Molecular aspects of the potato — Phytophthora infestans interaction

The fungal pathogenPhytophthora infestans is the causal organism of late blight, one of the most devastating diseases of potato. In the past, various aspects of the potato-P. infestans interaction have been studied extensively. In this paper we briefly review the current knowledge of the molecular events associated with the interaction and in addition we discuss a new approach for analyzing the molecular basis of pathogenicity ofP. infestans.     

Molecular aspects of the potato — Phytophthora infestans interaction

The fungal pathogenPhytophthora infestans is the causal organism of late blight, one of the most devastating diseases of potato. In the past, various aspects of the potato-P. infestans interaction have been studied extensively. In this paper we briefly review the current knowledge of the molecular events associated with the interaction and in addition we discuss a new approach for analyzing the molecular basis of pathogenicity ofP. infestans.     

Quantification of late blight resistance of potato using transgenic Phytophthora infestans expressing β-glucuronidase

A transgenic Phytophthora infestans strain that constitutively produces and secretes -glucuronidase (GUS) was used in detached leaf assays to quantify the levels of resistance to late blight in potato cultivars Surprise, Irene, Pimpernel, Alpha and Bintje. Four days after inoculation levels of GUS activity were determined in infected leaves. Significant differences between the various cultivars were observed. Discrimination between resistant and susceptible cultivars was possible based solely on levels of GUS activity. Regression analysis revealed a positive correlation between in planta GUS levels and field resistance expressed as Area under Disease Progress Curve (ADPC).     

Phenotypic and genotypic structure of Phytophthora infestans populations on tomato and potato in the North of Thailand in 2000–2002

A total of 80 single–lesion isolates of Phytophthora infestans were collected from tomatoes and potatoes in several locations in Chiang Mai and Tak provinces in 2000–2002. These isolates were analyzed for mating type, metalaxyl sensitivity, mitochondrial DNA (mtDNA) haplotype RFLP pattern as determined by probe RG57, and for microsatellite markers. All isolates were A1 mating type. Isolates from tomato were usually sensitive to metalaxyl, but isolates from potato were usually resistant to metalaxyl. With one exception, all tomato isolates were related to the US-1 clonal lineage. With two exceptions, all potato isolates were related to two European lineages. In these two provinces, the populations of P. infestans on tomatoes are clearly different from those on potatoes.     

What is the evidence for sexual reproduction of Phytophthora infestans in Europe?

The biology of late blight of potato and tomato, caused by Phytophthora infestans, changed when sexual reproduction by the pathogen became possible in many parts of the world, including Europe. In northern Europe, especially Scandinavia, there is increasing evidence that the pathogen is reproducing sexually on a regular basis, although in other regions further south or to the west it appears to reproduce primarily in a clonal manner. The presence of both mating types, the production of viable oospores, and observations of fields with soilborne sources of inoculum are consistent with sexual reproduction. Studies with different marker systems have revealed a population structure without any dominating clonal lineages in Scandinavia, and that is most easily explained by sexual reproduction. Phytophthora infestans recovered from the soil can also be linked to parental genotypes using likelihood‐based methods when codominant markers are used. A synthesis of all the available data points to a second centre of sexual reproduction in northern Europe.     

Transdisciplinary weed research: new leverage on challenging weed problems?

