Skip to main content
SpringerLink
Log in

RT-PCR/PCR analysis detected mixed infection of DNA and RNA viruses infecting sugarcane crops in different states of India

  • Research Article
  • Published:
Sugar Tech Aims and scope Submit manuscript

Abstract

A sensitive assay based on the polymerase chain reaction detected mixed infection of four viruses, viz. Sugarcane mosaic virus (SCMV), Sugarcane streak mosaic virus (SCSMV), Sugarcane yellow leaf virus (SCYLV) and Sugarcane bacilliform virus (SCBV) on sugarcane crops of India. Thirteen sugarcane varieties exhibiting mosaic, chlorotic streaks, mid-rib yellowing and without symptoms (from the vicinity of symptomatic fields) that originated from Uttar Pradesh, Andhra Pradesh, Tamil Nadu, Madhya Pradesh, Kerala, Bihar and Haryana states of India were evaluated for virus association through PCR and RT-PCR assays with specific designed primers for SCMV (SCMV-F3 and SCMVR3), SCSMV (SCSMV-ST2 and SCSMV-P1), SCYLV (SCYLV-615F and SCYLV-615R) and SCBV (SCBV-F and SCBV-R).The expected 0.9 kb SCMV fragment was amplified by RT-PCR with the SCMV-F3 and SCMV-R3 primers from sugarcane varieties of Kerala and Uttar Pradesh. The expected 0.5 kb SCSMV fragment was amplified by RT-PCR with the SCSMV-ST2 and SCSMV-P1 from sugarcane varieties of Uttar Pradesh, Kerala, Andhra Pradesh and Tamil Nadu. However, a 610 bp SCYLV fragment (by RT-PCR with the SCYLV-615F and SCYLV-615R primers) and 580 bp SCBV fragment (by SCBV-F and SCBV-R) was respectively amplified from all the 13 symptomatic and non-symptomatic sugarcane varieties in the study. Interestingly, mixed infection of all the four viruses SCMV, SCSMV, SCBV and SCYLV was detected in two sugarcane varieties of Uttar Pradesh and Kerala and mixed infection of three viruses (SCSMV+SCYLV+SCBV) was detected in the four states (Uttar Pradesh, Kerala, Andhra Pradesh and Tamil Nadu). However, mixed infection of SCYLV and SCBV was reported in all the seven surveyed states.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  • Agnihotri VP (1996). Current sugarcane scenario and management strategies. Indian Phytopathol. 49: 109–26.

    Google Scholar 

  • Alegria O M, Royer M, Bousalem M, Chatenet M, Pterschmitt M, Girard J C, Rott P (2003). Genetic diversity in the coat protein region of eighty six Sugarcane mosaic virus isolates from eight countries particularly from Cameroon and Congo. Arch Virol. 148: 357–372.

    Article  CAS  PubMed  Google Scholar 

  • Autrey L J C, Saumtally S, Dookun A, Boolell S (1990). Occurrence of Sugarcane bacilliform virus in Mauritius. Proc. S. Afri. Sugar Techn. Assn. 64: 34–39.

    Google Scholar 

  • Autrey L J C, Boolell S, Jones P, Lockhart B E L, Nadif A (1995). Distribution of Sugarcane bacilliform virus in various geographical regions. Proceedings ISSCT Congress, 21: 527–539.

    Google Scholar 

  • Bharathi V, Kishan Reddy, Nagamalleswari P (2006). Mixed infection of sugarcane streak mosaic and sugarcane yellow leaf virus infecting sugarcane crops in A P. India Sugar 56: 37–42.

    Google Scholar 

  • Bhargava KS (1975). Sugarcane mosaic-Retrospect and Prospects. Indian Phytopathology 28: 1–9.

    Google Scholar 

  • Chatenet M, Mazarin J C, Girard E, Fernandez D, Rao G P, Royer M, Lockhart B, Rott P (2005). Detection of Sugarcane streak mosaic virus in sugarcane from several Asian countries. Sugar Cane Internl 23: 12–15&28.

    Google Scholar 

  • Choi Y G, Croft B J, Randles J W (1999) Identification of sugarcane striate mosaic associated viruses by partial characterization of its double stranded RNA. Phytopathology 89: 877–883.

    Article  CAS  PubMed  Google Scholar 

  • D’Arey CJ, Domier LL (2005) Luteoviridae in: CM Fauquet, MA Mayo, J Maniloff, U Desselberger, LA Ball. (eds) Virus Taxonomy. VIIIth Report of the International Committee on Taxonomy of Viruses. New York, Academic Press, pp 891–900.

