The purpose of the 2016 Smarter Irrigation Technology Tour (an intensive three day tour to Northern Victoria and Southern NSW) had several objectives. To examine a range of surface irrigation layouts, the hydraulics, performance and suitability.To learn about automation technologies currently adopted in the irrigation industry, and see these technologies in action. To understand the application of automation equipment currently available, and how it could potentially benefit a farmers irrigation system. Improve participants understanding of various water management technologies (precision application, soil moisture sensors, EM survey). To showcase the irrigation research undertaken in the Smarter Irrigation for Profit Project and other CRDC funded irrigation research and provide a networking opportunity for irrigators, consultants and industry personnel from the rice, cotton, dairy and sugar industries.

The 'Tales from Cotton' Tour was designed as a cross-sector shared learning experience between the cotton and dairy industries on water and energy use efficiency. The event was an activity of the Smarter Irrigation for Profit- Tamworth Optimised Irrigation Dairy Farm Project. The tour was co-sponsored by the Australian Government Department of Agriculture and Water Resources as part of its Rural R&D for Profit programme, Dairy Australia, the Cotton Research and Development Corporation, Dairy NSW, and the Australian Government through Dairy Australia’s – Profitable Dairying in a Carbon Constrained Future Project. It was also supported locally by in kind support from North West Local land Services, Aquanorth irrigation, Hazell’s farm and Fertiliser Services, Davey and NSW DPI.

• Cotton aphid, two-spotted mite (TSM), banana or strawberry spider mite (SSM), cotton seedling thrips, western flower thrips (WFT) and green mirid were collected from Australian cotton growing regions.

• TSM regularly showed discriminating dose survivors against bifenthrin (Talstar®) and abamectin (Agrimec®) but seldom propargite (Comite®) or etoxazole (Paramite® or Zeal®) and never diafenthiuron (Pegasus® as CGA140408).

• Bifenthrin (Talstar®) and abamectin (Agrimec®) resistance detected in TSM was often at high frequency so may fail. The reason for this is not clear because pyrethroid use in cotton is limited and TSM do not fly so their immigration from sprayed crops other than cotton must be limited. It is speculated that the continuing increase in abamectin (Agrimec®) resistance is due to its use as a preventative treatment with mirid sprays. Mirid sprays are disruptive to beneficials so the inclusion of abamectin reduces the risk of subsequent mite flare.

• SSM was the most found mite species in Australian cotton confirming anecdotal observations that the cotton mite complex has changed and is no longer TSM dominant. Additionally TSM was restricted to NSW only and bean spider mite (BSM) was not collected so remains absent from Australian cotton.

• To allow resistance monitoring SSM baseline data was established for abamectin (Agrimec®), propargite (Comite®) and diafenthiuron (Pegasus® as CGA140408) and monitoring commenced but none was detected.

• A DNA based method to identify SSM, TSM and BSM was developed and successfully deployed by Biosecurity Australia where it has been used to identify more than 2000 quarantine mite intercepts.

• Cotton aphid was tested for pirimicarb (Pirimor®), OP-specific, pyrethroid, clothianidin (Shield®), diafenthiuron (Pegasus® as CGA140408), thiamethoxam (Actara or Cruiser®) and sulfoxaflor (Transform®) resistance. Interestingly pyrethroid resistance was often detected although it is not registered for this use in cotton and pirimicarb (Pirimor®) and OP-specific resistance was not detected so these chemicals can be used with confidence. Neonicotinoid survivors were detected in some strains but later thought vigour tolerant rather than resistant requiring discriminating dose adjustment to eliminate those false positives.

• Methods to transport and culture green mirid were developed making resistance detection possible with established laboratory based bioassay technology. Green mirid was screened for fipronil (Maestro® or Albatross®) resistance using a molecular-based diagnostic and none was detected.

• Neonicotinoid resistance was detected in cotton seedling thrips confirming anecdotal consultant / grower observations that seed treatments may not be working as well as they did. Unexpectedly WFT was the most abundant thrips found and worryingly spinetoram (Success® Neo)(the only registered control in cotton) resistance was detected in some strains.

