Completed projects and reports

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Sugar Research Australia, Sugar Research Development Corporation and BSES reports from completed research projects and papers.

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Prospects for a genetic solution to the management of ratoon stunting disease : ASSCT peer-reviewed paper
(ASSCT, 2021) Bhuiyan, SA; Eglinton, J; Magarey, RC
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. Developing varieties with resistance to RSD has been proposed at different times as a possible solution. This paper provides a review of the resistance status of the sugarcane germplasm, the effective range in reactions to the disease, and the efficacy of current practices used for RSD management. Examination of the Australian germplasm and historical resistance records show that material with effective RSD resistance has never been identified. Published literature has occasionally suggested that there are resistant varieties/clones, but these putative sources of resistance have failed to demonstrate commercially-effective disease control. 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. A genetic solution for RSD may only be considered if an effective source of resistance can be identified and validated.
Pachymetra root rot surveys of the Tully district update 2018 : ASSCT peer-reviewed paper
(ASSCT, 2019) Shannon, GJ; Magarey, RC; Macgillycuddy, L; Stringer, JK; Lewis, M
Pachymetra root rot is a soil-borne disease that impacts all sectors of the Australian sugar industry. The disease attacks the root system of sugarcane crops, affecting yields and leading to stool loss and shortened crop cycles, thus impacting the farming, harvesting and milling sectors. Monitoring the disease is, therefore, important so that optimised management practices are adopted, so bringing benefits to the entire value chain. A survey of the Tully district conducted in 2004 showed that pachymetra root rot was widely distributed across the Tully mill area; a second survey undertaken in 2013 sought to determine trends in disease incidence after some significant changes occurred in the cultivar mix. Crop resistance had shifted significantly with a change in cultivar resistance and there was a consequent increase in disease severity. Financial losses from reduced yield were estimated at $5.5 million in 2013; this compares to just under $1.0 million in 2004. This paper reports on a third survey in 2018 that is a five-year update to provide snapshot of the status of this disease in the Tully sugar industry. While the disease is still widespread, its severity has decreased with financial losses estimated to be $3.5 million.
Sugarcane streak mosaic; researching a relatively new disease in Indonesia
(ASSCT, 2018) Magarey, RC; Kristini, A; Achadian, E; Thompson, N; Wilson, E; Reynolds, M; Sallam, N; Goebel, R; Putra, L
SUGARCANE STREAK MOSAIC occurs in the south and south-east Asia regions and was first identified in Indonesia in 2005. Its relatively recent recognition means that much remains to be learnt about this viral disease. ACIAR-funded research has been investigating molecular and serological assays for the virus, yield losses, important modes of transmission, and an integrated disease management strategy to manage and minimise losses. So far our findings include: molecular variation in the virus around its geographic range; yield losses amount to approximately 20% in a susceptible variety; transmission may occur via application of infested sap to leaves; mechanical transmission (as on infested machinery surfaces) is unlikely to be significant. Surveys have shown the disease to be present in various parts of Indonesia (Java, Sumatera, Sulawesi and probably West Papua). Much remains to be learnt about its epidemiology.
Innovation in disease management; where to next : ASSCT peer-reviewed paper
(ASSCT, 2019) Magarey, RC
New technologies offer considerable scope for the refinement of disease management in the Australian sugarcane industry. While resistant cultivars, disease-free plant sources, crop termination and quarantine have provided a strong foundation for good disease management, the development of new technologies offers the possibility to make changes to data accumulation, analysis and application to industry. DNA- and NIR-based assay technology, remote sensing, drones, data digitisation, GIS and information databases offer the ability to capture huge additional amounts of relevant field data, enabling a better understanding of disease issues and the management required to minimise losses. This will also enable targeted extension of management strategies to individual farmers and industry sectors. Automated pathogen assays may also be possible, centred on the sugar factory. Step changes in disease management are likely in the next 5-10 years.
Effects of pachymetra root rot and nematodes on some elite sugarcane clones in Australia
(ASSCT, 2016) Bhuiyan, SA; Croft, BJ; Wong, E; Ogden-Brown, J; Turner, M; Parfitt, R; Magarey, RC; Bull, J; Cox, MC
PACHYMETRA ROOT ROT and nematodes are the two most important soil-borne pathogens of sugarcane in Australia. An experiment was established in Yandaran, Queensland in grey forest soil with high Pachymetra spore counts (>100 000 spores/kg). Fifteen elite varieties and one advanced clone, from pachymetra root rot susceptible, intermediate and resistant categories, were planted in the experiment. The experiment was maintained until the second ratoon crop and Pachymetra and nematode populations were assessed in each crop. In addition, the incidence of smut was recorded before harvesting. Cane yield (TCH), commercial cane sugar (CCS) and sugar yield (TSH) were also measured in each crop. Pachymetra spore counts remained significantly lower in resistant varieties compared to susceptible and intermediate varieties until the second ratoon. In intermediate and susceptible varieties Pachymetra spore counts increased substantially, in particular, in second ratoon. In intermediate varieties such as Q232A and Q208A Pachymetra spore counts increased more than three times from plant crop to second ratoon. Numbers of nematodes, in particular root-lesion nematode, more than doubled in the second ratoon crop compared to the plant and first ratoon crops. Only Q248A had significant levels of smut, with 25% and 30% infected plants in the first and second ratoon crops, respectively. Yield reduction was substantial in the second ratoon compared to the plant and first-ratoon crop. Sugar yield decreased by 45% in the second ratoon compared to the first ratoon. Mostly, poor or negative correlations were observed between both Pachymetra spore counts and nematode numbers and yield.
