Domestication to crop improvement: Genetic resources for sorghum and saccharum (Andropogoneae)

Background Both sorghum (Sorghum bicolor) and sugarcane (Saccharum officinarum) are members of the Andropogoneae tribe in the Poaceae and are each other's closest relatives amongst cultivated plants. Both are relatively recent domesticates and comparatively little of the genetic potential of these taxa and their wild relatives has been captured by breeding programmes to date. This review assesses the genetic gains made by plant breeders since domestication and the progress in the characterization of genetic resources and their utilization in crop improvement for these two related species. Genetic Resources The genome of sorghum has recently been sequenced providing a great boost to our knowledge of the evolution of grass genomes and the wealth of diversity within S. bicolor taxa. Molecular analysis of the Sorghum genus has identified close relatives of S. bicolor with novel traits, endosperm structure and composition that may be used to expand the cultivated gene pool. Mutant populations (including TILLING populations) provide a useful addition to genetic resources for this species. Sugarcane is a complex polyploid with a large and variable number of copies of each gene. The wild relatives of sugarcane represent a reservoir of genetic diversity for use in sugarcane improvement. Techniques for quantitative molecular analysis of gene or allele copy number in this genetically complex crop have been developed. SNP discovery and mapping in sugarcane has been advanced by the development of high-throughput techniques for ecoTILLING in sugarcane. Genetic linkage maps of the sugarcane genome are being improved for use in breeding selection. The improvement of both sorghum and sugarcane will be accelerated by the incorporation of more diverse germplasm into the domesticated gene pools using molecular tools and the improved knowledge of these genomes.

Phylogenetic placement of the sugarcane orange rust pathogen Puccinia kuehnii in a historical and regional context

Sugarcane orange rust, caused by Puccinia kuehnii, was once considered a minor disease in the Australian sugar industry. However, in 2000 a new race of the pathogen devastated the high-performing sugarcane cultivar Q124, and caused the industry Aus$150–210 million in yield losses. At the time of the epidemic, very little was known about the genetic and pathogenic diversity of the fungus in Australia and neighbouring sugar industries. DNA sequence data from three rDNA regions were used to determine the genetic relationships between isolates within two P. kuehnii collections. The first collection comprised only recent Australian field isolates and limited sequence variation was detected within this population. In the second study, Australian isolates were compared with isolates from Papua New Guinea, Indonesia, China and historical herbarium collections. Greater sequence variation was detected in this collection and phylogenetic analyses grouped the isolates into three clades. All isolates from commercial cane fields clustered together including the recent Australianfield isolates and the Australian historical isolate from 1898.The other two clades included rust isolates from wild and garden canes in Indonesia and PNG. These rusts appeared morphologically similar to P. kuehnii and could potentially pose a quarantine threat to the Australian sugar industry. The results have revealed greater diversity in sugarcane rusts than previously thought.

Experimental study of Australian sugarcane bagasse pulp permeability

In this experimental study the permeability of Australian bagasse chemical pulps obtained from different bagasse fractions were measured in a simple permeability cell and the results compared to one another as well as to eucalypt, Argentinean bagasse and pine pulps. The pulps were characterised in terms of the permeability parameters, the specific surface area, Sv, and the swelling factor, α. It was found that the bagasse fraction used affects these parameters. Fractionation of whole bagasse prior to pulping produced pulps that have permeability properties that compare favourably with eucalypt pulp. The values of Sv and α for bagasse pulp also depend on whether a constant or a variable Kozeny factor is used.

An ecological assessment of secondary poisoning risk in the Australian sugarcane industry

