Browsing by Author "Braithwaite, KS"

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Assessing the impact that pathogen variation has on the sugarcane breeding program : SRDC final report BSS258
(BSES, 2005) Braithwaite, KS
In recent years, two fungal diseases of sugarcane have had a huge impact on the Australian sugar industry and the BSES CSIRO breeding and pathology programs. Sugarcane smut, caused by Ustilago scitaminea, first appeared in Australia in 1998, whilst orange rust, caused by Puccinia kuehnii, was a minor pathogen until an epidemic devastated the industry in 2000. In the case of both pathogens, the industry had to respond to the outbreaks without a full understanding of the pathogen's population structure. Successful disease-management strategies and deployment of resistance require an understanding of variation in the pathogen population. This project has clarified the genetic makeup of the two pathogens and has identified a number of quarantine issues that could place the Australian sugar industry at risk.
Australian component Genetic diversity within Sugarcane yellow leaf virus : ICSB final report 99-15
(2001) Borg, Z; Braithwaite, KS; Smith, GR
Sugarcane yellow leaf virus (SCYLV) is widespread in many sugarcane growing countries of the world. The aim of this study was to determine the extent of genomic variation in SCYLV isolates from various countries. Isolates were obtained from Mauritius, Reunion, South Africa, Australia, Papua New Guinea, Hawaii, U.S.A. and Brazil. Four regions of the SCYLV genome (ORF 1, Replicase, Coat Protein and Readthrough) were analysed for variation using both RFLP analysis and sequence comparisons. Of the fifty isolates used, several did not produce RT-PCR amplicons in one or more of the regions covered, suggesting variation in regions where the primers bind. Of the amplicons produced across the four regions studied, RFLP analysis and sequencing results revealed the Coat Protein (CP) region to be the most conserved, followed by the Replicase (REP) region. These areas should be targeted for diagnosis of SCYLV and for use in viral mediated transgenic resistance in sugarcane varieties. Phylogenetic studies of the nucleotide and protein sequences of the four regions covered were performed using eighteen isolates. Representative isolates from each country were used where possible. In a second round of phylogenetic studies, covering the REP and CP regions, nine isolates from North, South and Central America, sequenced by our American collaborators on this project, were included. Variation in nucleotide and protein sequences revealed that many haplotypes of SCYLV exist across the countries tested. Most isolates from the various countries are very closely related across all four regions. Phylograms produced from REP and CP sequences in Phylogeny study #2 revealed that isolates from Hawaii and Australia tend to group together as do isolates from Mauritius and Reunion. Phylogenetic analyses on the sequences used in this study have not identified any significant variants of SCYLV. In conclusion, we recommend that the YLS111 and 462 RT-PCR primers originally developed by Mike Irey and colleagues continue to be used for routine SCYLV diagnosis. Also, the viral coat protein and replicase regions being the most conserved, should be targeted in research to genetically engineer resistance to SCYLV.
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.
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.
Innovative approaches to identifying the cause of chlorotic streak and new management strategies : final report 2013/357
(Sugar Research Australia Limited, 2017) Braithwaite, KS
Chlorotic streak is one of the major diseases in the Australian sugar industry. The disease occurs in areas of high rainfall and poorly drained fields and is a limitation to productivity, particularly during seasons that are wetter than average. The cause of the disease was unknown for 87 years before being identified through a combination of modern molecular techniques, particularly Next Generation Sequencing, and traditional pathology and microscopy. The causal agent is a novel biflagellated cercozoan and Phytocercomonas venanatans has been assigned as the tentative name. It is the first plant pathogenic cercozoan able to systemically infect higher plants and also the first to be successfully grown in axenic culture on common microbiological media. The ability to culture the organism opens the way to developing innovative methods of control. Until now, there has been no reliable method to screen varieties for resistance to chlorotic streak due to the difficulty of setting up replicated screening trials with controlled infection. The project assessed both field-based and glasshouse-based screening. Using the cultured organism as inoculum was considered the most promising way of delivering a rapid resistance screening method. Other outcomes include improved diagnostic screening methods to assist Productivity Services staff, an understanding of epidemiology and a better understanding of the biology of the causal agent.
Maintaining access to foreign germplasm by developing methods to detect unidentified viruses in sugarcane in quarantine : SRDC final report BS116S
(1998) Braithwaite, KS; Smith, GR
Four types of gneeric tests for detecting unidentified viruses in plants were trialed for their suitability for sugarcane. The tests were; double stranded RNA (dsRNA) analysis, sap inoculation of indicator plants, sap examination by electron microscopy and polymerisation chain reaction (PCR) amplification using 'group-specific' primers. The aim of this project was to develop and implement general diagnostic tests for unidentified viruses in sugarcane germplasm held in quarantine. The availability of these general tests has provided an opportunity to significantly improve the security of sugarcane quarantine.