Organic matter in soil can supply more than 50% of the nitrogen (N) to cotton crops, but this pool of N supply is dynamic and difficult to predict. Soil bacteria are responsible for mineralising soil organic N and hydrolysing dissolved urea to ammonium. Most plants can take up both ammonium and nitrate forms. However, nitrate is susceptible to leaching and can be denitrified into inert and greenhouse gases. Filterable organic N (dissolved organic nitrogen, DON) is the most readily available form for microbial mineralisation and can also leach. The type and timing of N fertiliser and irrigation may regulate N supply and loss, as the severity of soil drying between irrigation events regulates microbial activity. The ‘Optimising nitrogen and water interactions in cotton’ project investigated how ammonium, nitrate and organic N in soil is affected by urea and DMPP-treated urea fertilisers during wetting and drying cycles of irrigated cotton. DMPP urea is an enhanced efficiency fertiliser that slows the conversion of ammonium to nitrate in soils.

The main objectives of this research were to: (1) investigate how N fertiliser formulations; namely: urea and DMPP-treated urea, and wet/dry cycles affect within- season patterns of soil N supply, (2) identify how well a rapid soil test based on water extraction and measurement of dissolved organic N or potassium chloride-extractable inorganic N species can inform predictions of soil mineralisable N, and (3) suggest how currently available nutrient management DSSs can be improved by improved knowledge of within-season patterns of soil N supply.

The research was conducted in soils established to overhead irrigated cotton on commercial farms over the 2016/17 and 2017/18 seasons in the Darling Downs of south-east Queensland. Soil was sampled after key irrigation or rainfall events, and at critical cotton growth stages. Soil was sampled from outside and inside root exclusion tubes that were placed in the soil to a depth of 300 mm at the beginning of each season,

to monitor the plant-available pools of soil and fertiliser N in the presence and absence of roots, respectively. Novel, low-cost, rapid methods were used to measure nitrate, ammonium and total dissolved N (mineral N and DON). The results were compared with conventional N testing methods for their ability to predict crop N availability.

This project aimed to enhance and support the sustainability of the Australian cotton industry by: providing continued capacity in plant virology expertise and diagnostics, building industry awareness of viral disease threats, and developing preparedness for viral diseases that pose serious biosecurity threats to the Australian cotton industry.

Disease surveys targeting viruses in northern Australia were done over 4 years in areas that may be exposed to possible incursion pathways for biosecurity threats and also in emerging cotton production regions in far northern Western Australia and Queensland. No viruses were detected in cotton production areas of Kununurra and northern QLD. However, six different polerovirus species were detected in other hosts. None of the newly detected poleroviruses are likely to affect cotton but it does indicate there is a diverse range of poleroviruses in northern Australia and emerging cotton production regions may be exposed to new virus threats.

Disease surveys were also done in commercial cotton in Queensland. From 158 disease counts from 35 farms, no symptoms typical of exotic viruses were seen. Generally, there was very low incidence of virus-like symptoms for endemic viruses (Cotton bunchy top virus – CBTV and Tobacco streak virus - TSV) in cotton crops inspected with the exception of a few sporadic disease outbreaks of CBTV. Old volunteer or ratoon cotton appears to be the major source of infection for CBTV moving into crops and as such it is recommended to maintain effective crop hygiene to break the infection cycle and reduce the risk of virus disease outbreaks.

This project has confirmed that two distinct polerovirus species infect cotton in Australia, CBTV-1 and CBTV-2. We found that CBTV-2 is always associated with disease symptoms in cotton while CBTV-1 is not. All symptomatic plants were infected with CBTV-2, either with or without CBTV-1. This will help to focus any future work on the control of CBTV-2 which is likely the only causal agent for disease while it appears that CBTV-1 is most likely non-symptomatic in cotton and of little concern.

Three virus surveys were done in Timor-Leste (East Timor) with the primary focus to establish how common Cotton leafroll dwarf virus (CLRDV) is and what potential threat there may be for incursion into Australia. Gossypium samples were collected from across much of the country and CLRDV was detected from more than 30% of plants tested from several sites. Hence, CLRDV in Timor-Leste was found to be relatively common and widespread in three Gossypium species (G. arboreum, G. barbadense and G. hirsutum). Improved diagnostics developed for CLRDV strains from Timor-Leste, Thailand and other countries will support preparedness for this biosecurity threat.

