Methods Manual Edited by P. Lava Kumar and F. Waliyar Mycotoxicology and Virology Laboratory International Crops Research Institute for the Semi-Arid Tropics METHODS MANUAL Diagnosis and Detection of Viruses Infecting ICRISAT Mandate Crops Editors P. Lava Kumar and Farid Waliyar For the training course on Methods for Studying Plant Virus-Insect Vector Interactions and Virus Disease Diagnosis 15 – 19 January 2007 Mycotoxicology and Virology Laboratory, ICRISAT, Patancheru 502 324, AP, India Sponsored by National Research Centre for Groundnut (NRCG) Junagadh, India International Crops Research Institute for the Semi-Arid Tropics Patancheru 502 324, AP, India © International Crops Research Institute for the Semi-Arid Tropics, 2007 AUTHORS P. LAVA KUMAR Scientist – Virology Virology and Mycotoxin Diagnostics Laboratory ICRISAT, Patancheru 502 324, India e-mail: [email protected] FARID WALIYAR Principal Scientist (Pathology) and Managing Director, Agri- Science Park@ICRISAT ICRISAT, Patancheru 502 324, India e-mail: [email protected] Material from this manual may be reproduced for the research use providing the source is acknowledged as: KUMAR, P.L., and WALIYAR, F. (Eds) (2007). Diagnosis and detection of viruses infecting ICRISAT mandate crops: Methods Manual. International Crops Research Institute for the Semi-Arid Tropics, Patancheru 502 324, India. pp133. (http://www.icrisat.org) FOR FURTHER INFORMATION: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) Patancheru - 502 324, Andhra Pradesh, India Telephone: +91 (0) 40 30713071 Fax: +91 (0) 40 30713074 +91 (0) 40 30713075 Web site: http://www.icrisat.org DISCLAIMER: The designations employed and the presentations of the material in the publication do not imply the expression of any opinion whosoever on the part of the ICRISAT concerning the legal status of any country, territory and city, or area, or of its authorities or concerning delimitation of its frontiers or boundaries. Where trade names are used this does not constitute endorsement of or discrimination against any product by the institute. ©ICRISAT-2007. Cover page and manual designed by P Lava Kumar. 2 INDEX Contents Page no. Preface 5 6 Abbreviations Section – I Virus diseases of current importance in Asia 1 Virus diseases of ICRISAT mandate crops 11 P Lava Kumar and F Waliyar 2 Pigeonpea sterility mosaic disease 15 P Lava Kumar, AT Jones, F Waliyar, P Sreenivasulu, V Muniyappa, TKS Latha and K B Saxena 3 Groundnut bud necrosis and spotted wilt 22 P Sreenivasulu and P Lava Kumar 4 Peanut stem necrosis 26 RDVJ Prasad Rao, AS Reddy, F Waliyar, P Sreenivasulu and P Lava Kumar 5 Chickpea stunt disease 29 SV Reddy, P Lava Kumar and F Waliyar 6 Plant virus diseases of quarantine importance 32 RDVJ Prasad Rao and KS Varaprasad Section – II Virus disease diagnosis and screening for resistance 7 Diagnosis of virus diseases 39 P Lava Kumar, P Sreenivasulu and F Waliyar 8 Plant virus isolation and purification 49 P Lava Kumar and P Sreenivasulu 9 ELISA and RT-PCR methods for the detection of plant viruses 53 P Lava Kumar and P Sreenivasulu 10 Screening genotypes for virus resistance 63 P Lava Kumar, AT Jones, F Waliyar, SN Nigam and KB Saxena Section – III Protocols for virus detection 11 Mechanical Sap Inoculation for Virus Detection and Assay 69 P Lava Kumar, SV Reddy and AS Reddy 3 12 Enzyme-linked immunosorbent assay (ELISA) 72 P Lava Kumar, AS Reddy and SV Reddy Extraction IgGs and preparation of enzyme conjugate 75 Double antibody sandwich (DAS)-ELISA 77 Direct antigen coating (DAC)-ELISA 78 Virus testing in seed 79 Western immuno-blotting 83 13 Nucleic acid-based methods 89 P Lava Kumar PCR and RT-PCR 89 Isolation of total RNA from leaf tissue 89 RT-PCR 93 Gel Electrophoresis of PCR and RT-PCR products 97 Agarose Gel Electrophoresis 97 Polyacrylamide Gel Electrophoresis (PAGE) for separation of DNA 99 and Proteins 14 Screening for virus resistance 105 P Lava Kumar, SV Reddy and AS Reddy Section – IV Appendices 1 Certain economically important virus diseases of crops in India 113 2 List of commonly used methods for the detection of plant viruses 114 3 Common conversions 115 4 ICTV classification of plant viruses 116 5 Further reading 117 6 Glossary 118 7 List of contributors 131 4 Preface Crop losses as a result of plant disease caused by viruses come second only to fungal diseases, but plant viruses are much more difficult to control. Of the various virus disease control strategies, cultivating the disease resistant varieties are by far the most effective and economical choice. Any efforts to control virus disease in the field should proceed first by accurately identifying the causal virus involved in the disease etiology. Virus identification based on symptoms is unreliable, as different viruses can cause similar symptoms on different host species or strains of same virus can cause different symptoms on a same host. Methods for the diagnosis and detection of plant viruses are described in this manual with particular emphasis on detection of important virus