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
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 |
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.
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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