Advertisement

Application of PCR based diagnostics in the exploration of Parastagonospora nodorum prevalence in wheat growing regions of Himachal Pradesh

  • S. Katoch
  • S. K. Rana
  • P. N. Sharma
Original Article

Abstract

Stagonospora leaf and glume blotch (SLGB) of wheat caused by Parastagonospora nodorum (formerly Stagonospora nodorum) has recently emerged as a major problem in changing climatic conditions of Himachal Pradesh (HP), especially during delayed winter rains. In the present studies symptomatology, morpho-cultural as well as molecular marker based identification showed the prevalence of disease in the state and conclusively proved that leaf and glume blotch of wheat is caused by P. nodorum. The test pathogen showed 100% homology with other reported P. nodorum isolates by rDNA (ribosomal DNA) analysis. In addition, the amplification of rDNA region of 36 P. nodorum isolates representing various agro-ecological areas of HP and one infected wheat leaf sample generated an amplicon of ~ 449-bp with JB433 (5′-ACACTCAGTAGTTTACTACT-3′) and JB434 (5′-TGTGCTGCGCTTCAATA-3′) P. nodorum specific primer pair whereas no amplification was observed with the genomic DNA of Septoria titici, Stemphylium vesicarium and healthy wheat leaf sample. This study on integration of morpho-cultural and microscopic methods along with PCR based technique could form basis for routine diagnosis of the SLGB in wheat samples during early growth stages of crop in the seed production fields.

Keywords

Glume blotch Wheat Prevalence Stagonospora nodorum PCR 

Abbreviations

SLGB

Stagonospora leaf and glume blotch

MAM

Minimal agar medium

CTAB

Cetyl trimethylammonium bromide

DNA

Deoxyribonucleic acid

PCR

Polymerase chain reaction

ELISA

Enzyme linked immunosorbent assay

NCBI

National Centre for Biotechnology Information

MEGA

Molecular Evolutionary Genetics Analysis

ITS

Internal transcribed spacer

rDNA

Ribosomal DNA

Notes

Acknowledgements

The corresponding author is grateful to Department of Science and Technology, Govt of India for financial assistance.

Compliance with ethical standards

Conflict of Interest

All the authors declare that there has no conflict of interest.

Supplementary material

13562_2018_481_MOESM1_ESM.doc (58 kb)
Supplementary material 1 (DOC 58 kb)

