This study examines the effectiveness of publicly-available data to identify farm-scale regions of similarity, and classifies the distribution of physical (available water capacity (AWC)) and chemical (pH and electrical conductivity (ECe)) soil constraints in a northern NSW dryland cotton system. The incorporated open-source information could identify spatial variability in key soil attributes, though further data accuracy improvements will be increasingly valuable. ECe (salinity) levels were low, and there was no relationship between AWC and cotton or wheat yield. However, a strongly alkaline pH within a crops capable rooting depth across 70% of the property was identified, with an easily interpretable depth to pH constraint map produced. While depth to pH constraint had a major impact on wheat yield, no impact on cotton yield was observed. Such a discrepancy highlights the importance of analysing multiple years of crop yield monitor data as the most limiting soil constraint may vary based on seasonal conditions. The accurate characterisation of depth to pH constraint across both the property and region will assist in classifying its influence on other crop types and growing seasons in an overall bid to overcome its possible negative implications on productivity and profitability via the adoption of best management practices. Further work will focus on using the developed approach to map the depth to other important soil constraints, such as sodicity.

The Nucleopolyhedroviruses (NPV) are dsDNA invertebrate-specific obligate pathogens of the insect orders Lepidoptera, Hymenopteran and Dipteran belonging to the family Baculoviridae (Baculovirus). An NPV consists of a genome with lengths between 80 and 180 kbp and a community of phenotypically and genetically diverse virus strains that are co-occluded within a protein body. NPVs are widely used in biological control of Lepidopteran pests, and understanding isolate dynamics, diversity and evolution is important in resistance management strategies and developing next generation biopesticides with desired phenotypic traits.

The aim of this study was to apply next generation sequencing and develop bioinformatic techniques to expand and accelerate current knowledge of baculoviruses by studying the dynamics, diversity and evolution. This included the development of a new bioinformatic pipeline to analyse the within-isolate and within-strain diversity, applying this pipeline to monitor the change in genotype abundance during the infection cycle and derivatisation of in vitro and in vivo selected strains from a wild type isolate of commercial importance, Helicoverpa armigera Single Nucleopolyhedrovirus (HaSNPV) isolate AC53 (AC53). Derived genomes were analysed to identify trait or isolation technique specific mutations, and the global relationships of these strains to all known HaSNPV isolates.

Phylogenetic analysis of all known HaSNPV and H. zea SNPV isolates with the addition of AC53 and some of its derivatives supported the claim that these viruses are the same viral species, and suggests that the HaSNPV species may have originated in Australia. The use of whole genomes in phylogenetic analysis gave greater resolution than the more commonly used analysis using selected open reading frames.

Five strain derivatisation approaches were applied: two in vitro (in tissue culture) and three in vivo. Analysis of both in vitro and in vivo -derived strains genomes identified selection specific mutations, with fast speed of kill, slow speed of kill and maximum virus production strains containing trait specific mutations. Biological characterisation of these trait-specific strains identified significant virulence-transmission trade-offs such as enhanced speed of kill but reduced efficacy which implicates commercial optimisation of strains.

A new software pipeline called the ‘Meta-barcoding Genotyping and Abundance Pipeline’ (MetaGaAP) was developed to identify genotypes and their relative abundance within the AC53 isolate. This was validated by Sanger sequencing and comparison to the AC53-T2 strain. The pipeline was applied to monitor AC53 during the infection cycle and identified two evolutionary effects occurring within the population; weak-negative selection with mutation bias and a ‘drift barrier’ to limit the effects of genetic drift. Furthermore, time-course assays revealed a significant reduction in dominant genotype abundance with an increase in minor genotype abundance when the initial viral stock is compared to the final viral product. This implicates commercial production as the starting material and the produced material contain different genotype abundance profiles, however, both products contain the same genotype composition.

In addition, results presented throughout this study suggested that NPVs fit the viral quasispecies model as mutations that arose were the result of mutational robustness and genotype cooperation. Limitations observed with current NGS and bioinformatic techniques partially impacted the described results but may eventually resolve with advent of third-generation sequencing

In 2017-18, CRDC invested $25.1 million into 318 RD&E projects in collaboration with 118 research partners and growers who conducted on-farm trials, across five key program areas: farmers, industry, customers, people and performance.

