One step in the production of transgenic cotton is the regeneration of whole plants from undifferentiated cells (calli) in which the gene of interest has been inserted. The first stage is a crucial one and involves producing plant embryos from callus cells (somatic embryogenesis). The frequency of embryo formation is low and the process is poorly understood. Of the cultivars that can form embryos, most are no longer grown commercially (e. g., Coker). To introduce a gene into commercially important cultivars, the standard international practice is to transform a Coker cultivar, produce plants that are homozygous for the gene inserted and then enter these plants into a backcross breeding program (Wilkins et al. 2000). This process delays the commercial release of transgenic cotton by several years' A method that allows commercial cotton cultivars to be transformed and regenerated directly would be a significant advance in cotton biotechnology (Rajasekaran et al. 2001).

Cotton fibres, or lint, are very long single cells containing almost pure cellulose. The fibres develop in the weeks after flowering from single cells on the surface of the young seed. Each fibre cell is small at first but elongates and develops rapidly, eventually forming the mature cotton fibre. These processes require the ordered expression of genes which make enzymes, structural proteins and signalling molecules that together determine the properties of the fibre. Domestication has modified fibre development to produce cotton varieties with greatly improved fibre length, strength and quality. However, the selection and breeding of plants with desirable fibre characteristics is slow and expensive. As such, future crop improvement is likely to depend upon genetic engineering and the cotton industry has been a leader in both research and commercialisation of transgene technology, with momentous consequences for the agronomic properties of the crop such as insect and herbicide resistance. However, the potential for fibre modification by biotechnology has yet to be realised Apart from their commercial significance, the single-celled nature of cotton fibres and their synchronous growth inside the cotton boll has made them an attractive system for the study of plant cell elongation and cell wall biogenesis. Such fundamental studies have resulted in the identification of a number of genes with proposed roles in cotton fibre growth, and have led to the creation of the first molecular and cellular model of fibre development (Wilkins and Jernstedt, 1999). The model has provided the basis for limited early success in the alteration of fibre growth, but not on a commercial scale,

The broad aims of CCC CRC 5.2.03 ‘Delivering science to agribusiness: Smart approaches to cotton irrigation management’ were to; conduct irrigation research for emerging crop management issues and alternative cotton cropping systems; provide industry with an enhanced version of HydroLOGIC; and document a decision framework for integrating irrigation management tools. This project formed a key application and feedback link within the Cotton Management Support System Team, which developed targeted, cotton specific management tools for the Australian industry. This project also supported the CSIRO Plant Industry water research team of Mr Stephen Yeates (scientific development), Mr Dirk Richards (DSS development and application) and Mr James Neilsen (plant water relations).

Key research findings and outcomes were:

* Bollgard water use and scheduling

* Extraction patterns and the depth of rooting were similar in the Bollgard and conventional treatments by the end of the season.

* Bollgard®II had the potential to use less water whilst maintaining a yield advantage.

* Bollgard®II may be more sensitive to larger deficits (>55-60% PAWC), late in flowering and should be watered before conventional fields.

* A reduction in gross and irrigation water use efficiency was only found in Bollgard®II where moisture stress was experienced at or close to cut-out.

Application and use of HydroLOGIC in the industry

* Feedback from HydroLOGIC trial co-operators and users indicated a mixture of strategic and tactical use including; area to plant depending on water available; confirming scheduling decisions (consultants); benchmarking crop water use after harvest. A key application of the software was late in the season and when determining the last irrigation, with HydroLOGIC often indicating that the final irrigation was not required.

* HydroLOGIC user surveys indicated great value in this decision support tool with:

* 36% of respondents using the software to compare water use across farms,

* 44% of respondents finding the software easy to use, while recognising that the tool addresses complex issues and this requires significant training,

* 50% of respondents finding the data required by the software easy to collect,

* 78% of respondents saw HydroLOGIC fitting into their enterprise, and

* 60% of respondents indicating their wanted to learn more about HydroLOGIC.

* The greatest value in HydroLOGIC was in the areas of limited water (18%), irrigation scheduling (11%) and first irrigation (8%).

Documentation and integration of irrigation decision tools

* Research over two seasons demonstrated the value in using the Irrimate™, WaterTrack™, and HydroLOGIC tools to assist in separate aspects of water management. These experiments indicated the combined use of these products can result in significant water savings through improved irrigation efficiency, optimised water scheduling, identification of on-farm losses, and changes in farm management and infrastructure.

* All tools provided good commercial estimates of crop water use and use of any would result in better irrigation practice.

Research results from this project were successfully communicated to the Australian cotton industry via industry publications, media release, presentations and all other relevant media. An essential component of the projects success was the close collaboration with commercial cotton growers, consultants and the Cotton CRC extension network.

