Application of the LAMP Assay as a Diagnostic Technique for Rapid Identification of Thrips tabaci (Thysanoptera: Thripidae)

Mitochondrial genetic diversity of Thrips tabaci (Thysanoptera: Thripidae) in onion growing regions of the United States

Onion thrips (Thrips tabaci Lindeman, Thysanoptera: Thripidae) causes severe damage to many horticultural and agronomic crops worldwide. It also acts as a vector of several plant viruses. T. tabaci is a key pest of Allium cepa in the United States. However, there is limited information available on the genetic variation within and between T. tabaci populations in the United States and its key evolutionary parameters. In the current study, 83 T. tabaci specimens were collected from A. cepa from 15 different locations comprising four states of the United States. A total of 92 mtCOI gene sequences of T. tabaci from A. cepa were analyzed to understand the genetic diversity and structure of T. tabaci collected from onion host. Seven distinct haplotypes of T. tabaci infesting A. cepa were identified from the current collection, while nine T. tabaci sequences retrieved from GenBank comprised 5 haplotypes. Overall, 15 haplotypes of T. tabaci infesting A. cepa were identified in the world that includes the ten haplotypes in the United States. In the phylogenetic analysis, all the populations collected during the study clustered with thelytokous lineage, while T. tabaci sequences retrieved from GenBank corresponded to leek-associated arrhenotokous lineage. The highest genetic variation was found in Elba and Malheur populations with 3 haplotypes identified in each. The results suggest that haplotypes 1 and 7 are more frequently prevailing haplotypes in the north-western United States, with haplotype 1 being the predominant all over the country. The eastern United States appears to have a more diverse group of haplotypes. The populations from Hungary constituted distinct haplotypes and a haplotype from Kingston linked it with the predominant haplotype.

Frontiers Approaches to the Diagnosis of Thrips (Thysanoptera): How Effective Are the Molecular and Electronic Detection Platforms?

Simple Summary

Thrips are important agricultural and forest pests. They cause damage by sucking plant sap and transmitting several plant viruses. Correct identification is the key for epidemiological studies and formulating appropriate management strategies. The application of molecular and electronic detection platforms has improved the morphological character-based diagnosis of thrips species. This article reviews research on molecular and automated identification of thrips species and discusses future research strategies for rapid and high throughput thrips diagnosis.

Abstract

Thrips are insect pests of economically important agricultural, horticultural, and forest crops. They cause damage by sucking plant sap and by transmitting several tospoviruses, ilarviruses, carmoviruses, sobemoviruses, and machlomoviruses. Accurate and timely identification is the key to successful management of thrips species. However, their small size, cryptic nature, presence of color and reproductive morphs, and intraspecies genetic variability make the identification of thrips species challenging. The use of molecular and electronic detection platforms has made thrips identification rapid, precise, sensitive, high throughput, and independent of developmental stages. Multi-locus phylogeny based on mitochondrial, nuclear, and other markers has resolved ambiguities in morphologically indistinguishable thrips species. Microsatellite, RFLP, RAPD, AFLP, and CAPS markers have helped to explain population structure, gene flow, and intraspecies heterogeneity. Recent techniques such as LAMP and RPA have been employed for sensitive and on-site identification of thrips. Artificial neural networks and high throughput diagnostics facilitate automated identification. This review also discusses the potential of pyrosequencing, microarrays, high throughput sequencing, and electronic sensors in delimiting thrips species.

Alien Invasive Pathogens and Pests Harming Trees, Forests, and Plantations: Pathways, Global Consequences and Management

Forest health worldwide is impacted by many invasive alien pathogens and pests (IAPPs) that cause significant harm, with severe economic losses and environmental alterations. Destructive tree pathogens and pests have in the past devastated our forests, natural landscapes and cityscapes and still continue to represent a serious threat. The main driver of pathogen and pest invasions is human activities, above all global trade, which allows these invasive species to overstep their natural distribution ranges. While natural transport occurs according to a regular, expected colonization pattern (based on the dispersive capacity of the organism), human-mediated transport takes place on a larger, unpredictable scale. In order for a pathogen or pest species to become invasive in a new territory it must overcome distinct stages (barriers) that strongly affect the outcome of the invasion. Early detection is crucial to enabling successful eradication and containment. Although sophisticated diagnostic techniques are now available for disease and pest surveillance and monitoring, few control and mitigation options are usable in forestry; of these, biological control is one of the most frequently adopted. Since invasion by pathogens and pests is an economic and ecological problem of supranational relevance, governments should endorse all necessary preventive and corrective actions. To this end, establishing and harmonizing measures among countries is essential, both for preventing new introductions and for diminishing the eventual range expansion of IAPPs present at a local scale. Research is fundamental for: (i) developing effective and rapid diagnostic tools; (ii) investigating the epidemiology and ecology of IAPPs in newly introduced areas; and (iii) supporting policymakers in the implementation of quarantine regulations.

