Australia contributes approximately 12% of the world’s total cotton production, and is the third largest exporter of cotton fibre. Most Australian cotton is cultivated in New South Wales, (70% of the total production), with the remainder cultivated in Queensland, an area that extends from Emerald in Queensland to Hay in New South Wales (Hearn and Fitt, 1992). Australian cotton is generally furrow irrigated with only a small proportion rainfed. There has been a dramatic increase in cotton production in Australia from 45,000 tonnes in 1970s to 600,000 tonnes in 2000s, with an average increase in lint yield of 1.8% per year (Constable, 2004). Despite this enormous improvement in cotton production systems, the cotton yield in Australia remains substantially subject to various abiotic stress factors including drought, heat, waterlogging and cloudy conditions.

Waterlogging is an important factor that adversely affects cotton yield. Australian cotton is cultivated on heavy clay soils with inherently low drainage and a summer dominant rainfall pattern poses significant risk of intermittent waterlogging. In addition, the reproductive phase of cotton, which starts by late December through January, often coincides with heavy summer rains in cotton producing regions. As the reproductive phase of cotton growth is most sensitive to stress-induced damage, exposure to waterlogging at this phase can significantly reduce yield. A degree of damage to cotton is expected if heavy rainfall occurs just after an irrigation event. Heavy lint yield losses have been recorded in Australian cotton under persistent rainfall and cloudy weather during the 2009-2010 and 2010-11 cotton seasons (CRC, 2010-11).

Waterlogging-induced growth and yield reduction are the result of a complex syndrome caused by O2 deficiency in the soil. Soil hypoxia impairs root growth and subsequent water and nutrient uptake. An inhibited supply of nutrients and water influences leaf development, light interception and photosynthetic efficiency leading to growth reduction. In addition, soil waterlogging alters the level of phytohormones in root tissues; specifically it accelerates biosynthesis of 1- aminocyclopropane 1-carboxylic acid (ACC). This ACC is converted into ethylene in the presence of O2 and ACC oxidase in aboveground plant parts (Bradford and Yang, 1980). Elevated ethylene accumulation in cotton tissues can stimulate leaf senescence and fruit abortion (Lipe and Morgan, 1973).

Tolerance to waterlogging in plants is a complex phenomenon that depends on tolerance to by-products of anaerobiosis and elemental/molecular toxicities. Plants exhibit a variety of modifications to survive in O2-deficient environments. Development of aerenchyma is one of the most common responses in many plant species at the anatomical level. Aerenchyma facilitates oxygen diffusion into root tissues (Jackson et al., 2008). Other morphological changes include increased root porosity via development of adventitious root and hypertrophied lenticels, and rapid shoot elongation in some waterlogging-tolerant species. Modifications of water relations, stomatal changes, decreased transpiration and photosynthesis are the physiological adaptive responses in plants. Metabolic adaptations, including energy production via fermentation, metabolic adjustments and anaerobic protein synthesis are also crucial for survival of plants exposed to low O2 concentration.

Absence of any apparent changes in cotton roots in terms of aerenchyma formation (Conaty et al., 2008), as well as the slow rate of energy production through anaerobic respiration, make cotton relatively sensitive to waterlogging. Cotton roots rapidly respond to soil O2 deficiency, showing symptoms of growth inhibition under mildly hypoxic conditions (O2 < 10%) within a short time (Huck, 1970). Inhibited root growth restricts nutrient uptake and interferes with various physiological process, causing overall yield reduction. Yield loss in cotton is directly associated with the duration for which root roots remain under O2 deficient environments. For example, an inundation period of 4 to 16 h (when soil O2 < 10 %) caused a 8% reduction in cotton lint yield, while prolonging inundation time to 32 h increased yield losses to 18% (Hodgson, 1982). Similarly, 27 – 30% yield reduction was recorded in response to 4 to 9 d of waterlogging, respectively (Wu et al., 2012). Despite significant improvements in cotton production systems, limited effort has been made in improving tolerance to waterlogging. Waterlogging tolerance in cotton is a complex trait, which depends on several environmental and physiological factors. Screening and breeding for waterlogging tolerance alone may not be adequate, as the waterlogging-tolerant cultivars identified in one experiment may appear intolerant in other trials. Therefore, understanding the impact of environmental factors and plant adaptation to waterlogging is critical for developing efficient waterlogging tolerance strategies. Physiological and biochemical modifications can provide clues to understanding plant tolerance mechanisms to waterlogging and assist in devising techniques for reducing yield losses under stressful conditions.

Viral diseases of cotton are of economic significance in many parts of the world. Only two virus diseases have been reported from Australian cotton crops, Cotton bunchy top (CBT) and Tobacco streak virus (TSV). However, many of the most economically damaging virus diseases of cotton remain serious biosecurity threats. These include Cotton leaf curl disease (CLCuD), Cotton leaf roll dwarf virus (CLRDV; causing Cotton blue disease) and Cotton leaf crumple virus (CLCrV).

Insect vectors for Cotton leaf curl disease, Cotton leaf crumple and Cotton blue disease are common and widespread in many cotton growing regions of Australia. Surveillance in Australia for viral diseases of cotton will be important to help protect the cotton industry from these serious biosecurity threats. Unusual virus-like symptoms in NSW cotton crops such as tall sterile plants have also been observed by CSIRO staff in several locations. If found, transmissibility studies may be able to determine if the cause is pathogenic.

While significant progress has been made by previous researchers into several aspects of the biology of Cotton bunchy top disease, it is still unclear what natural alternative hosts this pathogen has in and around cotton crops. This information will be important to effectively minimise the risk of this disease entering crops. Results from current CRDC project (DAQ0002) indicate that while TSV appears to be currently restricted to Central Queensland, some of the alternative hosts such as Fleabane and Crownbeard are commonly found in many other cotton growing regions.

