The cotton boll contains the seeds of the plant to which long, white fibres are attached. The cotton industry takes advantage of these fibres to spin yarns for textile production. A major challenge facing the cotton industry is that of crop loss to insect attack. The primary insect pests of cotton preferentially attack the boll, causing damage to the commercially important fibres. The recent introduction of Bt-transgenic varieties, containing genes with anti-pest properties from the soil bacterium Bacillus thuringiensis, has had positive impacts on pest control and pesticide usage. These transgenes are under control of constitutive promoters, resulting in endotoxin expression in all parts of the plant. This constant high level transgene expression may have several detrimental effects, such as placing strong selective pressure on pest populations to develop resistance, non-target effects of the transgene on other organisms, a yield penalty to the plant, and the presence of transgenic protein in secondary commercial products. For these reasons, this project aims to identify promoters that could be used for tissue-specific expression of anti-pest molecules in only the boll wall of the plant. A differential screening approach was used to identify several boll wall-specific mRNAs and the temporal and spatial abundance of these transcripts was determined using Northern analysis. The promoters corresponding to these transcripts were identified using Genome Walker® PCR and isolated from genomic DNA by PCR. Transient transformation of various cotton tissues with these promoters driving reporter expression resulted in predominant boll wall expression. The cotton promoters identified here provide an alternative tool to constitutive promoters for use in future transgenic varieties.

SIRATAC is an on-line computer-based pest management system for irrigated cotton. It makes recommendations for insect control on the basis of samples collected from individual management units. Daring the 1980s, the SIRATAC methodology was marketed through SIRATAC Ltd. A reimplementation of SIRATAC was initiated in 1986 (SIRATACPlus). However, by 1988, it had become clear that on-line management systems were an evolutionary dead end. SIRATAC Ltd went into liquidation in mid-1989. The SIRATAC Plus project was abandoned in early 1990. During the 1989/90 and 1990/91 cotton seasons, SIRATAC was operated by a newly-formed User Group (SUG). The collapse of the SIRATAC framework coincided with the initiation of Project CS51L, Economic optimisation in SIRATAC. The abandonment of the SIR ATAC framework also coincided with increasing doubt concerning the ability of cotton to compensate for early insect damage. This circumscribed the usefulness of the SIRATAC crop model for formal optimisation. Thus, during the course of the project, the emphasis shifted from mathematical optimisation using validated simulation models towards the development of a novel approach to decision support as a replacement for SIRATAC.

This project has part funded maintenance of HVI900 and FMT3 cotton fibre testing instruments in CSIRO’s fibre testing laboratory at ACRI for the 2005/06 season. The laboratory supports measurements of fibre quality from cotton experiments in CSIRO’s breeding program and research projects by other organisations and projects.

More than 20,000 samples were tested by HVI and 10,000 samples by FMT.

Global cotton production and market dynamics indicate Australia needs a future edge with fibre quality to ensure buyers will want our cotton in preference to our competitors. This means developing varieties, management and processing to ensure we deliver better fibre. There may be opportunities for premium fibre products in future. Thus the CSIRO cotton breeding program raised the emphasis on developing improved fibre varieties to address these needs.

Negative associations between yield and fibre quality present challenges for variety development. We have accurately measured these associations and developed breeding population sizes to ensure the rare combinations of high yield and quality can be identified. Accurate measurement of fibre quality is an important component of that work.

A number of new breeding lines have been developed to address the objective of improved fibre quality and at high yield levels. In addition there are lines with excellent fibre properties to potentially target speciality (premium) markets. These lines are under further evaluation and are also used in developing speciality Bollgard®II varieties. Sicala 350B, released in 2005, has very long fibre and is attracting interest in the market. We have identifies possible superior lines of this type.

The VIII International Colloquium on Invertebrate Pathology and Microbial Control and the

VIth International Bacillus thuringiensis Conference were held at Iguassu Falls, Brazil,

August 18-23,2002.

