Molecular assay of major soilborne sugarcane pathogens for better exploitation of commercial varieties : final report 2016/047

Abstract

A commercial assay service, based on specific DNA tests for soil-borne pathogens, has been developed for various cropping industries by the South Australian Research and Development Institute (SARDI), Adelaide. A unique feature of the DNA testing service is the ability to assay 500 g of soil in a single test, a breakthrough made possible by SARDI researchers, enabling the reliable, sensitive detection of root pathogens. The assay service now provides feedback on a range of deleterious, as well as beneficial, organisms in the grains and horticultural industries across southern Australia and in cereals in NSW and southern Queensland. This has provided important decision-making information for the application of better soil-borne disease management strategies. The service is now expanding further into northern Australia. Specific DNA assays were developed in this project for the major root pathogens / parasites in the Australian sugarcane industry (Pachymetra chaunorhiza and Pratylenchus zeae; Meloidogyne species tests were developed much earlier. The results from these assays were compared to traditional manual assessment. There was very good agreement between manual counts and the DNA results for Pachymetra chaunorhiza, and the two major nematode root parasites, Pratylenchus zeae (root lesion) and Meloidogyne species (root knot). This suggests that the SARDI laboratory could provide an assay service for these organisms in the sugarcane industry. Advantages of the SARDI service include the ability to rapidly assay large sample numbers (>80 in a batch), to be able to apply multiple tests to single soil samples, and to potentially do this testing at a reduced cost compared to the normal manual tests. In addition, the molecular nematode assays do not require nematode viability to be as carefully maintained for accurate assay results. Disadvantages of the molecular assay method are the potential for increased assay costs with small sample batch sizes; a slightly less-sensitive assay for Pachymetra chaunorhiza (compared to the traditional counting method) and potential slower turnaround times with limited sample numbers flowing through the laboratory. Southern experience suggests that additional tests will be added once the service is initiated, with better all-round information on soil biology resulting. A recommendation from the project is for SARDI to be contracted to undertake the molecular assays while the Tully soil assay laboratory maintains assay recommendation and data warehousing roles. Results from this project were extended to industry, which is now in a place to adopt the assay service provided by SRA / SARDI.