The importance of research and development to the Australian cotton industry is unquestionable. History details the achievements such as plant breeding that have contributed to significant improvements in cotton yield and quality. Worldwide recognition exists for much of the research including the management of chemical resistance in heliothis. Thirst for the latest research results and technology drives the industry extension efforts at an increasing pace. One can only contrast the success of the Australian cotton industry with the failures of those countries that do not have strong R&D programs. As growers we have become accustomed to researchers providing the basis for solutions to whatever challenges we have experienced. But there is no room for complacency. The question now is how can we maintain the efficacy of our R&D efforts to meet the challenges created by the increasing complexity of crop management, community and environmental scrutiny.

Plants can utilise an array of biochemical mechanisms to protect themselves against viral, bacterial, fungal and nematode pathogens. Systemic induced resistance can be achieved by using an activator, either an organism or a chemical, at the early stage of a crop. The activator 'switches on' the host plant's defence mechanisms. There are few reports of induced resistance against soil born and vascular pathogens. A significant reduction in the severity verticillium wilt in cotton disease was observed under field conditions after the use of isonicotinic acid (Colson-Hanks and Devera11, 2000). Application of the Novartis product Bion 50WG (a. I. bellzothiadiazole 50%) to grapevines resulted in a reduced the incidence of root knot nematodes. The rate of maturity of nematodes and egg production appearing to reduced (Owen et al 1999). Colonisation of roots by mycorrhizal fungi (VAM) may also induce systemic resistance in plants and protect them from pathogens (Dassi et al 1998). Rotation with non-host crops (eg. cereals) does not prevent the build-up of spores of T basicola in the soil with each cotton crop (see paper by Nehl et al this proceedings). Rotation with susceptible hosts, such as certain legumes, may add to the build-up of spores in cotton fields. Hence, the increasing interest in rotation with legumes presents a challenge to management of black root rot in cotton farming systems. In this paper we examine the potential for induced resistance to decrease the severity of black root rot in both cotton and legumes.

Irrigation in the Australian cotton industry has traditionally been dominated by the use of furrow irrigation practiced almost exclusively on the heavy clay soils associated with riverine flood plains. However, increasing pressures on water availability, expansion onto more marginal soils, the potential yield benefits of improved control of soil-water in the root zone, and the potential for reduced labour, fertiliser and pesticide costs have raised grower interest in alternative irrigation application techniques. In order to make informed investment decisions regarding irrigation application systems, it is necessary to understand the characteristics and performance of both the existing and alternative systems available. This paper draws on the results of recent studies looking at the in-field irrigation performance of furrow irrigation, large mobile irrigation machines (LMIM's) and subsurface drip irrigation (SDl) within the cotton industry. However, in discussing alternative irrigation options, it is important to realise that no single application system and management practice will be appropriate for all growers in all environments. As with most things in life, one size does not fit all! Hence, it is important to understand the nature of the alternatives and the factors which influence the performance, operation and management of each option

Black root rot is an intractable soil borne disease that threatens the sustainability of Australian cotton fanning. In this paper we describe the factors contributing to the spread of black root rot, the effects of black root rot on the maturity and yield of cotton, and prospects for its management and control. Black root rot was first observed in Australian cotton in 1989 (Allen, 1990). Annual disease surveys have shown an exponential increase in the number of fields with black root rot in NSW (Figure I) and the disease now occurs in all cotton glowing regions of NSW except Menindee. Black root rot is also widespread in south west Queensland and the Darling Downs (J. Kochman, personal communication). All understanding of the life cycle of the pathogen, Thielaviopsis basicola (Figure 2), is a key factor in explaining the increasing spread and severity of black root rot. T basicola is a soil borne fungus that produces two types of spores; thick walled chlamydospores and thin-walled endospores (Figure 2). Both spore types can cause disease. The spores of T basicola are primarily soil borne but may also occur internally with stem rot (Figure 2). Consequently, most spread of T basicola is by movement of soil, carried either in moving water or on vehicles and machinery.

Limited genetic variation in cotton has presented a significant challenge for the isolation of DNA markers linked with valuable traits such as resistance to Verticillium wilt and Fusarium wilt. Nevertheless, effective new techniques are now yielding DNA markers that can be used by cotton breeders to select for disease-resistant varieties in the absence of the pathogens.

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