• Much effort was put into transitioning resistance detection away from conventional bioassay to DNA based techniques. To this end indoxacarb resistance in cotton bollworm Helicoverpa armigera was extensively studied via genotype-by-sequencing and a diagnostic developed. Unexpectedly a second resistance mechanism was found preventing practical use of that diagnostic.

• A molecular diagnostic was successfully developed and deployed against TSM and etoxazole (Paramite® or Zeal®).

• Molecular methods to detect neonicotinoid in cotton seedling thrips and spinetoram (Success Neo®) in WFT were developed but require further validation.

Arbuscular mycorrhizal fungi (AMF) are important symbiotic partners to the majority of land plants. AMF depend on the plant community for photosynthate-derived energy. In return, AMF provide the plant with a range of nutritional benefits, increased protection against plant pathogen and environmental stresses. In natural ecosystems, AMF can significantly influence plant community structure and plant community stability. In cropping systems, AMF are important contributors to sustainable, low-input plant production. Excessive reduction in the diversity of AMF has occurred in some intensively managed soils as the result of intensive farming practices. Low taxonomic diversity in AMF communities may have important implications for ecosystem function. This thesis examined some of the whether AMF taxonomic diversity is reduced a cotton cropping system.

AMF were identified in the roots of mycorrhizal host plants and directly in field soil using PCR-based techniques. An AMF-targeted PCR primer was designed that enabled the specific amplification of AMF DNA in the presence of plant DNA and other non-target organism templates (Chapter 2). The primer was used to amplify AMF rDNA living in the roots of trap plants baited with field soil. The trap plants were grown in soil from long-term fallow, monoculture and rotation crops to examine whether rotation crops can influence the taxonomic diversity of AMF in cropped soils (Chapter 3). Trap plants harboured the same overall diversity of AMF in monoculture and rotation cropped field soils. The same taxa occurred in each of the fields. AMF in the cotton cropping vertisols appear to be robust. Spore dormancy may be common in many AMF (Chapter 5), and may account for the survival of the majority of AMF taxa in the long-term fallow soil.

TRFLP profiles were used to compare AMF communities in soil under different land management practices. DNA was extracted directly from soil to obtain community profiles. TRFLP analysis revealed that AMF are distributed more evenly in

cultivated than uncultivated soils. This finding has important implications for the design of sampling strategies for AMF community diversity studies.

Water allocation and access arrangements affect the livelihoods and well-being of a diverse range of water users, including irrigators and the environment increasing pressures on surface and groundwater resources have seen a shift in water management towards decision Processes that attempt to represent the interests of these diverse groups. Decision makers are increasingly being asked to take account of trade-offs between different users of water so as to make fair, equitable and/or efficient decisions that achieve a balance of social, economic and environmental outcomes.

In NSW, changes to water allocations and access through the design and implementation of Water Sharing Plans, involved negotiation between stakeholders representing many different interests and concerns. A key gap identified by many stakeholders involved in these negotiations was open access to integrated, scientifically sound and generally agreed upon information on the socioeconomic trade-offs likely to result from changes in access, allocation ~d pricing. In addition, estimates of impacts on the flow regime and on river health are also required. The Water Allocation Decision Support System (WAdss) has been

Developed and applied to two NSW catchments the Namoi and Gwydir River catchments for considering the trade-offs between environmental and socioeconomic outcomes resulting from changes in water allocation, access and pricing in the unregulated and regulated surface water systems and the groundwater system of these catchments.

The WAdss has been developed to be used in a workshop situation, allowing for analysis of a library of pre-run scenarios, sharing of scenarios between users, and creation of new scenarios live in meetings and workshops. I t also allows for reports to be generated which can be accessed from outside the system. The system has been tested in workshops situations with a broad range of potential users and found to have potential for considering water allocation issues.

Development of the WAdss has involved substantial stakeholder involvement. This has been aimed at giving stakeholders a greater sense of ownership of the models, results and WAdss, by incorporating their comments and ideas into the system. It was also important for obtaining information and data necessary for ground-truthing or calibrating the models in the system and for increasing the awareness of stakeholder groups of the existence of WAdss, its potential uses and limitations.