Rapid Detection of Pityophthorus juglandis (Blackman) (Coleoptera, Curculionidae) with the Loop-Mediated Isothermal Amplification (LAMP) Method

The walnut twig beetle Pityophthorus juglandis is a phloem-boring bark beetle responsible, in association with the ascomycete Geosmithia morbida, for the Thousand Cankers Disease (TCD) of walnut trees. The recent finding of TCD in Europe prompted the development of effective diagnostic protocols for the early detection of members of this insect/fungus complex. Here we report the development of a highly efficient, low-cost, and rapid method for detecting the beetle, or even just its biological traces, from environmental samples: the loop-mediated isothermal amplification (LAMP) assay. The method, designed on the 28S ribosomal RNA gene, showed high specificity and sensitivity, with no cross reactivity to other bark beetles and wood-boring insects. The test was successful even with very small amounts of the target insect’s nucleic acid, with limit values of 0.64 pg/µL and 3.2 pg/µL for WTB adults and frass, respectively. A comparison of the method (both in real time and visual) with conventional PCR did not display significant differences in terms of LoD. This LAMP protocol will enable quick, low-cost, and early detection of P. juglandis in areas with new infestations and for phytosanitary inspections at vulnerable sites (e.g., seaports, airports, loading stations, storage facilities, and wood processing companies).

Development of a loop-mediated isothermal amplification (LAMP) assay for the identification of the invasive wood borer Aromia bungii (Coleoptera: Cerambycidae) from frass

The red-necked longhorn beetle Aromia bungii (Faldermann, 1835) (Coleoptera: Cerambycidae) is native to east Asia, where it is a major pest of cultivated and ornamental species of the genus Prunus. Morphological or molecular discrimination of adults or larval specimens is required to identify this invasive wood borer. However, recovering larval stages of the pest from trunks and branches causes extensive damage to plants and is timewasting. An alternative approach consists in applying non-invasive molecular diagnostic tools to biological traces (i.e., fecal pellets, frass). In this way, infestations in host plants can be detected without destructive methods. This paper presents a protocol based on both real-time and visual loop-mediated isothermal amplification (LAMP), using DNA of A. bungii extracted from fecal particles in larval frass. Laboratory validations demonstrated the robustness of the protocols adopted and their reliability was confirmed performing an inter-lab blind panel. The LAMP assay and the qPCR SYBR Green method using the F3/B3 LAMP external primers were equally sensitive, and both were more sensitive than the conventional PCR (sensitivity > 10³ to the same starting matrix). The visual LAMP protocol, due to the relatively easy performance of the method, could be a useful tool to apply in rapid monitoring of A. bungii and in the management of its outbreaks.

Population Genetic Diversity and Structure of Thrips tabaci (Thysanoptera: Thripidae) on Allium Hosts in China, Inferred From Mitochondrial COI Gene Sequences

Thrips tabaci Lindeman is a widely distributed agricultural pest China, which causes damage to many vegetables and cash crops. However, the population genetic variation of this pest in China remains unknown. In this study, the genetic diversity and structure of T. tabaci on Allium hosts collected from 12 geographic locations were evaluated based on mitochondrial cytochrome oxidase subunit I (COI) sequences. Six haplotypes were identified in 247 T. tabaci individuals from 12 geographic locations. All the identified T. tabaci haplotypes were thelytokous populations. The strongest genetic differentiation and relatively low gene flow were found between QHXN and other locations, which might be due to geographic barriers, such as high altitude Qinghai-Tibet Plateau. The lowest genetic variation was found in eastern and southern regions, with only one haplotype identified. The Mantel test showed no correlation between genetic distance and geographical distances. High gene flow between locations with substantial geographical distances suggested that migration of T. tabaci across China might be facilitated through human activities. The results of demographic analysis suggested that T. tabaci in China have undergone a recent demographic expansion. The possible influences of T. tabaci invasion history and human activities on the current haplotype geographical distribution were interpreted and the implications of these findings for T. tabaci management were discussed.