Other new poleroviruses were also found in Timor-Leste and northern Australia, suggesting there may be natural movement of virus-infected aphids in wind currents from Timor-Leste. This example of potential virus movement may be of concern for the expansion of cotton production in northern Australia.

Host plant resistance has long been a focus of the CSIRO cotton breeding program with emphasis on both morphological (okra leaf, frego bract) and biochemical factors (high gossypol) for resistance to insects. Some of this work was reported at the last cotton conference (Fitt et at 1994). Conventional breeding for pest resistance makes small incremental improvements in the tolerance of varieties to insect feeding and damage. With the advent of genetically engineered cotton the stage is set for quantum leaps in pest resistance, through the introduction of the INGARD Bt gene. However, this does not mean conventional approaches are no longer useful. Ally change to the plant to make it less attractive to pests or more tolerant to damage will only enhance the value of genetically engineered traits by providing a stronger, more stable basis on which to manage those genes. We have continued our work on conventional pest resistance, though now with the added aim of screening breeding lines and other genotypes for resistance to sucking pests like minds, in addition to Helicoverpa and mites. With increasing concern about the possible emergence of Bemisia tabaci Type B (silverleaf whitefly) as a major pest of cotton following its recent introduction to Australia we have also taken the opportunity to evaluate genotypes against whitefly and aphids. This opportunity arose when the unsprayed plots at one of our study sites (Plant Breeding institute, Narrabri) became quite heavily infested with these pests during the 1995/96 season. Here we report the results of these evaluations for the 36 cotton genotypes grown at the PBl site

Achieving reliable, even crop establishment has been identified through the Dryland Cotton Research Association (DCRA) project meetings as one of the major concerns dryland cotton growers face. This issue has gained significant importance with the current commercial varieties available which typically have poorer seed vigour than their predecessors due to the small seed size. Planting, particularly in marginal moisture conditions, is therefore a crucial process in dryland cotton production.

There are various manufacturers producing cotton planters incorporating a range of styles from older style tine planters to single and double disc planters. The goal behind this construction project was to mount different styles of commercial cotton planting units onto a single bar so that the establishment achieved could be compared between units while planting into exactly the same conditions at the same time over a range of soil types and moisture levels.

To demonstrate the influence of the diesel engine’s speed over the energy consumption and performance of large lateral move (LM) irrigation machines, 10 field tests were conducted on four LMs on the Darling Downs of South East Queensland. A key objective of the research was to identify if a relationship existed between the performance (uniformity) and energy consumption of the machines, allowing an optimum point to be established.

The main findings of the field testing and analysis were: 1) in general, the emitter discharges were found to decrease with increasing distance from the supply pump; 2) the uniformity was found to decrease in all cases when the engine speed decreased the total flow rate below that of the design; 3) the energy consumption increased with each increase in engine speed; 4) the energy consumed per ML of water pumped, and hence energy cost per year, increased significantly with each increase in engine speed; and

5) a relationship was found to exist for two of three LMs whereby the highest uniformity was achieved at engine speeds that put the pump operating point closest to that of the design.

This project funded bronze sponsorship of the Science Protecting Plant Health 2017. With delegates from around the world, severalfrom Australasia, Science Protecting Plant Health 2017 offered an unparalleled opportunity to showcase CRDC's research, products and services to key players and decision-makers on the world stage. Conference themes focused on the latest science, research and practice from leaders in their fields.

This international event displayed the latest research on plant biosecurity and pathology

science and practice from leaders in their fields and included a strong plant pathology stream as

it incorporated the 21st Australasian Plant Pathology Society conference.

Plant health is an issue of priority and concern to government, agricultural industries and

environmental organisations globally. As international trade in agricultural products grows,

the changing threats of plant pests and diseases mean that meaningful scientific exchange

among researchers and industry is vital to address new challenges to plant health and crop

protection.

