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Molecular characterisation of Meloidogyne enterolobii and other Meloidogyne spp. from South Africa

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Abstract

Identification of Meloidogyne spp. is challenging when using only the classical techniques since some species share similar characteristics. In this study, 37 Meloidogyne populations were obtained from four provinces in South Africa during 2015 and 2016 and molecularly characterised. We used SCAR-PCR markers and sequencing of four DNA fragments, viz. the D2-D3 segment (28S rDNA), COI, viable region between COII and 16S rDNA and NADH5 (mtDNA) genes. Using SCAR-PCR, M. enterolobii, M. javanica, M. incognita and M. hapla (in descending order of prevalence) were identified. According to D2-D3, COI, COII/16S and NADH5 sequence analyses, the 23 M. enterolobii populations identified clustered together in a well-supported clade, while M. javanica (9 populations) and M. incognita (5 populations) grouped in another. Results showed that D2-D3 and COI genes were appropriate for accurate identification of M. enterolobii, but not to differentiate among M. arenaria, M. incognita and M. javanica. Conversely, SCAR-PCR and NADH5 were more accurate in distinguishing among different Meloidogyne spp. In conclusion, SCAR-PCR was best for the situation of mixed populations.

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Acknowledgments

This research has been partially funded by the National Research Foundation under Grant CPRR160424162946. Any opinion, finding and conclusion or recommendation expressed in this material is that of the author(s) and the NRF does not accept any liability in this regard. Partial funding, by the North-West University and the Agricultural Research Council – Institute for Tropical and Subtropical Crops and use of infrastructure of these institutions, is acknowledged. The authors also convey their gratitude towards Proffs. Gerrit Karssen (NPPO, Wageningen, The Netherlands) and Wim Wesemael (ILVO, Merelbeke, Belgium) for supplying standards of cryophilic Meloidogyne spp. for SCAR-PCR analysis.

Funding

This study was partially funded by the National Research Foundation (Grant number CPRR160424162946).

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Authors and Affiliations

  1. Unit for Environmental Sciences and Management, North-West University, Private Bag X6001, Potchefstroom, North West, 2520, South Africa

    Milad Rashidifard, Charlotte M. S. Mienie & Hendrika Fourie

  2. Nematology Unit, Biosystematics, Agricultural Research Council - Plant Health and Protection (ARC-PHP), Private Bag X134, Queenswood, Gauteng, 0121, South Africa

    Mariette Marais

  3. Agricultural Research Council - Tropical and Subtropical Crops (ARC – TSC), Private Bag X11208, Mbombela, Mpumalanga, 1200, South Africa

    Mieke Stefanie Daneel

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  1. Milad Rashidifard
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Correspondence to Milad Rashidifard.

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Figure S1

Bayesian inference (BI) of Meloidogyne spp. obtained from South Africa, based on 50 sequences of partial D2-D3 28S rDNA region with length of 540 bp each under HKY + G model (those populations which are from this study are shown in bold). (PNG 634 kb)

High Resolution Image (TIF 62902 kb)

Figure S2

Bayesian inference (BI) of Meloidogyne spp. obtained from South Africa, based on 50 sequences of COI of mtDNA with length of 250 bp each under HKY + G model (those populations which are from this study are shown in bold). (PNG 854 kb)

High Resolution Image (TIF 62841 kb)

Figure S3

Bayesian inference (BI) of Meloidogyne spp. obtained from South Africa, based on 39 sequences of region between COII and 16S rDNA with length of 425 bp each under HKY + G model (those populations which are from this study are shown in bold). (PNG 365 kb)

High Resolution Image (TIF 28426 kb)

Figure S4

Bayesian inference (BI) of Meloidogyne spp. obtained from South Africa, using 46 sequences of NADH5 mtDNA with length of 395 bp each under ATR model (those populations which are from this study are shown in bold). (PNG 838 kb)

High Resolution Image (TIF 63075 kb)

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Rashidifard, M., Marais, M., Daneel, M.S. et al. Molecular characterisation of Meloidogyne enterolobii and other Meloidogyne spp. from South Africa. Trop. plant pathol. 44, 213–224 (2019). https://doi.org/10.1007/s40858-019-00281-4

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