The 2019-20 CRDC Researchers' Handbook is a key resource for all researchers working with, or interested in applying for funding from, the CRDC. Updated annually, the Handbook outlines the key information researchers need to know, including key dates, the application process, funding and stipends available, the payment, evaluation and reporting processes and the CRDC’s intellectual property policy. These, and other critical details needed by researchers are provided in the Handbook.

The CSIRO cotton breeding program based at Narrabri has been very successful in developing varieties adapted to all cotton production regions in Australia. At least 90% of the cotton grown in Australia are varieties developed at Narrabri. The breeding program includes many objective including: high yield, high fibre quality, disease resistance and tolerance to insect damage. These targets are applied to cotton production areas that range from hot locations such as central Queensland to cool districts such as the upper Namoi valley and southern NSW. Such diverse locations require different characteristics for optimum production. Breeding requires large numbers of experiments and breeding lines. This program now has in excess of 15,000 yield plots at 15 different locations; there are also about 30,000 single plants harvested at the early generation stage of the breeding process. New varieties released to the Australian cotton industry in recent years include conventional types Si okra S-101, Sicot 189, Si okra V-16 and Sic ala 40 and transgenic varieties Siokra L-23i, Sicot 189i, SicaJa V-2i, Siokra V-15i and Sicot SOL There are new breeding lines close to commercial release.

CRDC 2015/16 Summer Scholarships (S/S ) Purpose- Strategic Plan Targets 1.Farmers 2. Industry 3.Customers 4. People 5.Performance Summer Scholarship Programme - 8 weeks

Ongoing research at ACRI into cotton diseases confirmed the need for best practice to be exercised to avoid disease transfer from one location to another.The need for this was confirmed by pathology staff at ACRI who tested vehicles visiting ACRI and found Black root Rot , Veticilium and Fusarium pathogens present . This clearly presented a risk to the research trials at ACRI especially if Fusarium Wilt was to be imported onto the farm. It was also recognised that ACRI is a hub of the Cotton Industry with many grower visitors and that many off station sites are visited by ACRI staff. The pathology staff advised that in order to prevent disease transfer it would be necessary to improve the washdown facilities at ACRI and adopt a come clean go clean policy.The facility would also double as a best management practice demonstration facility to industry.

The effects of rotation crops and their management on soil properties of Vertosols, cotton yield and profitability were monitored from 1993 to 2001 in 3 irrigated field trials in NSW (Warren in the Macquarie valley, and Merah North and Wee Waa in the lower Namoi valley), and 2 dryland trials in Queensland (Warra in the Darling Downs and Emerald in the Central Highlands).

Measurements taken in all trials were: soil physical and chemical properties to a depth of 0.6m in (e. g. soil organic matter, plastic limit, strength with a penetrometer, soil structure, exchangeable Ca, Mg, K and Na, pH, electrical conductivity). Profile water content to 1.2m, nutrient uptake, 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. Commencing from the 2000-01 cotton season spatial and temporal deep drainage (with the chloride mass balance model) and nutrient leaching were measured at ACRI (cotton sown into standing wheat stubble), Wee Waa (wheat-cotton) and 3 rotations (continuous cotton, wheat-cotton and doIichos-cotton) at Merah North.

The winter edition of CRDC's magazine, Spotlight, acknowledges the role of women in the industry with the celebration of International Day for Women and Girls in Science and International Women’s Day with some words of encouragement and advice from just some of our many female scientists and industry leaders. This is timely, given the announcement that Senator the Hon. Bridget McKenzie has been appointed to the Agriculture portfolio – becoming Australia’s first female Agriculture Minister.

In this edition, we also look at the results of a recent sleep study that confirms cotton sleepwear and bedding creates a better environment for a good night’s sleep. While cotton has always had a reputation as the premier fibre for bedding, to have quantified this scientifically gives cotton a powerful marketing tool to take to brands and consumers.

Additionally, in the lead-up to the industry’s biosecurity preparedness simulation Exercise Blueprint, this edition includes an update on Dr Murray Sharman’s investigations into cotton blue disease, and a collaboration with GRDC and the grains industry to manage an old foe of the cotton industry, Helicoverpa.

It also includes articles on the outcomes of CRDC's Grassroots Grants investment funding, including record breaking crowds at field days to introduce growers to ag technology, farmers from the Northern Territory travelling south to investigate cotton growing, and more than 10 weather stations erected across the growing regions. The grants have also led to practice change in the way the industry manages insects such as mealybug and whitefly.

