Energy costs are the second largest gross margin cost item for Australian cotton growers after wages. Half of this cost is consumed in pumping water for irrigation. Therefore, small improvements in pump efficiency make significant improvements to the bottom line of cotton production. Pump efficiency improvements significantly reduce greenhouse gas emissions from cotton production. Improvements in pump efficiency can also result in increased water harvest volumes. Production and gross income is directly proportional to available water. Small improvements in water harvest volumes have a large, positive impact on gross income, profit and viability of the Australian cotton industry.

The primary aim of this project was to obtain a better understanding of the energy efficiency of pump installations in the Australian cotton industry. To do this, the project undertook a number of areas of investigation. Broadly, these areas are:

1. Characterise Pumping Systems in the Australian Cotton Industry.

2. Improve Pumping System Performance in the Australian Cotton Industry.

3. Increase industry awareness of pump operating parameters and opportunities for improvement.

This project is principally reported in the attachment: ‘The performance of pumping systems in the Australian cotton industry.’ (the report). This report outlines, in detail, the objectives, methods, results, outcomes and opportunities resulting from the project. The report is intended to be a document containing the current knowledge of pumps in the Australian cotton industry and present technical aspects in a reader-friendly manner. This report is intended for public release.

Since the inaugural Field to Fabric course in August 2005 the course has been

presented 3 times in 2006 and twice in 2007. Feedback from participants has been

overwhelmingIy positive and despite the drought, two further courses were

presented in July and November 2008 to a total of 33 participants.

In total 185 participants from various sectors of the cotton production pipeline

have attended the course.

The course, which is a formal three 3 day course, is presented in Geelong at

CSME. It gives participants an opportunity to interact with leading researchers

on allaspects of the cotton production pipeline including global perspective,

fibre properties, agronomy, picking, ginning, classing, marketing, yarn

formation, fabricformation and dyeing and finishing. A strong emphasisis

placed on the impacts offibre quality on textile processing. Information is

presented by way of lectures and practical demonstrations using the modem

commercial cotton spinning and processing equipment available at CTF

The course is constantly updated with all practical suggestions considered, to

ensure that the course stays relevant and current.

In this 25th anniversary special edition of Spotlight, we take a look back at 25 years of innovation and the 25 major achievements of cotton RD&E during this time.

Even though the cotton industry is relatively successful, it continually faces a range of critical issues from drought and water supply; yield and profitability; fibre quality and export price; nutrition; sustainability and catchment management. In an effort to help the industry remain successful, the industry has committed significant resources into the industry’s Best Management Practice system – myBMP.

This project has facilitated linkages between research and extension through myBMP. This is fundamental for the ongoing success of myBMP ensuring that the latest research and development is integrated, information is up-to-date and tools and information are developed to improve the implementation of Best Management Practices.

Taking on a part time role (5 days/fortnight), Sandra Deutscher was uniquely positioned to undertake such an initiative with its underlying complexity.

The project objectives focused on effectively delivering the latest research and technology to the industry. This was achieved through 3 key areas:

1. Improving the flow of research outcomes and its adoption by identifying linkages and

synergies between research, extension and BMP initiatives.

2. Facilitating the development of timely, relevant and consistent extension tools and

information from research.

3. Explicitly supporting the industry’s implementation of its BMP program.

Sandra’s role as a research co-ordinator for myBMP, required significant effort involving the research community in its development. The first step was the formation of several small focus groups which consisted of researchers and extension specialists who worked together to review and develop the myBMP modules. Sandra’s role was to help facilitate some of the group meetings and refine the final practices. In addition to this, Sandra also spent a significant amount of time identifying the resources needed to support some of the new modules i.e. Fibre and Energy and Input Efficiency Modules.

Supporting user friendly web tools to deliver the latest research and technology to the industry required significant effort in development and support. Sandra’s main role involved liaising with the researcher involved to help web developer Loretta Clancy with the design specifications and functionality. E.g. Working with Dr. Richard Sequeira to develop the Silverleaf Whitefly Tool. Sandra also carried out rigorous testing before any new tool or upgrade was released. A large proportion of Sandra’s time was dedicated to supporting and promoting the CottASSIST web tools. From keeping the user manual up-to-date and writing promotional articles to hands-on training, demonstrations and phone support.