Rodenticide use in agriculture can lead to the secondary poisoning of avian predators. Currently the Australian sugarcane industry has two rodenticides, Racumin® and Rattoff®, available for in-crop use but, like many agricultural industries, it lacks an ecologically-based method of determining the potential secondary poisoning risk the use of these rodenticides poses to avian predators. The material presented in this thesis addresses this by: a. determining where predator/prey interactions take place in sugar producing districts; b. quantifying the amount of rodenticide available to avian predators and the probability of encounter; and c. developing a stochastic model that allows secondary poisoning risk under various rodenticide application scenarios to be investigated. Results demonstrate that predator/prey interactions are highly constrained by environmental structure. Rodents used crops that provided high levels of canopy cover and therefore predator protection and poorly utilised open canopy areas. In contrast, raptors over-utilised areas with low canopy cover and low rodent densities, but which provided high accessibility to prey. Given this pattern of habitat use, and that industry baiting protocols preclude rodenticide application in open canopy crops, these results indicate that secondary poisoning can only occur if poisoned rodents leave closed canopy crops and become available for predation in open canopy areas. Results further demonstrate that after in-crop rodenticide application, only a small proportion of rodents available in open areas are poisoned and that these rodents carry low levels of toxicant. Coupled with the low level of rodenticide use in the sugar industry, the high toxic threshold raptors have to these toxicants and the low probability of encountering poisoned rodents, results indicate that the risk of secondary poisoning events occurring is minimal. A stochastic model was developed to investigate the effect of manipulating factors that might influence secondary poisoning hazard in a sugarcane agro-ecosystem. These simulations further suggest that in all but extreme scenarios, the risk of secondary poisoning is also minimal. Collectively, these studies demonstrate that secondary poisoning of avian predators associated with the use of the currently available rodenticides in Australian sugar producing districts is minimal. Further, the ecologically-based method of assessing secondary poisoning risk developed in this thesis has broader applications in other agricultural systems where rodenticide use may pose risks to avian predators.

Some aspects of calcium phosphate chemistry in sugarcane clarification

This paper reviews some aspects of calcium phosphate chemistry since phosphate in juice is an important parameter in all sugar juice clarification systems. It uses basic concepts to try and explain the observed differences in clarification performance obtained with various liming techniques. The paper also examines the current colorimetric method used for the determination of phosphate in sugar juice. In this method, a phosphomolybdate blue complex formed due to the addition of a dye is measured at 660 nm. Unfortunately, at this wavelength there is interference of the colour arising from within the juice and results in the underestimation of the amount of soluble inorganic phosphate content of juice. It is suggested that phosphate analysis be conducted at the higher wavelength of 875 nm where the interference of the juice colour is minimised.

Enhancing agrobacterium-mediated transformation efficiency of sugarcane : progress towards an efficient, genotype-independent method

Several key issues need to be resolved before an efficient and reproducible Agrobacterium-mediated sugarcane transformation method can be developed for a wider range of sugarcane cultivars. These include loss of morphogenetic potential in sugarcane cells after Agrobacterium-mediated transformation, effect of exposure to abiotic stresses during in vitro selection, and most importantly the hypersensitive cell death response of sugarcane (and other nonhost plants) to Agrobacterium tumefaciens. Eight sugarcane cultivars (Q117, Q151, Q177, Q200, Q208, KQ228, QS94-2329, and QS94-2174) were evaluated for loss of morphogenetic potential in response to the age of the culture, exposure to Agrobacterium strains, and exposure to abiotic stresses during selection. Corresponding changes in the polyamine profiles of these cultures were also assessed. Strategies were then designed to minimize the negative effects of these factors on the cell survival and callus proliferation following Agrobacterium-mediated transformation. Some of these strategies, including the use of cell death protector genes and regulation of intracellular polyamine levels, will be discussed.

Demonstration of cellulosic ethanol production from sugarcane bagasse in Australia : the Mackay Renewable Biocommodities Pilot Plant

The ready availability of sugarcane bagasse at an existing industrial facility and the potential availability of extra fibre through trash collection make sugarcane fibre the best candidate for early stage commercialisation of cellulosic ethanol technologies. The commercialisation of cellulosic ethanol technologies in the sugar industry requires both development of novel technologies and the assessment of these technologies at a pre-commercial scale. In 2007, the Queensland University of Technology (QUT) received funding from the Australian and Queensland Governments to construct a pilot research and development facility for the production of bioethanol and other renewable biocommodities from biomass including sugarcane bagasse. This facility has been built on the site of the Racecourse Sugar Mill in Mackay, Queensland and is known as the Mackay Renewable Biocommodities Pilot Plant (MRBPP). This research facility is capable of processing cellulosic biomass by a variety of pretreatment technologies and includes equipment for enzymatic saccharification, fermentation and distillation to produce ethanol. Lignin and fermentation co-products can also be produced in the pilot facility.