This project supported the training and development of auditors for myBMP, the refinement of the myBMP auditing framework, and rationalisation and clarification of practices to be audited. myBMP audits are undertaken on farm and farms are audited every five years to remain compliant. Seventy two farms are myBMP accredited an increase from 5 at project inception with 20 farms participating in the Better Cotton Initiative. Currently demand for myBMP accredited bales and BCI cotton is increasing and is providing momentum to the myBMP accreditation program. This is being further supported by Monsanto through a system to support the cost of an audit. The number of myBMP bales produced and shipped has increased significantly over the last few years rising from 15,000 bales in 2013 to 65,000 bales in 2015.

A major issue facing the cotton industry in Australia is the potential for surface and groundwater contamination from the inefficient application of nitrogenous fertilisers. This dissertation appraises the merits of applying site-specific nitrogen management to irrigated cotton in Australia, as this system has been hypothesised as being economically and environmentally more sustainable than the traditional 'blanket' approach to the application of crop production inputs. Site-specific crop management (SSCM) utilising new technologies such as Global Positioning System (GPS), yield monitors, orbital-satellites and variable-rate crop applicators to identify within-field crop and soil variability as well as their causes. The rational behind SSCM is 'by identifying within-field variability in crop and soil attributes and their origin', it then becomes possible to optimise crop production inputs such as pesticides and fertilisers on a point- by-point basis. Implicitly, this lowers the potential for their over- and under-application.

Cotton fibres are the fastest growing and among the longest single cells in the plant kingdom. In the space of about16 days, these single cells can expand from a few micrometers to 3 cm in length. When the fibres stop growing they then thicken with cellulose, becoming over 90% cellulose by the end of maturation. As long fibres are important for cotton fibre quality, we set out to study cotton fibre elongation using biochemistry and molecular genetics. We identified several potential gene targets for improving this process of elongation. We have shown that 2 key processes are important in controlling fibre growth. 1. Sucrose metabolism in the fibre and 2. Solute transport into the fibre. Using transgenic cotton we have shown that early in fibre growth, an enzyme of sucrose metabolism (sucrose synthase; SuSy) limits fibre elongation. Also, in fuzz fibre, SuSy activity is low and delayed. Later in elongation, the movement of solutes into the fibre control fibre elongation. The fibre must inflate analogous to a filling balloon. We have shown that solute (sucrose and potassium) transporters play a key role in this process and that the pores (plasmodesmata or PD) between the fibre and the seed coat must close to allow the fibre to inflate with solutes pumped into the cell and expand to full length. Importantly, we have shown that in short fibre cultivars and in fuzz fibres, the timing of this process of PD closure is not optimal. The longer the period of PD closure, the more the fibre expands. We have identified candidate genes which could be manipulated to improve fibre length through the control of this process. We have also demonstrated that during cell wall thickening the enzyme SuSy also plays a key role in supplying sugars for cellulose biosynthesis and that a small decrease in the level of this enzyme has a large negative effect on fibre cellulose content. We have produced transgenic cotton plants with increased seed SuSy and will analyse fibre properties in these plants. We hope to use the genes we have identified to produce cultivars with longer fibres and more consistent cellulose content.

The Cotton Research & Development Corporation’s 5 year Strategic R&D Plan commenced in 2013, setting out the key priority areas for R&D investment.

sought

• a framework by which to measure their success against this plan

• a set of metrics of what to measure, when to measure it and how to measure it in order to track achievements and impact of the CRDC Strategic Plan.

• mapping of existing data sources

• recommendations for future data collection and collation

• a benchmark of Cotton Industry practices and situation in 2013.

There is a need to clearly identify what metrics are core to monitoring impact of the 2013-­‐18 CRDC Strategic Plan and to identify the necessary sources and frequency of data to report against these requirements. This process will identify how existing and historical information sets can contribute to measuring success of the CRDC 2013-­‐18 plan, which of these need to continue to be gathered and what gaps need to be filled.

A 6 step methodology is proposed.

1. Develop a framework for monitoring achievements of the CRDC 5 year strategic plan This framework is to provide a clear process to map investments, activities, outputs and achievements. Linkages will be drawn from Clarity where possible. A relatively simple program logic framework is proposed to identify Inputs (investments), Activities, Outcomes of projects and Outcomes for industry.

2. Review strategic requirements for monitoring

a. Review strategic plans of CRDC to distill core objectives and potential measures (immediate priority)

b. Review other relevant plans and processes underway in the global cotton industry and in Australia (eg CottonInfo AOP, SEEP, BCI, CottonLeads, Sustainable Australia, etc) [this will be done through Guy’s new project]

We will participate in a meeting with ABARE and CRDC in December.

3. Distill a set of core metrics

to measure success of the CRDC plan whilst being cognizant of other initiatives. This will be done iteratively with Step 4 to enable alignment of core metrics with historical data sets where relevant.

4. Map existing data sources and identify ongoing needs and gaps

Recent and historical data sets (surveys, research projects, national data) will be reviewed to map out which data can be used in relation to the core metrics.

