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.

Stinkbugs are emerging pests in cotton. In conventional cotton the use of broad-spectrum insecticides to kill Helicoverpa spp. effectively controlled the stinkbugs, but with the introduction of transgenic Bt cotton the use of broad-spectrum insecticides to control Helicoverpa spp. has been reduced. Further reduction of insecticides is expected with the increasing adoption of Bollgard II and IPM will aggravate the stinkbug problem. Little was known about their damage, thresholds, IPM tools, etc. This project addressed these issues.

In Australia there are six different types of stinkbugs- green vegetable bug (GVB), Nezara viridula (Linnaeus), red banded shield bug (RBSB), Piezodorus hybneri (Gmelin), green stink bug (GSB), Plautia affinis (Dallas), brown stink bug (BSTB), Dictyotus caenosus (Westwood), harlequin bug (HRLQB), Tectocoris diopthalmus (Thunberg), cotton stainer bug (CSB), Dysdercus sidae (Montrouzier).

Stinkbugs move to cotton from wild winter or spring crop (early mungbean) hosts when these hosts dry off or are harvested after Christmas at boll setting stage and pass at least one generation causing considerable damage to cotton. All stinkbugs cause similar damage. Damage is characterised by black spots, warty growths inside boll walls, brown coloured lint and tight lock. The damage caused by stinkbugs cannot be distinguished from the damage cause by mirids at the boll stage. The most damaging stinkbug is GVB, causing damage 2, 3 and 4 times more than GSB, RBSB/CSB and HRLQB respectively. BSTB caused negligible damage. Fourth and fifth instar nymphs and adult GVB cause equivalent damage. Third instars cause half the damage caused by 4th and 5th instar nymphs and adults. First instars do not feed and 2nd instar nymphs cause negligible damage. Bolls up to 20 days old suffer significant damage from GVB but compared to older bolls, the preferred age is 10 days or less. Bolls up to 7 days can shed due to GVB feeding. Bolls older than 25 days suffer very negligible damage and therefore do not need protection at that stage.

The most efficient method to monitor stinkbug is beat sheet sampling. In the field, distribution of stinkbugs is patchy; therefore thorough inspections at least once in a week throughout a crop are necessary. Stinkbugs are most visible during the early to mid morning when they move to the top of the crop to bask in the sun, making crop inspections easier at this time.

Once stinkbugs number reach the threshold level, control option should be selected in the light of the IPM strategy. The threshold for GVB is 1 bug (adult, 4th and 5th instar nymphs)/m with beat sheet or 0.5 bugs/m with visual counting. When calculating threshold, 3rd instar are equivalent to 0.5, and 1st or 2nd instars, clumped around the egg remnants, are equivalent to 1 4th or 5th instar nymph or adult. The thresholds for GSB, RBSB/CSB and HRLQB are 2, 3 and 4/m with beat sheet and 1, 1.5 and 2/m with visual counting respectively. As well as the insect threshold, a damage threshold can be used for management decision. US guidelines suggest a damage threshold of 20% damage to small bolls (14 days old). At least 100 bolls from a management unit should be selected randomly to assess damage and the presence of warts or stained lint deems a boll to be damaged.

For managing stinkbugs, soybean strip or bulk can be used as a trap crop. Since soybean is a preferred host of whitefly, it can be replaced with mungbean where whitefly is an issue. Since stinkbugs preferred podding stage of soybean/mungbean, the trap crop should be planted in such a way that they start podding in early January when stinkbugs move to cotton from wild hosts.

Salt mixture is an effective and profitable IPM option to manage stinkbugs. Salt at 10 g/L water mixed with reduced rate (1/2 to ¼ of full rate) chemical increase chemical efficacy by 40 % compared to low rate of chemical alone. Salt mixture increased palatability of the chemical. Mixing salt with chemicals should be approached cautiously. Chemicals that are registered for Helicoverpa, mites, whitefly and aphids should not be mixed at the low rate with salt if one of these pests is present in the field. The stinkbug spray at lower rate may have resistance implications for those pests. In terms of the IRMS, a low-rate application is counted the same as a full-rate application. If there is a maximum of three applications allowed then three low-rate applications is equivalent to three full-rate applications.

There are a number of issues that were considered before TANDOU LIMITED began trailing UNR (ultra narrow row cotton). The first was to understand the concept and visualise its best fit for our operation.

Electromagnetic (EM) surveys in combination with computer models, like Sodium-SaLF, and chloride mass balance models have been used to estimate deep drainage under irrigated soils with high clay content (Wills and Black 1996; Triantafilis et al. 1998; Zischke and Gordon 2000). In addition to these surveys and models we can also add field lysimeters. These have been used in southeast Queensland and northwest NSW to monitor nutrients that leach below the root zone of cotton crops (Zischke and Gordon 2000). This form of evaluating nutrient leaching is accurate, however, it is also expensive and requires a lot of time to install. They are a permanent fixture in the field to be studied and cannot be readily relocated to monitor multiple locations across a field.

Rising energy costs are no surprise to farmers. Peak oil and an exponentially expanding world population are maintaining strong upward pressure on the price of energy.Cotton is sensitive to energy price because it is a high-input crop that relies on energy intensive inputs such as diesel fertilisers and chemicals. This is why the Cotton Research and Development Corporation (CRDC) has initiated projects to meet the energy challenge for Australian cotton production into the future.

Water-use efficiency of cotton production and minimising the impact of the cotton industry on the environment have emerged as issues of great importance. To improve these issues two major questions need to be answered: 1. How much water is draining from the irrigation system? 2. Where does the water go once it moves below the root zone.

The following is a summarised version of a paper written on research into two potential reference methods for a NIR fibre maturity and fineness instrument being developed at the United States Department of Agriculture's (USDA) Southern Regional Research Center (SRRC). The objective of the research was to compare values of perimeter and wall thickness derived from the values given by two instruments; the Shirley Micromat and the Zellweger Uster Advanced Fibre Information Systems Fineness and Maturity Module (AFIS F&M). The aim was to choose one of the instruments as a reference method for calibrating NIR spectroscopy. Comparisons were made on the level of error associated with each method and the degree to which data from each method conformed with theoretical relationships.