Plants may look simple and defenceless, however on-going genetic research is revealing a complex system that detects harmful organisms and triggers a battery of plant defence responses. We are studying this process of recognition and response in the cotton plant, with the aim of developing molecular tools to ensure that broadly based and effective disease resistance is incorporated into commercial cotton cultivars.

Micro-organisms can be identified by the size or sequence of a portion of their DNA, and this information can suggest if they are likely to cause disease. Molecular plant pathology could revolutionise disease diagnosis in cotton crops by enabling fast and accurate identification of harmful fungi before severe disease symptoms develop

Bacterial blight of cotton is caused by the bacterium Xanthamonas campestris pv. malvacearum (Xcm). This infection attacks leaves and bolls and causes early leaf drop and affects boll development and normal boll opening. In Australia the CSRO breeding program has developed varieties that are resistant to Xcm infection. The use of these resistant cultivars has meant that the importance of this disease has been reduced. The resistance locus was introduced into the breeding program from the USA in the 1970's; however, the identity of the resistance gene or genes has not been fully clarified. G. barbadense or Pmia varieties are susceptible to Xcm, and a breeding program is in place aimed at introgressing Xcm resistance into the Pima cottons from G. hirsutum. Further work is needed to characterise the source of the resistance, and possibly to develop molecular markers linked to the resistance locus in order to assist with breeding efforts. In order to map this resistance locus a mapping population was set up using backcrosses between the resistant G. hirsutum variety CSSO and the susceptible G. barbadense variety Pima S-7.

The resistance of commercial cultivars of cotton to bacterial blight, caused by Xanthomonas campestris pv. malvacearum, in, is due to the interaction of resistance gene products in cotton and avirulence gene products in the pathogen. This interaction triggers a hypersensitive response at the site of infection that leads to localised cell death and hence containment of the pathogen. Associated with the localised hypersensitive response is a more generalised induced resistance that can be detected elsewhere in the plant. This induced resistance can be effective against a range of other pathogens. We are conducting experiments to determine if it is possible to utilise the interaction of bacterial avirulence genes expressed in transgenic plants already containing blight resistance genes to trigger defence responses including generalised induced resistance.

Fusarium wilt of cotton has emerged as a major threat to cotton production, since it was first recorded in Australia in 1993. Control of Fusarium wilt depends on understanding genetic diversity within the fungus that causes the disease, Fusarium oxysporum f.sp vasinfectum (Fov). We have analysed genetic diversity within Fov by DNA amplification fingerprinting (DAF), and restriction fragment length polymorphism (RFLP) and sequence analysis of the intergenic spacer (IGS) region of the ribosomal (r) DNA. The Australian isolates of Fov were compared to overseas isolates that represented races I, 2, 3, 4, 5, 7, 8 and A of the pathogen, and also to other formae speciales of F. oxysporum and species of Fusarium. We have identified two distinct genotypes amongst the Australian isolates of Fov that correspond with vegetative compatibility groups (VCGs) 01111 and 01112. We are using the information we have obtained on genetic diversity among Australian isolates of Fov to develop a polymerase chain reaction (PCR)-based DNA diagnostic system for the rapid detection of Fov directly from infected plants and seed, and infested soil. This diagnostic test will be an invaluable tool for the cotton industry, as early detection of Fusarium wilt is critical to the containment and control of the disease

A plant disease is an interaction between a plant host, a pathogen and the environment. Most plants are immune or completely resistant to almost all plant pathogens. When a virulent pathogen is dispersed onto a susceptible host and the environmental conditions are suitable then a plant disease develops and symptoms become evident. Disease control strategies must therefore focus on the host, the pathogen and/or the environment. 'Integrated Disease Management' involves the selection and application of a harmonious range of control strategies that minimise losses and maximise returns.

A field experiment comparing irrigation treatments of 100% of predicted ETCrop applied with subsurface drip irrigation with 50%, 75% and 125% ETCrop was conducted at Warren in the 1999/2000 season. Cotton yield of 7.8 bales/ha was greatest in the 100% treatment followed by the 75% and 125% treatments with lowest yield coming from the 50% treatments. This yield trend, combined with similar soil moisture contents in the 100% and 125% treatments indicated that the 100% treatment was supplying adequate water to satisfy crop demand. Neutron probe readings showed that treatments receiving insufficient water to satisfy crop demand were able to extract water from part of the soil profile that was not wet by irrigation. Use of this water allowed the 50% and 75% treatments to grow at similar rates to the 100% and 125% treatments for I month in peak growing conditions after the soil was saturated by rain moisture in late December.

An understanding of likely impact of water stresses on yield and quality is important for developing optimum irrigation practices for cotton in the region. Irrigationg a crop for 12 h to 24 h depending upon the bed length (between 200 in and 500 m) is a common practice in the valley (Wood et al 1998). This practice of extended duration of irrigation is commonly associated with shallow rooted crops on 1.8 m wide beds. This might contribute to water logging stress in dins cracking clay son as Hearn and Constable (1984) and Hodgson and Chan (1982) reported inadequate soil aeration for cotton in a clay soil after furrow irrigation. Furthermore, a rapid onset of water deficit stress, particularly in the top 30 cm soil profile which dries out within 5 to 10 days of watering has also been observed due to a hot and dry conditions in the Ord (Muchow and Keating, 1998). The aim of his study was to compare the relative magnitude of water logging and water deficit stresses on plant water status and yield between wide and ridge beds for a range of irrigation management systems Gravimetric and volumetric soil water contents and air-filled porosity were measured to a depth of 1.2 my before and 48 h after irrigation.

The theme of the conference is "Meeting the Challenge". Amongst the many challenges the cotton industry faces are a host that relate to water. Uppermost in most people's minds are probably the increasing restrictions on access to irrigation water resulting from the COAG reform process. However, I am not addressing the reform process itself, which is economic and political, but the technical challenges that led up to it, or follow from it.

Water is one of the key resources for industry and economic development in Australia. It is one of the main inputs to maximise the production of the cotton plant. Due to the rising pressures on the use and allocation of the national water resource (and in particular the Murray Darling Basin) "water use efficiency" has gained an ever increasing profile. The term typically means different things to different people. If one thing were common however it would be to maximise the opportunities for benefit from the water through optimal management of that water.