The overall objective to provide a high quality scientific conference for plant health

researchers and stakeholders to:

» Learn, workshop, network and exchange knowledge on agricultural and

environmental biosecurity and plant pathology

» Facilitate engagement and exchange of ideas between researchers and the endusers

of their research, such as industry and regulators

» Provide a unique opportunity to showcase the diversity of science, innovation and

new technologies and knowledge that is protecting plant health around the world

» Build cross-disciplinary networks across all biosecurity and plant pathology

related disciplines

» Help Australia, partner organisations and sponsors, as world leaders in

plant pathology, agricultural and environmental biosecurity research and

management to support and stimulate collaboration, innovation and

networksew technologies and knowledge that is protecting plant health around the world

» Build cross-disciplinary networks across all biosecurity and plant pathology

related disciplines

» Help Australia, partner organisations and sponsors, as world leaders in

plant pathology, agricultural and environmental biosecurity research and

management to support and stimulate collaboration, innovation and

networks

Fusarium oxysporum f.sp vasinfectum (FOV) has merged as a very serious pathogen of cotton, which apparently lacks good sources of endogenous resistance to Fusarium wilt. In contrast, there are several well defined genes in tomato for resistance to the related pathogen Fusarium oxysporum f.sp lycopersici (FOL) and tomato has the best characterised system of plant interaction with Fusarium. The tomato I-2 gene for resistance to FOL has been cloned and found to encode a coiled-coil-nucleotide-binding site- leucine-rich repeat(CC-NBS_LRR) protein similar to proteins encoded by a number of resistance genes to various plant pathogens in various plant species.

Under previous CRDC funding, we engineered the I-2 gene to allow its expression/over expression under the control of a strong constitutive promoter (the 35S from cauliflower mosaic virus) and, in collaboration with CSIRO Plant Industry, attempted to produce 35S:I-2 transgenic cotton. However, we were unable to generate transgenic cotton lines containing 35:SI-2. We interpreted this result to indicate that over expression and/or inappropriate temporal or spatial expressions of the I-2 protein caused inappropriate activation of cotton defence mechanisms leading to cell death. Interestingly, this finding is consistent with the expression of some disease resistance genes in different plant species eg. the flax L6 resistance gene expressed in tobacco causes the constitutive activation of tobacco plant defences.

We continued to test I-2 function in cotton by Agrobacterium-mediated transient expression of the 35S:I-2 gene in cotton leaves. We found that over expression of the I-2 in cotton leaf tissues resulted in necrosis consistent with activation of cotton defences. Again, this finding is consisitent with results that would be expected following over expression of an active resistance gene. More importantly, it indicated that the I-2 was biologically active in cotton.

Given that over expression of I-2 caused inappropriate activation of cotton defence mechanisms, we explored the possibility of using the I-2 promoter in place of the 35S promoter. A glucuronidase (GUS) reporter gene was fused to the I-2 promoter and the fusion construct was expressed in hairy roots of cotton induced by Agrobacterium rhizogenes. Staining for GUS activity showed that the I-2 promoter was active and showed a similar pattern of expression in cotton to that in a tomato ie: in cells adjacent to to the vascular tissues of the root. We therefore made a DNA construct with the I-2 gene driven by its own promoter for use in cotton transformation experiments.

following the conclusion of our previous CRDC funding, we proceeded, in collaboration with the CSIRO Plant Industry, to produce transgenic cotton with the I-2 gene under the control of its own promoter. Twenty two T0 lines were produced, with 9 of these identified as independent lines. In this project, we have analysied the progeny of these primary transformers to determine how many transgenic loci are present. Many of the primary transformants carry multiple I-2 loci. All I-2 lines were screened for their resistance/tolerance towards FOV in glasshouse trials. Whilst the preliminary results from an initial glass house trial were encouraging, later FOV bioassays demostrated that the possession of the I-2 gene appeared to have no effect on resistance/tolerance in cotton against FOV.

The presence of an active interaction between plants and microbiological life in soil has been accepted for many years. This interaction is particularly important in the rhizosphere, where plant exudates and other rhizodeposits directly feed the microbial population, which in turn is responsible for nutrient cycling, production of growth promoters, disease suppression, agrochemical degradation and occasionally development of pathogenicity. These factors are important to plant health and productivity. However, the difficulties of studying such interactions in the soil and the inability to grow the majority of soil microorganisms in the laboratory (for example, at present <10% of microbial life in soil is cultured in the laboratory) have resulted in limited research in this area. Up to 40% of photosynthetically fixed carbon is released by plant root.

