Genetic engineering techniques allow the transfer of novel genetic material from one organism to another and hence has the potential to augment classical plant breeding techniques by extending the gene pool accessible for crop improvement We have established a program of research and development aimed at using this new technology to improve the performance of Australian cotton cultivars under our intensive production systems. The major limitations to cotton production in Australia, other than the availability of water, is competition from other organisms, be they insect pests (such as HeIicoverpa larvae), weeds or fungal pathogens (such as the wilt pathogens Ventcillium and Fusarium). The first generations of genetically engineered cotton plants will inevitably be aimed at minimising the impacts of these other organisms, while maintaining and improving the level and quality of Australian cotton production. Already transgenic cotton (INGARD and Roundup Ready varieties) coming through this program are making a major impact on pesticide usage and the weed control options available to the Industry. In the future, as our understanding of plant growth and development expands, other targets for genetic engineering such as improvements in quality or plant physiology will become possible. The aim of this project has been to develop and maintain the basic technology and expertise to produce new cotton cultivars using genetic engineering. In particular, to use the currently available molecular and tissue culture skills to produce herbicide tolerant, insect tolerant and disease tolerant cotton plants by the introduction of novel genes from other organisms. It complements and extends the more traditional cotton breeding program (CSP96C) by providing access to molecular biology and laboratory skills necessary for the breeding of transgenic cotton varieties.

SiroMat is an instrument that measures cotton fibre maturity directly and accurately. It was

developed by CMSE with financial support from the CRDC and CCC CRC. Its advantage

over other test methods is that it measures maturity directly and is able to measure the fibre to-

fibre distribution of maturity in a specimen. During this project a license to manufacture

and market SiroMat was sold to an Australian SME (BSC Electronics) with a good track

record in instrument development and manufacture. The licensing agreement was signed in

June 2009. A new prototype of the SiroMat instrument has already been built (now called

Cottonscope) by BSC Electronics and trials of it are planned for later this year.

During this project a number of studies were undertaken to demonstrate the value of SiroMat

and SiroMat data to a variety of end-users from research agronomists interested in monitoring

and measuring fibre development in immature bolls to spinners requiring more information to

predict dye uptake and yarn quality.

The overall objective is to develop soil and agronomic management techniques to improve the aeration of irrigated clays and hence their productivity for cotton. Specific objectives: * To quantify waterlogging influences on the growth and yield of cotton. * To quantify waterlogging influences on the physical and chemical properties of the cracking grey clays. * To develop management techniques to overcome or ameliorate ate the effects of waterlogging .

The Cotton Research and Development Corporation have demonstrated a strong commitment to supporting research in water use efficiency across the industry. One component of water use in irrigation is the identification of the risk of water being wasted through deep drainage, which is defined as the rate of water that is lost below the depth of plant roots. The cotton industry also recognises that excessive deep drainage can also potentially lead to the development of shallow water tables often blamed for root zone salinisation affecting crop performance. There are many methods that exist to estimate the deep drainage however they need specialised and expensive instrumentation and, the measurement is often tedious requiring highly specialised skills. With this in mind the CRDC supported this project with the charge to develop a cheap and easy protocol to estimate the risk of deep drainage. The method should not require any specialised equipment, should not be time consuming, and can be operated by growers and IDO’s within the industry.

The initial work involved the successful completion of experiments that determined the minimum number of observations that need to be taken to in a cotton field to give a good estimate the potential deep drainage and the implementation of a modified sub-soil hydraulic conductivity using the falling head lined-borehole technique (FHLBT) appropriate for a cotton growing system. The readily available Microsoft EXCEL was chosen as the platform to develop the user-friendly interface for managing the data to estimate the potential and required deep drainage. Testing of the method was conducted on Field 11 at Auscott Moree, which was chosen as this site is representative of the soil in the cotton growing area, having heavy clays derived from alluvial material and less clayey and/or leaky soil traversing the field. Results showed that the method could successfully identify the significant difference in the potential deep drainage occurring within Field 11, corresponding to soil with different soil clay contents and leaky areas. To make the estimate of potential deep drainage more meaningful the Potential and Required Deep Drainage Interface incorporates a leaching requirement that is needed to prevent excess salts build up in the sub-soil that may affect crop.

