After much consideration the project grant for a thermocycler (CRDC197C) was used to purchase an Eppendorf Mastercycler gradient machine. This choice of machine gave not only the obvious advantages of having a dedicated machine for the CRC29C project, it also had advanced features that were not available with the previous instruments in use. Being able to use gradient functions to optimise multiple annealing temperatures during a single reaction contributed a five-fold reduction in time taken for primer screening. The ability to optimise speed of temperature ramping and to preform touch-down PCR is giving higher quality results in the molecular marker work, additionally faster ramping rates have greatly reduced reaction times; allowing faster turn around of samples.

The ability to purchase a new thermocycler has greatly improved the ability to meet project aims, while increasing the skill base of the primary researcher as well as cotton honours project students. This instrument continues to be an asset to this project and too any other CRDC/CRC projects conducted through the botany department at the University of Queensland.

The Beltwide cotton conference is well worth attending as it is one of the few conferences specifically devoted to all aspects of cotton research. There are too many concurrent sessions to attend all topics, but this also provides for some variety as well. I endorse the CRDC’s continued support of sending at least one researcher to attend every year in order for the Australian research community to benefit from this information source and communication exchange.

Problems associated with pesticide application on the Darling Downs have not been solved by conventional strategies and alternate chemicals. Associated with these chemical use patterns is the development of resistance to insecticides in H. armigera. The use of molecular technologies for identification of Heliothis populations can provide answers to fundamental questions of population movement and development of insecticide resistance. These technologies will be applied in area wide management strategies presently under investigation in DAQ442 and in DAQ364 and from other recently developed Area Wide Management programs outside the Darling Downs. The proposed work will give precise information about local recruitment and migration of H. armigera and H. punctigera by providing an ability to track and study seasonal cohorts at a property management unit level. The microsatellite markers developed in UQ117 detect local population recruitment. It is now possible to measure local population recruitment and migration. The thrust of this project is to monitor local recruitment and the extent of migration over a further three growing seasons. The project will also begin the process of determining the source of migrating Heliothis populations. It is expected that this project will provide several major outputs.

This report presents the key outcomes of a collaborative research study between NSW Department of Primary Industries (DPI) and Cotton Research and Development Corporation (CRDC). The study used the science-based method of Life Cycle Assessment (LCA) and aimed to:

(1) produce a clear picture of the greenhouse gas (GHG) emissions profile for a representative cotton production system in North West NSW;

(2) identify the most plausible set of emission reduction opportunities;

(3) create a platform in SimaPro (an LCA tool), through the North West NSW LCA, from which industry can routinely test emission mitigation options or the consequences of new productivity-based technologies in an ongoing way; and,

(4) undertake sensitivity analysis to check whether the case study region is representative of other regions.

We followed the LCA principals, as defined by ISO 14040:2006 Standard [1] and ISO 14044:2006 Standard [2]. The functional unit of the assessment was 1 t (1000 kg) of cotton lint at port, produced between 2011- 2014 by a continuous (back-to-back) cotton production system. A mixture of irrigated and rainfed cotton was modelled, in which irrigated cotton predominated. The system boundaries of the assessment included all processes involved in pre-farm, on-farm, and post-farm stages. The foreground data included that from questionnaires sent to some ginning plants, interviews conducted with some cotton farmers, gross margin data, industry surveys and case study research. Data were also validated by obtaining expert opinion from industry representatives. The background data (e.g. fertiliser production) were accessed from the different sources mainly from the Australian life-cycle inventory (AusLCI).

To assign the calculated CC impact between cotton lint and cotton seed, we followed the relevant hierarchy recommended by ISO 14044:2006. We initially applied the system expansion approach in which the total CC impact of the cotton system is assigned to cotton lint but it is credited for the avoided CC impacts of the products displaced by cotton seed (i.e. animal feed and oilseeds). Through this approach, we calculated the CC impact of the functional unit to range from 1254 kg CO2e to 1307 kg CO2e for four investigated scenarios. As other scenarios are also possible, these results should be treated as subjective. Given this uncertainty, we finally applied the economic allocation approach in which we allocated around 86% of the total CC impact to cotton lint and around 14% of the impacts to cotton seed, in proportion to their revenue.

In a two season study, results from large scale field trials, supported by laboratory bioefficacy experiments showed that the adoption of Large Droplet Placement (LDP) techniques for the aerial application of insecticides, (endosulfan and chlorpyrifos) did not have a significant effect in reducing the biological efficacy of the pesticides when compared to aerial Ultra Low Volume (ULV) and ground rig application.

