Survey of viruses infecting open‐field pepper crops in Côte d'Ivoire and diversity of Pepper veinal mottle virus and Cucumber mosaic virus

The prevalence of viruses in pepper crops grown in open fields in the different agro‐ecological zones (AEZs) of Côte d'Ivoire was surveyed. Pepper veinal mottle virus (PVMV; genus Potyvirus) and Cucumber mosaic virus (CMV; genus Cucumovirus) were the most frequent viruses among those surveyed, while tobamoviruses (genus Tobamovirus) were detected at low frequency. PVMV showed a high heterogeneity across AEZs, which may be related to climatic, ecological or agronomical conditions, whereas CMV was more homogeneously distributed. The molecular diversity of CMV and PVMV were analysed from partial genome sequences. Despite the low number of CMV isolates characterized, two molecular groups were revealed, one corresponding to subgroup IA and the other to reassortants between subgroups IA and IB. RNAs 1 and 3 of the reassortants clustered with the IB subgroup of CMV isolates, whereas their RNA 2 clustered with the IA subgroup. Importantly, RNA 1 of CMV isolates of the IB subgroup has been shown to be responsible for adaptation to pepper resistance. The diversity of PVMV in the VPg‐ and coat protein‐coding regions revealed multiple clades. The central part of the VPg showed a high level of amino acid diversity and evidence of positive selection, which may be a signature of adaptation to plant recessive resistance. As a consequence, for efficient deployment of resistant pepper cultivars, it would be desirable to examine the occurrence of virulent isolates in the CMV or PVMV populations in Côte d'Ivoire and to follow their evolution as the resistance becomes more widely deployed.     

Occurrence and diversity of Tomato spotted wilt virus isolates breaking the Tsw resistance gene of Capsicum chinense in Yunnan,southwest China

Widely used resistant peppers (Capsicum spp.) bearing the Tsw locus triggered the rapid emergence of resistance‐breaking (RB) isolates of Tomato spotted wilt virus (TSWV) around the world. However, although TSWV‐induced diseases have rapidly increased in Yunnan, southwest China, in recent years, no information is available about the diversity of TSWV isolates in this region. In this study, the occurrence of natural TSWV RB variants among isolates collected in Yunnan is reported. Initially, a TSWV isolate from asparagus lettuce (TSWV‐LE) was collected in Yunnan in 2012. Surprisingly, this isolate of TSWV induced systemic necrosis on pepper carrying the Tsw resistance gene. Novel TSWV isolates, collected in 2015, included a tomato isolate (TSWV‐YN18) and a tobacco isolate (TSWV‐YN53) that also overcame Tsw‐mediated resistance. TSWV‐YN18 induced systemic ringspots, whereas TSWV‐YN53 caused systemic chlorotic mottling. Variations in the TSWV nonstructural (NSs) protein are the key determinants associated with Tsw resistance‐breaking isolates. It was found that TSWV‐LE NSs retained the hypersensitive response (HR) induction, whereas TSWV‐YN18 and TSWV‐YN53 NSs were unable to induce HR. However, the NSs of all three RB isolates suppressed RNA silencing. Sequence analysis of the NSs revealed that RB isolates of Yunnan have no amino acid mutation sites common to other previously reported RB isolates. However, two amino acids (F74 and K272) on TSWV‐LE NSs make it distinct from TSWV‐YN18 and TSWV‐YN53. The occurrence of different RB isolates and the failure of Tsw‐mediated resistance control pose serious threats to domestic pepper crops in southwest China.     

Genetic variation and evolutionary forces shaping Cucumber vein yellowing virus populations: risk of emergence of virulent isolates in Europe

