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Development of SNP-based assays for identification of Globodera rostochiensis and Globodera pallida

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Abstract

Potato cyst nematodes (PCNs), Globodera rostochiensis and G. pallida, are one of the major pathogens of potato and cause significant losses worldwide. These species, which are on the worldwide quarantine list, can survive in infected areas for more than 20 years. Therefore, these species need to be identified accurately and quickly. Although different molecular methods have been developed for the detection of G. rostochiensis and G. pallida, new techniques are being studied to identify these species. Kompetitive Allele-Specific PCR (KASP) based on single nucleotide polymorphisms (SNP) is a novel molecular technique. This technique is used for marker-assisted selection of genes that confer resistance in plants, for determining genetic variation of pathogens and for species identification. In this study, G. rostochiensis and G. pallida specific KASP primers were developed from the available DNA sequences of all Globodera species retrieved from GenBank. The KASP assay successfully identified the species G. rostochiensis and G. pallida. The developed KASP assays were able to distinguish these species from each other and from other nematode species. Results shown that even one cyst of these species can be sufficient for identification. This is the first study to develop KASP primers to identify PCNs. These assays can be used for accurate and rapid identification PCNs in laboratories.

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References

  • Abd-Elgawad MMM (2020) Biological control agents in the integrated nematode management of potato in Egypt. Egypt J Biol Pest Control 30:1–13. https://doi.org/10.1186/s41938-020-00325-x

    Article  Google Scholar 

  • Ahuja A, Joshi V, Singh G, Kundu A, Bhat CG, Kumar S, Rao U, Somvanshi VS (2021) Rapid and sensitive detection of potato cyst nematode Globodera rostochiensis by loop-mediated isothermal amplification assay. 3 Biotech 11(294):1–8. https://doi.org/10.1007/s13205-021-02830-8

    Article  Google Scholar 

  • Aydınlı G, Mennan S (2019) Reproduction of root-knot nematode isolates from the middle Black Sea Region of Turkey on tomato with Mi-1.2 resistance gene. Türkiye Entomoloji Dergisi 43(4):417–427. https://doi.org/10.16970/entoted.582406

    Article  Google Scholar 

  • Baldwin JG, Mundo-Ocampo M (1991) Heteroderinae, cystand non-cyst-forming nematodes. In: Nickle WR (ed) Manual of agricultural nematology. Marcel Dekker, pp 275–362

    Google Scholar 

  • Bulman SR, Marshall JW (1997) Differentiation of Australasian potato cyst nematode (PCN) populations using the polymerase chain reaction (PCR). N Z J Crop Hortic Sci 25:123–129. https://doi.org/10.1080/01140671.1997.9513998

    Article  CAS  Google Scholar 

  • Camacho MJ, Inacio ML, Mota M, De Andrade E (2021) Development and validation of a loop-mediated isothermal amplification diagnostic method to detect the quarantine potato pale cyst nematode, Globodera pallida. Pathogens 10(744):1–16. https://doi.org/10.3390/pathogens10060744

    Article  CAS  Google Scholar 

  • Devran Z, Göknur A (2020) Development and validation of a SNP-based KASP assay for rapid identification of Aphelenchoides besseyi Christie, 1942. Crop Prot 136:105235. https://doi.org/10.1016/j.cropro.2020.105235

    Article  CAS  Google Scholar 

  • Devran Z, Kahveci E (2019) Development and validation of a user-friendly KASP marker for the Sw-5 locus in tomato. Australas Plant Pathol 48:503–507. https://doi.org/10.1007/s13313-019-00651-1

    Article  CAS  Google Scholar 

  • Devran Z, Söğüt MA (2009) Distribution and identification of root-knot nematodes from Turkey. J Nematol 41(2):128–133

    CAS  PubMed  PubMed Central  Google Scholar 

  • Devran Z, Göknur A, Mesci L (2016) Development of molecular markers for the Mi-1 gene in tomato using the KASP genotyping assay. Hortic Environ Biotechnol 57(2):156–160. https://doi.org/10.1007/s13580-016-0028-6

    Article  Google Scholar 

  • EPPO (2017) PM 7/40(4) Globodera rostochiensis and Globodera pallida. Bull OEPP 47:174–197

    Article  Google Scholar 

  • EPPO (2022) EPPO datesheet: Globodera pallida. https://gd.eppo.int/taxon/HETDPA/datasheet/. Accessed 18 Feb 2023

  • Fenwick DW (1940) Methods for the recovery and counting of cysts of Heterodera schachtii from soil. J Helminthol 18:155–172

    Article  Google Scholar 

  • Gamel S, Letort A, Fouville D, Folcher L, Grenier E (2017) Development and validation of real-time PCR assays based on novel molecular markers for the simultaneous detection and identification of Globodera pallida, G. Rostochiensis and Heterodera Schachtii. Nematology 19:789–804

