Summary

Following significant impacts from root disease of chickpea in 2017, a three-year survey of legume and canola samples began in 2018. Growers submitted 329 samples and 850 fungal, oomycete and nematode organisms were identified in the diseased roots using DNA techniques, many of which appear to be important pathogens.

Phytophthora megasperma was identified as the likely cause of the 2017 chickpea disease and several potentially important pathogens were identified.

Culture collections focusing on Phytophthora, Fusarium, Phoma and Aphanomyces spp. have been established for research into host ranges and disease potential, yield impacts, and development of Predicta®B type soil tests to enable pre-sowing detection.

Background

In 2017, the failure of several chickpea crops in South East SA and severe disease in faba beans on Kangaroo Island highlighted the need for greater awareness of root disease in pulse crops across the state. As a result, SAGIT funded a survey of pulse root diseases for the 2018, 2019 and 2020 growing seasons. In 2019, the survey was extended nationally by GRDC (DJP1907-002RMX).

Research Aims

The core objectives of the project were to:

• Identify the cause of chickpea crop failure in the South East during 2017 and support development of molecular (PREDICTA®B type) testing.
• Survey pulse crops more widely across the high and medium rainfall zones of SA for this disease.
• Establish the spread of Aphanomyces euteiches following severe damage to faba bean crops on Kangaroo Island during 2017.

In The Field

Growers and advisers were asked to collect and submit samples comprising around 12 plants from the outer edges of any poorly performing areas of pulse crops.

Samples were received from across the South East, Kangaroo Island, Mid North, Yorke Peninsula and Eyre Peninsula.

As each sample was received by SARDI, the roots were washed and the plant tops removed 5cm above the crown. Researchers visually inspected each plant, photographed it, and scored the root health from 0 to 3 (2019 and 2020 samples only). The sample was divided into two random groups of six plants and dried. One group was used for DNA extraction and the other group stored for pathogen isolation at a later date.

Twenty-four qPCR tests were used to quantify the presence of soilborne pathogens and nematode pests known to be present in SA. Additional oomycetes, fungi and Fusarium species were detected using next generation sequencing (NGS) protocols developed by GRDC project DAS1907-001BLX.

To investigate the pathogenicity (disease risk) of commonly detected pathogens, experiments were conducted under controlled growing conditions across faba bean, chickpea, field pea, lentil and lupin.

Results

SA growers submitted 329 legume root samples to the survey (63 in 2018, 140 in 2019, 126 in 2020) which were analysed with qPCR testing. In all, 850 species were identified, including common cereal pathogens such as root lesion nematodes and Rhizoctonia solani AG8. The most common legume pathogens were Pythium Clade F and Phoma pinodella.

Phytophthora megosperma or closely related species were detected in 65 per cent of faba bean and lucerne samples from the South East and 67 per cent of broad bean samples from Kangaroo Island.

Aphanomyces eutiches was detected in 25 per cent of faba bean samples from the Upper South East, 29 per cent of faba bean samples from the Mid South East and 67 per cent of broad bean samples from Kangaroo Island.

Both Aphanomyces and Phytophthora spp. are recognised as important pathogens in high rainfall regions and may pose a serious risk to SA crops in wet seasons.

Fusarium was also very common and numerous species were detected. Many were shown to be weakly pathogenic but several SA isolates of F. oxysporum caused serious root disease on either chickpea or faba bean. Isolates of F. tricinctum, F. acuminatum and F. solani were pathogenic on a range of crops. Most isolates of F. avenaceum were highly pathogenic on a range of hosts.