 1·3 and 6·5%, of cases respectively. Maximum disease incidence, as well as the number of cultivars expressing disease symptoms, increased over the years of this study, indicating an increase in the prevalence of the disease. Severe disease incidence was observed on cvs Dita, Rodeo, Desiree, Mondial, Tomensa and Jelly. Of the 55 imported seed lots from which disease was recorded in the field, 49 originated from the Netherlands, four from Germany and two from France. None originated from Scotland.