Past survey questions / research processes will be mapped against core metrics. Future questions / research will be proposed with the desired frequency of monitoring identified. This is proposed to be presented as a timeline of historical information and a 5 year timeline for gathering new information.

Economist review – during this stage it is proposed to contract an economist experienced in Cost Benefit Analysis of agricultural research programs to review the proposed metrics for their suitability for economic assessment.

5. Prepare a benchmark snapshot of the cotton industry in 2013

Report on the state of the cotton industry in 2013 in relation to practices and condition based on existing data and information. Drawing on current and historical information this report will present current situation and trends.

6. Recommend a framework and process for benchmarking and gathering future data.

To include: specification of the data needs, sources, frequency and mode of collection.

Centre Pivot and Lateral Move (CF&LM) irrigation machines are gaining popularity within

the Australian cotton industry, as they can provide high application efficiency and

uniformity, low labour requirements, improved crop management flexibility, and fertigation

and chemigation potential. Growers and consultants who have not yet had experience with

these machines can be daunted by the choice and design considerations available whilst those

individuals using CP&LM machines often struggle with the increased level of management

required over their previous furrow irrigation operations.

This project has developed a number of extension, adoption and training tools to allow end

users to increase their understanding of CF&LM machines. These tools form a resource of

information that can be readily accessed as stand alone materials or delivered in a structured

manner.

The information resource developed consists of a number of articles and case studies to

provide opportunities for awareness raising and increasing adoption. In addition, a significant

training package has been developed that can be delivered to growers, consultants or

extension personnel to increase their understanding of the design and management

considerations and practicalities involved with CP&LM machines. Finally, chapters have

been contributed to the WaterPak manual and provide a readily accessible reference source

for information as required.

Much of this information has been developed including practical tips obtained from a series

of interviews of seven leading and innovative CP&LM users to incorporate the experience

that these practitioners have gained.

Fusarium wilt disease has the potential to cause significant yield losses and the removal of some areas from cotton production. It is therefore likely to impact on the long-term sustainability of the cotton industry. Conventional breeding techniques have made some progress towards generating resistance to Fusarium wilt in the cotton plant, but breeding efforts would be enhanced by knowledge of the factors that contribute to resistance. In addition, knowledge of the factors controlling the pathogenicity of the pathogen could provide the basis for the development of novel techniques that allow minimisation of the impact of the disease.

Resistance to the wilt pathogens is complex and probably controlled by many genes. This makes the task of breeding for resistance complex and difficult. In order to determine suitable approaches for improving cotton’s resistance by breeding or by the use of genetic engineering, we need an improved understanding of the existing plant responses that are effective at giving some resistance to Fusarium wilt. Identification of the genes deployed by cotton during infection by the Fusarium wilt pathogen, particularly those associated with the response of more resistant species or cultivars, could indicate new targets for effective breeding or for manipulation by genetic engineering. In this project, we aimed to develop tools for the large-scale study of gene expression in cotton and Fusarium, and to apply these tools to investigate gene expression in the host and the pathogen during the infection process.

During the course of this project, we developed effective microarray and model infection systems for the analysis of gene expression in Fusarium-infected cotton. This is a resource of potential use to the cotton industry in the identification of potential targets for generation of improved resistance to Fusarium wilt.

The most striking observation made during analysis of gene expression patterns was that in infected seedlings, gene expression changes in roots and hypocotyls appear to be different.

We found that repression of gene expression, particularly repression of genes for water-regulating proteins, such as aquaporins, was consistently observed in roots and hypocotyls. This repression appears to be associated with susceptibility. This identifies aquaporins as potentially important in the development of wilt symptoms.

In the Fusarium wilt pathogen, expression of a homologue of the AtsC gene from Agrobacterium may be important for pathogenicity, and expression of the retrotransposon foxy may provide a mechanism for rapid adaptation, and hence pathogenicity evolution, in Fusarium populations.

Fusarium wilt, caused by Fusarium oxysporum f. sp. vasinfectum (Fov), is a serious disease

of cotton in Australia responsible for substantial yield reductions. Since its detection on the

Darling Downs in 1993, Fov has spread to all major eastern cotton growing districts except

the lower Namoi. The significant crop losses that have already occurred and the increasing

incidence and severity of Fusarium wilt make Fusarium wilt the most significant challenge

to long term sustainable cotton production in Australia.

Improved farm management strategies can reduce yield losses and disease spread, but

developing resistant cultivars is by far the most effective long-term means of combating

fungal diseases of agricultural plants. Australian cotton breeders have significantly

improved the Fusarium wilt resistance of their cultivars, and new selections with even

greater resistance are nearing commercial release. Despite the admirable progress that has

been made, however, the current assessment is that new sources of Fusarium wilt resistance

are needed.