The commonly used Micronaire value for cotton is related to both fibre fineness (weight per unit length) and maturity. There is a need for a new measurement technique to separate these. This is of particular importance to the Australian industry where varieties of fine, mature cotton have the potential to be wrongfully discounted commercially if a low Micronaire value is taken as indicating immaturity.

The CRDC is currently funding research at CSIRO Textile and Fibre Technology aimed at developing techniques to measure fibre fineness and maturity to overcome this deficiency in the micronaire measurement.

One difficultly with research in this area is that there are no internationally recognised standard cotton samples that can be used for checking the accuracy of new measurement approaches or for that matter for checking the calibration and accuracy of existing instrumentation.

Researchers at USDA in New Orleans and Texas Tech. University have been tackling this problem by coordinating the development of a standardised set of cotton samples specifically for this purpose. The cottons in this set will each have well characterised values of both fibre fineness and maturity and the set will cover a wide commercial range in these parameter values. This set will then be of extensive value to the cotton community.

Utilising our expertise in measuring cotton fibre fineness and maturity, CSIRO Textile and Fibre Technology, has participated in these trials as an independent measurement test laboratory.

The use of the new round module builder pickers has grown very quickly in Australia, reaching about 90% in 2015. As the round module is wrapped by plastic film, concern has been expressed by cotton gins that the moisture content of the round modules may be higher than expected, resulting in increased drying cost and potential impacts on fibre quality.

A continuous module monitoring system which includes a temperature & humidity sensor connected by cable to a datalogger is used. The sensor is inserted into the middle of the round module using special hand tools. Relative humidity (RH) and temperature inside the module are recorded in the datalogger every 15 to 30 minutes for up to eight months without intervention. This gives us the full history of a round module from harvesting to ginning.

The temperature and relative humidity at the top part of the round module fluctuates significantly while conditions in rest of the module were very stable. After a long period of storage, the top part of the module dries out and the bottom part becomes the wettest region. Covering the modules by a tarpaulin significantly reduces the fluctuation of temperature and relative humidity and slows down the drying of cotton at the top part of the module. The orientation of modules during storage has an influence on the conditions of the modules. Core temperatures of modules stored with axis in North-South direction were about 2˚C higher than those stored in the East-West direction during the hot months of the year.

Several cotton quality attributes (length uniformity, strength and colour) displayed statistically significant changes between modules ginned at the beginning of trial and that ginned at the end of the storage period.

This Guide provides you with a comprehensive summary of the key cotton crop protection issues, and is brought to you by CRDC and the Australian cotton industry's joint extension program, CottonInfo, in partnership with Crop Consultants Australia (CCA).

Deep drainage (DD) - water that passes beyond the root zone - can be an important

contributor in terms of recharging ground water as well as leaching salts from the root

zone. Excessive DD is economic poor practice and a potential source of rising ground

water tables with increased solute concentrations; potentially challenging issues for

irrigated agricultural landscapes and the communities therein. The project’s prime aim

was the direct quantification of DD across a wide, yet representative range of cotton soils

and management systems, while concurrently assessing both salt balances of collected

leachates and around-lysimeter soils, as well as crosschecking the measured DD data with

less expensive, indirect methods of predicting DD (eg SODICS, SaLF and ET/SIRMOD).

Secondly, to monitor irrigation efficiencies in terms of recent technology utilisation in the

cotton industry, specifically the comparative efficiency of a lateral move irrigator (LM) vs

adjoining furrow irrigation, in terms of lessened water applied and DD; LM considered as

having great potential for positive impacts on water savings. Thirdly, to investigate

linkages (if any) between surface water events (DD, irrigation, river flows, etc) with

historic and current (logged) groundwater levels in the St George irrigation area (SGIA);

checking for rising water and salinity risk. Instrumentation was 35 drainage lysimeters

(constant suction) at three locations in one field on each of 10 commercial farms and at

the Australian Cotton Research Institute. Up to five irrigation seasons have been

monitored (2002 to present). Results show a maximum DD of 310 mm (3.1 ML/ha) in

one season has been measured (representing ~39% of the applied irrigation water).

However, of 69 sampling occasions across four growing seasons and all the lysimeter

sites, only 14 occasions (~20%) provided DD values of >100 mm (1 ML/ha).

Additionally, DD has been found to vary strongly across fields - from head to tail ditches,

and there is strong between-seasons’ variation in the lysimeter data at any one site,

apparently linked to during-season weather and water (irrigation water) availability. Some

sites that provided >150 mm (1.5 ML/ha) of DD in one season, gave a zero reading the

following season. These unexpected variabilities in the DD data, though important to

know and to begin to rationalise in terms of site practice and seasonal weather, cause

difficulties in rationalisation of the main drivers (of DD) towards the development of

industry-applicable BMPs. Water quality analysis of the DD leachates apparently shows

salt loads being mobilised under all sites. Soil chloride analysis (over five years at some

of the DD sites) shows increased salts in the root zone of certain fields. Close

investigation of both data sets is current. The indirect methods of predicting DD have

proven most poor in providing matches to the measured lysimeter DD values; in terms of

both magnitude (of DD volumes) and correspondence with (at times large) measured infield

and seasonal variability in DD. Preliminary analysis of the historic borehole logs

and real-time logging of groundwater levels suggests that the shape of the groundwater

contours does not particularly illustrate the presence of a broad groundwater mound in the