The main outcomes to benefit the cotton industry are:

• the Development of a protocol that can be used to assess the potential deep drainage on a cotton farm

• demonstrating the importance of strategically placing sampling sites to capture the within field soil variability, which will increase the opportunity for a better representation of the potential deep drainage.

• the development of a user-friendly interface in commonly available software to calculate the potential deep drainage.

• and the incorporation a module into the Potential and Required Deep Drainage software to allow growers to determine the drainage required to avoid subsoil salinisation that could potentially reduce crop performance.

Section J of WeedPak -Herbicide damage on cotton, Symptoms guide and production outcomes from known levels of exposure to herbicides.

Healthy soils are fundamental to the profitability and sustainability of cotton ecosystems. However, whilst soil fauna such as earthworms have been widely shown to be capable of markedly influencing soil structure and fertility (e.g. porosity, nutrient cycling, retention of nutrients on-farm), disease and pest incidence, and plant production and quality in other agricultural ecosystems, very little is known of their biology and functional role under cotton.

Cotton farming has presented several potential hazards for soil fauna (e.g. heavy pesticide use, tillage), but recent trends in the industry such as reduced (& softer) pesticide use, less tillage and retention of organic matter would seem likely to open opportunities for population growth and (re)colonisation of soil fauna such as earthworms. This project aimed to survey the status of the current earthworm fauna in and near to cotton fields in the Namoi Valley and to determine some of the major factors influencing its abundance there. Preliminary glasshouse experiments were conducted to evaluate the potential of earthworms to improve cotton production. The research was conducted in a period of drought in northern N.S.W. The results need to be considered in light of this (e.g. the field abundance that was observed may have been unusually low as a result of prolonged, low soil moisture).

Earthworms were more common in cropping soils used in recent times for cotton production than in less disturbed soils nearby. This result ran counter to expected, in that tillage is well known to reduce earthworm abundance. Possibly, greater availability of soil moisture in irrigated crops contributed to this result. Earthworm abundance within the cropping soils was most strongly correlated with measures of particle size (especially % silt) and electrical conductivity. Species richness was greatest in the undisturbed soils.

This research project was a preliminary foray into the importance of one component of the soil biota, earthworms, in soil health and cotton production. It focused on surveying just one cotton production valley. It primarily used one soil type for the evaluation of earthworm effects on cotton production and only considered earthworm influences in the short term. More extensive research, in particular considering the most common earthworm species within cotton fields, earthworm influences on soil physical and chemical properties, plant diseases and the dynamics of other pest and beneficial species.

There is evidence the nep and short fibre content of Australian cotton is too high compared

with other growths of similar quality. These characteristics are a result of the productive and

efficient harvest and ginning practices utilized by the Australian industry but the problem is

exacerbated by current lint cleaner design. In particular, the combination of lint cleaner

elements, i. e. the feed rollers and feed bar, grid bars and the doffing brush around the lint

cleaner saw, and the transfer ratios between these elements affect fibre quality.

The broad aim of this project was to adapt and re-engineer the widely used fixed batt saw lint

cleaner to reduce short fibre and nep content. The main adaption proposed at the start of this

project was an auto-levelling system for the lint cleaner feed such that the weight of fibre

transferred onto the saw would always be constant. Typically the unit is powered by a single

30kW motor, which regardless of the rate of fibre flow runs at fullspeed.

Currently in lint cleaners there are no sensors to regulate fibre flow or draft settings.