    Article  Google Scholar 

  • Golden AM (1986) Morphology and identification of cyst nematodes. In: Lamberti F, Taylor CE (eds) Cyst nematodes. Plenum Press, pp 23–45

    Chapter  Google Scholar 

  • Hooper DJ (1986) Extraction of free living stages from soil. In: Southey JF (ed) Laboratory methods for work with plant soil nematodes. Her Majesty’s Stationary Office, pp 5–30

    Google Scholar 

  • Jones JT, Haegeman A, Danchin EG, Gaur HS, Helder J, Jones MG, Kikuchi T, Manzanilla-Lopez R, Palımares-Rius JE, Wesemael WML, Perry RN (2013) Top 10 plant-parasitic nematodes in molecular plant pathology. Mol Plant Pathol 14(9):946–961. https://doi.org/10.1111/mpp.12057

    Article  PubMed  PubMed Central  Google Scholar 

  • Khanal C, Kularathna MT, Ray JD, Stetina SR, McGawley EC, Overstreet C (2019) Single nucleotide polymorphism analysis using KASP assay reveals genetic variability in Rotylenchulus reniformis. Plant Dis 103:1835–1842. https://doi.org/10.1094/PDIS-11-18-1975-RE

    Article  CAS  PubMed  Google Scholar 

  • Lima FSO, Mattos VS, Silva ES, Carvalho MAS, Teixeira RA, Silva JC, Correa VR (2018) Nematodes affecting potato and sustainable practices for their management. In: Yıldız M (ed) Potato: from Incas to all over the world. IntechOpen, pp 107–124

    Google Scholar 

  • Madani M, Subbotin SA, Moens M (2005) Quantitative detection of the potato cyst nematode, Globodera pallida, and the beet cyst nematode, Heterodera schachtii, using real-time PCR with SYBR green I dye. Mol Cell Probes 19:81–86. https://doi.org/10.1016/j.mcp.2004.09.006

    Article  CAS  PubMed  Google Scholar 

  • Mburu H, Cortada L, Haukeland S, Ronno W, Nyongesa M, Kinyua Z, Bargual JL, Coyne D (2020) Potato cyst nematodes: a new threat to potato production in East Africa. Front Plant Sci 11:1–13

    Article  Google Scholar 

  • Mıstanoğlu İ, Özalp T, Devran Z (2019) The efficacy of molecular markers associated with virulence in root-knot nematodes. Nematology 0:1–8

    Google Scholar 

  • Mıstanoğlu İ, Uysal G, Devran Z (2022) Distribution and identification of important plant parasitic nematodes in anise growing areas. Türkiye Entomoloji Dergisi 46(3):323–333. https://doi.org/10.16970/entoted.1098172

    Article  Google Scholar 

  • Nowaczyk K, Dobosz R, Kornobis S, Obrepalska-Steplowska A (2008) TaqMan REAL-Time PCR-based approach for differentiation between Globodera rostochiensis (golden nematode) and Globodera artemisiae species. Parasitol Res 103:577–581. https://doi.org/10.1007/s00436-008-1012-6

    Article  PubMed  Google Scholar 

  • Oliveira CMGD, Monteiro AR, Blok VC (2011) Morphological and molecular diagnostics for plant-parasitic nematodes: working together to get the identification done. Trop Plant Pathol 36(2):65–73

    Google Scholar 

  • Özalp T, Konül G, Ayyıldız O, Tülek A, Devran Z (2020) First report of root-knot nematode, Meloidogyne arenaria on lavender in Turkey. J Nematol 52:1–3. https://doi.org/10.21307/jofnem-2020-008

    Article  CAS  PubMed  Google Scholar 

  • Rehrig WZ, Ashrafi H, Hill T, Prince J, Van Deynze A (2014) CaDMR1 cosegregates with QTL Pc5.1 for resistance to Phytophthora capsici in pepper (Capsicum annuum). Plant Genome 7(2):1–12. https://doi.org/10.3835/plantgenome2014.03.0011

    Article  CAS  Google Scholar 

  • Semagn K, Babu R, Hearne S, Olsen M (2014) Single nucleotide polymorphism genotyping using Kompetitive Allele Specific PCR (KASP): overview of the technology and its application in crop improvement. Mol Breed 33:1–14. https://doi.org/10.1007/s11032-013-9917-x

    Article  CAS  Google Scholar 

  • Shi Z, Liu S, Noe J, Arelli P, Meksem K, Li Z (2015) SNP identification and marker assay development for high-throughput selection of soybean cyst nematode resistance. BMC Genom 16(314):1–12. https://doi.org/10.1186/s12864-015-1531-3

    Article  CAS  Google Scholar 

  • Siddiqi MR (2000) Superfamily Hoplolaimina. In: Siddiqi MR (ed) Tylenchida parasites of plants and insects. CABI Publishing, pp 387–412

