Development of a DNA microarray for species identification of quarantine aphids

Lee, Won Sun; Choi, Hyun-Ki; Kang, Jin-Seok; Kim, Ji Hoon; Lee, Si Hyeock; Lee, Seung Hwan; Hwang, Seung Yong

doi:10.1002/ps.3520

Cited by 5 publications

(3 citation statements)

References 18 publications

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“…Microarrays have been widely used for species diagnosis, detection of functional genes and gene expression (Sessitsch et al, ). Diagnostic microarrays were the earliest high‐throughput identification methods that enabled targeting specific pre‐selected taxa of viruses, bacterial and fungal pathogens and pests at species level (Lee et al, ; Szemes et al, ; Wilson et al, ). The first diagnostic (macro)arrays for selected plant pathogenic fungi and oomycetes included just >10 species and enabled quantification of pathogens present at low abundance (<0.1% in mixed DNA samples; Lievens et al, ; Szemes et al, ).…”

Section: The Emerging Methodsmentioning

confidence: 99%

High‐throughput identification and diagnostics of pathogens and pests: Overview and practical recommendations

Tedersoo

Drenkhan

Anslan

et al. 2018

Molecular Ecology Resources

109

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High-throughput identification technologies provide efficient tools for understanding the ecology and functioning of microorganisms. Yet, these methods have been only rarely used for monitoring and testing ecological hypotheses in plant pathogens and pests in spite of their immense importance in agriculture, forestry and plant community dynamics. The main objectives of this manuscript are the following: (a) to provide a comprehensive overview about the state-of-the-art high-throughput quantification and molecular identification methods used to address population dynamics, community ecology and host associations of microorganisms, with a specific focus on antagonists such as pathogens, viruses and pests; (b) to compile available information and provide recommendations about specific protocols and workable primers for bacteria, fungi, oomycetes and insect pests; and (c) to provide examples of novel methods used in other microbiological disciplines that are of great potential use for testing specific biological hypotheses related to pathology. Finally, we evaluate the overall perspectives of the state-of-the-art and still evolving methods for diagnostics and population-and community-level ecological research of pathogens and pests. K E Y W O R D S community ecology, crop disease, forest pathology, high-throughput sequencing, metabarcoding, metagenomics, molecular diagnostics, plant pathogens, sentinel plantations play a key role in maintaining diversity and primary productivity in ---

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Section: The Emerging Methodsmentioning

confidence: 99%

High‐throughput identification and diagnostics of pathogens and pests: Overview and practical recommendations

Tedersoo

Drenkhan

Anslan

et al. 2018

Molecular Ecology Resources

109

View full text Add to dashboard Cite

show abstract

“…Microarray technology has been extensively used in disease forecasting, diagnostics, screening of drugs, crop improvement, food safety analysis, and environmental monitoring [ 209 , 210 , 211 ]. DNA chips are preferred in insect diagnosis because of their high throughput, high sensitivity, and many practical applications [ 212 , 213 ]. To date, only two studies report the use of microarray/DNA chip technology in thrips identification.…”

Section: Pcr-based Identification Of Thrips Using Molecular Markersmentioning

confidence: 99%

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

Ghosh

Jangra

Dietzgen

et al. 2021

Insects

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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.

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“…It is essential to develop a more efficient method for simultaneous screening of mass samples. In the past decade, the microarray assay routinely used in pathogen investigation has been used rarely for insect pest identification (Chung et al ., 2011; Yeh et al ., 2012; de Luca et al ., 2013; Lee et al ., 2013).…”

Section: Introductionmentioning

confidence: 99%

Agronomically important thrips: development of species-specific primers in multiplex PCR and microarray assay using internal transcribed spacer 1 (ITS1) sequences for identification

Yeh

Tseng

Chang

et al. 2014

Bull. Entomol. Res.

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Thrips, the sole vector of plant Tospovirus, are major pests of many agricultural crops throughout the world. Molecular approaches have been applied in recent decades to identify these minute and morphologically difficult to distinguish insects. In this study, sequences of internal transcribed spacer 1 (ITS1) region of 15 agronomically important thrips, including several virus transmission species, have been analyzed in order to design species-specific primers for multiplex PCR and probes for microarray assay. That the ITS1 sequence distances within species were smaller than those among species suggests that the ITS1 fragment can be used for thrips species identification. The specificity and stability of these primers, combined with universal paired primers, were tested and verified in multiplex PCR. Using these specific primers as probes, microarray assay showed that PCR products of all thrips species hybridized consistently to their corresponding probes, though some signals were weak. We have demonstrated that multiplex PCR using specific primers based on ITS1 sequences is a simple, reliable, and cost-effective diagnostic tool for thrips species identification. Moreover, the DNA microarray assay is expected to extend into a reliable high-throughput screening tool for the vast numbers of thrips.

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Development of a DNA microarray for species identification of quarantine aphids

Abstract: A microarray has been developed to distinguish aphid species. DNA microarray technology provides a rapid, easy, cost-effective and accurate method for identifying aphid species for pest control management.

Cited by 5 publications

References 18 publications

High‐throughput identification and diagnostics of pathogens and pests: Overview and practical recommendations

High‐throughput identification and diagnostics of pathogens and pests: Overview and practical recommendations

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

Agronomically important thrips: development of species-specific primers in multiplex PCR and microarray assay using internal transcribed spacer 1 (ITS1) sequences for identification

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