Transdisciplinary weed research (TWR) is a promising path to more effective management of challenging weed problems. We define TWR as an integrated process of inquiry and action that addresses complex weed problems in the context of broader efforts to improve economic, environmental and social aspects of ecosystem sustainability. TWR seeks to integrate scholarly and practical knowledge across many stakeholder groups (e.g. scientists, private sector, farmers and extension officers) and levels (e.g. local, regional and landscape). Furthermore, TWR features democratic and iterative processes of decision‐making and collective action that aims to align the interests, viewpoints and agendas of a wide range of stakeholders. The fundamental rationale for TWR is that many challenging weed problems (e.g. herbicide resistance or extensive plant invasions in natural areas) are better addressed systemically, as a part of broad‐based efforts to advance ecosystem sustainability, rather than as isolated problems. Addressing challenging weed problems systemically can offer important new leverage on such problems, by creating new opportunities to manage their root causes and by improving complementarity between weed management and other activities. While promising, this approach is complicated by the multidimensional, multilevel, diversely defined and unpredictable nature of ecosystem sustainability. In practice, TWR can be undertaken as a cyclic process of (i) initial problem formulation, (ii) ‘broadening’ of the problem formulation and recruitment of stakeholder participants, (iii) deliberation, negotiation and design of an action agenda for systemic change, (iv) implementation action, (v) monitoring and assessment of outcomes and (vi) reformulation of the problem situation and renegotiation of further actions. Notably, ‘purposive’ disciplines (design, humanities and arts) have central, critical and recurrent roles in this process, as do integrative analyses of relevant multidimensional and multilevel factors, via multiple natural and social science disciplines. We exemplify this process in prospect and retrospect. Importantly TWR is not a replacement for current weed research; rather, the intent is to powerfully leverage current efforts.     

Phenotypic and genotypic changes in French populations of Phytophthora infestans: are invasive clones the most aggressive?

The main objective of this investigation was to test the ‘always more aggressive’ hypothesis, often advocated to explain lineage replacements in clonal populations of the potato late blight oomycete Phytophthora infestans. To this end, genotypic and pathogenicity data on 1274 French isolates of P. infestans, collected over the period 2001–2008, were analysed. Overall, the populations sampled showed limited genetic diversity, with four multilocus lineages (1_A1, 2_A1, 8_A1 and 13_A2) accounting for over 80% of the isolates collected. As in other West European countries, drastic changes in these dominant clonal lineages were observed over the course of the 8 years, particularly in the appearance and propagation of the clone 13_A2. However, invasiveness of clones was not associated with higher aggressiveness; on the contrary, dominant clones had generally low or moderate aggressiveness relative to others present at the same time within the same populations. This finding challenges the link between invasive behaviour and increased aggressiveness often assumed for this biotrophic pathogen, and could reflect the existence of a trade‐off between intra‐season and inter‐season transmission. This would be consistent with the concept of inclusive fitness, which involves the abilities to both reproduce and survive.     

The dynamics of Phytophthora infestans populations in the major potato-growing regions of Asia – A review

Asia is now the largest potato-producing region of the world and late blight, caused by Phytophthora infestans, is the most important pathogen limiting production. This review documents, in both the historical and the current context, the population structure of P. infestans in the major areas of potato production in Asia. Information from diverse sources regarding the stated or inferred clonal pathogen lineages present, population changes, and possible migration routes of the pathogen into the countries of this region have been reviewed to aid researchers and those involved in managing late blight in Asia. The single most important factor for population change and resultant epidemics in this region has been found to be migration of pathogen genotypes from Europe and the Americas. Reducing the impact of such migration in the future will necessitate putting in place improved phytosanitary measures. To achieve this, data sharing using global networks such as AsiaBlight and EuroBlight is imperative.     

Invasion of Phytophthora infestans at the landscape level: how do spatial scale and weather modulate the consequences of spatial heterogeneity in host resistance?

Strategic spatial patterning of crop species and cultivars could make agricultural landscapes less vulnerable to plant disease epidemics, but experimentation to explore effective disease-suppressive landscape designs is problematic. Here, we present a realistic, multiscale, spatiotemporal, integrodifference equation model of potato late blight epidemics to determine the relationship between spatial heterogeneity and disease spread, and determine the effectiveness of mixing resistant and susceptible cultivars at different spatial scales under the influence of weather. The model framework comprised a landscape generator, a potato late blight model that includes host and pathogen life cycles and fungicide management at the field scale, and an atmospheric dispersion model that calculates spore dispersal at the landscape scale. Landscapes consisted of one or two distinct potato-growing regions (6.4-by-6.4-km) embedded within a nonhost matrix. The characteristics of fields and growing regions and the separation distance between two growing regions were investigated for their effects on disease incidence, measured as the proportion of fields with ≥1% severity, after inoculation of a single potato grid cell with a low initial level of disease. The most effective spatial strategies for suppressing disease spread in a region were those that reduced the acreage of potato or increased the proportion of a resistant potato cultivar. Clustering potato cultivation in some parts of a region, either by planting in large fields or clustering small fields, enhanced the spread within such a cluster while it delayed spread from one cluster to another; however, the net effect of clustering was an increase in disease at the landscape scale. The planting of mixtures of a resistant and susceptible cultivar was a consistently effective option for creating potato-growing regions that suppressed disease spread. It was more effective to mix susceptible and resistant cultivars within fields than plant some fields entirely with a susceptible cultivar and other fields with a resistant cultivar, at the same ratio of susceptible to resistant potato plants at the landscape level. Separation distances of at least 16 km were needed to completely prevent epidemic spread from one potato-growing region to another. Effects of spatial placement of resistant and susceptible potato cultivars depended strongly on meteorological conditions, indicating that landscape connectivity for the spread of plant disease depends on the particular coincidence between direction of spread, location of fields, distance between the fields, and survival of the spores depending on the weather. Therefore, in the simulation of (airborne) pathogen invasions, it is important to consider the large variability of atmospheric dispersion conditions.     