References

  1. Atkins SD, Clark IM (2004) Fungal molecular diagnostics: a mini review. J Appl Genet 45:3–15PubMedGoogle Scholar
  2. Aureli G, Scala V, Niglio A, L’Aurora A, Fabbri AA, Iori A (2015) Durum wheat infected by Stagonospora nodorum: survey on electrophoretic protein pattern modifications. J Plant Pathol 97:315–319.  https://doi.org/10.4454/JPP.V97I2.016 CrossRefGoogle Scholar
  3. Beck JJ, Ligon JM (1995) Polymerase chain reaction assays for the detection of Stagonospora nodorum and Septoria tritici in wheat. Phytopathology 85:319–324CrossRefGoogle Scholar
  4. Bhathal JS, Loughman R, Speijers J (2003) Yield reduction in wheat in relation to leaf disease from yellow (tan) spot and Septoria nodorum blotch. Eur J Plant Pathol 109:435–443.  https://doi.org/10.1023/A:1024277420773 CrossRefGoogle Scholar
  5. Chona BL, Munjal RL (1952) Glume blotch of wheat in India. Indian Phytopathol 5:17–20Google Scholar
  6. Consolo VF, Albani CM, Beron CM, Salerno GN, Cordo CA (2009) A conventional PCR technique to detect Septoria tritici in wheat seeds. Australas Plant Pathol 38:222–227CrossRefGoogle Scholar
  7. Cowger C, Murphy JP (2007) Artificial inoculation of wheat for selecting resistance to Stagonospora nodorum blotch. Plant Dis 91:539–545.  https://doi.org/10.1094/PDIS-91-5-0539 CrossRefGoogle Scholar
  8. Druzhinina IS, Kopchinskiy AG, Komoj M, Bissett J, Szakacs G, Kubicek CP (2005) An oligonucleotide barcode for species identification in Trichoderma and Hypocrea. Fungal Genet Biol 42:813–828CrossRefPubMedGoogle Scholar
  9. Engle JS, Lipps PE, Minyo RJ (2006) Reaction of commercial soft red winter wheat cultivars to Stagonospora nodorum in the greenhouse and field. Plant Dis 90:576–582.  https://doi.org/10.1094/PD-90-0576 CrossRefGoogle Scholar
  10. Eyal Z, Scharen AL, Prescott JM, Ginkel MV (1987) The septoria diseases of wheat: concepts and methods of disease management. CIMMYT, MexicoGoogle Scholar
  11. Fraaije BA, Lovell DJ, Rohel EA, Hollomon DW (1999) Rapid detection and diagnosis of Septoria tritici epidemics in wheat using a polymerase chain reaction/PicoGreen assay. J Appl Microbiol 86:701–708.  https://doi.org/10.1046/j.1365-2672.1999.00716.x CrossRefGoogle Scholar
  12. Gaurilcikiene I, Ronis A (2006) The effect of strobilurin fungicides on the development of foliar diseases of winter wheat. Agron Res 4:177–180Google Scholar
  13. Geiser DM, Jiménez-Gasco M, Kang S, Makalowska I, Veeraraghavan N et al (2004) FUSARIUM-ID v. 1.0: a DNA sequence database for identifying Fusarium. Eur J Plant Pathol 110:473–479CrossRefGoogle Scholar
  14. Glass NL, Donaldson GC (1995) Development of primer sets designed for use with the PCR to amplify conserve genes from filamentous ascomycetes. Appl Environ Microbiol 61:1323–1330PubMedPubMedCentralGoogle Scholar
  15. Glazek M, Krzyzinska B, Myczynska A (2005) Occurrence of Stagonospora nodorum glume blotch of wheat in the region of middle-southern Poland. Acta Agrobot 58:23–28.  https://doi.org/10.5586/aa.2005.004 CrossRefGoogle Scholar
  16. Gummer JPA, Trengove RD, Oliver RP, Solomon PS (2012) A comparative analysis of the heterotrimeric G-protein Gα, Gβ and Gγ subunits in the wheat pathogen Stagonospora nodorum. BMC Microbiol 12:131.  https://doi.org/10.1186/1471-2180-12-131 CrossRefPubMedPubMedCentralGoogle Scholar
  17. Joshi LM, Saari EE, Wilcoxson RD (1971) Epidemic of glume blotch on wheat and reaction of wheat varieties to Septoria nodorum L. Indian Phytopathol 24:413–415Google Scholar
  18. Joshi LM, Singh DV, Srivastava KD (1986) Problems and progress of wheat pathology in South Asia. Malhotra Publishing House, New Delhi, pp 197–207Google Scholar
  19. Kamle M, Pandey BK, Kumar P, Kumar M (2013) A species-specific PCR based assay for rapid detection of mango anthracnose pathogen Colletotrichum gloeosporioides Penz. and Sacc. J Plant Pathol Microbiol 4:184.  https://doi.org/10.4172/2157-7471.1000184 CrossRefGoogle Scholar
  20. Katoch A, Prachi Sharma, Sharma PN (2017) Identification of Colletotrichum spp. associated with fruit rot of Capsicum annuum in North Western Himalayan region of India using fungal DNA barcode markers. J Plant Biochem Biotechnol 26:216–223.  https://doi.org/10.1007/s13562-016-0384-4 CrossRefGoogle Scholar
  21. Kihara J, Ueno M, Arase S (2015) PCR-mediated detection of endophytic and phytopathogenic fungi from needles of the Japanese black pine, Pinus thunbergii. Open J For 5:431–442Google Scholar
  22. Klos KLE, Vásquez-Siller LM, Wetzel HC III, Murray TD (2012) PCR-based detection of Cephalosporium gramineum in winter wheat. Plant Dis 96:437–442.  https://doi.org/10.1094/PDIS-07-11-0568 CrossRefGoogle Scholar