The genetic variation and evolutionary mechanisms shaping Cucumber vein yellowing virus (CVYV) populations were investigated by analysis of nucleotide sequences coding for P1b, P1b/P3 and coat proteins (CP) from isolates collected in different countries. The complete genome sequence of isolate ISM from Israel was also determined and compared to those of isolates Jor from Jordan and ALM32 from Spain. This isolate had overall nucleotide identities of 94·23 and 94·96% with ALM32 and Jor, respectively. Nucleotide variation among isolates was not homogeneously distributed, with the 5′ half of the genome being more variable than the 3′ half. A Bayesian phylogenetic tree of the CP showed that CVYV isolates clustered into two main clades: isolates from the Middle East region (Lebanon, Israel and Jordan) clustered in both clades whereas the isolate from Tunisia clustered in clade I and the European isolates clustered as a homogeneous phylogroup in Clade II. A similar topology was observed for P1b but with incongruences with respect to the CP, suggesting genetic exchange among virus isolates, which were confirmed with recombination algorithms. The low genetic diversity within the European phylogroup with respect to the other isolates, neutralist tests and genetic differentiation analyses suggest that the Middle East region is the cradle of CVYV and that a unique virus introduction event occurred in Europe, where the virus spread rapidly. Taken together, these findings indicate a risk of emergence of virulent CVYV isolates in Europe either through migration from the Middle East or by genetic changes of the European isolates.     

Induction of systemic resistance against Cucumber mosaic virus by Penicillium simplicissimum GP17‐2 in Arabidopsis and tobacco

The plant growth‐promoting fungus, Penicillium simplicissimum GP17‐2, was evaluated for its ability to induce resistance against Cucumber mosaic virus (CMV) in Arabidopsis thaliana and tobacco plants. Treatment with barley grain inoculum (BGI) of GP17‐2 significantly enhanced fresh weight, dry weight and leaf number of A. thaliana and tobacco plants 6 weeks after planting. Two weeks after CMV inoculation, all plants treated with BGI of GP17‐2 or its culture filtrate (CF) showed a significant reduction in disease severity compared with non‐treated control plants, which exhibited severe mosaic symptoms by the end of the experiment. The enzyme‐linked immunosorbent assay (ELISA) demonstrated that CMV accumulation was significantly reduced in plants treated with GP17‐2 or its CF relative to control plants. Based on RT‐PCR, plants treated with GP17‐2 (BGI or CF) also exhibited increased expression of regulatory and defence genes involved in the SA and JA/ET signalling pathways. These results suggested that multiple defence pathways in A. thaliana and tobacco were involved in GP17‐2‐mediated resistance to CMV, although neither the transgenic NahG line, nor the npr1, jar1 or ein3 mutants disrupted the response in A. thaliana. This is the first report to demonstrate the induction of systemic resistance against CMV by GP17‐2 or its CF.     

Quantification of Mirafiori lettuce big‐vein virus and its vector,Olpidium virulentus,from soil using real‐time PCR

Big vein disease of lettuce (Lactuca sativa) is an economically important disease transmitted through soil by Olpidium virulentus, and has occurred in most production areas worldwide. The disease is assumed to be caused by Mirafiori lettuce big‐vein virus (MiLBVV). To understand the dynamics of the virus and its vector, MiLBVV and O. virulentus were directly detected in soil. DNA and RNA were extracted from 5 g soil using a bead beating method, followed by purification using adsorption to a column. Detection and quantification were performed using real‐time PCR and a TaqMan probe that was prepared based on the CP region of MiLBVV and the rDNA‐ITS region of O. virulentus, respectively. Furthermore, using a visual assessment of the incidence rate of big vein disease on lettuce in agricultural fields, the C_t values of MiLBVV and O. virulentus from soil were also determined using real‐time PCR. The results showed that MiLBVV concentrations in the soil were high in the field, as also determined by a visual assessment of the incidence rate of big vein disease on lettuce. However, the amount of O. virulentus in soil was not directly correlated with the incidence of MiLBVV. From these results, it is suggested that the risk of lettuce crops developing big vein disease can be estimated using an index of the amount of MiLBVV in the soil.     

Evidence for two predominant viral lineages,recombination and subpopulation structure in begomoviruses associated with yellow vein mosaic disease of okra in India

Yellow vein mosaic disease (YVMD) caused by whitefly‐transmitted begomoviruses is an economically significant viral disease of okra. In this study, a survey of begomoviruses associated with YVMD was carried out in eight states and two union territories of India. A total of 92 full‐length DNA‐A components were sequenced and characterized. Sequence comparisons and population structure analysis revealed the existence of four begomovirus species. Two novel species were detected with several recombinationally derived genome fragments that probably originated from begomoviruses known to infect malvaceous and non‐malvaceous hosts. Among the four species, Bhendi yellow vein Maharastra virus (BYVMaV) and Bhendi yellow vein Madurai virus (BYVMV) were found to be predominant in okra, with BYVMV having a pan‐India distribution. There was evidence for a high degree of genetic variability and subpopulation structure within these four species. Neutrality tests suggested the occurrence of purifying selection acting upon these populations. The results of the current study have uncovered the diversity and genetic structure of okra‐infecting begomoviruses in India and generated potentially useful information for developing management strategies for YVMD.     