diseases of ICRISAT mandate crops. These include protein-based (ELISA and Western immunoblotting) and nucleic acid-based (PCR, RT-PCR and dot-blot hybridization) techniques, and methods for studying plant-virus vector interactions. Though the technology may appear complicated to beginners, every effort has been made to simplify the procedures by providing technical details in a step-wise manner, with description of underlying principles. The techniques described are applicable for the detection of any plant virus in general, albeit suitable modifications made to optimize the performance as per the needs. This is a revised version of a manual originally prepared for a training course entitled ‘Serological and Nucleic Acid Based Methods for the Detection of Plant Viruses’ held at ICRISAT, Patancheru 502 324, India, from 12 – 20 April 2004. This manual is based on our experience and expertise built over the years with the help of past and present research staff. Some basic procedures have been adapted from other people’s work and credit given where applicable. We sincerely thank all authors for their contributions. Lava Kumar & Farid Waliyar 5 Abbreviations ALP Alkaline phosphatase BND Bud necrosis disease BTB Bromothymol blue cv Cultivar DAC-ELISA Direct antigen coating-enzyme-linked immunosorbent assay DAS-ELISA Double antibody sandwich-enzyme-linked immunosorbent assay DNA Deoxyribonucleic acid dH2O Distilled water dNTPs Deoxynucleotide phosphates ELISA Enzyme-linked immunosorbent assay EM Electron micrograph Ig Immunoglobulin IgG Immuno-γ-globulin mol. wt. Molecular weight kb Kilo base kbp Kilo base pair kDa Kilo Dalton PAGE Polyacrylamide gel electrophoresis PBS Phosphate buffer saline PCR Polymerase chain reaction pi Post-inoculation PNC Penicillinase PSND Peanut stem necrosis disease RNA Ribonucleic acid RT-PCR Reverse transcription-polymerase chain reaction SEM Scanning electron microscope SMD Sterility mosaic disease TAS-ELISA Triple antibody sandwich-ELISA TEM Transmission electron microscope VLP Virus-like particles WIB Western immuno blotting Symbols/Units A Absorbance cm Centimeter 0C Degree centigrade g grams h hours l Liter lb/sq.in Pounds per square inch M Moles mM Millimoles min minutes ml Milliliter mg Milligram µl Microliter µg Microgram 6 ng Nanogram nm Nanometer OD Optical density pH Hydrogen ion concentration % Percent rpm Revolutions per minute sec Seconds v Volume w Weight Virus Acronyms CCDV Chickpea chlorotic dwarf virus CMMV Cowpea mild mottle virus CpSDaV Chickpea stunt disease associated virus GRAV Groundnut rosette assistor virus IPCV Indian peanut clump virus MYMV Mungbean Yellow mosaic virus PBNV Peanut bud necrosis virus PCLSV Peanut chlorotic streak virus PCV Peanut clump virus PPSMV Pigeonpea sterility mosaic virus PSV Peanut stunt virus PStV Peanut stripe virus PYSV Peanut yellow spot virus MStV Maize stripe virus TSV Tobacco streak virus TSWV Tomato spotted wilt virus 7 8 Section - I Virus Diseases of Current Importance in Asia 9 10 1. Virus Diseases of ICRISAT Mandate Crops P Lava Kumar and F Waliyar ICRISAT, Patancheru 502 324, AP, India International Crops Research Institute for The Semi-Arid Tropics (ICRISAT) is one of the 15 Centers of the Consultative Group on International Agricultural Research (CGIAR) devoted to science-based agricultural development. ICRISAT works mainly in the semi-arid tropical (SAT) areas of the world - a home for 1/6th of the world populations, Fig. 1. Semi-Arid Tropics of the world, and which is typified with unpredictable rainfall location of ICRISAT centers and poor soils. Some of the worlds poorest Virus diseases of ICRISAT mandate of the poor live in the SAT (Fig. 1). crops ICRISAT centers are in India (Asia), Mali, Virus diseases are important constraints for Zimbabwe and Nairobi (Africa) provide the productivity of food crops in Asia and hubs for ICRISAT and collaborating Africa. Several economically important virus national institutions across Africa and Asia. diseases have been reported on ICRISAT ICRISAT crop mandate includes three crops (Table 2). Most of these viruses infect cereals: sorghum, pearl millet, and finger legume crops, especially groundnut, millet - and three legumes: chickpea, consequently extensive work was done on pigeonpea, and groundnut (Table 1), with an viruses infecting this crop in Asia and Africa. agenda for the improvement of these crops Although fewer, but all major viruses infecting for higher productivity to benefit poor pigeonpea, chickpea and millets in SAT have farmers. been characterized. Details of the certain important viruses of ICRISAT mandate are Table 1. ICRISAT mandate crops given in Table 2. Virus diseases caused by Cereals Pigeonpea sterility mosaic virus (PPSMV), Peanut Pearl millet: One of the hardiest crop and is bud necrosis virus (PBNV), Tobacco streak virus the food staple in the driest parts of the SAT. (TSV) and chickpea stunt disease is discussed Sorghum: It is a major source of food and in detail in other chapters. fodder in many countries in the world.