    Google Scholar 

  • Gaur R K, Singh Maneesha, Rao G P (2003) Molecular characterization of Sugarcane mosaic virus isolate from North Eastern Region of India. Sugar Cane 5:149–53.

    Article  CAS  Google Scholar 

  • Gaur RK, Singh M, Singh A, Mishra LC, Rao GP (2006). Identification and molecular characterization of Sugarcane streak mosaic virus in North India. Sugar Cane Internl 24(2): 13–17.

    CAS  Google Scholar 

  • Gillaspie Jr. A G, Mock R G, Hearon S S (1984) Status of identification of Sugarcane mosaic virus strains worldwide. Maize virus diseases Newsletter 1: 30–32

    Google Scholar 

  • Grisham MP (2000). Mosaic. Rott, P., Bailey, R.A., Comstock, J.C., Croft, B.J. and Saumtally, A.S. (Eds), A Guide to Sugarcane Diseases. CIRAD-ISSCT, Montepellier, France, CIRAD Publication Services, 249–254.

    Google Scholar 

  • Hema M, Joseph J, Gopinath K, Sreenivasulu P, Savithri HS (1999a) Molecular characterization and interviral relationships of a flexuous filamentous virus causing mosaic disease of sugarcane (Saccharum officinarum L.) in India. Arch Virol 144: 479–490.

    Article  CAS  PubMed  Google Scholar 

  • Hema M, Venkatramana M, Savithri H S, Sreenivasulu P (1999b) Biological antigenic and genomic relationships among the virus isolates causing mosaic disease of sugarcane in South India. Current Science, 77:698–702.

    CAS  Google Scholar 

  • Hema M, Kirthi N, Sreenivaslu P, Savithri HS (2003). Development of recombinant coat protein antibody based IC-RT-PCR for detection and discrimination of Sugarcane streak mosaic virus isolates from South India. Arch Virol. 148:1185–1193.

    Article  CAS  PubMed  Google Scholar 

  • Hema M, Savithri H S, Sreenivasulu P (2001) Sugarcane streak mosaic virus: Occurrence, Purification Characterization and Detection. Pp. 37–69. In: Sugarcane Pathology Vol II viral and Phytoplasma Disease (eds: G.P. Rao, R.E. Ford, M. Tosic, D.S. Teakle). Science Publishers Inc., Enfield, NH, USA.

    Google Scholar 

  • Hema, M., Sreenivasulu, P. and Savithri, H.S. (2002). Taxonomic position of sugarcane streak mosaic virus in the family Potyviridae. Arch Virol 147: 1997–2007

    Article  CAS  PubMed  Google Scholar 

  • Hema M, Sreenivasulu P, Gopinath K, Kiranmani G, Satyanarayana T (1997) Partial characterization of a poty virus causing mosaic disease of sugarcane in Andhra Pradesh. Indian Jour. Virol. 13:125–129.

    Google Scholar 

  • Hughes FL (1994). Sugarcane Streak. In: Current Trends in Sugarcane Pathology. (Prof. K.S. Bharagava Fetschcrift). Pp. 130–140 (eds. G.P. Rao, A.G. Gillaspie, jr., P.P. Upadhyaya, A. Bergamin, V.P. Agnihotri and C.T. Chen). International Books and Periodicals Supply Services, Pitampura, Delhi, India.

    Google Scholar 

  • Izaguirre-Mayoral M L, Carballo O, Alceste C, Romano M, Nass H A (2002) Physiological performance of asymptomatic and yellow leaf syndrome-affected sugarcanes in Venezuela. J Phytopathol 150:13–19.

    Article  CAS  Google Scholar 

  • Lockhart BE, Cronje CPR (2000). Yellow leaf syndrome. In: A guide to sugarcane diseases. P. Rott, R.A. Bailey, J.C. Comstock, B.J. Croft and A.S. Saumtally (Eds), Centre de Cooperation international en recherché agronomique pour le development (CIRAD) & International Society of Sugar Cane Technologists (ISSCT) Montpellier, France pp. 291–295.

    Google Scholar 

  • Lockhart BEL, Autrey IJC (1988). Occurrence in sugarcane of a bacilliform virus related serologically to Banana streak virus. Plant Disease 72:230–233.