Drift studies undertaken simultaneous with this project by the Centre for Pesticide Application & Safety, (CRDC UQ 27C, Optimisation of large droplet placement (LDP) technology for the aerial application of insecticides in cotton) showed that the use of LDP application techniques reduced the downwind drift ten to fifteen times, compared to ULV applications. This finding shows that LDP techniques can be adopted to reduce the potential for spray drift resulting from the aerial application of pesticides whilst maintaining the effectiveness of certain contact insecticides on heliothis mortality.The results from this study will have a significant effect upon reducing the potential for spray drift resulting from the use of insecticide in the Australian cotton industry. By showing that the efficacy of insecticides was not compromised with the adoption of low spray drift aerial application techniques, the use of LPD technology in BMP can be extended and used with greater confidence. For the CRDC it will increase the Corporations capacity to support be more sustainable and profitable cotton industry by providing significant benefits. Based upon these data and subsequent modelling undertaken by CPAS, the National Registration Authority (now the Australian Pesticides and Veterinary Medicines Authority, APVMA) developed the 1999/2000 endosulfan cotton label in response to the detection of endosulfan residues in beef cattle during the 98/99 cotton season. The APVMA consequently focussed solely upon reducing off target contamination and aerial transport of droplets, not the biological efficacy of the product.

AN ENERGY efficiency audit of the new overhead irrigation system on Adam McVeigh's Darling Downs farm in southern Queensland has set him on the path to reducing emissions and making big savings in energy costs.

The green mirid, Creontiades dilutus (Hemiptera: Miridae), is a serious pest of cotton in Australia (Adams and Pyke, 1982). Minds are sucking insects which feed preferentially on the actively growing points of young plants. The damage they inflict to the tips of pre-squaring cotton and to early squares can result in delayed maturity of the plants and a reduced yield (Bishop, 1980). Current control of the green mirid relies on early season chemical sprays. The use of chemical insecticides is disruptive to beneficial insect populations as well as being expensive and environmentally harmful. One new strategy for insect control is the use of genetic engineering to produce plants resistant to insect attack. Chemical control of Heliothis armigera has already been augmented with the use of cotton plants expressing Bacillus thuringiensis (Ali and Young, 1993). A similar strategy for control of the green mind would be a desirable alternative to chemical insecticides.

To examine the genetic similarity of cotton cultivars available in Australia, twelve cultivars of Gossypium hirsutum, together with an American Pima cotton (G. barbadense) cultivar, were subjected to genetic fingerprint analysis using the technique of RAPD-PCR 1 The study revealed that it is possible to differentiate each of the CSIRO cultivars, even though the majority of these cultivars possess greater than 90% of their genetic material in common (Figure 1 ). As would be expected from their wide pedigrees, cul ti vars such as CS 50 and DP 90, together with the G. barbadense cultivar Pima S-7. reveal much less genetic similarity. From these results we can assume that if such an analysis were extended to cultivars with unknown pedigrees, it would be possible to obtain a detailed picture of their genetic relatedness.

Fov is the causal organism of Fusarium wilt disease in cotton. This disease is of serious concern to the cotton industry in terms of potential yield loss. Existing CRDC projects in progress to identify genes associated with cotton’s response to Fov infection (CSP114C) including those genes associated with the expression of moderate resistance. Once potential genes have been identified as being associated with resistance responses, it is necessary to confirm that these genes are playing an active role in the expression of this resistance. One approach that may be used to verify the role of any particular gene in resistance is to generate transgenic plants in which the expression of this gene has been altered and to look for a change in disease resistance. This is not feasible in cotton but would be feasible in the model plant Arabidopsis thaliana, where suitable genomics tools (e.g. rapid and simple transformation, complete genome sequence, diploid plant) are available. One of the aims of this project was therefore to establish a model Arabidopsis/Fusarium oxysporum system to complement studies with cotton and Fov. We wished to know if the importance of genes detected in the cotton microarray work (CSP114C) could be assessed rapidly in Arabidopsis and if it would have been feasible to perform gene discovery work in the system for application to the cotton system. In order to achieve this we needed to set up and develop expertise in the Arabidopsis/Fusarium infection system.

The second part of the pilot project dealt with developing the tools required to undertake a study of the molecular basis of pathogenicity of Fov. This may have lead in the long term to the development of novel disease resistance strategies. In order to undertake molecular analysis of the pathogen, a transformation system for Fov is required. We wished to apply an Agrobacterium-based transformation method developed for Fusarium oxysporum pathogens of Arabidopsis to the cotton pathogen Fov. Initially we planned to introduce reporter genes into the fungus to generate transgenic strains with immediate practical use in studying Fov infection dynamics in experimental systems and in the glasshouse.

It was hoped that development of these technologies would form the basis for a further project aimed at verification of the role of genes already discovered, the discovery of novel plant genes and the elucidation of pathogenesis mechanisms in Fov.

Since the late 1980's secondary soil salinisation has been recognised as a potentially threatening problem in many of the irrigated cotton growing areas. This has been most apparent in the lower Macquarie valley and at Bourke where large earthen storage dams constructed from semipermeable soil materials have leaked. Owing to the presence of subsurface textural boundariesshallow water tables have been created in adjacent irrigated fields which have redistributed stored soluble salts within the rootzone. In Dalby and the Lockyer valley, the application of poor quality irrigation water has resulted in minorproblems with salinisation of surface soil. Fortunately, there have been no widespread occurrences of secondary soil salinisation as a result of rising water tables or the prolonged use of poor quality irrigation waters.