Workplace health and safety legislation introduced in 2012 means farm owners and managers are responsible for the safety of everyone working on their farm, including contractors and volunteers.

Despite the long history of cotton production and research, little is known about the genes that control the initiation and growth of the cells on the outer surface of the seed that become fibres. The work described in this thesis uses cDNA microarray technology to study global gene expression differences between normal linted cotton and two lintless mutants to uncover the genetic control of lint production. By comparing differences in gene expression between the mutants and the wild-type, a small number of genes that might be important for fibre development were identified, including a transcription factor GhMyb25, which was assumed to be the best candidate for a master fibre control gene. During normal lint production this gene is predominantly expressed in the cells on the surface of the seed at the same time that fibre cells start to grow, but also in the trichomes on the leaf and stem of developing plants.

Over-expression of GhMYB25 in transgenic tobacco led to an increase in the number and branching of multicellular trichomes on the adaxial leaf surface. By contrast, ectopic expression of GhMyb25 in Arabidopsis had no effect in trichome development suggesting that Arabidopsis and tobacco trichomes are regulated differently.

Over-expression and silencing of Myb25 in transgenic cotton was also performed to validate its role in fibre development. Analysis of primary transformants revealed that the RNA interference (RNAi) of GhMyb25 caused a significant reduction in fibre development, as well as, the production of distorted fruits with aborted seeds. Apparently the suppression of GhMyb25 in the embryo has inhibited the development of the seed entirely. Trichome development on the petiole and leaves of the transgenic lines was also affected by the suppression of the GhMyb25. The inhibition of the trichome development correlated inversely with the over-expression phenotype, where an increase in trichome production on leaves and stems was observed from a preliminary analysis of a number of primary transformants.

The outcomes of this project will provide a better understanding of the genes controlling fibre development and should enable genetic engineers to design new strategies using biotechnological approaches to genetically improve cotton fibre yield and quality.

Final report of high yielding grains project

A technique to identify the host crop of Heliothis moths by analysis of elemental content has been progressively developed over several seasons(CRC Project CS13L, Fin 1986). In this grant period we finalised statistical analyses of the existing database for individuals from known hosts and have developed a procedure for allocating unknown individuals collected in cotton crops to probable hosts (developed by Dr. Richard Motton CSRO Biometry Unit). The procedure (based on Newton's method with gradient matrix calculated by formula) allows for moths to be allocated to one of five major host crops or to a class derived from none of the major crops and includes a facility to use only a subset of possible hosts in an allocation run. The procedure gives acceptably accurate estimates of the proportion of a sample of moths derived from major hosts, though to date it has been validated using the same database as used to produce it. Further data for individuals from known hosts is being collected this season for validation purposes. We have commenced processing elemental data for unkonwns collected in 1985/86 using the procedure but have encountered a problem which may be due to dust contamination of field caught moths. The elements Fe, P, and Mn are the most important in discriminating moths from different crops (accounting for 85-90% of the variation), but most of the moths taken from traps show levels of Fe (and Al and Si) outside the range of any of those reared from crops, while levels of other elements are similar to those for moths reared on crops. Elevated concentrations of Fe, Al and Si are characteristic of sample being contaminated with soil, which may easily occurring pheromone traps from which the moths are collected.

The development of population dynamics models of heliothis populations in multi cropping systems required information on reproductive development, longevity and lifetime fecundity of adult female Heliothis in order to simulate the daily input of white eggs to each simulation unit. Studies with H. armigera and other species overseas have shown Heliothis spp. to be highly fecund. In the laboratory females may commence laying after a prereproductive period of2-3 days and lay 1000-2000 eggs during their reproductive lifetime of5-8 days. However only limited laboratory data was available for Australian H. armigera and little or no data is available for H. punctigera. Potential fecundity in many insects is related to adult body size which in turn may be influenced by the quality of food consumed by the larvae. Heliothis develop on a range of cultivated and non-cultivated host plants which may vary considerably in their suitability for larval growth. Differences in weight of pupae produced on different crops have been recorded (Fitt unpub. data) which may influence potential fecundity and longevity. What was needed was areIative measure of the effects of host plant on reproductive performance to provide coefficients for the simulation models. In addition we required data on the effects of seasonal climatic factors, particularly temperature and day length on rate of reproductive maturation and longevity of both sexes and of egg production in females at different times of the season. No quantitative data was available on such effects.