CRDC’s role is to invest in RD&E on behalf of cotton growers and the government, with the outcomes boosting the productivity and profitability of our industry. RD&E, and its resulting innovations, are a key driving force behind the Australian cotton industry’s continued success.

The findings from these research projects continue to be extended through a range of methods, including the industry’s joint extension program CottonInfo. The adoption of best management practices is also encouraged via the industry program myBMP. CRDC is a founding partner of both programs.

The Green Vegetable Bug, Nezara viridula, has recently become a more significant pest of Australian cotton but it is not a problem every season. This project addressed aspects of the multiple host use and movement of N. viridula as they relate to cotton, as well as the genetic relationship between Australian N. viridula and the global populations of this pest.

Samples of N. viridula were collected from northern and eastern Australia and from a variety of weed and crop hosts, with an emphasis on cotton. The abundance of N. viridula was low for the duration of the project but about 800 adult insects were collected overall. Comprehensive phylogenetic and population genetics methods were used to address each of the questions. The methods developed during this study will be made available to other researchers through scientific publications.

The Australia populations of N. viridula come from two different evolutionary lineages, one European and one Asian. The former is distributed across eastern Australia and the other across northern Australia. At some point in the past some individuals of the Asian lineage have mated with individuals of the European lineage in northern Queensland but these events appear to have occurred only rarely. Across the different host plant species there are no genetic differences between N. viridula that would indicate separate host-specific gene pools.

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The N. viridula in eastern Australia are more genetically distinct from one another the greater the geographic distance that separates the sampling localities from which they were collected. This slight genetic differentiation over geographic distance is present in insects collected across two years and this indicates that N. viridula populations remain relatively localised in the short term. This result indicates that the host plants available to N. viridula within each cotton growing region will be the most relevant for predicting the abundance of this insect in cotton. Pest pressure from N. viridula was low for the duration of the project and so this pattern may be different during seasons when N. viridula is present in high numbers. In years of high abundance host plants might be found between growing regions, and allow for the recruitment of N. viridula over a wider area.

Future research that addresses the host use of N. viridula should investigate populations from each cotton growing region independently, as local conditions, such as the crop and weed host plants used by N. viridula each season before cotton becomes attractive, will be the most relevant to late season numbers of this insect in cotton. A previous CRDC funded project has already addressed N. viridula host use in central New South Wales. If cotton is grown regularly in northern Australia then it would be prudent to treat the N. viridula population there as a separate entity, as there may be significant differences in their biology which could affect their host use and abundance in cotton. Any differences would therefore influence the development of management strategies.

Cotton is now a significant crop in the irrigated Riverina region of southern NSW, Australia, increasing in area from approximately 39,000 ha in 2013 to 90,050 ha in 2018 and contributing from between 10-30% of Australia’s total cotton production (Cotton Info, 2018). Many cotton crops and processing facilities in the region (Whitton, Hay, Carathool) are located in close proximity (< 50 km) to chicken production (meat and eggs), which has also increased significantly in recent years. Around Griffith, NSW, it is estimated that poultry production is currently generating approximately 10,000 m3/week of manure and chicken litter (raw manure + bedding material which is usually rice hulls or sawdust). There is quite significant variability in the nutrient content and dry matter mass of manures and wastes that are cleaned out of chicken sheds (Griffiths, 2007). However, considering average values of plant total nutrients as 2.9%N, 1.2% P, 2.8 % K and 60% dry matter, our estimates suggest that on an annual regional basis, there maybe 5400 tonnes of TN, 2246 tonnes of total P and 5200 tonnes of total K. These are sizeable amounts of nutrient resources which have the potential to be relatively easily reused for productive purposes in an economically attractive way for farmers. Coincidentally, this re-use may contribute to offsetting the amount of artificially produced fertilizers that are applied regionally, which offers positive environmental outcomes.

A significant number of growers (> 50%) are applying the available chicken wastes to their land, mainly with a view to maintain or enhance yield through the soil fertility benefits that organic amendments can offer (nutrient efficiency and biological and physical property maintenance and improvement). Typically application rates are between 2-5 t/ha, spread and surface incorporated early in the winter when field conditions are optimal and nutrient mineralisation and losses are minimised due to low microbial activity under relatively cold winter conditions. When temperatures start to increase in spring, mineralisation of nutrients and other physical and biological beneficial effects of manure amendments are considered to potentially become available from planting through the growing season and long term.