Cotton blue disease has caused economic losses in cotton from Brazil and Argentina but little is known about the diversity of the Asian or African strains. There is also currently no expertise in Australia for diagnostics of Cotton blue disease. It is important to identify the diversity of the viruses that cause Cotton blue disease to determine the likely effectiveness of resistance currently available.

Transgenic resistance to viruses has been successfully used in a range of plant species. It is possible that this may be a useful strategy to utilise in cotton as preparedness for an incursion of Cotton leaf curl disease.

A warmer and drier climate has been projected in Australia especially for the inner part of Australia (CSIRO, 2007) which covers the cotton production regions. This change will have significant implications for the sustainable development of the cotton industry, as it is highly sensitive to climate and relies heavily on water for irrigation. To better address the challenges and opportunities of future climate change in the cotton industry, local climate change including changes in the mean climate, climate variability, and resultant water availability needs to be understood, its impacts need to be quantified, and effective and economical adaptation options need to be identified. Given the resilience of cotton production to current climate variability, the context of this existing resilience also needs to be assessed in a changing climate.

Atmospheric C02 and water are fundamental substances for crops to synthesis carbohydrate. Climate is the major driving force of crop production systems. Even though most cotton production in Australia is under irrigated conditions, water is a precious and costly resource for irrigated farming system and dependent on rainfall amount and pattern. Greenhouse gas induced climate change will inevitably impact on cotton production. It has been projected that annual temperature over inland Australian including the cotton production regions will increase l to l .2°C and annual rainfall will decrease 2-5% for the period 2020-2040 (CSIRO, 2007). This will have significant implications for the cotton industry. For example, increase in temperature will increase water use and the frequency of exceeding critical temperature thresholds, which will adversely impact on cotton growth, boll production, fibre quality and resultant farm profitability. A drier environment means less rainfall on average or more frequent and severe droughts placing increased pressure on precious water resources. Even though increased atmospheric CO, concentration have some positive effects on cotton production, these effects are constrained or impacted by high temperature, soil water and nutrient conditions (Bange et al., 2009). For cotton industry to continue to thrive into the future, there is a strategic need to quantify the combined impacts of changes in temperature, rainfall, water availability and atmospheric C02 concentration on cotton production, and to identify and evaluate existing and potential adaptation options in dealing with projected negative impacts and in capitalising the potential growth opportunities of climate change.

Plant Health Australia (PHA) has reviewed and updated the Biosecurity Plan for the Cotton Industry.The cotton industry remains under constant threat from exotic and endemic pests, diseases and weeds. To ensure its future viability and sustainability, it is vital that the Australian cotton industry minimises the risks posed by exotic pests and responds effectively to pest threats. The Biosecurity Plan for the Cotton Industry is a framework to coordinate biosecurity activities and investment for Australia’s cotton industry. It provides a mechanism for industry, governments and stakeholders to better prepare for and respond to, incursions of pests that could have significant impacts on the cotton industry.

The 2013-2018 Cotton Research and Development Corporation (CRDC) Strategic Research and Development Plan therefore has a focus on biosecurity preparedness for the industry. Two key biosecurity strategies identified for the industry include: Respected Stewardship (Cotton crops protected from pest, weed and disease threats); and Successful Crop Protection (Cotton crops protected from pest, weed and disease threats).

A number of the objectives identified by these strategies are achieved by the review of the Biosecurity Plan for the Cotton Industry. These include the investigation of new and emerging cotton pests and diseases, identifying biosecurity capacity, knowledge and preparedness, and by supporting the industry’s ability to effectively respond to biosecurity threats and meet biosecurity obligations.

Through this review of the Biosecurity Plan for the Cotton Industry the following components were delivered:

• Identification and update of all exotic pest threats to the cotton industry, including an analysis of the entry, establishment and spread potentials together with the potential economic impact should the pest become established in Australia.

• Prioritisation of pest threats to the cotton industry to provide direction for the allocation of biosecurity resources within the industry and from governments.

• Identification of key areas for investment within the cotton industry through the “Implementing biosecurity for the Australian cotton industry 2015-2020” section of the Biosecurity Plan.

• Identification of what risk mitigation activities are currently undertaken by the industry and what could be implemented in the future to reduce biosecurity threats to cotton production.

• Identification of what surveillance activities are undertaken and diagnostic capabilities that are available for pests and diseases that could impact on the cotton industry.

• Identification of the established pests and weeds of biosecurity significance to the cotton industry

The Cotton Field Awareness map is an industry initiative which has been designed to highlight the location of cotton fields. Initially implemented in 2012/13, the decision to create this mapping capability annually was agreed would be funded annually for a set period of time by the Sponsors. The original project was CA1304. The service is provided free of charge, with the purpose of minimising off target damage from downwind pesticide and herbicide application, particularly during fallow spraying.

The Cotton Field Awareness map is an industry initiative which has been designed to highlight the location of cotton fields, was first intitiated by the sponsors in 2012/13. The service is provided free of charge, with the purpose of minimising off target damage from downwind pesticide and herbicide application, particularly during fallow spraying.

The AgTech Finder is a direct response to challenges facing the industry relating to barriers to new technology adoption - namely, the ability for agribusinesses to know what is available and understand the essential features and decide whether it meets their specific needs. AgTech Finder will be designed as a sophisticated online application that aims to help Australian producers quickly and confidently match the right digital tools to their needs. Using AgTech Finder, producers will be able to search, sort and compare digital solutions. Ultimately, AgTech Finder will help accelerate digital adoption for the agribusiness sector, assist with digital literacy, and provide a rich data source for future research.

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.