Chlorotic streak resistance screening in the Tully district
(ASSCT, 2016) Magarey, RC; Sevntek, K; Bull, JI; Stringer, JK; Zamora, R
CHLOROTIC STREAK DISEASE (CSD) was first recognised more than 85 years ago and is present in most cane-growing countries around the world. An important management strategy is the use of resistant varieties; past research has shown there is significant variability in resistance in the Australian sugarcane germplasm. Data are reported from a variety resistance screening trial conducted in the Tully district (2013–2015 period) that was subjected to at least five flooding events over a two-year period. Maximum ‘% stools diseased’ infection levels were over 60% in the most susceptible variety. Several current commercial varieties appear very susceptible, including Q241A and Q251A. The data show that a much higher disease incidence is evident when data on ‘% stools diseased’ are recorded rather than ‘% stalks diseased’. Recording data on a stools basis therefore may provide a shorter time frame for assessing varietal susceptibility. Crop inspections are also significantly easier using this parameter, especially in mature crops where symptom expression is often higher (and therefore desirable to undertake at this time). Major flooding events provide optimum conditions for disease transmission in field trials, as long as shoot survival is not unduly affected.
Biosecurity research in PNG 2015-2017
(ASSCT, 2018) Magarey, RC; Braithwaite, KS; Kuniata, LS; Thompson, NP; Korowi, K; Samson, PR; Tom, L; Sallam, N; Derby, L
PAPUA NEW GUINEA is the centre of diversity for several species in the genus Saccharum, including S. officinarum, selections of which constituted the first commercial sugarcane varieties in Australia. Apart from providing germplasm for commercial sugarcane production world-wide, PNG is also home to pests and diseases that pose a unique and serious threat to commercial sugarcane production in Australia. These include members of the noctuid moth borer group, an oomycete causing downy mildew and the viral disease, Ramu stunt. Australian scientists have been working alongside PNG counterparts to develop management strategies that will assist with pest and disease management in PNG and enable effective preparation for a possible incursion into Australia. Over the past three years, significant outputs from the research have included a much better understanding of causal agents, specific diagnostic tests, an understanding of pest and disease distribution and faster methods for varietal resistance screening.
Incidence and economic effects of ratoon stunting disease on the Queensland sugarcane industry : ASSCT peer-reviewed paper
(ASSCT, 2021) Magarey, RC; McHardie, R; Hession, M; Cripps, G; Burgess, D; Spannagle, B; Sutherland, P; Di Bella, L; Milla, R; Millar, F; Schembri, A; Baxter, D; Hetherington, M; Turner, M; Jakins, A; Quinn, B; Kalkhoran, SS; Gibbs, L; Ngo, C
Ratoon stunting disease (RSD) has had a significant influence on productivity and profitability in the Australian sugarcane industry for at least the last 76 years. There have been few attempts to objectively quantify the incidence and economic influence of the disease across the industry. Most Cane Productivity Service (CPS) groups routinely monitor RSD in plant sources and, in some cases, in commercial crops. Surveys by 12 Queensland CPSs were conducted in 2017- 2020 with sampling of different proportions of commercial crops (5-25% of farms) in each region. The latest molecular technology was adopted to assay samples. RSD incidence varied between 0 and 60% in commercial crops and 0 and 41% in plant source inspections. The data suggest that implementation of the three pillars of RSD management (disease-free seed-cane, equipment sanitation and planting into fallow ground devoid of volunteers) were essential to minimise RSD incidence. Failure to adequately address any one of these pillars often compromised RSD management. An economic analysis suggested that RSD led to an annual loss of $25m in the study areas in the 2019 crop. This is significant, but it is unlikely to be the largest single disease constraint on productivity.
Chlorotic streak transmission and crop dynamics research
(ASSCT, 2016) Magarey, RC; Sventek, K; Bull, JI; Braithwaite, KS
CHLOROTIC STREAK DISEASE (CSD) is transmitted in water, specifically drainage, flood or irrigation water. Research showed that transmission in water was increased by the addition of oxytetracyline (Terramycin). A two-hour inoculation period, where roots were dipped in infected hydroponic solution containing the antibiotic, was sufficient to lead to significant disease levels in test plants grown in a hydroponic system. A hydroponic system incorporating no water circulation (still-hydroponics) was found more effective than one where the solution was regularly circulated. Monitoring of the disease at field sites showed that disease levels build up over time and that different lengths of inundation associated with flooding events may lead to uneven distribution of the disease in a commercial crop.
Integrated disease management of sugarcane streak mosaic in Indonesia : final report 2012/083
(Australian Centre for International Agricultural Research (ACIAR), 2019) Magarey, RC
Sugarcane streak mosaic (SCSM) caused by sugarcane streak mosaic virus (SCSMV) is a relatively recently recognised disease of sugarcane that is now widespread through S.E. Asia and widely infecting commercial crops, both in terms of incidence and in the percentage of plants infected within individual fields. Crop losses, though not spectacular in individual plants, is very significant since whole crops are very often affected meaning that accumulated smaller losses in individual plants leads to very significant losses for cane farmers. A number of aspects related to the disease were unknown at initiation of this research, including: distribution across Indonesia (Sumatera, Sulawesi, and the eastern archipelago); transmission mechanisms (mechanical or insects or planting material only); the epidemiology and speed of spread; crop resistance; sensitive, specific and cheap detection technologies; and an effective integrated disease management (IDM) strategy. All these points were addressed in associated research activities.

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