Distinct strains of the re‐emergent Cassava common mosaic virus (genus: Potexvirus) infecting cassava in Argentina

Cassava common mosaic disease (CCMD) has been reported in all regions where cassava is grown in the Americas and the causal agent, Cassava common mosaic virus (CsCMV), has been identified as a mechanically transmitted potexvirus (Alphaflexiviridae). In Argentina, cassava is grown mainly in the northeast (NEA) region that shares borders with Brazil and Paraguay. Increasing incidences of CCMD were observed during the years 2014 to 2016 associated with severe leaf mosaic symptoms and yield reductions where the occurrence of CsCMV was confirmed by RT‐PCR and sequencing. In this work, the virus has been successfully purified and a double‐antibody sandwich (DAS‐) ELISA test has been developed from an Argentinean isolate of CsCMV to extend the diagnostics of the disease. A collection of 726 samples was screened and CsCMV was detected with 100% prevalence in the NEA region. Additional co‐infecting viruses were detected in some plants (64.4%); in these, CCMD symptoms correlated with CsCMV only, although more severe symptoms could be observed in mixed infected plants. Sequence analysis of the conserved RdRp domain showed a wider diversity of CsCMV isolates. Interestingly, a separate phylogenetic cluster was formed by isolates from the NEA region that only shared 77.1% to 80.3% nucleotide identity with the other clusters. These results indicate the presence of mixed strains occurring in the NEA region and suggest the presence of geographically distinct strains of CsCMV in South America.     

Biology of Southern rice black‐streaked dwarf virus: a novel fijivirus emerging in East Asia

Southern rice black‐streaked dwarf virus (SRBSDV) was first reported in southern China in 2001 and causes a striking disease on rice and maize that leads to serious yield losses in several East Asian countries, such as China, Vietnam and Japan. A large research effort has been directed to understanding the virus and controlling the disease. Its geographic distribution, disease cycle via its insect vector, genome organization, relationship with host plants, and epidemiology are summarized in this review and the important role played by the vector, the white‐backed planthopper (Sogatella furcifera), is emphasized. Countermeasures to control the disease that have been developed and applied include molecular detection for precise forecasting, chemical, physical, and ecological pest management. There is widespread insecticide resistance in the vector population but it is hoped that current efforts to develop rice cultivars resistant to the virus will eventually provide effective and cost‐effective control.     

Biochemical and physiological responses to long‐term Citrus tristeza virus infection in Mexican lime plants

Reactions that occur when a plant is subjected to Citrus tristeza virus (CTV) infection often result in triggering of numerous defence mechanisms to fight the infection. The reactions vary according to virus strain, host genotype, time of exposure to the infection and environmental conditions. To date, no study has examined in detail the consequences of 10‐year exposure to CTV infection on the biochemical and physiological status of susceptible Mexican lime plants (Citrus aurantifolia). To understand the reaction of such plants, changes in nutrient status, total proteins, enzyme activity involved in scavenging of reactive oxygen species, photosynthetic and transpiration rates, chlorophyll content, membrane permeability and water content were analysed in plants infected with different CTV isolates and in healthy plants. The activity of superoxide dismutase and polyphenol oxidase significantly decreased in the infected leaves, and membrane permeability was lower in the infected plants. Macro‐ and micronutrient elements were significantly changed: concentrations of leaf nitrogen, zinc, magnesium and iron were elevated but potassium concentration depressed in comparison to noninfected control leaves. Levels of other analysed nutrient elements, enzymes, photosynthesis and stomatal conductance, chlorophyll content and relative water content were unchanged. Clear physiological changes were found among infected and noninfected control plants but none between plants infected with different CTV isolates. The data suggest that some of the defence mechanisms investigated here were suppressed due to the continuous and long‐term pressure of biotic stress.     

