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Development of real-time PCR systems based on SYBR® Green I and TaqMan® technologies for specific quantitative detection of Phoma tracheiphila in infected Citrus

Demontis, Maria Antonietta and Cacciola, Santa Olga and Orrù, Marcella and Balmas, Virgilio and Chessa, Valentina and Maserti, Bianca Elena and Mascia, Laura and Raudino, Francesco and Magnano di San Lio, Gaetano and Migheli, Quirico (2007) Development of real-time PCR systems based on SYBR® Green I and TaqMan® technologies for specific quantitative detection of Phoma tracheiphila in infected Citrus. European Journal of Plant Pathology, Vol. 120 (4), p. 339-351. eISSN 1573-8469. Article.

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DOI: 10.1007/s10658-007-9222-9

Abstract

Real-time PCR assays based on SYBR® Green I and TaqMan® technologies were developed for in planta detection and quantification of Phoma tracheiphila, the mitosporic fungus causing ‘mal secco’ disease on citrus. Primers and a hybridization probe were designed on the basis of the internal transcribed spacer (ITS) region of the nuclear rRNA genes. The real-time PCR assays were compared with a classic isolation method in two separate experiments carried out on 6 and 24 month-old sour orange seedlings, artificially inoculated with a conidial suspension of the pathogen. Both technologies made it possible to follow the progression of infection by P. Tracheiphila, enabling detection and quantification of the target fungus prior to the development of symptoms. The detection limit was 10 copies of the cloned target sequence and 15 pg of genomic DNA extracted from fungal spores. The values of the cycle threshold (Ct) were linearly correlated with the concentration of the target DNA, indicating that the method is suitable as a qualitative and quantitative assay. The presence of non-target fungal DNA had no effect on the specificity of the assay, but resulted in a 10-fold reduction of sensitivity. Total inhibition of the reaction occurred when conidia of the target pathogen were mixed with an organic soil substrate before extracting DNA using the standard protocol, while an alternative purification kit resulted in a significant decrease in sensitivity. Compared to classic methods, real-time PCR proved faster and easier to perform and showed a higher sensitivity. These results suggest that real-time PCR, based on both chemistries, has a great potential for early diagnosis of ‘mal secco’ disease and for quantitative estimation of fungal growth within host tissue.

Item Type:Article
ID Code:495
Status:Published
Refereed:Yes
Uncontrolled Keywords:‘Mal secco’ disease, Citrus, lemon, molecular diagnostics, real time polymerase chain reaction, nuclear rRNA genes
Subjects:Area 07 - Scienze agrarie e veterinarie > AGR/12 Patologia vegetale
Divisions:001 Università di Sassari > 01 Dipartimenti > Protezione delle piante
002 Altri enti e centri di ricerca del Nord Sardegna > Istituto nazionale biostrutture e biosistemi, Unità di ricerca, Sassari
Publisher:Springer Netherlands
eISSN:1573-8469
Copyright Holders:© KNPV 2007
Deposited On:18 Aug 2009 10:02

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