Image-based weed recognition and control: Can it select for crop mimicry?

As highly adaptable plants, weeds have evolved numerous mechanisms to evade control in agroecosystems. For example, reliance on herbicides has resulted in widespread evolution of resistance in many species. Minimising weed adaptation is a major driver for integrated weed management strategies. Crop mimicry is a notable example of weed adaptation, where weed species evolve to avoid control by mimicking aspects of the crop phenotype. Visual selection by hand weeding has been documented to select for crop mimics that are difficult to distinguish from the crop at the vegetative stage. With recent advancements in weed recognition technologies, image-based weed recognition for in-crop, site-specific weed control is on the cusp of becoming widely adopted. Whilst the control methods used in site-specific weed control will be varied (e.g., spot spraying or lasers), they will share weed recognition technology. Visual selection via image-based deep learning represents a selection pressure for weeds that can evade detection by mimicking crops. This mimicry may reduce weed recognition accuracy and thus weed control efficacy over time and result in difficult to manage mimetic weed phenotypes. Therefore, it is timely to explore the potential for selection of crop mimics by image-based weed recognition algorithms.     

Focus on ecological weed management: what is hindering adoption?

Despite increased concerns regarding the heavy reliance of many cropping systems on chemical weed control, adoption of ecological weed management practices is only steadily progressing. For this reason, this paper reflects on both the possibilities and limitations of cultural weed control practices. Cultural weed control utilises a number of principles, predominantly: (i) a reduced recruitment of weed seedlings from the soil seedbank, (ii) an alteration of crop–weed competitive relations to the benefit of the crop and (iii) a gradual reduction of the size of the weed seedbank. Compared with chemical control, the general applicability, reliability and efficacy of most measures is only moderate, and consequently, cultural control strategies need to consist of a combination of measures, resulting in increased systems complexity. Combined with the trade‐offs connected to some of the measures, this hampers large‐scale implementation. It is argued that tailoring cultural weed management strategies to the needs and skills of individual farmers would be an important step forward. Research can aid in improving the utilisation of cultural weed control strategies by focussing on a broadening of the range of available measures and by providing clear quantitative insight in efficacy, variability in outcome and trade‐offs of these measures.     

Can the storage effect hypothesis explain weed co‐existence on the Broadbalk long‐term fertiliser experiment?

Understanding how plant species with similar resource requirements co‐exist has been a long‐standing ecological question with several theoretical explanations. One potential mechanism is the storage effect hypothesis. According to this hypothesis, species co‐exist because they differ in when they are most actively using resource and, therefore, respond differently to environmental perturbation. The hypothesis is based on two main assumptions: (i) two competitors have different responses to climate and (ii) the responses to climate are mediated by changes in the relative importance of intra‐ and interspecific competition. The hypothesis could provide useful insights into the role of climate in maintaining weed species diversity and potential shifts in dominant species under climate change. This study tested the basic principles of the storage effect hypothesis on weed communities using data from the Broadbalk long‐term fertiliser experiment. Relative abundance of weeds in 10 plots with contrasting fertility but no herbicides was assessed for 21 years. Multivariate analyses and generalised additive mixed models were used to analyse the data. The following pairs of species were found to be adapted to similar fertiliser levels, but diverged in their response to climate: (i) Papaver rhoeas–Tripleurospermum inodorum, (ii) Medicago lupulina–Vicia sativa and (iii) Scandix pecten‐veneris–Ranunculus arvensis. Contrasting responses to spring temperature within these species pairs modified the competition balance providing evidence for the storage effect hypothesis and helping to explain weed co‐existence in the Broadbalk experiment.     

