Ratoon Stunting Disease (RSD) Impact on Australian Sugar Industry and the Great Barrier Reef

Ratoon Stunting Disease (RSD) Impact on Australian Sugar Industry

Take Home Messages

• RSD is possibly the most widespread disease of sugarcane in Australia.
• Significantly under-diagnosed and under-estimated by highly placed individuals (estimated by 2-3 people).
• Costing Australia >200M annually.
• Contributing to the death of the Great Barrier Reef.
• Sugar Research Australia (SRA) are called upon to invest in addressing the issue.

Mossman Mill Closure

• Mossman Mill closure has left workers and growers in fear for their families and the town.
• The Mossman Central Mill went into liquidation after a potential sale fell through.
• The Australian Sugar Milling Council expressed sadness and disappointment at the announcement that the operation of the Mossman Mill is being transitioned into liquidation.
• An unnamed investor stepped in at the last minute with plans to save the mill, but later pulled out.
• The mill's parent company, the Daintree cane went into voluntary administration last week.
• Ash Salardini stated it was a sad day for employees, growers, associated businesses and the community.
• The Sugar Milling Council also expressed concerns about the broader regulatory and policy environment and the need for government support to invest in new diversified economic opportunities.

Soil Impacts

• Planting cane requires significant soil disturbance:
  • Loss of beneficial biology
  • Loss of organic matter (OM)
  • Compaction
  • Degradation
• Ratooning cane does not require significant soil disturbance.

Yield Example

• 1 hectare (ha) yields 10 tonnes/ha under certain conditions.
• Example field produces 90 tonnes.

RSD Symptoms and Management

• Ratoon Stunting Disease (RSD) yield losses are dramatic in dry seasons.
• Managed by seed selection and farm hygiene.
• Spectrum of heritable susceptibility to RSD.
• Significant higher RSD rate in replant fields.
• SRA does not recommend resistant varieties as part of a control strategy.
• For 20 years, it was claimed to be present “in fewer than 5% of fields”.
• RSD symptoms may not always be obvious externally but can be observed through red discoloration of vascular bundles when an infected stalk is sliced longitudinally.

RSD Control

• Hot Water Treatment (or TC) is conducted by Production Boards to generate 'clean seed'.
• Seedbed inspections are important.
• 'Phytosanitation' practices are necessary.

RSD Susceptibility

• Higher susceptibility translates to:
  • More damage to plant/crop
  • Greater transmission rates
  • Lower Hot Water Treatment (HWT) efficacy
• Uninfected:
  • Few colonized vascular bundles (cvb) = low expressed titre = ‘Resistant’
• Infected:
  • Many colonized vascular bundles (cvb) = high expressed Lxxtitre = ‘Susceptible’
• RSD “resistance” is based on colonized vascular bundles (cvb).

Expressed Xylem Sap Diagnostics

• It’s easier to get sap out of thicker stalks than thinner stalks.
• It’s easier to get sap out of uninfected xylem than infected xylem.
• It’s easier to get sap out of distal nodes, despite highest Lxx concentrations at basal nodes.

ELISA and RSD Detection

• ELISA can dilute Lxx to undetectable limits.
• Usually, sap from 16 stalks is sampled and pooled into 4 sample tubes, with each tube containing sap from 4 stalks.
• There is the potential to dilute out the Lxx, leading to false negatives, particularly for varieties that support low titers.
• If detection limit is > 1 X 10^6 ml-1, need > 4 X 10^6 ml-1 to hope to detect 1 infected stalk with 3 clean stalks.

RSD Incidence

• Generally, RSD is present in fewer than 5% of fields in Australia, although in some districts incidence is much higher.
• Questioning how much this depends on the diagnostic used, sample collection, and the fields targeted for diagnosis.

RSD Testing

• 2003-13 Harwood RSD rates of approximately 9% recorded, but only testing the best of the best (seedbeds).
• Commercial fields were never tested due to cost.

Leaf Sheath Biopsy (LSB)-qPCR

• Lxx is a systemic bacterial infection found throughout the plant.