The aims of the project were to determine the effect of selected management practices on carbon sequestration, soil quality and hydrology, crop agronomy and profitability in irrigated and dryland Vertosols using a combination of field and laboratory experiments, and desktop studies. Management practices were tillage systems, rotation crops, soil amendments, irrigation and stubble management. Measurements included environmental variables such as soil quality, carbon storage and sequestration, greenhouse gas emissions, deep drainage and soil water storage, and agronomic variables such as above- and below-ground crop growth and cotton lint yield. Economic returns in irrigated sites at ACRI were evaluated by comparing seasonal and cumulative gross margins. Partial life cycle analyses of greenhouse gas emissions were made using a desktop approach. The &quote;Mulch Manager&quote;, a machinery attachment which was able to kill vetch while reducing herbicide application rates and trafficking was completed and assessed.In general, SOC stocks in the 0-60 cm depth ranged between 50 and 70 t/ha. Legumes, although contributing large amounts of carbon to the soil were unable to retain it because their low C/N ratio facilitated rapid microbial decomposition. Carbon inputs of C4 crops such as sorghum and corn were much larger than those of C3 crops such as wheat. A major proportion of that carbon came from their root systems. Increasing water availability and reducing tillage improved root growth. SOC sequestration rates were generally negative or neutral, except where a stressed soil (disease, sodicity, salinity) was in the process of recovering. Estimates of carbon inputs, based on above-ground and root dry matter, together with measured sequestration rates indicated that large losses of carbon were occurring, probably due to a combination of accelerated erosion, runoff and microbial decomposition. SOC storage was positively related to dry matter inputs, average maximum temperature, soil aeration and water availability but was negatively associated with N fertiliser inputs. Except for temperature, the other variables can be manipulated by cotton growers. Average maximum temperature and soil organic carbon in the 0-60 cm depth had a curvilinear relationship. The temperature optima were higher in the Namoi valley (27-28 oC) than in the Macquarie (25.5 oC). Farming practises that could reduce emissions include eliminating inversion tillage, minimising use of groundwater, sowing winter crops in rotation with cotton, reducing/optimising mineral N fertiliser rates, substituting a legume an thus, fixed N for mineral N fertiliser. Long-term cropping-related K depletion may be minimised by regular application of cattle manure. Gypsum application did not improve subsoil structure under dryland conditions, probably because of the erratic rainfall pattern.Water losses through drainage can be reduced and soil water storage increased (i.e. water conservation improved) by including a wheat crop in the rotation with in situ stubble retention under less frequent irrigation. Management systems that conserve all rainfall received in situ, thereby reducing irrigation water requirements can contribute greatly to the sustainability of irrigated cropping. Deep drainage in cropped plots under normal or low rainfall conditions was many times higher than that in fallow plots, and reflects the higher water inputs in the former. When rainfall was frequent and no irrigation was required, drainage was higher under fallow, with fallow length being positively correlated to drainage. A model was developed that used rainfall and potential evaporation to estimate soil evaporation from beds where stubble was either incorporated or retained in situ. A model that used EM38 measurements, soil water storage and sodicity (ESP) was able to accurately estimate chloride in non-saline soils. These values could then be used to estimate drainage using chloride mass balance models.Cotton yields and gross margin/ML were generally higher when wheat was included in the rotation with highest values occurring on permanent beds. Amendments such as gypsum or manure did not improve crop yields under dryland conditions, even though soil quality wasimproved. Including vetch in the rotation did not result in sufficient improvements in cotton yield to compensate for the increase in production costs. In years of plentiful water (or when crop area is the limiting factor) reducing water application rates on a continuous cotton crop was a false economy.Cotton lint yields, in general, were positively related to water and N inputs, soil aeration in some sites and average annual daily maximum temperature in cooler or poorly-drained sites but were lowered by higher average annual daily minimum temperature. In a sodic soil, a high frequency of the tillage practices intended to aerate the soil may have caused yield decreases, presumably due to exposure of more sodic soils. Depth and frequency of tillage, average annual maximum and minimum temperature, N and SOC directly affected WUE of cotton.Except for SOC, which had no effect, all of the above variables directly affected NUE of cotton, particularly N fertiliser rate, which was negatively related, and legumes, which were positively related. The relative importance of individual variable differed among sites for yield, WUE and NUE.The &quote;Mulch manager&quote; reduced use of herbicides, decreased labour, lowered risk to operators and had a lower carbon footprint. In comparison to spraying with an 8-row boom sprayer, depth of compaction was more when this 4-row implement was used, although the former resulted in more intense and shallower compaction.Between 2008 and 2011, two postgraduate students, two honours student and a visiting fellow from Pakistan were hosted by the project. Project outputs were: 7 journal articles, 11 conference papers and 5 cotton industry and extension. A total of 16 public presentations were given by project and associated staff.Key outcomes included: Identifying soil and crop management practices, and climatic variables that had direct impacts on soil carbon stocks, yield, water and nitrogen use efficiency in irrigated cotton soils. Quantifying rainfall harvested, and associated drainage and evaporation, and thus, water saved by retaining rotation crop stubble as in situ mulch.Identifying practices that could reduce carbon footprint of cotton farming systems with life cycle analysis. A machinery attachment for managing prostrate cover crops bed-furrow systems.Simplified field methods to estimate soil evaporation and deep drainage. whole-farm model of profitability for cotton farming systems that can be used as an analytical research tool.