During this project Sandra actively coordinated the update of, ‘Pests and beneficials in Australian Cotton Landscapes’. Sandra collaborated with catchment extension and research staff to incorporate into the ute guide outcomes from biodiversity research. These outcomes will educate growers and consultants about the role that native vegetation can play as an alternate habitat for beneficials. The new guide is integrated into myBMP as a resource to support both the IPM and Natural Assets modules. This has been one of Sandra’s major project highlights as this publication is unique as it is a first to integrate outcomes of biodiversity research in a production focused guide.

Advances in our knowledge of the genes expressed in cotton fibres make biotechnology a viable means to improve fibre characteristics. Most genetic modification uses ubiquitously expressing promoters that often result in yield penalty. We have developed a strategy which uses fibre-specific promoters to manipulate and confine gene expression to fibre cells.

We used several fibre-specific gene promoters to drive expression of an expansin gene that is native to cotton and fibre-specific as well. Expansin is a protein known to be involved in cell elongation and growth, and therefore could impact on fibre traits such as length. Normally, the fibre-specific expansin gene expresses predominantly in the first 18 days of fibre development. By assembly of the expansin gene with a promoter (FS18) that usually drives expression of a lipid transfer-like protein that is active late in fibre development, we have been able to extend expansin expression for a further 4-10 days in transgenic plants. The chimeric gene increased the total amount of expansin in fibre cells and altered the morphology of the fibre in ways that are potentially advantageous to the industry. Linked experiments in which this promoter was used to drive a GUS reporter gene in a separate set of transgenic plants showed that the FS18 promoter can drive a high level of transcription specifically in fibre cells to a much later stage of fibre development. The FS18 promoter could be used to express any gene of interest in an effective and predictable manner in cotton fibre cells, and could be an important tool in fibre biotechnology.

Transgenic plants containing the FS18-expansin construct have modified fibre characteristics that could be incorporated into existing breeding programs. In this way new fibre variants could be generated, contributing to germplasm stocks and helping to maintain the reputation of the Australian cotton industry as a producer of premium quality cotton. Our strategy of manipulating gene expression in a tissue-specific manner by utilising native cotton genes is feasible and potentially beneficial to the cotton industry.

Soil nutrients, in particular phosphorus (P) and potassium (K), are being depleted in the clay soils supporting the grains and cotton industries of northern NSW and Queensland, especially in the deeper layers of the soil profile. Current commercial soil tests used to measure these reserves do not detect some of these changes because previously unrecognised pools of nutrients have been replenishing those measured by the extractants. Even when enough fertiliser is applied to maximise yields, inorganic pools of P and K which are not measured by commercial tests are decreasing. Across soil types these backup pools of nutrients range in size and their rate of supply, and in the case of K, the availability to plants can be moderated by high levels of other elements like Na. It is therefore important to quantify the size of these pools, their interaction with applied nutrients in fertiliser and their capacity to supply plant nutrient requirements in our current farming systems.     

In conditions where nutrient limitations are identified or where nutrient replacement strategies have been adopted for long term sustainability, effective fertilisation strategies need to be developed to ensure efficient use of those nutrients by plants. The experiments needed to make these assessments are expensive and time consuming, and so certainty of selecting responsive sites becomes important. The uncertainty with current P and K diagnostic tests, due mainly to the existence of variable sized pools of nutrient reserves, has complicated this selection process.

This small preliminary project was conducted to assess the potential of new P and K diagnostic tests to clearly identify sites with low levels of available P and K on which future fertiliser trials could be conducted. It was also part of an initial assessment of the variability in P and K reserves in different soils and cropping systems across the region. Findings from this project will feed directly into a joint GRDC and CRDC project in which laboratory, field and glasshouse studies will develop new guidelines to ensure profitable use of P and K fertilisers as well as long term sustainability of grains and cotton farming systems.