    Chapter  Google Scholar 

  • Subbotin SA, Franco J, Knoetze R, Roubtsova TV, Bostock RM, Del Prado Vera IC (2019) DNA barcoding, phylogeny and phylogeography of the cyst nematode species from the genus Globodera (Tylenchida: Heteroderidae). Nematology 0:1–29. https://doi.org/10.1163/15685411-00003305

    Article  CAS  Google Scholar 

  • Toyota K, Shirakashi T, Sato E, Wada S, Min YY (2008) Development of a real-time PCR method for the potato-cyst nematode Globodera rostochiensis and the root-knot nematode Meloidogyne incognita. Soil Sci Plant Nutr 54:72–76. https://doi.org/10.1111/j.1747-0765.2007.00212.x

    Article  CAS  Google Scholar 

  • Turner SJ, Rowe JA (2006) Cyst nematodes. In: Perry RN, Moens M (eds) Plant nematology. CAB International, Oxfordshire, pp 90–122

    Google Scholar 

  • Vejl P, Skupinova S, Sedlak P, Domkarova J (2002) Identification of PCN species (Globodera rostochiensis, G. pallida) by using of ITS-1 region’s polymorphism. Rostlinna Vyroba 48(11):486–489

    CAS  Google Scholar 

  • Viaene N (2016) Ring testing of diagnostic methods for the identification of potato cyst nematodes and assessing resistance of potato cultivars. İn: Poster at the report of the joint EEC-EPPO workshop on Euphresco, (Moscow: Eurasian Economic Commission (EEC) and the European and Mediterranean Plant Protection Organisation (EPPO))

  • White TJ, Bruns T, Leeand S, Taylor I (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis MA, Gefand DH, Sninsky JJ, White TJ (eds) PCR protocols: a guide to methods and applications. Academic Press, pp 315–322

    Google Scholar 

  • Zhao S, Li A, Li C, Xia H, Zhao C, Zhang Y, Hou L, Wang X (2017) Development and application of KASP marker for high throughput detection of AhFAD2 mutation in peanut. Electron J Biotechnol 25:9–12. https://doi.org/10.1016/j.ejbt.2016.10.010

    Article  Google Scholar 

  • Zouhar M, Rysanek P, Kocova M (2000) Detection and differentiation of the potato cyst nematodes Globodera rostochiensis and Globodera pallida by PCR. Plant Prot Sci 36(3):81–84

    Article  Google Scholar 

Download references

Acknowledgments

The authors would like to thank Hülya Demirbaş Pehlivan (Adana Biological Control Research Institute) for providing G. rostochiensis samples; Halil Toktay (Niğde Ömer Halisdemir Universıty) for providing G. rostochiensis samples; Gülten Kaçar Avcı (Niğde Potato Research Institute) for providing G. rostochiensis samples; Emre Evlice (Sivas University of Science and Technology) for providing G. rostochiensis and G. pallida samples, The French Agency for Food Environmental and Occupational Health & Safety (ANSES) for providing G. rostochiensis, G. pallida, D. destructor samples; Valeria Orlando (Fera Science Ltd.) for providing G. rostochiensis, G. pallida, M. hapla samples; Nevşehir Directorate of Provincial Agriculture and Forestry for providing M. chitwoodi; Niğde Directorate of Provincial Agriculture and Forestry for providing M. chitwoodi; Gökhan Aydınlı (Ondokuz Mayıs University) for providing M. luci; Elif Yavuzaslanoğlu (Karamanoğlu Mehmetbey University) for providing D. dipsaci; Atilla Öcal (Atatürk Horticultural Central Research Institute) for providing D. dipsaci; and Mustafa İmren (Bolu Abant İzzet Baysal University) for providing H. filipjevi, H. avenae and H. latipons.

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Authors and Affiliations

  1. Antalya Directorate of Agricultural Quarantine, 07010, Antalya, Türkiye

    Mustafa Çatalkaya

  2. AtiTECH LLC, 525 Junction Rd. Suite 6500, Madison, WI, 53717, USA

    Atilla Göknur

  3. Department of Plant Protection, Faculty of Agriculture, Akdeniz University, 07058, Antalya, Türkiye

    Zübeyir Devran

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  1. Mustafa Çatalkaya
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  2. Atilla Göknur
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Contributions

MÇ contributed to formal analysis, validation, visualization, writing—original draft. AG contributed to methodology, software. ZD contributed to conceptualization, methodology, software, validation, visualization, writing—original draft, review and editing, project administration.

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Correspondence to Zübeyir Devran.

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Çatalkaya, M., Göknur, A. & Devran, Z. Development of SNP-based assays for identification of Globodera rostochiensis and Globodera pallida. J Plant Dis Prot 130, 1041–1048 (2023). https://doi.org/10.1007/s41348-023-00767-z

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