SYBR Green I based RT-qPCR assays for the detection of RNA viruses of cereals and grasses
T. Dráb A , E. Svobodová A , J. Ripl A , J. Jarošová A , F. Rabenstein B , U. Melcher C and J. K. Kundu A D
+ Author Affiliations
- Author Affiliations
A Division of Crop Protection and Plant Health, Crop Research Institute, Drnovska 507, 16106 Prague, Czech Republic.
B Institute of Epidemiology and Pathogen Diagnostics, Julius Kühn Institute-Federal Research Centre for Cultivated Plants (JKI), Erwin-Baur-Straße 27, D-06484 Quedlinburg, Germany.
C Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA.
D Corresponding author. Email: jiban@vurv.cz
Crop and Pasture Science 65(12) 1323-1328 https://doi.org/10.1071/CP14151
Submitted: 3 June 2014 Accepted: 7 July 2014 Published: 21 October 2014
Abstract
Less prevalent viruses of family Poaceae are usually excluded from the focus of interest, even though they represent a possible threat to agricultural production. We designed and validated a set of primer pairs suitable for detection and quantification of five RNA viruses, Lolium latent virus (LoLV), Oat necrosis mottle virus (ONMV), Ryegrass mosaic virus (RgMV), Soil-borne cereal mosaic virus (SBCMV), and Spartina mottle virus (SpMV), by means of one-step RT-qPCR based on SYBR Green I. These primers were used together with primers for Brome mosaic virus (BMV) and Wheat streak mosaic virus (WSMV) described elsewhere to screen grass and cereal samples from the Czech Republic. The results revealed a high prevalence of WSMV and RgMV, which pointed to possible local epidemics. We also make the first report of LoLV presence in the Czech Republic.
Additional keywords: crop protection, molecular diagnostics, plant pathogens, plant viruses.
References
Chen SN, Gu H, Wang XM, Chen JH, Zhu WM (2011) Multiplex RT-PCR detection of Cucumber mosaic virus subgroups and tobamoviruses infecting tomato using 18S rRNA as an internal control. Acta Biochimica et Biophysica Sinica 43, 465–471.| Multiplex RT-PCR detection of Cucumber mosaic virus subgroups and tobamoviruses infecting tomato using 18S rRNA as an internal control.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3MXntF2gs7o%3D&md5=941b148a29e19ce57459b93290637e11CAS |
Christian ML, Willis WG (1993) Survival of Wheat streak mosaic virus in grass hosts in Kansas from wheat harvest to fall wheat emergence. Plant Disease 77, 239–242.
| Survival of Wheat streak mosaic virus in grass hosts in Kansas from wheat harvest to fall wheat emergence.Crossref | GoogleScholarGoogle Scholar |
Coutts BA, Kehoe MA, Webster CG, Wylie SJ, Jones RAC (2011) Zucchini yellow mosaic virus: biological properties, detection procedures and comparison of coat protein gene sequences. Archives of Virology 156, 2119–2131.
| Zucchini yellow mosaic virus: biological properties, detection procedures and comparison of coat protein gene sequences.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3MXhsFCmsLnM&md5=d45c54cb4cd3de61e30a919278f00efcCAS | 21935626PubMed |
De Jong W, Ahlquist P (1995) Host-specific alterations in viral RNA accumulation and infection spread in a Brome mosaic virus isolate with an expanded host range. Journal of Virology 69, 1485–1492.
Ferns RB, Garson JA (2006) Development and evaluation of a real-time RT-PCR assay for quantification of cell-free human immunodeficiency virus type 2 using a Brome mosaic virus internal control. Journal of Virological Methods 135, 102–108.
| Development and evaluation of a real-time RT-PCR assay for quantification of cell-free human immunodeficiency virus type 2 using a Brome mosaic virus internal control.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD28XltVelu7c%3D&md5=3a351530b9080a5baa1ef24e33064c0eCAS | 16563526PubMed |
Gadiou S, Kundu JK (2010) Complete genome sequence of a Brome mosaic virus isolate from the Czech Republic. Czech Journal of Genetics and Plant Breeding 46, 178–182.