Analysis of Iris yellow spot virus replication in vector and non‐vector thrips species

Iris yellow spot virus (IYSV, genus Tospovirus) is a viral disease of bulb and seed onion crops and is transmitted by Thrips tabaci. Foliage damage of up to 75% has been reported in Kenya and Uganda. In this study, the rate of IYSV replication in the larva, pupa and adult stages of T. tabaci and other non‐vector thrips species and colour forms such as Frankliniella occidentalis, F. schultzei (dark) and F. schultzei (pale) was evaluated by monitoring relative levels of nucleocapsid (N) and non‐structural (NSs) proteins using N‐ and NSs‐specific antibodies. The effect of IYSV replication on mortality of thrips was also determined. N protein levels increased in all three stages of IYSV‐fed T. tabaci, indicating replication of IYSV. In IYSV‐fed non‐vector thrips, the increase of N protein levels in the larval stage was lower than IYSV‐fed T. tabaci but higher than their healthy counterparts. The N protein levels did not increase at pupal and adult stages. NSs protein was not detected in first instar of either vector or non‐vector thrips species. After a 4 h post‐acquisition period, a significant increase in NSs proteins was only observed in IYSV‐fed T. tabaci, clearly differentiating vectors and non‐vectors of IYSV. IYSV replication did not influence the survival of the vector thrips species, T. tabaci populations or the non‐vector thrips species. This study indicates the effectiveness of monitoring non‐structural proteins such as NSs, compared to nucleocapsid proteins, for differentiating vectors and non‐vectors of IYSV.     

Increased bacterial endophyte populations in Nicotiana benthamiana with a branched‐chain alkane mixture

The aim of this study was to determine if treatment of soil with a branched‐chain alkane mixture known to induce resistance against Colletotrichum orbiculare also changes populations of bacterial endophytes from Nicotiana benthamiana. Eight culturable bacterial endophyte types matching six species of Bacillus and two species of Pseudomonas were found in roots, stem + petioles and/or leaves. Application of the branched‐chain alkane mixture resulted in significantly higher endophyte populations compared to the water or emulsifier controls for the Pseudomonas sp. LW3, Bacillus simplex LW4 and Bacillus pumilis LW5 colony types in roots and the B. simplex LW4 colony type in stem + petioles. The Pseudomonas sp. LW3 and B. simplex LW4 colony types also had higher populations in pure cultures under in vitro conditions with the branched‐chain alkane mixture compared to the controls. Inoculation with each of the eight colony types increased their population in the plant and induced resistance against C. orbiculare, with the most effective being Pseudomonas sp. LW3 and Pseudomonas alcaligenes SW1. Most of the endophytes could inhibit C. orbiculare growth in vitro, but the level of resistance in planta was not correlated to the ability of the colony type to inhibit C. orbiculare in culture. Thus, a branched‐chain alkane mixture can selectively affect the biomass of a subset of bacterial endophytes, demonstrating that it is a novel in planta endophyte growth promoter.     

A Variant of Cucumber mosaic virus Is Restricted to Local Lesions in Inoculated Tobacco Leaves with a Hypersensitive Response

A variant of Cucumber mosaic virus, CMV(Y/GM2), was isolated from a tobacco plant with mild green mosaic symptoms that was regenerated in vitro from a yellow strain of CMV [CMV(Y)]-infected tobacco leaves by tissue culture. CMV(Y/GM2) has two amino acid substitutions at 36 and 111 positions in the coat protein encoded on RNA3. CMV, assembled by mixing in vitro transcribed CMV(Y) RNA1 and RNA2 plus infectious RNA3 transcribed in vitro from cDNA to RNA3 of CMV(Y/GM2), was prepared and designated as CMV(Y/GM2)tr. When tobacco (Nicotiana tabacum cv. Xanthi nc) plants were inoculated with CMV(Y/GM2)tr, large necrotic local lesions in which the virus was localized, developed on the inoculated leaves. This host response unique to CMV(Y/GM2)tr was similar to the hypersensitive response (HR), which is a common resistance response to avirulent pathogens and was observed in five cultivars of Nicotiana tabacum and eight Nicotiana species. The revertant virus, however, accumulated to quite different levels in the various hosts. CMV(Y/GM2)tr induced pathogenesis-related 1 (PR-1) protein accumulation and systemic acquired resistance (SAR) which were generally observed in the HR. However, when tobaccos were inoculated with CMV(S36P)tr and CMV(V111I)tr, which have an amino acid substitution at either the 36 or 111 position in the coat protein of CMV(Y), respectively, CMV(S36P)tr was restricted to the primary infection site without necrotic local lesion formation and PR-1 protein and SAR induction. CMV(V111I)tr, however, systemically spread and induced mild green mosaic symptoms, while the host had the HR to CMV(Y/GM2)tr. The localization of CMV(Y/GM2)tr at the primary infection site may not only be caused by the HR, but also by the restriction of virus systemic movement resulting from the amino acid substitution at position 36 in the coat protein of CMV(Y). Received 15 December 1999/ Accepted in revised form 18 April 2000     

