Identification of Pathogens Directly from Plant Parts

Wed, 25 Apr 2012 | Biological Control

Examples of studies using molecular methods to identify pathogens directly from plant parts are given in Table 2. Most of these involve identification of fungal species using RAPDs or PCR of the ITS-rDNA.

Developing methods for direct isolation of specific fungal DNA from plant tissues is more difficult than isolating DNA from a pure fungal strain, but the potential impact of the former methods is tremendous. These assays have demonstrated the presence of the pathogens in asymptomatic plants (Doohan et al. 1998). Some of these procedures take only seven to 24h to perform (Lee et al. 2001; Lovic et al. 1995), compared with several days to a week for traditional methods or methods requiring that the fungus be isolated prior to DNA

Table 1 Examples of studies on molecular identification of fungal plant pathogens in vitro
Fungal genus	Host	Level of discrimination	Method	Citation
Alternaria	Umbellifers	Species	RAPD	Pryor and Gilbertson 2002
Botrytis	Onion	Species subgroup	PCR-ITS/rDNA	Nielsen et al. 2001
Claviceps	Sorghum	Species/populations	AFLP and RAM	Tooley et al. 2000
Colletotrichum	Alfalfa	Species	AFLP	O'Neill et al. 1997
Elsinoe	Citrus	Species	RAPD	Hyun et al. 2001
Fusarium	Tomato	Virulence within race	RAPD	Mes et al. 1999
Fusarium	Cucumber	Forma specialis	RAPD	Vakalounakis and Fragkiadakis 1999
Gaeumannomyces	Turf-grass	Variety	PCR-ITS/rDNA	Goodwin et al. 1995
Gibberella (Fusarium)	Banana/corn	Species/toxicity/host	RAPD	Jimenez et al. 2000
Gibberella (Fusarium)	Banana/corn	Species	PCR-ITS/rDNA	Jimenez et al. 2000
Macrophomina	Bean, corn+	Population	AFLP	Mayek-Perez et al. 2001
Rhizoctonia	Various	Anastomosis grp subsets	PCR-ITS/rDNA	Carling et al. 2002
Rhynchosporium	Barley	Species	PCR-ITS/rDNA	Lee et al. 2001
Tilletia	Wheat	Species	TaqManPCR-MtDNA	Frederick et al. 2000
Venturia	Pear	Species	PCR-ITS/rDNA	Le Cam et al. 2002

Table 2 Examples of studies on molecular identification of fungal plant pathogens in vivo
Fungal genus	Host	Method	Level of discrimination	Citation
Alternaria	Carrot	PCR-ITS/rDNA	Species	Konstantinova et al. 2002
Fusarium	Wheat	RAPD	Species	Parry and Nicholson 1996
Fusarium	Wheat	RAPD	Species/variety	Doohan et al. 1998
Leptosphaeria	Crucifers	PCR/GenBank M77515a	Virulence	Taylor 1993
Melampsora	Willow	RAPD	Stem/leaf variants	Pei et al. 1997
Monosporascus	Cucurbits	PCR-ITS/rDNA	Species	Lovic et al. 1995
Monilinia	Stone fruits	dot blots and PCR	Species	Boehm et al. 2001
Mycosphaerella	Banana/plantain	PCR-ITS/rDNA	Species	Johanson and Jeger (1993)
Peronosclerospora	Sorghum	dot blots-genomic DNA	Species	Yao et al. 1990
Phakopsora	Soybean	TaqMan-PCR-ITS/rDNA	Species	Frederick et al. 2002
Pythium	1 ■ b 3 species	PCR-ITS/rDNA	Species	Kageyama et al. 1997
Rhynchosporium	Barley	PCR-ITS/rDNA	Species	Lee et al. 2001

aSeed cultured in liquid medium. b Cucumber, sugar beet, and Chinese cabbage.

extraction. Moreover, fungi that do not grow in pure culture may be studied with these techniques. On the other hand, amplifying DNA of nonviable fungi would lead to false-positives for disease potential, but would nevertheless provide useful information for researchers interested in mycotoxins.

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