Two key soil-borne diseases suspected to be emerging threats for SA pulse crops are the subject of laboratory research, DNA sequencing and efforts to develop Predicta B testing framework.
Phytophthora root rot and Aphanomyces root rot are the two suspect diseases being targeted in a survey of paddock samples being conducted across the state through agronomists with the support of South Australian Grain Industry Trust funding, in collaboration with researchers supported by the GRDC/SARDI bilateral program.
The SAGIT project is led by SARDI senior research officer Tara Garrard, who is using traditional lab methods alongside next generation sequencing technologies used by SARDI molecular biologist Kelly Hill.
The pair are analysing samples collected via a network of local agronomists from most of the 2018 season and expect results from spring chickpea samples they are presently receiving to come through in the new year.
“We’re seeing issues on pulse roots but so far we don’t know culprit, we need to investigate further to find out what is happening and work towards getting a solution for growers,” Dr Garrard says.
Dr Hill is developing NGS technology that is providing sequence information on broad groups of organisms, such as fungi, bacteria or nematodes, present in the sample.
This means diseases such as the Phytophthora root rot and Aphanomyces root rot that are difficult to culture using traditional lab methods will be found through this technology.
Researchers can search the data for sequences that match particular organisms of interest or use international databases to assign species’ names to the DNA sequences that have been detected.
Sequences that do not match an existing database entry can mean the organism has not been found previously or its DNA sequences have yet to be entered.
“Predicta B tests will be developed for those pathogens that have a track record of causing losses overseas,” Dr Garrard said.
Our access to the international database of DNA sequences means we’re able to leverage work from countries that have identified problems before they have manifested in Australia
“I am looking to Canada for inspiration on these, as they seem to be ahead of Australia in terms of the prevalence of root diseases of pulses and oilseeds and their development of management strategies.”
Dr Garrard says the NGS protocol and Predicta B complement each other well. While NGS is able to reveal what is present in a sample, it takes time to do so.
Predicta B is a quick and cheap option to quantify the target pathogens present.
“Our access to the international database of DNA sequences means we’re able to leverage work from countries that have identified problems before they have manifested in Australia,” Dr Garrard said.
She says SARDI suspects Phytophthora megasperma is the cause of 2017 South East crop failures, but the organism is proving difficult to isolate.
“We know it is not Phytophthora medicaginis, which is a problem in northern NSW and southern Qld, because we have a good test for it,” she said.
Dr Hill has also been focused on selecting primers to amplify DNA of a broad group of organisms known as water moulds, which include Phytophthora and Pythium species that may be present in the samples. The sequences developed from this work can also be used to help design a test for Predicta B.
Agronomists are invited to attend the Predicta B Root Disease Risk Management course at the Waite Campus on Thursday, November 15