A Diagnostic Loop-Mediated Isothermal Amplification Method to Distinguish Helicoverpa armigera (Lepidoptera: Noctuidae) From Other Related Species in the New World

Helicoverpa armigera (Hübner) is a notorious agricultural pest native to the Old World. Recently, its invasion into South and Central America has become a serious problem in the New World. The rapid detection of invasive pests is essential to eradicate them and prevent establishment. However, an extremely similar species, H. zea (Boddie) distributed in the New World makes identification difficult. Helicoverpa armigera and H. zea have only minor differences in male genitalia to separate them morphologically. Both species are attracted to the same pheromone lure, and it takes considerable time and effort to identify them from bulk samples obtained during trap monitoring. Although several molecular approaches based on PCR have been reported, these methods require expensive equipment and are unsuitable for onsite diagnostics. Here, we developed a rapid and convenient diagnostic method based on the loop-mediated isothermal amplification to distinguish H. armigera from related species: H. zea, H. assulta (Guenée), H. punctigera (Wallengren), and Chloridea virescens (Fabricius). The diagnostic method makes it possible to detect H. armigera within 90 min only using simple equipment. The method also worked with mixed DNA templates containing excess DNA from H. zea at the ratio of 1:999 (H. armigera:H. zea). This method can be an effective tool for onsite diagnostics during monitoring surveys for invasive H. armigera.

Loop-mediated isothermal amplification (LAMP) for the identification of invasive Aedes mosquito species

Invasive Aedes mosquito species (Diptera: Culicidae) are of public health concern in Europe because they are either recognized or potential vectors of pathogens. Loop-mediated isothermal amplification (LAMP) is a rapid and simple method for amplifying DNA with high specificity and efficiency, with the technique having potential for application in the field, including in high-throughput format. Specific LAMP assays based on rDNA internal transcribed spacers 1 or 2 sequences, considering intraspecies variability at these loci, were developed for Aedes aegypti, Aedes albopictus, Aedes japonicus, Aedes koreicus and the indigenous Aedes geniculatus. No such assays could be developed for Aedes atropalpus and Aedes triseriatus because both loci were too short to serve as target. The assays rely on the clearly visible colour change from violet to sky blue after successful amplification. Sensitivity of egg detection was confirmed with ratios of up to one mosquito egg in 99 other eggs. Simple sample preparation of adults or eggs by mechanical homogenization in water required an additional heat treatment or centrifugation step to avoid non-specific colour changes. Thus, further technical improvements are needed to render these assays truly field-applicable, which would greatly facilitate surveillance of these invasive mosquito species and allow for prompt implementation of control measures.

Loop-Mediated Isothermal Amplification Combined with PCR for Rapid Identification of the Ethiopian Fruit Fly (Diptera: Tephritidae)

Nowadays, with increasing trend of trans-boundary transportation of agricultural products and higher probability of introduction of many invasive species into new areas, fast and precise species diagnosis is of great significance particularly at the port of entry, where morphological identification often requires adult insect specimens especially with specialist insects. The cucumber fruit fly, Dacus ciliatus Loew (Diptera: Tephritidae), ranks as one of the most destructive agricultural pests attacking mainly fruits of Cucurbitaceae. This pest is also widespread and highly invasive; thus, it is a high priority for pest detection and quarantine programs. Although cucumber fruit fly adults can usually be identified and distinguished from the other species by morphological keys, it is often difficult or impossible to distinguish this species from the other tephritids that share host plants by using material from other stages of development. In such situations, using a quick and robust alternative species diagnostic tool would be valuable. In this study, we assessed a technique combining loop-mediated isothermal amplification (LAMP) with PCR (PCR-LAMP) for the rapid detection and discrimination of cucumber fruit fly DNA from some other common tephritid species attacking Cucurbitaceae, using material from different stages of development. The described method was species-specific and sensitive and provided a rapid diagnostic tool to detect D. ciliaus even by non-experts.