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.

The emergence of multiple resistance to insecticides in Helicoverpa populations has had a significant impact on the production of most major field crops in Australia. This, coupled with industry's increasing awareness of the need to reduce environmental impacts from pesticide use, has led to the demand for effective alternatives to traditional pesticides. Current alternative control options for Helicoverpa available to cotton growers include the use of 'Gemstar', a nucleopolyhedrovirus (NPV) specific to Heliothine species. Gemstar has been widely used in cotton and grains crops throughout growing areas. It is often used in combination with other pesticides and, in Queensland, in repeated and low-rate applications.

This wide-scale and repeated use has led to industry concerns about the potential for emergence of resistance to Gemstar. There have been several examples in other insect species where resistance of between 5 and 800 times normal susceptibility to insect viruses has been generated in the laboratory, although there have been no reports of resistance to baculoviruses in the field. There is, therefore, a need to establish the baseline level of susceptibility against which future resistance can be assessed, to develop some understanding of the mechanisms of resistance to insect viruses, and to develop genetic markers that might lead to rapid identification of resistant populations.

The Australian Cotton Integrated Pest Management grower short course was

conceptualised and developed from a recommendation presented in a commission

report in 1997. This report focused on the adoption of IPM within Australian cotton

industry. The recommendation made from this study identified the need to develop

a package on IPM that could provide practical implementation strategies for

growers. Industry accepted this recommendation and development a “hands on”,

“practical focused”, and ” technical strong” short course. As well as assigning a

designated IPM Coordinator to develop and implement the course.

The IPM grower short course has had a series of coordinators; Mr Greg Kauter, Mr

Bill Dalton and Mr Mark Hickman. Each coordinator established, individual

milestones for the course’s development. Only through the collaborative nature of

the Australian Cotton CRC, and the leadership of Mr Kauter it possible to collate

industry and research documentation regarding IPM. This information focused on

the principles behind IPM management, utilising relevant industry examples of the

modern farming system to establish both grower and industry creditability. Mr

Dalton formulated the short course into a five day course conducted over a cotton

production season. It consisted of a 2 day workshop in winter, 2 field days within

crop and a review meeting post season for reflecting on practice change. This course

format and content achieve a national competency based accreditation mapped to

the unit RUAAG4302CTA at a Certificate IV level. Mr Dalton successful acquired

FarmBi$ funding for the program and was able to conduct in 2001 the 3 industry

pilot programs. Following these successful workshops Mr Hickman held the

position of IPM training coordinator during 2002‐2005. In this period of time Mr

Hickman implemented the pilot suggestions and modified the course to the

emerging transgenic cotton crops. During this time a DVD was commissioned to

NSW Agriculture and overseen by Mr Hickman to capture comments on leading

IPM adopter’s comments within the industry. The DVD is used in the course and

generates strong support from the participants. During the delivery period of this

project Mr Hickman was successful in up grading the level of competency to

Certificate V in agriculture addressing the unit RTE5006A “plan and manage longterm

weed, pest and/or disease control in crops”.

Since 2001, there have been 20 courses completed across 11 of the industries

production valleys. Statistics collected from the course indicated of the total 221

participants that participated (2001 to 2005), shows approximately 70% of

participants are cotton producers, 25 % cotton consultants and 5% industry

representatives. Excluding the 43 participants in 2004‐05 courses, since assessments

had not been completed at the time of compiling this report, indicates 169

participants (2001‐2004) have successful been awarded a statement of attainment

from either Murrumbidgee College of Agriculture or Dalby Agricultural College

relating to the above mentioned qualifications.

In the 2004, a BDA economic analysis of the Australia Cotton CRC stated research

and extension in the area of IPM had an estimated benefit of $315 millions over the

previous 5 year period. This project contributed towards this benefit. Participants

from the course completed a self‐evaluation before the course and at the completion

of the course 6‐9 months after starting. This indicated 72% of participants identified

a practice change in their operation as a result of the course. The main areas of

improvement were identified as increased and improved communication especially

with the consultant. Growers felt they were empowered to enter into dialogue

regarding management decisions suggested by the commercial consultants. Other

growers identified a greater level of importance regarding beneficial insects when

deciding on a management decision. Some growers simply increased the level of

plant monitoring through mapping techniques learnt in the field days to aid in

management decisions.