Key outcomes from this project included (i) evidence of strongly stratified reserves of P and K within the 0-30cm sampling depth in cotton growing soils across the industry, which may have significant implications for nutrient access by cotton crops; (ii) evidence that there is substantial variability in the P and K reserves in soils across the regions, and that the size of these reserves is often not related to existing soil test methods; and (iii) this variability is being used, in combination with in-crop tissue testing, to improve understanding of the relationship between soil tests and plant nutrient status, and to ultimately guide selection of sites for longer term experimentation to develop P and K fertiliser guidelines for the grains and cotton industries.

Research and development programs are under increasing pressure to demonstrate and

enhance their impacts towards the triple bottom lines of environment, economic and social

criteria. Cotton research, development and extension funders are looking for strategies

both to meet this reporting need and to build capability and impact-thinking amongst

research and extension providers. This research reviews literature and existing reports and,

through a series of unstructured and semi-structured interviews, explores the perspectives

of both research funders and researchers towards evaluation.

It has identified a low level of formal evaluation practice and understanding amongst

cotton researchers. However, many researchers regularly gather feed back from industry about their research

and are willing to further explore constructive evaluation. Strong

views are held about a lack of specialised skills, and the need to engage these rather than

build them solely within existing staff. Building an appreciation and understanding

evaluation amongst researchers was regarded important to aid evaluation and improve

projects.

A strategic, holistic view is needed for evaluation of Cotton RD&E to be efficient and

minimise the pressure on industry in gathering data. This efficiency as three core

elements: I) Finding a balance between projects and programs - it is suggested to look at

individual projects up to the level of outputs and at project clusters, programs or key

questions for evaluation of outcomes and impacts; 2) minimising the pressure on industry

by gathering data in smart & efficient ways, unobtrusively where possible; and 3) develop

and resource a clear evaluation strategy.

Also identified in this research are diverse values and roles for cotton research,

with a gradient of embeddedness in industry. There are some conflicts between perceived

industry needs and organisational needs for some scientists, particularily about the need for

peer reviewed publishing.

Development of the following manuals:

*Knowledge Management in cotton & Grain Irrigation

*Planning & conducting Focus Group Interviews

*Strategic Approaches for Evaluation in Agricultural & Natural Resource Management Research Programs

*Strategic approaches for Evaluation in australian Cotton Research Programs

Genomic technologies are set to revolutionise plant biology and we have already seen significant advances in the rate of gene discovery and new ideas engendered by the sequencing of genomes from two model plants, Arabidopsis and rice. This is pushing the frontiers with new developments in biotechnology as plant scientists start to now try to understand what all the genes in these plants do and how we might manipulate them to improve our crops. Monsanto, for example, is reported to be developing new drought stress tolerance transgenes for crops that has come out of studies of master stress regulator genes first identified in Arabidopsis. Some of the research from these model plants will flow through to cotton but to achieve the maximum benefit, particularly in the area of fibre, as these biological structures are not found in rice and Arabidopsis, we must develop a capacity for genomic studies in cotton. CSIRO has taken the first steps in this direction by developing cDNA microarray technologies for cotton that will help us understand better what genes are important in fibre development as well as in other aspects of cotton biology.

Microarrays are formed by robotically depositing specific fragments of DNA (genes) at indexed locations onto glass microscope slides. The microarrays can then be probed with the genes expressed in particular tissues or under particular conditions that have been chemically tagged with a coloured dye. Scanning the slide can then tell you, by the colour of the spots where the DNA has been printed, how much each genes is expressed in those conditions – thousands of genes at a time, giving a whole picture of the differences in gene expression. Knowing what sequence and hence inferred function of the different genes on the slide can then tell you what genes expression is contribution to the problem under investigation.