Overall the development process of the WAdss has been successful, given the maintained engagement of stakeholders in its development and support for its continued use and development. Initial development of the WAdss is complete. The WAdss is now moving into an adoption, extension and reapplication phase. Success in this phase will depend on the maintained engagement of stakeholders and the enthusiasm and input of researchers or other champions within Agencies or Catchment Management Authorities. With this support and adoption of the system by these groups for policy and planning processes it is hoped that the WAdss will lead to greater communication between irrigators and catchment management authorities and the development of policy options that lead to improved environmental outcomes at the least cost to production. The WAdss provides an important opportunity to

incorporate the opinions and knowledge of irrigators in the water allocation decision making process and debate. The potential of WAdss for use in other catchments and for incorporating the investigation of other issues (wetland ecology, salinity, vegetation change) is very high. WAdss has the framework and the analytic tools to examine trade-offs in these cases.

This travel Scholarship supported Dr Robert Mensah, who was invited by the International Cotton Advisory Committee (ICAC)and presented the topic “IPM is Key to Insecticide Management: Alternative Solutions for Insecticide Management in Cotton Crops” to the ICAC 77th Plenary Meeting on 6 December 2018. Dr Mensah’s presentation highlighted to the participants that over-reliance of synthetic insecticides to manage cotton pests worldwide has resulted in insecticide resistance, disruption of beneficial insect species, higher production costs and significant negative environmental impacts. Cotton industries worldwide require the development and adoption of alternative strategies and solutions for managing and controlling pests on cotton and other crops. Dr Mensah stressed that, although transgenic (Bt) cotton crops may be providing effective control for Helicoverpa spp., the development of sucking pest insect resistance to these crops remains a big threat.Attended and presented a paper at the 77th Plenary Meeting of the International Cotton Advisory Committee (ICAC). The theme for the event was “Cotton Challenges: Smart and sustainable solutions”. The meeting was attended by 385 persons including 20 member governments, six International organizations and 15 non-member governments. The agenda of the meeting included six open sessions (including “World Café” interactive session), six breakout sessions and two plenary sessions. The meeting discussed World Cotton Production, future cotton textile demand, governments support to the world cotton sector, combating effects of Climate Change on cotton, mechanization, drones and robotics for small scale cotton farms, combating pest resistance to biotech cotton and pesticides, Biotechnology, Cotton by-products and Inter-governmental policies on cotton seed exchange.

UNE1601 came about from a merger of two proposals. One proposed to develop a more detailed understanding of C under cotton, whilst the other focused on the potential for rotations to modify the soil microbial biology. To address the combined goals of the project, work was undertaken at ACRI on the long term rotational trial managed by Dr Guna Nachimuthu and broken down into three areas of investigation. These were; (i) Mechanisms of whole-profile C and N cycling, (ii) Microbial processes in the soil profile, and (iii) Below ground agronomy and constraints to plant growth.

Addressing the ‘Mechanisms of whole-profile C and N cycling’ became the focus for Dr Yui Osania. Her research in this area establishing that the maize rotation increased SOC stock in a Min Till/CW system. The mechanism for this was likely to be vertical movement of C in the form of DOC and that a strong correlation between SOC and soil N was evident, which indicated that C and N dynamics are interlinked. The conclusions from this were that agricultural management impacted SOC storage differently between the topsoil and the subsoil and that future research should explore the movement of C in the soil (i.e. leaching, root exudates), and the role of DOC in C stabilisation via microbial interactions or mineral interactions throughout the soil profile.

‘Microbial processes in the soil profile’ became the area of focus for Katherine Polain’s PhD candidature. Katherine’s work looked at both short and long term influence of the cotton rotaion under minimum tillage and found that microbial diversity was not influenced by rotational changes, which implied that there may be greater resistance and resilience in the system than previously presumed. Katherine’s work also highlighted that whilst the microbial biomass may be higher in the top 30 cm of the profile the activity can be as high in the 30-100 cm sub-soil of the cotton system profile as it is in the top. The implications from these observations are that we may need to look deeper in our systems if we want to truly understand the nutritional cycles that feed our plants nutrient demand and that might limit the losses of C from our soils.