SGIA, but rather the development of more localised groundwater mounds probably

reflecting zones of locally preferential accession of DD (most probably due to channel

leakage and leakage from on farm storages). The depth to groundwater data suggest that

groundwater levels have not yet approached the 2 m bGL level that is commonly viewed

as posing a risk for soil salinisation via capillary rise of groundwater. Currently there are

28 operational lysimeters (2 sites having been recently de-commissioned) and 18

borehole loggers (logging aquifer level twice daily) that will continue monitoring to 2011.

These additional data will aid clarity in the drivers of DD and associated groundwater

response. Further DD leachate and soil salinity data will be collected to continue the salt

mass balance study.

Cotton fibres are differentiated single cells, originating from the epidermal layer of

the cotton ovule. Cotton fibre quality is determined by its length, strength and

fineness properties, which are largely controlled by genetic factors. Genes that are

expressed predominantly in fibre cells are likely to control development of the fibre

and contribute to these fibre characteristics.

The promoter sequence of the fibre-specific gene FSltp6 was isolated (Orford,

unpublished) and the region necessary for fibre-specific expression was identified

through successive 5’ deletions of the promoter (DELANEY 2005). An 84 bp region

identified, was subsequently used in a yeast-one-hybrid assay to identify transcription

factors that may regulate expression of FSltp6 (DELANEY 2005). Three classes of

novel cotton proteins were identified; HMGA-like proteins, Mutator transposase-like

proteins and an AT-hook protein.

The main objective of this project was to analyse the Mutator transposase-like and the

HMGA-like partial cDNAs to verify that these proteins do contribute to the regulation

of the FSltp6 promoter. The initial aim was to isolate full-length cDNA sequences for

each protein. A further aim was to perform functional analysis to determine the subcellular

localisation and expression profiles of each of the proteins. A full-length

sequence was identified for the Mutator transposase-like cDNA that encodes a

predicted 771 amino acid peptide sequence. Preliminary functional analysis was also

performed on both of the partial cDNA sequences and each showed expression in all

of the cotton tissues tested. Expression of both mRNAs were higher in the ovule and

6 DPA fibre compared to 12 DPA fibre, suggesting a potential role for these genes in

early fibre development.

Results from this project contribute to the field of cotton fibre development. More

specifically, this work contributes to the understanding of cotton promoters and their

roles in regulating fibre-specific expression. The full-length cDNA isolated in this

project could encode a transcription factor required for fibre-specific expression, but

further functional analysis must still to be performed for confirmation. Information

about cotton fibre-specific promoters and the transcription factors that regulate them,

such as the ones investigated in this study, could be used in the development of

transgenic cotton with improved fibre quality and yield.

Two of the major fungal diseases of cotton in Australia are fusarium and verticillium wilts caused by the fungus Fusarium oxysporum. F.sp vasinfectum (Fov) and Verticillum dahliae respectively. Both pathogens infect seedlings via the root and cause wilting, stunted growth and for Fov, death of some plants. In Australia Fov is the major cause of crop losses due to fungal infection, however, the incidence of verticillium wilt has increased recently due to the planting of susceptible varieties (Johnson and Nehl, 2004). We have been studying NaD1, a naturally occurring antifungal protein from the ornamental tobacco (Nicotiana alata) (Lay et al 2003). NaD1 is a member of the plant defensin family, a group of small, basic peptides with similar 3-D structures (Thornma et al 2002). Plant defensins have a range of antifungal activities. Several plant defensins, when expressed in transgenic plants, enhance resistance to pathogen attack (Bart et al, 2002), and field trials by Monsanto, of transgenic potato expressing an alfalfa defensin, have demonstrated resistance to Verticillum dahliae in some lines (Gao et al. 2000). In a program funded by Hexima Ltd, we have produced transgenic cotton plants expressing NaD1 under the control of the 35S promoter. Four lines, carrying single copies of the Gene, were selected for further analysis. Expression of NaD1 was high in most plant tissues tested.

Cotton (Gossypium spp.) has retained its prominent position in the international arena despite stiff competition from synthetic fibre. One of the major cotton producing countries in the world, occupying the third place (2.6 million M. T.) and having the largest acreage (8.8 million ha. ), India is still lacking far behind in terms of cotton productivity (298 Kg lint/ha) as compared to the highest productivity level (1667 Kg lint/ha ) as achieved by Israel (Mayee et al. 2001). The figures indicate that the major genetic potential remains yet to be fully exploited. Seedlessness in cotton may prove to be an essential indirect selection index for increased lint yield.