With the realization that the best the G. hirsutum gene pool has to offer may not be good

enough, We have looked to related Australian Gossypium species for novel sources of

Fusarium wilt resistance, identifying one possible source of Fusarium wilt resistance in G.

sturtianum. Although some of the G. sturtianum accessions tested are susceptible to fusarium

wilt, many of the accessions are more resistant to fusarium wilt than the industry standards,

and this resistance is expressed in the G. hirsutum background. Genetic analysis of G.

hirsutum x G. sturtianum hybrids, however, suggests transferring the G. sturtianum genes to

G. hirsutum will be difficult. Nonetheless, breeding lines are currently in the Fusarium field

nurseries and this selection process will continue.

The other important outcome of this project was the development of new experimental

populations and molecular markers that will, in ongoing research, provide a much better

understanding the genetic control of fusarium wilt resistance in cotton. Under this grant,

five chromosomes of the G. sturtianum genome have been identified as carrying genes that

may contribute fusarium wilt resistance. The experimental populations and molecular

markers will contribute to a more explicit genetic understanding of Fusarium wilt resistance

that will facilitate our ability to effectively transfer genes from G. sturtianum as well as other

novel resistance sources. With the apparent lack of immunity in the G. hirsutum gene pool,

these novel germplasm resources will become increasingly important to cotton breeders.

The development of IPM systems in cotton hinges on the availability of information on a wide range of issues. Included among these is the response of plants to pest damage, the impact of specific pests on yield and the effects of insecticides on pests and beneficials. Each of these factors has the potential; to influence when and with what a crop is sprayed with and hence to strongly influence the costs associated with insecticide use, the conservation of beneficial insects, resistance selection against pest species and environmental pollution. This research project has focussed on (1) plant responses to early season damage with emphasis on interactions with agronomic factors that may influence the degree to which plants compensate (2) the effect of aphids on cotton yield and initial studies of their ecology and (3) the effect of insecticides on target and non-target species, with particular emphasis on beneficial species so that growers and consultants have more information on which to base insecticide choice decisions.

This project has led to a significant advance in our understanding of the feeding behaviour of the adult heliothis moth. It has used detailed studies in ecology and behaviour of H. armigera to examine novel control strategies based around luring and killing adult moths. Our results will assist the design of more effective lures through consideration of important behavioural effects and odour preferences. We designed and executed a series of detailed experiments using odour lures and extended these experiments to allow moths to forage freely on flowers; testing their preferences for odours. Our results demonstrated odour learning on a number of levels, and provided evidence that flower visiting history influences attraction to odours. In addition to this we discovered that the enantiomeric forms of odour compounds may differ in their attractiveness to adult female moths, a finding that may improve the selection of synthetic odours for lures. Our results have been submitted as 3 key papers to international scientific journals.

We show that the location of feeding sites for adult moths influences the distribution of heliothis eggs. Our results imply that adult feeding sites have the potential to draw in adult moths to feed and that moths may then lay on nearby cotton plants. In addition, we show that male and female adult H. armigera moths may have differences in nectar feeding preferences. Our findings help elucidate why certain crops may be more attractive than others and why certain stages of the plant life cycle receive more heliothis eggs than others.

We have collected data on nectar foraging moths, which suggests that virgin female and male moths may be flying specifically to certain crops to feed. Specifically, we have shown that pigeonpea (Cajanus cajan), used as a refuge and trap crop, is highly attractive as a host for feeding adult moths. We have backed field studies with controlled experiments carried out in outdoor flight cages. Our findings could be utilised to improve control methods and also cautions the use of some crops as refuges and trap crops, in that they may extend the lifespan and fecundity of this pest species.

In conclusion this work has contributed to the design of new heliothis control strategies, providing information that will help the improvement of lure and kill, trap cropping, refuge cropping and population monitoring strategies and the future production of new varieties of cotton with lower attractiveness to moths. It will benefit the Australian cotton industry and the Australian community by aiding the design and development of new economic and environmentally friendly methods of insect pest control.

INGARD® Cotton varieties express Bt toxin in all plant parts except for the flowers. Because Helicoverpa moths frequently target flower buds and flowers as oviposition sites, a proportion of their neonate larvae may establish themselves on or in the flowers in a Bt-free location on the cotton plant. This may allow them to develop to a size at which they are more tolerant of Bt toxin on other plant parts. Such larvae may subsequently be capable of damaging fruiting structures and other plant parts before they are affected by the Bt toxin.

Honey bees are known to visit cotton flowers, and this project set out to determine whether they may provide an efficient means of depositing HNPV (Heliothis nuclear polyhedrosis virus) propagules directly into cotton flowers, and thereby help to eliminate an otherwise safe haven on INGARD® plants. Honey bee hives can be readily modified to disseminate virus or other microbial biocontrol agents, and the hives are easily transported to required areas. Honey bees from such hives have been shown to successfully act as vectors of HNPV against Helicoverpa zea on Crimson Clover Flowers (Gross et al. 1994), and as vectors of Bt for control of Banded Sunflower Moth on Sunflowers (Jyoti and Brewer 1999). Results from both these studies were impressive. For example mortality of H.zea larvae, when fed crimson clover flowers that had been visited by bees, increased from 12% in Control fields to over 80% in fields treated with HNPV (Gross et al. 1994).