The final aspect of the project was the ‘Below ground agronomy and constraints to plant growth’, which initially had to become more aligned to other projects when the appointed candidate had to withdraw and could not be replaced. Oliver, Brendan, Katherine, Guna, Brian and Yui did their best to address this aspect of the project. The associated work showed that ~25% of cotton fields are affected by sub-soil constraint, whilst the work at ACRI clearly established that furrow traffic led to soil compaction and with this a loss in microbial activity. Field vehicular traffic remains a necessity of our production systems, but the work done here adds to the number of proponents pushing for farms not only to move to minimum tillage, but controlled traffic farming systems.

This project was undertaken to investigate how dryland cotton production and its place in the farming system could be improved, particularly with the release of Bollgard® 3 varieties. Changes to the Resistance Management Plan (RMP) for Bollgard 3 with the relaxation of planting windows and pupae busting requirements offer the potential for greater flexibility in how growers might utilise cotton within the dryland farming system.

The project commenced with a series of workshops to engage with dryland cotton growers from across the northern region to better understand the strengths and limitations of the overall farming system and dryland cotton’s place within it for the purpose of identifying opportunities for where RD&E could have the greatest impact. The topics, concerns and opportunities raised at the workshops were then subject to a broad-based review to determine where RD&E could best be targeted for the betterment of the dryland cotton industry. The review identified a number of R&D gaps around the:

• implications for changes to pupae busting on the farming system

• need to develop effective zero-tillage crop destruction tactics

• opportunity to combine modelling with farming systems research to answer some of the more difficult crop sequencing questions raised by growers

• need to ensure that weed management practices extend across the system and are not carried out in isolation within each commodity

• potential to better extend a large body of existing R&D together with local validation to answer the many questions that growers have in expanding dryland cotton regions (e.g. the Liverpool Plains).

The grower workshops and review identified that it was regions with more marginal dryland cotton production prospects (lower rainfall and/or duplex soils) or areas where dryland cotton has been recently expanding (Liverpool Plains) that would potentially see the greatest benefits from new RD or E.

At the same time that the review was undertaken, a number of pilot studies were also conducted to examine the potential to overcome marginal soil moisture conditions with water injection and to test the use of the ultra-high pressure water jet cutting technology AquaTill for end of season crop destruction. Water injection both alone and with the addition of the moisture attractant SE14 (Sacoa Pty Ltd) was found to have limited potential to aid crop establishment under marginal soil moisture conditions. The use of AquaTill for the delivery of herbicide to post harvest stub cotton showed promise as a zero tillage crop destruction technique. This technique will be further developed by the Dryland Cotton Research Association in cooperation with the South Australian No Tillage Farming Association.

A conclusion of this project was the region spanning the border at Goondiwindi to Rowena and east to Quirindi in NSW represented some of the areas that would most benefit from targeted RD&E. The Queensland-based Department of Agriculture as the lead agency was not ideally placed to deliver on the identified needs of this region and therefore the project was concluded after the completion of the review so that a localised delivery model could be developed.

Farming systems in cotton are changing and weed management is again becoming more complex. The rise of herbicide resistance, particularly to glyphosate and the imminent introduction of new herbicide tolerant traits to dicamba and glufosinate has changed the way weeds need to be managed. The project team undertook to pre-empt these changes.

Three new modelling and decision support products were created for industry. The BYGUM decision support tool predicts economic outcomes from summer grass weed management strategies. The tool can be used to create and compare five-year rotations of cotton, grains and fallows, including cover crops, demonstrating the effectiveness, cost and efficiency of herbicide and non-herbicide weed control. BYGUM has been used in workshops and to create extension materials, and has been downloaded by over 300 unique users to date. The Weeds of Australian Cotton ID app allows identification of 50 key weed species in cotton fields. The app uses the Lucid framework and an extensive image library. The app is among the first to include cotyledon shape as a factor for identification, meaning weeds can be identified while still small enough to control effectively. It is free to use and available in Apple and Google app stores for use offline, and via the Identic Lucid Key library for use on desktop and laptop computers.