In conclusion the IPM course has provided two valuable outcomes for the industry.

Firstly, there has been practice change at the farm level. Secondly, the competency based

framework of the course has established a workable model that can be.

The need and motivation for a workshop on modelling water movement in cracking soils arose out of the National Program on Irrigation and Development(NPIRD) Project DAN11,

'Improving water use efficiency by reducing groundwater recharge under irrigated pastures'. The main objectives included identifying problems associated with water movement in cracking soils ( including water balance issues) : identifying key technical and functional weaknesses in modelling approaches: assessing the ability of existing models to underpin water policy and planning decisions and recommendations to improve model capabilities.

The focus of this position is the promotion and adoption of new technologies and best management practices to ensure the industry’s sustainability and continued development. The Cotton Industry Development Officer for the given Valley forms a link between researchers and cotton growers and consultants. Regional grower reference group meetings are held to obtain feedback on what the research and extension priorities are for each region. These are then incorporated into extension programs along with national extension issues to ensure that both industry wide and regional issues are addressed.

This position involves continued support of grower groups. These groups are often used to facilitate other extension activities. The Cotton IDO position has assisted Cotton Australia with the implementation of the Australian cotton industry’s Best Management Practice’s (BMP) program. This has primarily been achieved through the ‘Cotton Tales’ newsletter and grower group meetings where Pesticide Application Management Plans and the new Land and Water module have been promoted. This position also assisted with technical support for the Land and Water module of the BMP program.

The promotion of IPM is also a core component of the Cotton IDO position. This has involved promotion of the IPM short course, monitoring of Trichogramma species parasitism levels which could influence pest management decisions. Demonstrations of attract and kill technology were also carried out with grower groups as another tool to be used in IPM programs.

This project aimed to minimise the adverse impact of glyphosate-resistant weeds on the cotton industry by assessing the prospect that genetic diversity of targeted weed species can be used to predict which species are at highest risk of glyphosate resistance. Through this project, the industry has been able to develop bioinformatics and next generation sequencing skills, which was a capacity gap in understanding herbicide resistance.

Resistance to herbicides can happen by changes to the target gene (target site resistance) or other genetic changes (non-target site resistance, NTSR). Non-Target site resistance is particularly difficult to decipher as it is usually polygenic and can be constitutive, stress-induced, or possibly both. Cross resistance between different herbicide groups is not possible with target site resistance; however, since NTSR is the result of both regulatory processes (signal production, reception, and response) and protective processes of several kinds, they have the potential to interact together and accumulate, and possibly provide resistance across herbicide groups.

This project examined four weed species from cotton growing regions. The only species investigated that had a fixed target site mutation is Feathertop Rhodes grass. Fleabane, barnyard grass and windmill grass all have glyphosate resistance by NTSR mechanisms.

Gene expression analysis was conducted to test for genes that are more highly produced or supressed in resistant barnyard grass and fleabane to explore NTSR mechanisms in these two species. In barnyard grass about 50 genes are differentially expressed in intermediate resistant lines, whereas about 300 are in strong resistant lines. This indicates that NTSR is a polygenic trait in this weed.

In fleabane only five genes were differentially expressed in the resistant lines, and these genes are involved in plant signalling pathways and transporter proteins. It is therefore likely that NTSR in fleabane is controlled by relatively few genes and involves the transport of glyphosate within the plant.

The genomic data generated during this project (UQ1301) will be leveraged in project UQ1501 to

establish the mechanisms of NTSR in cotton-system weeds so that the threat of cross resistance can be assessed as the industry moves to stacked herbicide resistance traits.