The threat of root‐knot nematodes (Meloidogyne spp.) in Africa: a review

Meloidogyne species pose a significant threat to crop production in Africa due to the losses they cause in a wide range of agricultural crops. The direct and indirect damage caused by various Meloidogyne species results in delayed maturity, toppling, reduced yields and quality of crop produce, high costs of production and therefore loss of income. In addition, emergence of resistance‐breaking Meloidogyne species has partly rendered various pest management programmes already in place ineffective, therefore putting food security of the continent at risk. It is likely that more losses may be experienced in the future due to the on‐going withdrawal of nematicides. To adequately address the threat of Meloidogyne species in Africa, an accurate assessment and understanding of the species present, genetic diversity, population structure, parasitism mechanisms and how each of these factors contribute to the overall threat posed by Meloidogyne species is important. Thus, the ability to accurately characterize and identify Meloidogyne species is crucial if the threat of Meloidogyne species to crop production in Africa is to be effectively tackled. This review discusses the use of traditional versus molecular‐based identification methods of Meloidogyne species and how accurate identification using a polyphasic approach can negate the eminent threat of root knot nematodes in crop production. The potential threat to Africa posed by highly damaging and resistance‐breaking populations of ‘emerging’ Meloidogyne species is also examined.     

Diversity of Avr‐vnt1 and AvrSmira1 effector genes in Polish and Norwegian populations of Phytophthora infestans

The oomycete Phytophthora infestans, the cause of late blight, is one of the most important potato pathogens. During infection, it secretes effector proteins that manipulate host cell function, thus contributing to pathogenicity. This study examines sequence differentiation of two P. infestans effectors from 91 isolates collected in Poland and Norway and five reference isolates. A gene encoding the Avr‐vnt1 effector, recognized by the potato Rpi‐phu1 resistance gene product, is conserved. In contrast, the second effector, AvrSmira1 recognized by Rpi‐Smira1, is highly diverse. Both effectors contain positively selected amino acids. A majority of the polymorphisms and all selected sites are located in the effector C‐terminal region, which is responsible for their function inside host cells. Hence it is concluded that they are associated with a response to diversified target protein or recognition avoidance. Diversification of the AvrSmira1 effector sequences, which existed prior to the large‐scale cultivation of plants containing the Rpi‐Smira1 gene, may reduce the predicted durability of resistance provided by this gene. Although no isolates virulent to plants with the Rpi‐phu1 gene were found, the corresponding Avr‐vnt1 effector has undergone selection, providing evidence for an ongoing ‘arms race’ between the host and pathogen. Both genes remain valuable components for resistance gene pyramiding.     

Characterization and pathogenicity assessment of Plectosphaerella species associated with stunting disease on tomato and pepper crops in Italy

This study follows a survey carried out in 2012 and 2013 on tomato and pepper crops in the Foggia province (southern Italy), for morphological, molecular and pathogenicity analyses of Plectosphaerella fungi. The Plectosphaerella genus includes several species that are pathogens of horticultural plants. The survey identified tomato and pepper crops that showed abundant wilt, leaf yellowing, and discolouration and necrosis of roots, plus collar and stem symptoms. Different fungi including Plectosphaerella spp. were isolated from tissues with and without symptoms. Subsequent molecular and morphological studies identified first records of P. citrulli infecting tomato and pepper, and P. pauciseptata and P. ramiseptata infecting pepper. Pathogenicity testing confirmed that most isolated species of Plectosphaerella caused symptoms on tomato and pepper, with P. ramiseptata the most aggressive. On the basis of these data, it is considered that Plectosphaerella species may cause stunting disease in tomato and pepper.