Gadiou S, Kudela O, Ripl J, Rabenstein F, Kundu JK, Glasa M (2009) An amino acid deletion in Wheat streak mosaic virus capsid protein distinguishes a homogeneous group of European isolates and facilitates their specific detection. Plant Disease 93, 1209–1213.
| An amino acid deletion in Wheat streak mosaic virus capsid protein distinguishes a homogeneous group of European isolates and facilitates their specific detection.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD1MXhtlyqu7%2FO&md5=378ad284e4ea35ba2ba4fd3c17d93b62CAS |
Gadiou S, Ripl J, Janourova B, Jarosova J, Kundu JK (2012) Real-time PCR assay for the discrimination and quantification of wheat and barley strains of Wheat dwarf virus. Virus Genes 45, 614
| Real-time PCR assay for the discrimination and quantification of wheat and barley strains of Wheat dwarf virus.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC38XhvVSqurjK&md5=169ae9fc215c0b687a0c4fcea714dfc5CAS |
Gomes-Ruiz AC, Nascimento RT, de Paula SO, da Fonseca BAL (2006) SYBR green and TaqMan real-time PCR assays are equivalent for the diagnosis of dengue virus type 3 infections. Journal of Medical Virology 78, 760–763.
| SYBR green and TaqMan real-time PCR assays are equivalent for the diagnosis of dengue virus type 3 infections.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD28Xlt1Kjs7c%3D&md5=d9add111ccea28ce3baa6149348fdedbCAS | 16628591PubMed |
Huth W (2000) Viruses of Gramineae in Germany—a short overview. Zeitschrift Fur Pflanzenkrankheiten Und Pflanzenschutz – Journal of Plant Diseases and Protection 107, 406–414.
Izzo MM, Kirkland PD, Gu X, Lele Y, Gunn AA, House JK (2012) Comparison of three diagnostic techniques for detection of rotavirus and coronavirus in calf faeces in Australia. Australian Veterinary Journal 90, 122–129.
| Comparison of three diagnostic techniques for detection of rotavirus and coronavirus in calf faeces in Australia.Crossref | GoogleScholarGoogle Scholar | 1:STN:280:DC%2BC38vptVKiuw%3D%3D&md5=90834510f7c65f9dcb6f6c193c8f41c6CAS | 22443326PubMed |
Jarošová J, Kundu JK (2010) Validation of reference genes as internal control for studying viral infections in cereals by quantitative real-time RT-PCR. BMC Plant Biology 10, 146
Jarošová J, Chrpová J, Šíp V, Kundu JK (2013) A comparative study of the Barley yellow dwarf virus species PAV and PAS: distribution, accumulation and host resistance. Plant Pathology 62, 436–443.
| A comparative study of the Barley yellow dwarf virus species PAV and PAS: distribution, accumulation and host resistance.Crossref | GoogleScholarGoogle Scholar |
Kuhne T (2009) Soil-borne viruses affecting cereals: known for long but still a threat. Virus Research 141, 174–183.
Kundu JK, Gadiou S, Cervena G (2009a) Discrimination and genetic diversity of Wheat dwarf virus in the Czech Republic. Virus Genes 38, 468–474.
| Discrimination and genetic diversity of Wheat dwarf virus in the Czech Republic.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD1MXksFejs7c%3D&md5=2a7a8ca87dc761193342b1ed51203050CAS | 19326201PubMed |
Kundu JK, Jarosova J, Gadiou S, Cervena G (2009b) Discrimination of three BYDV species by one-step RT-PCR-RFLP and sequence based methods in cereal plants from the Czech Republic. Cereal Research Communications 37, 541–550.
| Discrimination of three BYDV species by one-step RT-PCR-RFLP and sequence based methods in cereal plants from the Czech Republic.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3cXhsVylsrs%3D&md5=36d477b0c635769c1b465fb3afc52209CAS |
Lapierre H, Signoret PA (2004) ‘Viruses and virus diseases of Poaceae (Gramineae).’ (Institut National de la Recherche Agronomique, Science Publishers: Paris)
Lekanne Deprez RH, Fijnvandraat AC, Ruijter JM, Moorman AFM (2002) Sensitivity and accuracy of quantitative real-time polymerase chain reaction using SYBR green I depends on cDNA synthesis conditions. Analytical Biochemistry 307, 63–69.
| Sensitivity and accuracy of quantitative real-time polymerase chain reaction using SYBR green I depends on cDNA synthesis conditions.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD38XlsFKht70%3D&md5=3e55408eea7eadc3c484dfe22e6a83cbCAS | 12137780PubMed |
Mackay IM (2004) Real-time PCR in the microbiology laboratory. Clinical Microbiology and Infection 10, 190–212.
| Real-time PCR in the microbiology laboratory.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD2cXjtFylsbs%3D&md5=03d6247076cbd7ab6ac63b4c1bda087dCAS | 15008940PubMed |
Makkouk KM, Kumari SG (2009) Epidemiology and integrated management of persistently transmitted aphid-borne viruses of legume and cereal crops in West Asia and North Africa. Virus Research 141, 209–218.