The introduction of glyphosate tolerant cotton has significantly improved the

flexibility and management of a number of problem weeds in cotton systems.

However, reliance on glyphosate poses risks to the industry in term of glyphosate

resistance and species shift. The aims of this project were to identify these risks, and

determine strategies to prevent and mitigate the potential for resistance evolution.

Field surveys identified fleabane as the most common weed now in both irrigated

and dryland system. Sowthistle has also increased in prevalence, and bladder

ketmia and peachvine remained common. The continued reliance on glyphosate has

favoured small seeded, and glyphosate tolerant species. Fleabane is both of these,

with populations confirmed resistant in grains systems in Queensland and NSW.

When species were assessed for their resistance risk, fleabane, liverseed grass,

feathertop Rhodes grass, sowthistle and barnyard grass were determined to have

high risk ratings. Management practices were also determined to rely heavily on

glyphosate and therefore be high risk in summer fallows, and dryland glyphosate

tolerant and conventional cotton. Situations were these high risk species are present

in high risk cropping phases need particular attention.

The confirmation of a glyphosate resistance barnyard grass population in a dryland

glyphosate tolerant cotton system means resistance is now a reality for the cotton

industry. However, experiments have shown that resistant populations can be

managed with other herbicide options currently available. However, the options for

fleabane management in cotton are still limited. Although some selective residual

herbicides are showing promise, the majority of fleabane control tactics can only be

used in other phases of the cotton rotation.

An online glyphosate resistance tool has been developed. This tool allows growers

to assess their individual glyphosate resistance risks, and how they can adjust their

practices to reduce their risks. It also provides researchers with current information

on weed species present and practices used across the industry. This tool will be

extremely useful in tailoring future research and extension efforts.

Simulations from the expanded glyphosate resistance model have shown that

glyphosate resistance can be prevented and managed in glyphosate-tolerant cotton

farming systems. However, for strategies to be successful, some effort is required.

Simulations have shown the importance of controlling survivors of glyphosate

applications, using effective glyphosate alternatives in fallows, and combining

several effective glyphosate alternatives in crop, and these are the key to the

prevention and management of glyphosate resistance.

There have been reports of symphlans in early established crops. Symphla are a natural part of healthy soil biota, & can be found under healthy crops however at very high numbers may cause root damage. Seedlings particularly at risk are those with low vigour due to other stresses such

as poor planting conditions. Effected plants may appear stunted & wilt due to early water stress.

The overall objective of this project was to develop improved conventional and transgenic cotton varieties adapted to Australian growing conditions and producing fibre suitable for our markets. The project comprised key components of conventional breeding and development of markers for future use in marker-assisted breeding.

Conventional breeding experiments and line evaluation are done in all major production regions in Australia; our mobile sowing and harvesting equipment is used at 15 sites and comprises more than 20,000 yield plots each year. New elite lines have been identified with increased yield potential, improved fibre properties and increased resistance to diseases such as Fusarium wilt.

Up to eight Quantitative Trait Loci have been identified for resistance to Fusarium wilt. These results are being used to develop molecular markers for Fusarium resistance to enable quicker and more accurate breeding and development of new varieties. At present there are 9,000 plots per year in field Fusarium nurseries with variable success; markers would enable this process to be improved at cheaper cost.

There have been 36 new varieties released in the past three years. We have introduced high Fusarium resistance (Sicot F-1, Sicala 45, Sicot 14B); Bollgard®II (a large suite including Sicot 71B and Sicot 71BR); a fuller suite of Roundup Ready (Sicot 71RR, Sicot 80RR); premium fibre (Sicala 350B); and initial limited RRFlex release (Sicot 80BRF, Sicala 60BRF, Sicot 43BRF).

We have continued to discover better combinations of yield, fibre quality and disease resistance in conventional germplasm. Sicot 75 is one example and this will provide a new base for future conventional and transgenic varieties. Thus the 1.96% improvement in yield potential due to breeding from previous years will continue. Yield increases are needed to help keep cotton growers remain viable.

WATERpak provides technical information and practical advice to help irrigators improve irrigation practices, minimise environmental impacts and increase farm profits from irrigated cotton crops.

WATERpak brings together in one place the many years of irrigation research conducted by a variety of organisations in the Australian cotton and grains industries.