Direct qPCR on Concentrated Bacteria

• LSBs go into a zip-lock bag, then covered with distilled water.
• Lxx seep into the water, PCR performed on smaller volume suspension of putative Lxx pellet then concentrated by centrifugation.

LSB Sample Number Optimisation

• LSBs taken from stalk from each stool in first 5 rows of cane.
• Five more LSBs taken from same 5 stalks, plus 5 more stalks from next 5 stools (total of 10 LSBs).
• LSBs taken from first 10 stalks, then next 10 (total=20).
• LSBs taken from first 20 stalks, then next 20 (total=40).
• Optimization done on Known (EB-EIA/PCM) infected field of BN83-3120.

RSD Testing Using Diagnostic Platforms

• ~2,000 µL, 16 stalks, 4 stalks per tube.
• Transfer 25 µL 50 Leaf Sheath Biopsies
• EB-EIA/PCM
• LSB-PCR
• 100 fields of different varieties
• RSD testing using three diagnostic platforms:
  • LSB-qPCR
  • xylem PCR (xPCR)
  • EB-EIA/PCM

Diagnostic Results

• Comparative diagnostic results (number varies from 1 to 27 depending on the test).

RSD Review for Innisfail

• In 2019, 29% of Innisfail seedbeds were infected.
• Plenty of RSD in ‘resistant’ Q208.
• Now SRA rate Q208 as Intermediate-Resistant (up from ‘highly resistant’).
• 2020 ASSCT paper not presented due to covid cancellation.
• SRA finally did survey.

RSD much higher than "less than 5%"

• Table shows the proportion of RSD diseased crops in plant sources (PSI) and in surveys assessing sugarcane disease status in mill areas/regions across the Queensland sugarcane industry for various mill areas and years.
• Mean RSD percentage range from 13.3% to 19.2% based on survey type.
• For South Johnstone, 26% diseased crops was used for deriving economic losses.

SRA Conclusion and AY Calculation

• SRA conclusion: RSD costs 25M annually, but other diseases cost more (2021).
• AY calculated 126M annually.
• Magarey et al. 2021 used CCS=9 vs CCS=13.7.
• Today’s money: 185M.

Prospects for a Genetic Solution to the Management of ratoon stunting disease

• Ratoon stunting disease (RSD,) caused by a bacterium (Leifsonia xyli subsp. xyli), is one of the most important diseases of sugarcane in Australia.
• RSD is an inconspicuous and highly infectious disease and can spread unnoticed causing significant yield loss across entire regions and industries.
• Examination of the Australian germplasm and historical resistance records show that material with effective RSD resistance has never been identified.
• Currently, there are no validated sources of resistance available to be used as parents in the breeding program.
• Evidence from overseas and Australia demonstrates that RSD can be successfully managed through disease-free planting material and farm hygiene.
• SRA conclusion:
  • Can't be done.
  • Don't look here.
  • Leave it with us.

SmartCane Best Management Practice

• Modules include:
  • Soil health and nutrient management
  • Irrigation and drainage management
  • Weed, pest and disease management
  • Planting and harvesting
  • Farm business management
  • Natural systems management
  • Workplace health and safety
  • Pathway to sustainable sugar

Issues with SRA

• SRA receive taxpayer funding of over 13M annually.
• SRA fund external research and internal researchers.
• Multiple cases of SRA rejecting external proposals, then funding SRA projects.
• SRA have relied on “corporate knowledge” of RSD.
• The “experts” who led to the RSD disaster are still being funded.
• The SRA system is broken.

RSD Results

• Lower overall yields
• Premature ploughout
• Worse weed control
• Reduced NUE (Nutrient Use Efficiency)
• Greater sediment and nutrient run off
• Reduced grower profitability and confidence
• Wasted efforts in plant breeding

RSD and the Great Barrier Reef

• Improved RSD management is the single thing we can do in the short to medium term to help save the Great Barrier Reef.
• Taxes are supporting the opponents of improved RSD management.