With the introduction of genetically modified (GM) crops into agricultural production systems public concern resulted in renewed interest and research into the impacts of new varieties of cotton on plant growth, productivity and environmental health. (Gupta and Watson, 2004; Brookes and Barfoot, 2005). Results from the previous research indicated that although some differences exist between rhizosphere microbial communities of non-GM and GM crops, they were not specifically identified as being caused by the expression of the introduced transgenic material alone. The results did, however, imply that cotton variety groupings were more likely to be associated with differences in the rhizosphere microbiota. In this project, two years of field and laboratory trials were conducted to assess what level of influence cotton varieties have on their associated soil microbiota involved in key functions and if there might be potential to influence these as a management tool.

Results demonstrated that there is a very strong relationship between the bacterial communities that develop in the cotton rhizosphere from the start of the season. Although there were seasonal based differences in the populations of rhizosphere microbial communities, a clear varietal separation was observed. Differences in the genetic and catabolic diversity of microorganisms between varieties suggest that rhizosphere microbial communities may be adapted to the quantity and quality of root exudates from cotton plants. The released plant products act as selective carbon and nutrient sources enriching a select group of microbial communities. These diverse microbial communities demonstrated shifts in several functional capabilities, particularly relating to N cycling e.g. N mineralization, free-living nitrogen fixation. This could form the basis for development of lower input and more biologically orientated and efficient cotton farming systems. With the current increases in fuel and fertilizer costs such systems are likely to be beneficial in the near future, but more work would be required to capitalise fully on this potential.

Black Root rot (Thielaviopsis basicola) BRR is a major threat to cotton production in southern and central NSW. It has a wide host range of more than 230 species of plants (Pereg 2013). The fungus survives for long periods in the soil as resistant resting spores. Infection of cotton is favoured by soil temperatures below 20 °C, which is normal at planting time in these cooler regions. Research in the USA has shown that severe disease symptoms result when the population of the black root rot fungus reaches 100 spores/g. It delays crop development in a region which already has a constrained growing season.

Populations of 600–700 spores per gram of soil have been found in some Australian cotton fields. Black root rot fungus does not kill seedlings by itself, however severe infection will render cotton more susceptible to other seedling diseases such as Pythium and Rhizoctonia. Stand losses of 30% or more are common from combinations of these seedling diseases. Seedlings affected by black root rot are stunted and slow growing. In effect, the disease ‘steals’ time from the crop leading to delayed maturity and yield loss. As weather conditions and temperatures improve, infected cotton crops will recover but in poor establishment conditions, yield reductions of 25–50% have been attributed to severe black root rot. The use of Woolly pod vetch as a green manure crop has been shown in previous research to reduce the impact of BRR in fields. This project aims to investigate the use of a bio fumigant crop such as Woolly Pod Vetch based on previous research. The concept of biofumigation involves planting a crop that releases compounds that are toxic to pests or pathogens in the soil. It involves growing and harvesting the biofumigant plant as either a rotation crop or as a sacrificial crop that is sprayed out and incorporated (brown manuring) or freshly incorporated (green manuring) into the soil prior to planting cotton. The effectiveness of biofumigation relies on the bulk of the crop being incorporated at least four weeks before planting cotton to allow breakdown of the material so there are no phytotoxic effects on the following cotton crop. A number of crop types have been trialed over the years as biofumigant crops including woolly pod vetch, mustard, canola and fodder radish. Three seasons of trials on different fields in northern NSW resulted in a 28–70% reduction in black root rot disease severity from Indian mustard and a 24–61% reduction from woolly pod vetch (Nehl 2004 )

This capital item funding is for the purchase of the small tractor and trailer. It is anticipated by the researcher, that this equipment will greatly assist with spraying and minor tillage operations associated with field trials. Previously the project relied on farm staff for transporting and spraying of field trails on research farms and growers properties. This often coincided with other farm staff operations, which made it difficult to co-ordinate for timeliness of operations.

Ownership of the equipmeenables field trialsto be progressed more efficiently and effectively, particularly where a number of spraying applications need to occur (eg. double knock – second knock timing trials). This purchase will save approximately $1500 - 2000/year by not having to pay farm staff salary and operating costs.