Within cotton plants nutrients are taken up by roots and partitioned between plant structures. At boll filling, when the demand for nutrients is greatest due to the development of seeds and lint, nutrients from vegetative plant parts are mobilised and redistributed around the cotton plant. Higher-yielding Bollgard® II varieties are suspected to have higher nutrient demands than conventional cultivars, although the mechanisms and proportions of nutrients accumulated and redistributed in different plant parts is unclear. Yield and fibre development may be limited where nutrients are not efficiently redistributed to the developing bolls in sufficient quantities. Cotton plants with a high boll retention may enhance this problem.

Fertiliser programs aim to supply nutrients to the plants at peak growth stages when nutrient uptake is greatest. Foliar and soil fertiliser applications may be needed to supply nutrients to the developing plants. Some information is available on the total plant uptake of nutrients, but little on partitioning of nutrients between vegetative and reproductive plant structures. The timing of nutrient uptake redistribution has not been studied in detail. A better understanding of this process could aid in the development of timely and effective fertiliser programs for maximising yield and fibre quality of high yielding cultivars.

Examining the nutrient partitioning and redistribution mechanisms within conventional and transgenic cultivars may aid in establishing some key nutrient limitations to yield. Further understanding of the nutrient redistribution mechanisms under nutrient stressed conditions will aid in developing best management practices for fertiliser application.

This PhD project will test several hypotheses:

• That effective translocation of nutrients (largely nitrogen, potassium, phosphorus and zinc) is essential for high cotton yields.

• That nutrient uptake is not limited by root uptake but driven by fruit load and nutrient redistribution is driven by internal physiological mechanisms.

• That supplemental nutrients applied at critical developmental stages by either soil or foliar fertilization increases nutrient uptake and promotes higher yields.

• Nutrient uptake and redistribution is more efficient in high fruit retention crops

in previous studies we have indicated a relationship between a decline in macro-invertebrate population densities and riverine endosulfan concentrations measured using passive samplers (Hyne et al. , 1999; Leonard et al. , 2000). These passive samplers, constructed of low density polyethylene membrane bags containing the solvent 2,2,4-trimethylpentane (TRIMPS), were then used in the Department of Land and Water Conservation(ELWC) NW region water quality program for comparison to traditional grab sampling procedures (Muschal, 1999). The TRIMPS detected three pesticides in river water that were not detected by routine manual sampling. The TRlMPS were also able to show that endosulfan and profenofos concentrations were higher downstream of irrigated agriculture than upstream of this area (Muschal, 1999). Environment Australia has also drawn attention to the utilisation of passive samplers in the Existing Chemical Review Program (ECRP) for endosulfan and for the registration of certain organophosphorus pesticides.

There was a need to develop a field validated model of the operation of passive samplers. The kinetics of pesticide uptake and release from the passive samplers needed to be understood. The influences of changes in river flow, turbidity and biofouling or ageing on the absorption of pesticides into the passive samplers also needed to be assessed. In addition, the influence of solvent type and frequency of sampling needed to be assessed in laboratory studies.

DNA based diagnostics has become increasingly utilised in the agriculture sector both in the diagnosis of pathogens and pests as well as in molecular marker assisted breeding. Most DNA diagnostic tests for plant pathogens are based on specific amplification of the genomic material(either DNA or RNA) from the pathogen using the polymerase chain reaction or PCR and the subsequent detection of the amplified product. The simplest method of detection of the amplified product is agarose or polyacrylamide gel

electrophoresis. More sophisticated platforms have been developed particularly for the detection of multiple pathogens most of which are based on arrays.

The most important characteristics of a diagnostic protocol are that the protocol is both sensitive and specific. Thus, the major reasons that PCR diagnostics have become popularfor pathogen detection are that very small concentrations of the target organism can be detected and the specificity can be varied from highly specific to broad. However, there are a number of disadvantages that must be overcome for a PCR based diagnostic test to be sufficiently robust for it to be used in a clinical environment. The disadvantage of PCR is that it is prone to both false positive and false negative results.

False positives usually result from (a) poor primer design or amplification conditions such that organisms other than the target organism are amplified or (b) contamination of either the original sample or reagents involved in the procedure. False negatives usually result from (a) poor primer design or amplification conditions in that there are variants within the population of the target organism which are not amplified, (b) poor extraction of DNA from the sample material, ie insufficient DNA is extracted or (c) contaminants in the DNA sample that inhibit the amplification. Three laboratory were identified and examined for merit and validity.

Trichogramma limit pest damage to Ord River Irrigation Area (ORIA) cotton crops by killing the developing embryo of their insect host at the egg stage, effectively reducing the number of emergent pests ingesting transgenic tissue. Their impact on the potentially resistant species, Helicoverpa armigera (Hübner), is considered integral to the Insect Resistance Management (IRM) strategy for transgenic cotton production in the ORIA. This thesis examines aspects of Trichogramma ecology pertinent to this strategy.