Of the 347 registrants at the Colloquium, >l00 were from Latin America, primarily from

Brazil and Mexico. There was an unusually strong contingent from the UK, indicative of an upswing in there. The only Australian registrants were

Dudley Pinnock (Microbial Products, Adelaide), Cheryl Beard (CSIRO Entomology) and me.

The Colloquium had the usual full program of symposia, contributed paper, poster sessions

and workshops, including one on Ethics, Legal and Regulatory Concerns of Transgenic

Plants. The plenary session was devoted to baculoviruses, presumably because of the interest

of the Chairman of the Organising Committee because there appeared to be no new

developments flagged in any of the four presentations. As there were three concurrent

sessions, my attention was given largely to the bacterial presentations. The highlights of the

conference were the report of resistance to Bt in a natural populations of a second species, the

large interaction between plant variety and Bt toxins, and the absence of non-target effects of

Bt.

I presented two contributed papers and chaired a Contributed Papers session. At the Business

Meeting during the conference, I took over the role as secretary of the Society for

Invertebrate Pathology, having previously been elected by postal ballot.

The Leaf Chamber Fluorometer is an exciting new addtion to the physiological instrumentation available to the scientists at ACRI. The LCF has raised the investigative capabilities of the cotton research team and made it possible to study in greater depth stress related physiological responses in cotton. Its application will be broad encompassing stresses induced by pests and environmental extremes such as temperature and available water. Current and future projects will be measuring gas exchange and chlorophyll fluorescence concurrently, exploring and revealing the physiological origins of stresses in cotton that could result in declining yield and fibre quality. Significant findings using the LCF are expected over the next few years which will maintain research of an innovative standard in areas of cotton physiology for the team at ACRI.

Dr David Nehl attended the 9th International Fusarium Workshop, the and a workshop by Plant Health Australia on Developing a World Class Plant Pathology Diagnostic Network.

Outcomes

. New concepts in disease control and epidemiology are being incorporated in

current research projects on diseases of cotton, including:

- Biological soil disinfestation

- Fumigation of soil using nitrogen fertiliser with nitrification inhibitors

- Novel agents for induction of systemic acquired resistance, including nitric oxide and

silicon compounds

- Role of matric potential on reproduction of F. oxysporum f. sp. vasinfoctum on crop

residues

Established new links and strengthened existing links with plant pathologists

in the Ministry of Agriculture in Israel, at the University of Pretoria in South

Africa, at the University of Anzoria, at the University of Arkansas, at the

University of Sydney, at the Royal Botanic Gardens in Sydney.

Information on factors that may influence biological control of Fusarium wilt

with non-pathogenic strains of Fusarium oxysporum communicated to

Honours Student Christina Bakker at the University of Queensland.

Work on a draft biosecurity plan for cotton in Australia has commenced in

collaboration with Queensland DPI, Cotton Seed Distributors and the

Australian Cotton Growers Research Association.

Outputs

. Report and recommendations to the Cotton R&D Corporation

. Two posters presentations

. One keynote paper(at Fusarium Workshop)

. One invited review paper in a refereed journal based upon work in the

diseases of cotton project(see section 1.1)

. One oral presentation of highlights of the Congress given to peers at a NSW

Agriculture Crop Protection Workshop

A video was produced with the assistance and cooperation of a number of cotton

growers and processors. The final version of the OH&S video "Safety at Harvest" was

completed in December 2001.

An initial production run of 600 copies was followed in March 2002 with another 300

copies. Promotion and extension of the video was done by Industry Development and

Departmental Officers in both New South Wales and Queensland using pre-harvest

field days and meetings, the Cotton Trade Show and the 10"' Australian Cotton

Conference. The TRC also played an important role in its promotion and distribution.

The video has proved to be an excellent way for cotton growers and contractors to

clearly demonstrate the dangers and hazards involved in the harvest operation and to

provide training in the correct way to do the job. It was well received by growers and

contractors alike and was used as part of the on-farm pre-harvest OH&S induction

meetings on a number of properties. The video also complements the recently CRDC

funded OH&S module developed for the industry.