    Article  Google Scholar 

  • Lockhart BEL, Autrey LJC (2000). Sugarcane bacilliform virus. In: A guide to sugarcane diseases. P. Rott, R.A. Bailey, J.C. Comstock, B.J. Croft and A.S. Saumtally, (eds.), CIRAD and ISSCT, Montepellier France, p.268–272.

    Google Scholar 

  • Lockhart, BEL, Autrey LJC, Comstock J C (1992). Partial purification and serology of sugarcane mild mosaic virus, a mealybug-transmitted closterolike virus. Phytopathology 82:691–695.

    Article  Google Scholar 

  • Mali V R, Garud T B (1998) Studies on sorghum red strip virus disease in Maharashtra. Indian J Mycol & Pathol. 7: 201–203.

    Google Scholar 

  • Rao, G P, Jain R K, Varma A (1998). Identification of sugarcane mosaic and maiz dwarf mosaic potyviruses infecting poaceous crops in India. Indian Phytolpathol. 51: 10–16.

    Google Scholar 

  • Rao, G P, Jain R K, Tosic M, Kristic B, Ford R E (2001). Antigenic diversity, peptide profiling and coat protein sequencing relationship of a virus isolate causing mosaic disease of sugarcane in Uttar Pradesh, India. Proc. Interntl. Soc. Sugar Cane Technol. 24: 646–647.

    Google Scholar 

  • Rao G P, Singh M, Rishi N, Bhargava K S (2002). Century status of sugarcane virus diseases research in India. In: Sugarcane Crop Management Edited by S.B. Singh, G.P. Rao and S. Easwaramoorthy. Sci Tech Publishing, Houston, USA, ISBN 1-930813163. pp. 223–254.

    Google Scholar 

  • Rao G P, Gaur R K, Singh M (2003). Distribution and serological diagnosis of sugarcane mosaic potyvirus in India. Sugar Cane Internl 21(1): 6–11.

    Google Scholar 

  • Rao G P, Chatenet M, Girard J C, Rott P (2006). Distribution of sugarcane mosaic and Sugarcane streak mosaic virus in India. Sugar Tech 8: 79–81.

    Article  Google Scholar 

  • Rishi N, Rishi S (1985). Purification, electron microscopy and serology of strains A and F of Sugarcane mosaic virus. Indian Jour. Virol. 1: 79–86

    Google Scholar 

  • Rott P, Bailey R A, Comstock J C, Croft B J, Saumtally A S (2000). A guide to sugarcane disease. CIRAD. ISSCT, CIRAD publications services, Montepellier, France, p. 339.

    Google Scholar 

  • Rott P, Comstock J C, Croft B J, Kusalwong A, Saumtally S A (2005). Advances and challenges in sugarcane pathology. Proc Internl Soc Sugarcane Technol 25: 607–614.

    Google Scholar 

  • Rott P, Bailey RA, Comstock JC, Croft BJ, Saumtally AS (2000). A guide to sugarcane disease. CIRAD. ISSCT, CIRAD publications services, Montepellier, France, p. 339.

    Google Scholar 

  • Rott P, Chatenet M (2000). Red leaf Mottle. Pp. 255–258, In: A guide to sugarcane diseases, CIRAD-ISSCT, CIRAD Publications services, Montepellier, France, p 339.

    Google Scholar 

  • Rott P, Comstock JC, Croft BJ, Kusalwong A, Saumtally SA (2005). Advances and challenges in sugarcane pathology. Proc. Intl Soc. Sugarcane Technol 25: 607–614.

    Google Scholar 

  • Scagliusi SM, Lockhart BE (2000). Transmission, characterization and serology of sugarcane yellow leaf luteovirus. Phytopathology 90: 120–124.

    Article  CAS  PubMed  Google Scholar 

  • Schenck S (2001). Sugarcane yellow leaf syndrome: history and current concepts. In: Sugarcane pathology. Vol.11 Virus and Phytoplasma Disease. G.P. Rao, R.E. Ford, M. Tosic and D.S. Teakle (Eds). Science Publishers Inc, Enfield, USA pp. 25–35.

    Google Scholar 

  • Shukla DD, Ward CW (1994). Recent development in the identification and classification of viruses comprising the sugarcane mosaic subgroup of potyviruses. Pp. 185–198. In: Current Trends in Sugarcane Pathology G.P. Rao, A.G. Gillaspie, jr., P.P. Upadhyaya, A. Bergamin, V.P. Agnihotri and C.T. Chen (eds). International Books and Periodicals Supply Service, Delhi, pp. 141–150.

