Molecular Characterisation and Diagnosis of Root-Knot Nematodes (Meloidogyne spp.) from Turfgrasses in North Carolina, USA

Ye, Weimin; Zeng, Yongsan; Kerns, James P.

doi:10.1371/journal.pone.0143556

Cited by 63 publications

(54 citation statements)

References 33 publications

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“…The low genetic diversity observed for M. javanica isolates during the present study was similar to results reported for other populations of M. javanica from different crops (Carneiro et al, 1998;Randig et al, 2002;Cofcewicz et al, 2004;Medina et al, 2017). This finding might be attributed to the parthenogenetic mode of reproduction in M. javanica, which results in clonal progenies (Triantaphyllou, 1985). Measured individuals of the selected five populations of M. javanica in the present study could not be sorted in regard of none of the diagnostic characters ( Table 3).…”

Section: Discussionsupporting

confidence: 91%

“…Also, we try to use Mantel test in linear shape for searching correlation between different matrix produced by RAPD and ISSR. Bootstrapping was done using the Winboot with 1000 replicates (Yap and Nelson, 1996) and measurements under 60 were excluded. Frequency analyses were performed to estimate the variance components and their significance levels of genetic variation within and among populations using GenALEx version 6.5 (Peakall and Smouse, 2006).…”

Section: Issr and Rapd Data Analysismentioning

confidence: 99%

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Genetic intraspecific diversity of Meloidogyne javanica parasitizing vegetables in southern Iran

Ghaderi

Dehghan

Hesar

et al. 2020

Journal of Nematology

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In order to investigate different species of root-knot nematodes associated with vegetable production in southern regions of Iran, 37 populations of the most predominant species, Meloidogyne javanica, were recovered. Morphological and morphometric studies were carried on the characters of females, males, J2s and perineal patterns. Species-specific Sequence Characterized Amplified Region (SCAR) primers confirmed morphological studies, and all these populations produced specific band in 670 bp using Fjav and Rjav primers. Genetic diversity of different populations was studied by Inter Simple Sequence Repeats (ISSR) and Random Amplified Polymorphic DNA (RAPD) markers implementing 10 primers for each approach. Results revealed a relatively low genetic diversity (the percentage of polymorphic bands were 19.08 and 24.60 for ISSR and RAPD, respectively). The analyses of molecular variance indicated that the variation resulted from genotypic variations within region and variances among regions are 81% and 19% for RAPD, and 86% and 14% for ISSR, respectively. On the other hand, F ST and Nm values are 0.140 and 1.535 for ISSR while these values are 0.188 and 1.079 for RAPD. So it can be concluded that there is a great deal of gene flow between populations due to the movement of plant material contaminated with nematodes, which results in high mixing between populations. ISSR and RAPD datasets failed to group populations according to their geographic region. There were no pathotypes or other intraspecific biological entities observed in the species.

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Section: Discussionsupporting

confidence: 91%

Section: Issr and Rapd Data Analysismentioning

confidence: 99%

Genetic intraspecific diversity of Meloidogyne javanica parasitizing vegetables in southern Iran

Ghaderi

Dehghan

Hesar

et al. 2020

Journal of Nematology

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“…These were used to inoculate 20 guava plants (a single egg mass per plant), which had been grown from seed in sterile medium for 3 months. At 45 days after inoculation, five plants were randomly chosen and several females were removed from the roots to confirm their molecular identification (Ye et al, 2015); all other plants were discarded. The selected plants were used as an inoculum source for the remaining experiments.…”

Section: Nematode Culturementioning

confidence: 99%

The use of infrared spectroscopy and machine learning tools for detection ofMeloidogyneinfestations

San‐Blas¹,

Paba

Cubillán

et al. 2020

Plant Pathology

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Plant parasitic nematodes are generally soilborne pathogens that attack plants and cause economic losses in many crops. The infested plants show nonspecific symptoms or, often, are symptomless; therefore, diagnosis is performed by taking soil and root tissue samples. Here, we show that a combination of different infrared spectra analysis and machine learning algorithms can be used to detect plant parasitic nematode infestations before symptoms become visible, using leaves instead of roots and soil as samples. We found that tomato and guava plants infested with Meloidogyne enterorlobii produced different spectral patterns compared to uninfested plants. Using partial spectra from 1,450 to 900/cm as the "fingerprint region", principal component analyses indicated that after 5 (tomatoes) or 8 weeks (guava), plants with no visible symptoms of infestations were positively diagnosed. To improve the early detection response, we used machine learning modelling. A support vector machine (SVM) was used to obtain more robust, accurate models. The SVM model contained 34 support vectors, 17 for each level. The overall performance of the model was >97% and the total accuracy was significantly higher, demonstrating the absence of chance prediction. The best prediction of infestation was obtained at the second and fourth weeks for tomatoes and guavas, respectively, reducing the diagnostic time by half. The combined application of these techniques reduces the processing time from field to laboratory and shows enormous advantages by avoiding root and soil sampling.

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“…The PCR amplification using the designed primers was done as described by Ye et al (2015). The thermocycler conditions for amplification comprised initial denaturation at 94°C for 3 min, followed by 35 cycles of denaturation at 94°C for 30 sec, annealing for 45 sec at 55°C for ITS primers and 49°C for LSU primers, extension at 72°C for 1 min, and a final extension at 72°C for 10 min.…”

Section: Pcr Amplification Cleaning and Sequencingmentioning

confidence: 99%

Molecular approach to confirm traditional identification of Radopholus similis sampled in Tanzania

Mgonja

Temu

Ndunguru

et al. 2020

Journal of Nematology

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Banana (Musa spp. L.) is an important staple food and cash crop for about 30% of the population in Tanzania; however, the burrowing plant-parasitic nematode Radopholus similis causes black head disease and toppling in banana plants, which results in yield losses. We collected and identified 80 specimens of R. similis from four agroecological zones in Tanzania using morphological characters. We then used universal and specific R. similis primers to amplify the small subunit, internal transcribed spacer and large subunit of ribosomal DNA regions of these specimens. The amplicons were subsequently sequenced and analyzed using Bayesian inference. We identified two major clades, one that comprised all R. similis sequences derived from this study and another that included R. similis and Radopholus spp. sequences obtained from GenBank, indicating the separation of this species from congeneric sequences. Our findings provide a useful, simple and rapid method for identifying burrowing nematodes. This outcome could contribute to the development of permanent, integrated pest management strategies for the control of R. similis in banana and other crops in order to reduce associated yield losses in Tanzania. To our knowledge, this is the first study of nematodes to use combined morphological and molecular methods for the identification of R. similis in Tanzania.

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Molecular Characterisation and Diagnosis of Root-Knot Nematodes (Meloidogyne spp.) from Turfgrasses in North Carolina, USA

Cited by 63 publications

References 33 publications

Genetic intraspecific diversity of Meloidogyne javanica parasitizing vegetables in southern Iran

Genetic intraspecific diversity of Meloidogyne javanica parasitizing vegetables in southern Iran

The use of infrared spectroscopy and machine learning tools for detection ofMeloidogyneinfestations

Molecular approach to confirm traditional identification of Radopholus similis sampled in Tanzania

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