| Epidemiology and integrated management of persistently transmitted aphid-borne viruses of legume and cereal crops in West Asia and North Africa.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD1MXksVartLg%3D&md5=a6cbb29109b63eaf1d83f02abcb26995CAS | 19152820PubMed |
Ordon F, Habekuss A, Kastirr U, Rabenstein F, Kuhne T (2009) Virus resistance in cereals: sources of resistance, genetics and breeding. Journal of Phytopathology 157, 535–545.
| Virus resistance in cereals: sources of resistance, genetics and breeding.Crossref | GoogleScholarGoogle Scholar |
Papin JF, Vahrson W, Dittmer DP (2004) SYBR green-based real-time quantitative PCR assay for detection of West nile virus circumvents false-negative results due to strain variability. Journal of Clinical Microbiology 42, 1511–1518.
| SYBR green-based real-time quantitative PCR assay for detection of West nile virus circumvents false-negative results due to strain variability.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD2cXjvFylsbc%3D&md5=4d3410a4a89949bb1cfe52b1f43a8f3dCAS | 15070997PubMed |
Power AG, Borer ET, Hosseini P, Mitchell CE, Seabloom EW (2011) The community ecology of barley/cereal yellow dwarf viruses in Western US grasslands. Virus Research 159, 95–100.
| The community ecology of barley/cereal yellow dwarf viruses in Western US grasslands.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3MXhtVaitrfP&md5=fb98d9011bd9b7036b6e93f2ffc0a5c9CAS | 21641945PubMed |
Price JA, Blunt T, Burrows ME, Franc G, Ito D, Kinzer K, Olson J, O’Mara J, Rush CM, Stack J, Tande C, Ziems A (2009) Great plains wheat virus survey 2008. Phytopathology 99, S105
Rabenstein F, Huss H (2013) Studies on grass viruses in Austria. Tagung der Vereinigung der Pflanzenzüchter und Saatgutkaufleute Österreichs 63, 11–14.
Schubert J, Habekuss A, Kazmaier K, Jeske H (2007) Surveying cereal-infecting geminiviruses in Germany – diagnostics and direct sequencing using rolling circle amplification. Virus Research 127, 61–70.
| Surveying cereal-infecting geminiviruses in Germany – diagnostics and direct sequencing using rolling circle amplification.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD2sXlvVOntr0%3D&md5=9b236bb10a08b1664e9e57244ad54663CAS | 17449126PubMed |
Seifers DL, Martin TJ, Harvey TL, Fellers JP, Stack JP, Ryba-White M, Haber S, Krokhin O, Spicer V, Lovat N, Yamchuk A, Standing KG (2008) Triticum mosaic virus: a new virus isolated from wheat in Kansas. Plant Disease 92, 808–817.
| Triticum mosaic virus: a new virus isolated from wheat in Kansas.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD1cXmtFGru7g%3D&md5=e8f56c57f92b92499da44dcb2a68a1adCAS |
Sharma S, Dasgupta I (2012) Development of SYBR Green I based real-time PCR assays for quantitative detection of Rice tungro bacilliform virus and Rice tungro spherical virus. Journal of Virological Methods 181, 86–92.
| Development of SYBR Green I based real-time PCR assays for quantitative detection of Rice tungro bacilliform virus and Rice tungro spherical virus.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC38Xis1Oqtr0%3D&md5=a447ab2108ea219108e6b8508390ff44CAS | 22326276PubMed |
Tatineni S, Graybosch RA, Hein GL, Wegulo SN, French R (2010) Wheat cultivar-specific disease synergism and alteration of virus accumulation during co-infection with Wheat streak mosaic virus and Triticum mosaic virus. Phytopathology 100, 230–238.
| Wheat cultivar-specific disease synergism and alteration of virus accumulation during co-infection with Wheat streak mosaic virus and Triticum mosaic virus.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3cXjslSntbo%3D&md5=6f5fadcf88926bf063678a89cd6f4a05CAS | 20128696PubMed |
Varga A, James D (2006) Real-time RT-PCR and SYBR Green I melting curve analysis for the identification of Plum pox virus strains C, EA, and W: effect of amplicon size, melt rate, and dye translocation. Journal of Virological Methods 132, 146–153.
| Real-time RT-PCR and SYBR Green I melting curve analysis for the identification of Plum pox virus strains C, EA, and W: effect of amplicon size, melt rate, and dye translocation.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD28XhtlClsbw%3D&md5=64c57a8d84a299060e510a23a731ebafCAS | 16293321PubMed |
Zhang HM, Yang J, Chen JP, Adams MJ (2008) A black-streaked dwarf disease on rice in China is caused by a novel Fijivirus. Archives of Virology 153, 1893–1898.
| A black-streaked dwarf disease on rice in China is caused by a novel Fijivirus.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD1cXht1eitL3I&md5=d55ee16bb7a192f9338fc7d937172862CAS | 18820828PubMed |