Excessive speed and large draft or combing ratios, ie. a high saw surface speed to feed roller

speed, increase damage to the lint. Implementing an auto-levelling system requires sensors

and variable seed devices to maintain a consistent flow of material. It has been shown in

previous work that low combing ratios reduced short fibre content and improved fibre length

and length uniformity. Introducing constancy to the batt weight requires a greater degree of

control of this combing ratio effect. Thus, the initial focus in this project was to test the

possibility of sensor control of mechanical elements, in particular the feed mechanism, in the

standard fixed batt saw lint cleaner and CSIRO's Modified Lint Cleaner (MLC). As well as

testing fibre and batt weight variation through the lint cleaner machine, work also

concentrated on the application of additional mechanical elements, eg. a combed grid bar

heel, designed to even the transfer of fibre onto the saw.

Once achieved, the objective was then to link this mechanical control to moisture control

systems being developed as part of New Ginning Technology for Australian Cotton: Part H

(Moisture & Contamination) project.

However, observations from flow and mass sensors applied to a commercial gin in the first

year of the project, showed the delivery of fibre from the gin by the current system was too

fast and too uneven to be controlled. Work on the project subsequently defaulted to proving

and extending the veracity of the MLC to industry, with a view to commercialismg the MLC

technology.

Alternate fibre conveyor designs to give a more even feed and allow time for the batt to be

levelled and humidified were drawn up towards the end of this project. These designs require

greater intervention to the ginning system than was originally foreseen in this project. A new

project around these designs was proposed to the CRDC in a FRP in January 2009.

Cellulose is a crystalline B-I, 4 glucan found in all higher plants and comprises over 90% of the dry matter of the mature cotton fibre. Selection for improved cotton fibre properties has not usually targeted cellulose characteristics directly but comparisons of fibres with different properties suggest that varietal differences between fibres often reflect unconscious selection for differences in cellulose properties. For example, changes in the quantities of cellulose produced, in the timing of production and in physical properties such as chain length, all impact on fibre properties. For many years the genes involved in cellulose production in plants remained elusive.However, our work identified the first gene involved in this process. It encoded the catalytic subunit of cellulose synthase, the enzyme that sequentially adds the glucose units onto the growing cellulose chain. This gene is currently protected by patent. The work exploited our collection of cellulose mutants to identify the gene and most importantly to prove its function and its ability to change the physical properties of cellulose. (The cellulose deficiency causes radial swelling of the roots, so the mutants are referred to as rsw mutants. An Arabidopsis gene can be used to identify equivalent genes in cotton by standard methods of molecular biology and then the Arabidopsis mutant can be used to rapidly prove the function of the cotton gene by showing that it restores wild type function to the mutant.

The basis of this project was to identify the genes which were affected in two of the other cellulose deficient mutants of the collection, rsw2 and rsw3. Cellulose production, like most biosyntheses, is almost certain to be controlled by several genes whose products may, for example, activate or inhibit the already identified catalytic subunit in response to environmental or developmental changes or may be required in some other capacity for cellulose to be generated. It is the identification of those additional genes, their functional characterisation and their protection for use in Australian cottonbreeding that was the basis for undertaking this project.

The Australian cotton industry is heavily dependent on chemical insecticides for pest control. As a result, a number of environmental issues involving off-farm movement of these pesticides have been raised for the industry. One of the key issues in meeting the challenges of growing cotton in tomorrow’s world involves pest management in a more environmentally friendly way. This involves reduction of pesticide use and adoption of IPM approaches. Introduction of transgenic cotton in recent years and application of insecticides targeting individual species has enabled a drastic reduction in pesticide use. This enables the numbers of important beneficial insect to build up, aiding in pest control. On the other hand, species like the , cotton tipworm (crocidosema plebejana) and rough bollworm (Earias huegeliana) which were not major problems under intensive use of insecticides are forecast to be more significant pests, which will require a re-evaluation of IPM in cotton..