The Diversity model is a world-first multi-herbicide, multi-species, polygenetic model of herbicide resistance evolution. It determines and quantifies how much diversity is enough, to slow or prevent evolution towards resistance. We used the model to assess the resistance potential of weed management under new triple stack systems, such as Xtendflex® cotton. Our results suggest three key points:

1. That these systems are substantially more diverse than Roundup Ready, and with the right extra tactics can be the basis of long-term effective weed management;

2. Glyphosate, glufosinate and dicamba alone or with minimal extra modes of action are incapable of controlling our existing glyphosate resistant grasses and fleabane—systems are likely to fail due to poorly controlled resistant populations long before new resistances have time to develop;

3. The 2+2+0 strategy is predicted to remain effective, but modelling multiple species at once reminds us that both grasses and broadleaves need multiple effective options in the system.

Genetic exploration of the mechanisms of glyphosate resistance in key weed species led to the discovery of the key role of ploidy and gene copy number in the evolution of glyphosate resistance. Our work on gene expression in fleabane and the genome assembly showed that there are many copies of the target site EPSPS gene in this species. This makes it very hard for fleabane to evolve target site resistance to glyphosate because many copies have to have a mutation, instead, species with many copies of the target site gene have to evolve non-targetsite resistance and this is more difficult for the weed because it usually involves more than one mutation. Feathertop Rhodes grass was found to be diploid with one copy of the EPSPS gene, and this species evolved resistance over 10 times by target site mutations. This understanding explains why it took sowthistle so long to develop resistance to glyphosate, and allows us to make predictions about herbicide resistance evolution in the future. Diploid species with one copy of the target site gene will be more likely to readily evolve resistance to a herbicide than polyploid species or those diploid species with multiple copies of the target site gene.

Work on the population genetics of four key species led to some surprising results. Fleabane is considered a well-dispersed species, but had strong regional genetic structure indicating that wind dispersal may play less of a role than previously expected. Windmill grass and feathertop Rhodes showed very little evidence for outcrossing, but there may have been some admixture in the past. Outcrossing is important because it affects the ability of a weed to develop resistance to multiple modes of action (MOA). Fleabane and sowthistle had evidence for some outcrossing in the genetic data, but we were unable to find experimental evidence for outcrossing in 200 offspring of each species. This highlights how very low levels of outcrossing might still play an important role in the evolution of resistance in species like fleabane that we had previously thought to be only self-pollinating.

In windmill grass and feathertop Rhodes grass, their highly selfing reproductive mode can be used in the fight against herbicide resistance. These species are less able to ‘stack’ resistance to different modes of action.. Our work shows, however, that feathertop has evolved resistance multiple times and how these have spread across the cotton system, and that almost 1/3 of windmill grass populations are now resistant. Each glyphosate resistant individual has the potential to evolve resistance to a second MOA. and our work highlights the importance of controlling glyphosate resistant populations to avoid multiple MOA resistance. Overall, the population genetics work emphasises the importance of the ‘0’ in the 2+2+0 strategy survivor control is essential to prevent the spread of resistance and to avoid multiple MOA resistance.

Studies on the growth and development of awnless barnyard grass, feathertop Rhodes grass, windmill grass, fleabane and sowthistle were conducted. In general, with the summer grasses, plants that emerged at the start of summer grew larger and produced more seed than those emerging later. This is where the focus of control should be for the greatest impact. However, it is important to note that plants emerging later still produce seed and need to be controlled. Sowthistle now has the ability to emerge and grow well throughout the year. Fleabane also appears to be adapting to warmer temperatures, readily producing seed throughout spring, summer and autumn.

The addition of glufosinate and dicamba has the potential to improve control, particularly on the five key species tested. When glufosinate was used, as a double knock partner, effective control was achieved in both glyphosate-resistant and susceptible populations tested. The glufosinate double knock should prove an effective option in Xtendflex® cotton.

Research on cover crops was hampered with dry conditions, and as the result the effects on weed emergence were limited. However, growers have shown cover crops to be an effective option provided they start with a clean crop and ensure that the cover provided is adequate and evenly spread.

The 2+2 and 0 was shown to be an effective management strategy for long-term resistance management. Research also concluded that additional options will provide more effective control in years with more rainfall events and subsequent emergences.