  23. Kumar S, Stecher G, Tamura K (2016) MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874CrossRefPubMedPubMedCentralGoogle Scholar
  24. Kurtzman CP, Robnett CJ (2003) Phylogenetic relationships among yeasts of the Saccharomyces complex’ determined from multigene sequence analyses. FEMS Yeast Res 3:417–432.  https://doi.org/10.1016/S1567-1356(03)00012-6 CrossRefPubMedGoogle Scholar
  25. Kuzdralinski A, Szczerba H, Tofil K, Filipiak A, Garbarczyk E, Dziadko P, Muszyńska M, Solarska E (2014) Early PCR-based detection of Fusarium culmorum, F. graminearum, F. sporotrichioides and F. poae on stem bases of winter wheat throughout Poland. Eur J Plant Pathol 140:491–502.  https://doi.org/10.1007/s10658-014-0483-9 CrossRefGoogle Scholar
  26. Manandhar JB, Cunfer BM (1992) An improved selective medium for the assay of Septoria nodorum from wheat seed. Phytopathology 81:771–773CrossRefGoogle Scholar
  27. Mead O, Thynne E, Winterberg B, Solomon PS (2013) Characterising the role of GABA and its metabolism in the wheat pathogen Stagonospora nodorum. PLoS ONE 8:e78368.  https://doi.org/10.1371/journal.pone.0078368 CrossRefPubMedPubMedCentralGoogle Scholar
  28. Mirmajlessi SM, Destefanis M, Gottsberger RA, Mand M, Loit E (2015) PCR-based specific techniques used for detecting the most important pathogens on strawberry: a systematic review. Syst Rev 4:9.  https://doi.org/10.1186/2046-4053-4-9 CrossRefPubMedPubMedCentralGoogle Scholar
  29. Mukuma C (2016) Morphological and molecular identification and characterization of dry bean fungal root rot pathogens in Zambia. Theses, dissertations, and student research in agronomy and horticultureGoogle Scholar
  30. Puri S, Tiwari IK, Saraf RK (2015) Role of polymerase chain reaction in plant pathology. Int J Sci Nat 6:115–118Google Scholar
  31. Quaedvlieg W, Verkley GJM, Shin HD, Barreto RW, Alfenas AC, Swart WJ, Groenewald JZ, Crous PW (2013) Sizing up Septoria. Stud Mycol 75:307–390.  https://doi.org/10.3114/sim0017 CrossRefPubMedPubMedCentralGoogle Scholar
  32. Rana SK, Paul YS, Singh D (2000) Occurrence of glume blotch of wheat in Himachal Pradesh. J Mycol Plant Pathol 30:427–428Google Scholar
  33. Ronis A, Semaskiene R (2011) Relationship of AUDPC values of tan spot and Stagonospora glume blotch with grain infection in winter and spring wheat. ZEMDIRBYSTE 98:11–18Google Scholar
  34. Samson RA, Seifert KA, Kuijpers AFA, Houbraken JAMP, Frisvad JC (2004) Phylogenetic analysis of Penicillium subgenus Penicillium using partial b-tubulin sequences. Stud Mycol 49:175–200Google Scholar
  35. Shah DA, Bergstrom GC, Ueng PP (2001) Foci of Stagonospora nodorum blotch in winter wheat before canopy development. Phytopathology 91:642–647.  https://doi.org/10.1094/PHYTO.2001.91.7.642 CrossRefPubMedGoogle Scholar
  36. Sharma PN, Kaur M, Sharma OP, Sharma P, Pathania S (2005) Morphological, pathological and molecular variability in Colletotrichum capsici, the cause of fruit rot of chillies in the subtropical region of north-western India. J Phytopathol 153:232–237.  https://doi.org/10.1111/j.1439-0434.2005.00959.x CrossRefGoogle Scholar
  37. Smith OP, Peterson GL, Beck RJ, Schaad NW, Bonde MR (1996) Development of a PCR-based method for identification of Tilletia indica, causal agent of Karnal bunt of wheat. Phytopathology 86:115–122CrossRefGoogle Scholar
  38. Solomon PS, Tan KC, Sanchez P, Cooper RM, Oliver RP (2004) The disruption of a Gα subunit sheds new light on the pathogenicity of Stagonospora nodorum on wheat. Mol Plant Microbe Interact 17:456–466.  https://doi.org/10.1094/MPMI.2004.17.5.456 CrossRefPubMedGoogle Scholar
  39. Solomon PS, Lowe RGT, Tan KC, Waters ODC, Oliver RP (2006) Stagonospora nodorum: cause of Stagonospora nodorum blotch of wheat. Mol Plant Pathol 7:147–156.  https://doi.org/10.1111/j.1364-3703.2006.00326.x CrossRefPubMedGoogle Scholar
  40. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680CrossRefPubMedPubMedCentralGoogle Scholar
  41. Vincelli P, Tisserat N (2008) Nucleic acid-based pathogen detection in applied plant pathology. Plant Dis 92:660–669.  https://doi.org/10.1094/PDIS-92-5-0660 CrossRefGoogle Scholar
  42. Wiese MV (1987) Compendium of wheat diseases. The American Phytopathological Society, St PaulGoogle Scholar
  43. Zhao J, Wang XJ, Chen CQ, Huang LL, Kang ZS (2007) A PCR-based assay for detection of Puccinia striiformis f. sp. tritici in wheat. Plant Dis 91:1669–1674.  https://doi.org/10.1094/PDIS-91-12-1669 CrossRefGoogle Scholar

Copyright information

© Society for Plant Biochemistry and Biotechnology 2018

Authors and Affiliations

  1. 1.Department of Plant PathologyCSK HP Krishi VishvavidyalayaPalampurIndia

Personalised recommendations