One potential component of IPM involves the use of insect pheromones in mating disruption, monitoring, attract and kill and mass trapping. Pheromones could be used to predict oviposition on a field by field basis and also give useful indications of the overall abundance, of the pests mentioned above. Identified pheromones therefore could be used in area wide pest management schemes. Pheromones can also be used in attract-and-kill strategies, or for mating disruption. Although the Australian cotton industry has not previously made significant use of these techniques, there are ecological reasons for believing that they may be more applicable to some emerging pests than to the key pests of cotton under previous pest management regimes, Helicoverpa spp. This project was carried out to identify the pheromones of rough bollworm, cotton tipworm and green mirids, test attractive blends, and investigate their potential use as part of the general IPM system of the Australian cotton industry.

In this thesis, the sex pheromone of the rough bollworm worm was identified using GC-MS techniques from female glands and air collection. Identified compounds were formulated into a blend and tested in the field for attractiveness to males. The GC-MS analysis revealed four compounds, (E,E)-10, 12-hexadecadienal, (E,E)-10, 12-hexadecadienol, (Z)-11-hexadecenal, and (Z)-11-Octadecenal in a ratio of 4 : 1 : 1 : 1 in the gland extract. (E,E)-10, 12-hexadecadienol was not detected in the air collections. Field bioassay showed the two components, (E,E)-10, 12-hexadecadienal and (Z)-hexadecenal to be essential for activity of the blend. This blend was highly attractive to males only. Two trap designs, the AgriSense and Delta traps were tested, and the Delta trap was the better of the two. A weathering experiment to determine how long loaded septa would remain attractive in the field indicated that the lures could be used for a maximum of four weeks in the field. Male response to pheromone baited traps was found to be in the second half of the night, between 2 to 5 am. This was found to be synchronised to female calling time.

Sex pheromonal compounds from the glands of cotton tipworm have been identified as a mixture of octadecanal, 2-nonadecanone, acetic acid octadecyl ester and octadecanol in a ratio of 2:2:1:2 respectively. Most lepidopteran sex pheromone systems are multi-components and the relative composition may be critical to be effective attractants. Preliminary field trials however indicated the possibility of using only 18Ac as an effective trap attractant.

The calling behaviour of the cotton tipworm was studied in the laboratory at 25°C and 16:8 light: dark condition. The age at which C. plebejana called for the first time was the third scotophase. The mean onset time of calling was found not to advance with age, and was about 5 hours into the scotophase. Duration of calling ranged from 6 minutes on the 3rd scotophase to a maximum of 77 minutes on the 7th scotophase before dropping gradually to 4 minutes on the 12th scotophase. There was a high correlation between the number of calling bouts and age. Generally number of calling bouts increased with age. Calling behaviour and pheromone production of females is synchronous. Female gland extracts generally contained about 10-12 ng/female as compared to 2 ng/female in the air collections.

When calling C. plebejana had wings slightly raised above the abdomen with full protrusion of the ovipositor.

The produced by adult females of the green mirid was identified as a blend of hexyl hexanoate and (E)-2-hexenyl hexanoate. The pheromone was found to be sex and species specific, attractive only to conspecific adult males. Hexyl hexanoate was identified in both sexes, whiles (E)-2-hexenyl hexanoate was produced by only females. A blend in a ratio of 5:1 was estimated from field trapping experiments as the optimal, though ratios of 3:1 to 7:1 were equally effective. Influences of pheromone septa loading on male attraction to traps were studied using loadings of 2, 20 and 40 mg. Results indicated blend attraction was generally not affected by the loading levels used. In the field, male C. dilutus were observed to respond to pheromone baited traps in the night, especially the early part of the night, at least when the temperatures were high enough to permit night flight. Initial attempts at applying the pheromones in a sprayable formulation for mating disruption and attract-and-kill provided some encouraging results. The use of C. dilutus lures to provide an effective, economic, and environmentally sound monitoring tool for this pest is discussed.