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Development of a routine DNA-based testing service for soilborne diseases in Australia

Ophel-Keller, Kathy, McKay, Alan, Hartley, Di, Herdina, 0, Curran, John
Australasian plant pathology 2008 v.37 no.3 pp. 243-253
Bipolaris sorokiniana, DNA, Ditylenchus dipsaci, Fusarium pseudograminearum, Gaeumannomyces graminis var. tritici, Heterodera avenae, Mycosphaerella pinodes, Phoma medicaginis var. pinodella, Pratylenchus neglectus, Thanatephorus cucumeris, barley, crop losses, crops, cultivars, farms, fungi, growers, horticulture, pathogens, peas, planting, prediction, quantitative polymerase chain reaction, risk, soil, soil sampling, soil-borne diseases, wheat, Australia
A DNA-based soil testing service operates in Australia to assist grain growers in predicting the likely extent of losses from various soilborne diseases well before a crop is planted. Growers, therefore, have the option of changing cultivars or modifying cropping programs in situations where the risk of crop loss is high. The service was launched in 1997 and although the initial focus was on wheat and barley, pathogens of rotation crops are now included. Key features of the service include a unique high-throughput DNA extraction system to process 500-g soil samples and a series of specific real-time PCR assays that allow a range of fungal and nematode pathogens to be quantified in a single soil sample. Tests for Heterodera avenae, Pratylenchus neglectus, P. thornei, Gaeumannomyces graminis var. tritici, G. graminis var. avenae, Rhizoctonia solani AG-8, Fusarium pseudograminearum, F. culmorum and the pea pathogens Mycosphaerella pinodes and Phoma medicaginis var. pinodella are available at present, while tests for Bipolaris sorokiniana, Ditylenchus dipsaci and Pratylenchus teres are in development. This paper discusses issues that were addressed in establishing the service (e.g. sampling strategies, extraction of DNA from soil, development of specific tests, disease risk categories) and explains the training and accreditation programs that have been established to ensure that results are interpreted adequately at the farm level. It also outlines research being conducted to extend the service to horticulture.