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.

Final report for Managing environmental flows in an agricultural landscape: the Lower Gwydir floodplain The Lower Gwydir floodplain is recognised for its high-conservation value as aquatic plant and wildlife habitat. This, along with the significance of the terminal wetland areas for water bird breeding, has resulted in parts of the floodplain being listed in the late 1990s under the international Ramsar Convention. However, construction of Copeton Dam upstream in the mid 1970s and subsequent changes to the region&#39s irrigation, grazing and cropping industries has altered flow patterns into the wetlands and placed other pressures on the wetlands and their biodiversity values. The Gwydir Regulated River Water Sharing Plan was developed in the early 2000s, in part to counter further wetland degradation and to establish an allocation balance between consumptive and environmental needs. A broad stakeholder committee (the Gwydir Environmental Contingency Allowance Operations Advisory Committee; ECAOAC), currently administered through the NSW Department of Environment, Climate Change and Water, is the primary mechanism by which the subsequent flow allowance is used for environmental benefit. It is the overarching aim of the present study to determine the ecological responses to flow variability in the Lower Gwydir aquatic ecosystem, and to provide the ECAOAC with a model to guide the effective management of flows to maximise ecological responses in this system. The listing of wetlands on &quote;Old Dromana&quote;, &quote;Crinolyn&quote;, &quote;Goddard&#39s Lease&quote; and &quote;Windella&quote; with the Ramsar Convention will continue to be a major driver of delivering environmental flows into the Lower Gwydir floodplain.

This review also examines the competition for water resources between the key stake holders in the area. Water from the Macquarie River is shared between agricultural enterprises (mainly cattle and irrigated cotton production), town water supplies and the environment. The social and economic reliance on agriculture and the value and importance of the Macquarie Marshes must be taken into account when managing the water allocations of the Macquarie River.

The Study develops a framework and set of social, economic and environmental indicators that aid in understanding how some 'cotton communities' are performing against relevant state and national benchmarks. The first part of the study, reported in the Information Paper (CARE 2009), provides more straightforward measures of the contribution of cotton to regional economies. It reports on the contribution of cotton to GRP, the relative specialisation (economic diversity) of each region compared with state

In 2004, Helicoverpa armigera resistance management was a high priority issue for both conventional insecticides and transgenic Bt technology(Bollgard 11). Over wintering pupae busting represents one of the most vulnerable stages in the life cycle of the H.armigera, and management efforts have been directed at reducing survival of this stage through the use of 'pupae busting', or full surface disturbance by cultivation to a depth of 10cm. Pupae busting was mandatory for Bollgard II crops and recommended for conventiaonl (non Bt transgenic) crops.

Industry compliance with pupae busting compliance is generally considered high. Pupae busting is associated with some disadvantages, including loss of soil moisture through cultivation, the potential lost opportunity to double crop, alterations to soil structure under wet conditions and its adverse impacts on machinery under dry conditions.

Under some circumstances, there may be few or even no over wintering pupae under cotton crops and growers seriously question the need to pupae bust under these circumstances. One of the problems facing growers is the difficulty of accurately sampling for pupae. Labour intensive soil sampling operations are the most common. There is an identified need for improved pupae detection/sampling methods.

Following the highly successful use of detection dogs for locating organochlorine residues, the idea was promoted that dogs could be trained to locate pupae in fields. this was successfully demonstrated DAQ125C. the next study is to imprint, train and calibrate a pupae detection dog against known field densities of pupae and develop its capacity for field application.

A major impediment to effective management of soil and water resources in most agricultural and riverine environments of Australia is the lack of information on the spatial distribution of natural resources required for management planning and implementation. With respect to the soil resource the major problems are that traditional methods used for the acquisition of soil information, including soil survey, are time consuming and costly. The data collected is therefore usually sparse and because of time constraints was subjectively interpreted and therefore implications for land use management are uncertain.Numerical clustering algorithims such as fuzzy k-means (FKM) have over the last 15 years been used successfully to continuously classify multiple soil attributes. More recently, FKM combined with geostatistical methods have been used to create representations of the soil continuum using remotely sensed information such as Digital Elevation Model (DEM) and deep sensing electromagnetic (EM) data.The use of gamma radiometric data is increasingly being used to assist with the recognition of surface soil patterns. This is because gamma radiometric data, which consists of Potassium (K), Uranium (U), Thorium (Th) decay rates as well as the total radioactivity (i.e. Total Count-TC) of the soil and regolith, are related to the age and mineralogy of the soil.In this project, the aim is to explore the possible use of FKM analysis of gamma radiometric data (i.e. K, U, Th and TC in cps) and secondary data derived from a DEM to identify geomorphological and geological units and associated soil units within the Edgeroi district. The results suggest that the FKM approach, including the use of fuzzy performance index (FPI) and normalized classification entropy (NCE), provides a framework for identifying a small number of classes (c = 7) to investigate for interpretation. We conclude that the classes derived from radiometric data, were consistent with the known soil variability and broad geology and geomorphology of the Edgeroi district (i.e. erosional, depositional and dust-mantled plains). The best results were achieved within the depositional and dust-mantled plains where we were able to discern differences between the depositional Namoi floodplain and the first and second terraces from the third and fourth terraces of Namoi alluvium. The approach also discerned the location of the dust-mantled plains associated with the fourth and eroded fifth fans of local alluvium. The results with respect to the erosional landscape were equivocal.