Is the current state of the art of weed monitoring suitable for site‐specific weed management in arable crops?

Weed monitoring is the first step in any site‐specific weed management programme. A relatively large variety of platforms, cameras, sensors and image analysis procedures are available to detect and map weed presence/abundance at various times and spatial scales. Remote sensing from satellites or aircraft can provide accurate weed maps when the images are obtained at late weed phenological stages. Cameras located on unmanned aerial vehicles (UAVs) have been shown to be adequate for early‐season weed detection in a variety of wide‐row crops, providing images with relatively high spatial resolutions. Alternatively, weed detection/mapping systems from ground‐based platforms can achieve even higher resolutions using a variety of non‐imaging and imaging technologies. These ground systems are suited, in some cases, for real‐time site‐specific weed management. Despite this rich arsenal of technologies, their commercial adoption is, apparently, low. In this study, we describe the state of the art of remotely sensed and ground‐based weed monitoring in arable crops and the current level of adoption of these technologies, exploring major constraints for adoption and trying to identify research gaps and bottlenecks.     

Can phyllosphere yeasts explain the effect of scab fungicides on russeting of Elstar apples?

In 1999 and 2000, the effects of scab fungicides on yeast composition and russeting of Elstar apples were assessed. Yeast composition of fungicide-treated and untreated young apple fruit with or without russet symptoms was investigated and enzyme activity of the yeasts was studied. Cryptococcus albidus, C.laurentii,Rhodotorula glutinis, Sporobolomyces roseus andMetschnikowia pulcherrima dominated the apple fruit surface. Russeted apple fruitlets had a higher red yeast density than non-russeted fruitlets. Invitro fungicide susceptibility of the dominant yeast species varied. Dithianon and dodine were active against all tested species, captan and tolylfluanid showed specificity for certain species, whereas pyrimethanil and bupirimate were largely ineffective. Fungicide treatment in the field had a clear effect on the yeast composition. Metschnikowia etschnikowia pulcherrima was eliminated from the phyllosphere and cryptococco$ï species diminished by both captan and dithianon. The red yeast population was not significantly changed by either fungicide. Captan, dithianon, tolylfluanid and pyrimethanil reduced russet in the field in both years, dodine and kresoxim-methyl only in 2000. All yeast species had cutinolytic activity, all but M.pulcherrimaand Debaryomyces hansenii were lipolytic, and some of the isolates showed proteolytic activity.     

Are herbicides a once in a century method of weed control?

The efficacy of any pesticide is an exhaustible resource that can be depleted over time. For decades, the dominant paradigm – that weed mobility is low relative to insect pests and pathogens, that there is an ample stream of new weed control technologies in the commercial pipeline, and that technology suppliers have sufficient economic incentives and market power to delay resistance – supported a laissez faire approach to herbicide resistance management. Earlier market data bolstered the belief that private incentives and voluntary actions were sufficient to manage resistance. Yet, there has been a steady growth in resistant weeds, while no new commercial herbicide modes of action (MOAs) have been discovered in 30 years. Industry has introduced new herbicide tolerant crops to increase the applicability of older MOAs. Yet, many weed species are already resistant to these compounds. Recent trends suggest a paradigm shift whereby herbicide resistance may impose greater costs to farmers, the environment, and taxpayers than earlier believed. In developed countries, herbicides have been the dominant method of weed control for half a century. Over the next half‐century, will widespread resistance to multiple MOAs render herbicides obsolete for many major cropping systems? We suggest it would be prudent to consider the implications of such a low‐probability, but high‐cost development. © 2017 Society of Chemical Industry     

Genotypic and phenotypic characterization of Phytophthora infestans in South Korea during 2009–2016 reveals clonal reproduction and absence of EU_13_A2 genotype