This project has focussed on developing a microarray slide that contains unique representatives of large numbers of the genes expressed in cotton (concentrating on those expressed in fibres, but also some other tissues). While it will still be a long way from having all the genes present in cotton (Arabidopsis has at least 30,000 genes) it should have a large enough representation that it will be useful for dissecting many important problems in cotton biology and biotechnology. CSIRO had already printed and used a slide containing over 10,000 cotton genes, but only a small fraction had been sequenced. During this project we added new clones to the set and sequenced about a third of the genes and were able to get the rest sequenced by a collaborator in the US. To add to the genes we already had, we were able to purchase another 13,000 unique genes from the US Cotton Genomics Centre (Thea Wilkins, Director) and have been using bioinformatics programs to search through the gene sequences and weed out those that occur more than once, so that we can produce a so-called uni-gene set (where each different gene is only represented once). This allows us to put more informative genes on the slide as they currently have a limit of about 25,000 spots. The laborious process of amplifying up each gene to produce enough DNA to print hundreds of slides and checking that each gene has been amplified properly has been completed and all that remains now is to assemble the sequences into the unigene set ready for printing. The project has generated an important new tool for cotton researches and the array should contain about 25,000 unique genes - the biggest of its type for cotton available anywhere in the world. We will shortly start to use the slide in a project designed to discover what genes are important in determining fibre quality traits like length, strength and fineness and will hopefully help our breeder’s improve the quality of Australian cotton.

Fusarium wilt, caused by Fusarium oxysporum f. sp. vasinfectum (Fov), is a destructive disease of cotton (Gossypium hirsutum L) in almost all cotton producing countries of the world. First reported in 1993, this disease is now widespread in Australia and is causing substantial losses. There are also 17 native Gossypium species or wild cottons in Australia, some of which have ranges that overlap cotton-growing regions. Wild crop relatives are a traditional source of novel resistance genes for many plant diseases, and preliminary studies of Australian Gossypium species suggested they may contain some useful levels of Fusarium wilt resistance. At the same time, however, it was possible that the native species could be harbouring potential cotton pathogens. The main objectives of this project was to explore the risk and the potential of the Australian Gossypium species.

Screening the Australian Gossypium species identified a range of accessions that will be useful in the continuing efforts to develop new cotton cultivars with improved levels of Fusarium wilt resistance. Although there was considerable variation in Fusarium wilt resistance among the Australian Gossypium species, G. sturtianum emerged as a possible source of novel resistance genes. Subsequent analyses confirmed that G. sturtianum was resistant to Fusarium wilt, but genetic analyses have established that transferring the G. sturtianum genes to cultivated cotton will be extremely difficult.

Simultaneously, it has become clear that while the native Gossypium species are not harbouring cotton field pathogens. However, surveys of the pathogen in cotton fields suggest that pathogen is continuing to evolve and continuing vigilance would be appropriate.

This project aimed to investigate the expression and function of a number of genes that we believed were involved in the production of the secondary chemical gossypol in cotton. One of the key enzymes in cotton terpene synthesis is cadinene synthase that is encoded by several different members of a large gene family. The promoter of one of these genes was chosen for analysis based on it sequence and when linked to a reporter gene and inserted into cotton drove expression of that GUS reporter gene in an embryo-specific pattern. As we were after a promoter that would allow us to silence gossypol production in cotton seeds (ie embryos) but not elsewhere in the plant this now provides us with a useful molecular tool for delivering gene knockout constructs to the cells in the seed that are making gossypol.

In addition we had previously isolated a gene for an enzyme of the P450 hydroxylase class that are involved in many biochemical conversions of secondary defence chemicals, but we needed to demonstrate that it was involved in gossypol production not some other chemical in cotton. Gene silencing or knockout constructs have been developed for this gene and introduced into transgenic cotton. We hope to be able to analyse the chemical composition of the oils in the gossypol glands to see what effects plants that should be deficient in the hydroxylase have had in terms of terpene production. In an alternative strategy we are also expressing this gene in simple bread yeast to see what biochemical conversions it can achieve when fed with different intermediates in gossypol synthesis.

A third approach has been to clone a peroxidase we believe is involved in the last step of gossypol production and see what changes in chemical composition occur when this particular gene is silenced in transgenic cotton plants.

Overall we are trying to characterise some of the key enzymes and genes in gossypol synthesis and develop strategies for eliminating gossypol just from the seeds of transgenic cotton plants in an attempt to increase the nutritive value of cotton seed meal and oil without affecting the normal defensive role of these chemicals against pests and pathogens of cotton. Unfortunately, the project was suddenly terminated midstream by the resignation of the student for personal family reasons.