Ultra-narrow row (UNR) cotton, a production system with rows spaced less than 40cm apart, has been proposed as the ideal system for earlier maturity without substantial yield loss. However, trials in the USA and Australia have found yield and maturity benefits difficult to consistently achieve with UNR cotton production. This thesis aimed to improve the understanding of the differences in the growth and development of cotton conventionally spaced (1m) and UNR.

The 2003 National Cotton Council of America, Beltwide Cotton Conferences with the

theme "In Harmony-Research Resources Results" were held at the Gaylord Opryland

Hotel, Nashville TN from January 6' to January 11. The conference consisted of

four days of individual reports, panel discussions, hands-on workshops and seminars

on the latest developments in research, ginning, milling and marketing.

My attending the conference and visit to Texas has provided an opportunity to update

on recent Us research and experience and has enabled me to meet a number of Us

cotton researchers. This win16ad to continued networking and future collaboration

and enhance the effectiveness of my research activities.

The effects of rotation crops and stubble management (including the residual effects of past rotation crops) on soil quality, carbon sequestration, deep drainage, nutrient leaching, yield and profitability of succeeding cotton in irrigated and dryland Vertosols were studied in nine on-station and on-farm experiments located in New South Wales and SE Queensland from 2002 to 2005. Key management issues considered were tillage systems, rotation crops and stubble management systems, and in particular, sowing cotton into standing wheat and vetch stubble.

Soil physical and chemical properties were measured in all experiments. Soil water storage, crop growth, cotton lint yield and fibre quality were also measured. Economic returns in irrigated sites were evaluated by comparing seasonal and cumulative gross margins. Spatial and temporal deep drainage (with the chloride mass balance model) and nutrient leaching, and profile salinity change with an EM38 meter were measured in some NSW sites. Investigations were conducted into cotton crop management practices which could overcome problems associated with sowing cotton into standing (retained) rotation crop stubble.

Residual effects of the rotation crops sown were present up to a period of five years with respect to soil structure, sodicity, exchangeable K, deep drainage and nutrient and salt leaching. Deep drainage, nutrient and salt leaching were generally in the order of ex-cotton-wheat > ex-continuous cotton > ex-cotton-dolichos.

At the dryland site Qld, soil structural properties were affected primarily by tillage system (changing from conventional to zero tillage) with rotation crops affecting structure only during a period of relatively higher compaction. Least compaction occurred with double-cropped cotton-wheat.

In most locations, sowing cotton into standing wheat stubble improved soil organic carbon, rainfall harvesting and gross margins (during the cotton phase of the rotation), decreased sediment concentration in runoff, soil sodicity and salinity; and improved cotton yields and root growth. When cotton prices were low cumulative gross margins with either conventionally-tilled continuous cotton or minimum-tilled cotton-wheat were similar. Irrespective of price, gross margins of minimum-tilled continuous cotton were highest.

Sowing vetch as a rotation crop improved soil physical and chemical properties in good quality soil. In poor quality soil, vetch rotation crops reduced N fertiliser requirements and nitrate-N leaching, but no other soil improvement occurred. Cotton lint yield following vetch was similar to continuous cotton but less than after wheat or wheat followed by vetch. Gross margins of cotton-vetch were always lowest. At lint prices < $450/bale, gross margins of the cotton-wheat (standing stubble)-vetch rotation were highest.

Retaining crop stubble in-situ can cause several problems such as blocking of "gas knives" during injection of anhydrous ammonia as fertiliser and waterlogging during irrigation. In addition vetch regrowth can suffocate emerging cotton seedlings. These problems were overcome by attaching coulter discs to the front bar of the gas rig to cut through crop stubble, removing stubble in furrows at the start of the irrigation season and controlling vetch regrowth through a combination of mechanical methods herbicides.

Drainage was greater where cotton was sown into standing wheat stubble compared with stubble incorporation. Management practices which improved subsoil structure such as permanent beds or cereal rotation crops also resulted in more drainage. Stubble burning increased deep drainage. Yield losses of the order of 50% occurred when soil chloride levels in the 0-60 cm depth at sowing were of the order of 5.3 t/ha.