    Google Scholar 

  • Shukla D D, Ward C W, Brunt A A (1994). The Sugarcane mosaic virus subgroup. In: Potyviridae pp. 360–371 CAB International, Wellingford, UK.

    Google Scholar 

  • Shukla US, Singh V, Srivastava KM (1995). Association of mosaic symptoms with a virus new to sugarcane. Indian J. Mycol. Plant Pathol 25: 286–287.

    Google Scholar 

  • Singh M (2001) Studies on virus diseases of sugarcane with special reference to Identification, economic losses and varietal susceptibility. Ph.D. Thesis, D.D.U. Gorakhpur University, Gorakhpur.pp257.

    Google Scholar 

  • Singh S P, Rao GP, Singh SB (1997). Effect of Sugarcane mosaic potyvirus infection on metabolic activity, yield and juice quality. Sugar Cane 5: 19–22.

    Google Scholar 

  • Singh SB, Rao GP, Solomon S, Gopalasundaram P (2009). Sugarcane: Crop Production and Improvement, Studium Press LLC, Texas, USA.

    Google Scholar 

  • Smith G R (2000) Fiji Disease. Pp. 239–244. In: A guide to sugarcane diseases, CIRAD-ISSCT, CIRAD Publications services, Montepellier, France, p.339.

    Google Scholar 

  • Viswanathan R (2002). Sugarcane yellow leaf syndrome in India: Incidence and effect on yield parameters. Sugarcane International, 20(5): 17–23.

    Google Scholar 

  • Viswanathan R, Balamuralikrishnan M, Premachandran MN, Tripathi BK (1999). Sugarcane Bacilliform virus: Symptoms, detection and distribution in the world germplasm collection at Cannanore. Proc. Internl Soc Sugar Cane Technol 23: 347–354.

    Google Scholar 

  • Viswanathan R, Balamuralikrishnan M (2005). Impact of mosaic infection on growth and yield of sugarcane. Sugar Tech, 7:61–65.

    Article  CAS  Google Scholar 

  • Viswanathan R, Balamuralikrishnan M, Karuppaiah R (2007) Sugarcane mosaic in India: A cause of combined infection of sugarcane mosaic virus and sugarcane streak mosaic virus. Sugarcane International 25(2): 6–14.

    CAS  Google Scholar 

  • Viswanathan R, Balamuralikrishnana M, Karuppaiah R (2008a). Characterization and genetic diversity of Sugarcane streak mosaic virus causing mosaic in sugarcane. Virus Genes 36: 553–564.

    Article  CAS  PubMed  Google Scholar 

  • Viswanathan R, Balamuralikrishnana M, Karuppaiah R (2008b). Identification of three genotypes of Sugarcane yellow leaf virus causing yellow leaf disease from India and their molecular characterization. Virus Genes 37: 368–379.

    Article  CAS  PubMed  Google Scholar 

  • Viswanathan R, Karuppaiah R, Balamuralikrishnana M (2009). Identification of new variants of SCMV causing sugarcane mosaic in India and assessing their genetic diversity in relation to SCMV type strains. Virus Genes 39:375–386.

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Division of Plant Pathology, Sugarcane Research Station, Kunraghat, Gorakhpur, 273008, U.P., India

    Deepti Singh, Ajay K. Tewari & G. P. Rao

  2. Plant Pathology Section, Sugarcane Breeding Institute, Coimbatore, 641007, Tamil Nadu, India

    R. Karuppaiah & R. Viswanathan

  3. Advanced Centre of Plant Virology, Division of Plant Pathology Indian Agricultural Research Institute, New Delhi, 110012, India

    Meenakshi Arya & V. K. Baranwal

Authors
  1. Deepti Singh
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Ajay K. Tewari
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. G. P. Rao
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. R. Karuppaiah
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. R. Viswanathan
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Meenakshi Arya
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. V. K. Baranwal
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to G. P. Rao.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Singh, D., Tewari, A.K., Rao, G.P. et al. RT-PCR/PCR analysis detected mixed infection of DNA and RNA viruses infecting sugarcane crops in different states of India. Sugar Tech 11, 373–380 (2009). https://doi.org/10.1007/s12355-009-0064-y

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12355-009-0064-y

Keywords

Search

Navigation