In order to better understand the Phytophthora infestans population structure in South Korea, 172 isolates were collected between 2009 and 2016 from four major potato cultivation areas. Fungicide (metalaxyl and dimethomorph) response, mating type, and microsatellite (SSR) genetic fingerprints were analysed to characterize these isolates. Ten isolates collected in Gyeongnam Province, which specializes in protected winter cultivation in polytunnels, were A2 mating type. All other isolates were A1 mating type. Overall, 42% of the isolates were resistant to metalaxyl, and 43% were sensitive. All isolates were sensitive to dimethomorph. From the SSR fingerprints, 45 distinct genotypes were identified, which could be clustered into four clonal lineages: KR_1_A1, KR_2_A2, SIB-1, and US-11. KR_1_A1 was the predominant P. infestans genotype in South Korea. KR_2_A2 was only found in Gyeongnam Province; all isolates were A2 mating type and resistant to metalaxyl. SIB-1 was dominant until 2013 but its frequency has gradually decreased in more recent years. US-11 was first found in 2014, after which its frequency has increased to become codominant with KR_1_A1. The calculated standardized index of association (I_A) suggests that the South Korean P. infestans population is undergoing clonal reproduction. When compared with populations of P. infestans from the Netherlands, it has less genetic diversity and the dominant Netherlands P. infestans genotype, EU_13_A2 (Blue_13), was not found in South Korea. Such monitoring of the pathogen population contributes to a more efficient integrated pest management-based control strategy for potato late blight control in South Korea.     

Can we forecast the effects of climate change on entomophagous biological control agents?

The worldwide climate has been changing rapidly over the past decades. Air temperatures have been increasing in most regions and will probably continue to rise for most of the present century, regardless of any mitigation policy put in place. Although increased herbivory from enhanced biomass production and changes in plant quality are generally accepted as a consequence of global warming, the eventual status of any pest species will mostly depend on the relative effects of climate change on its own versus its natural enemies' complex. Because a bottom‐up amplification effect often occurs in trophic webs subjected to any kind of disturbance, natural enemies are expected to suffer the effects of climate change to a greater extent than their phytophagous hosts/preys. A deeper understanding of the genotypic diversity of the populations of natural enemies and their target pests will allow an informed reaction to climate change. New strategies for the selection of exotic natural enemies and their release and establishment will have to be adopted. Conservation biological control will probably become the keystone for the successful management of these biological control agents. © 2013 Society of Chemical Industry     

Role of weed hosts and the western flower thrips, Frankliniella occidentalis, in epidemiology of Tomato spotted wilt virus in the Çukurova region of Turkey

Surveys of thrips and Tomato spotted wilt virus (TSWV) on weeds were conducted in the eastern Mediterranean region of Turkey during the years 2004–2006. Thrips species were collected by vigorously shaking weedy plants into a white container for 15 sec. Plant material collected during field surveys and plants which were used for mechanical inoculation of TSWV, were tested by DAS–ELISA. The weed species Ranunculus muricatus, Melilotus officinalis, Sinapis arvensis and Portulaca oleracea were used for the virus transmission experiments in an enclosed high plastic tunnel and in cage experiments. Western flower thrips, Frankliniella occidentlis (Pergande) (Thysanoptera: Thripidae), was the most common thrips, inhabiting 80 of the 82 weed species sampled. Adults of F. occidentalis and thrips larvae were significantly more abundant on S. arvensis than on the other weed species sampled (P<0.05). Adult and larval thrips showed peak densities on most weeds in April or May. Summer annual weeds were not good hosts for reproduction of the thrips. A total of 90 samples from 17 plant species belonging to 11 plant families were ELISA positive for TSWV. No TSWV was detected on 65 weed species belonging to 26 plant families. High numbers of plant samples infected by TSWV were obtained in P. oleracea (21 samples) and in R. muricatus (15 samples). In field surveys symptoms of TSWV were detected on only R. muricatus. Incidence of the TSWV on weeds ranged between 5% and 25%. Transmission rates of TSWV by F. occidentalis to the weeds ranged from 33% to 83% in the pepper plastic tunnel and cage experiments.