The organic materials are not usually applied to fields by growers as fertilizer replacements, rather, in addition to conventional fertilizers as there is a lack of adequate manure management recommendations for use in cotton production under different soil types and cropping systems. The usual rates of 2-5 t/ha of animal manure applied are convenience based rather than research based and can’t be relied upon in high yield cotton systems without supplemental N and other nutrient fertilization. Application rates of chemical N and other fertilizers are determined from field tests, petiole tests and experience. However, there are few detailed studies on how amendments impact on soil processes and thus effect crop production (Flavel and Murphy, 2006). The productivity responses of cotton crops in major irrigated soil types of the Australian southern region to organic amendment types, rates and frequency and placement of application, alone or in combination with fertilizers is unknown. The nutritional value, extra profit and soil sustainability measures that the organic products provide in the short and long term compared with fertilizers are ambiguous and difficult to predict. One particular reason for this is that manures vary greatly in their composition and degree of stabilization. Chicken litter available N, P, K composition and moisture content can vary by 2-10 times from one batch to another (Griffiths, 2007, Azeez and Averbeke, 2010). To successfully manage nutrient cycling from chicken litter it is necessary to know their decomposition rate and the influence that may have on the biogeochemical processes in the soil to which they are being applied.

Overall, there is a large body of research that shows that application of organic amendments improves soil fertility (see reviews of Murphy, 2014, Macdonald and Baldock, 2010 and Krull, 2004). Soil organic matter affects water holding capacity, nutrient retention, cation exchange capacity, aggregate stability and buffering capacity to acidification. It has a clear effect on nutrient supply, nutrient cycling, soil strength and compaction, water infiltration and gaseous exchange. A number of studies have reported the positive effect of soil organic carbon on cereal, potato, corn and rice in tropical and sub-tropics, Russia, China, Argentina (Johnston et al, 2009, Lal, 2010, Chen et al 2018). However, there are now several reputable publications detailing rigorous meta-analysis of well-known long term crop trials that conclude, on average there are insignificant increases in yield which can be attributed to organic inputs (Edmeades, 2003; Oelofse et al, 2014; Hijbeek et al 2017). The major finding that came out of the original work of Rothamstead was that organic fertilizers gave the same yield as farmyard manure, not that synthetic fertilizers were necessarily better than organics or vice versa (Johnston and Poulton, 2018). Johnston et al (2015) has countered some of the misconceptions surrounding the effects of SOM by finding that as crop cultivars with increased yield potential have been introduced, yields in many Rothamstead long term experiments are now larger on soils with more SOM. In contrast, Oelofse et al (2014), argues that the evidence from a lot of published organic amendment trials is quite variable and obtained from one location and therefore generalisations are difficult. In many studies, the analyses are dependent on, or fail to account for other factors that can affect yield such as the mineralizable C fraction, soil fertility status and managerial inputs such as nutrients and water (Lal, 2010).

Favourable agronomic, profit and soil conditioning effects for poultry litter application in cotton production have been documented within 3-5 years, in Alabama and Mississippi on silt loam soils (Reddy et al 2007; Tewolde et al, 2007; Tewolde et al 2016) and degraded upland soils in Louisiana (Lofton et al 2014). In other studies, the benefit of poultry litter to cotton production was stated as far exceeding the nutrient concentrations through soil conditioning (Tewolde et al 2010). Mitchell and Tu (2005) found broiler litter increased cotton yield in both no till and conventional till over a 13 year period in silty clay loam non-irrigated soils and residual effects in the year after application were found to be beneficial to yield.

Fertilizer replacement value of manure is affected by a number of factors including the form of nutrients, organo-metallic complexes, in the amendment, soil type and pH, crop type, application method, timing and manuring history (Jensen, 2013). It is well known that organic amendments including chicken litter cannot be depended on in commercial situations as a soul source of crop nutrients, even when applied at high rates due to nutrient imbalances and asynchronic release of nutrients that do not match plant requirements. Supplementary synthetic fertilizers are necessary in commercial food and fibre crops but little systematic research has been undertaken to evaluate the fertilizer replacement value of organic amendments and any improvements in nutrient use efficiency they may offer.

The current project has aimed at more thoroughly establishing how to optimise the management and application of manure that is available in the southern cotton growing region for tangible productivity and nutrient use efficiency benefits. Field experiments have focussed on incorporating the use of chicken manure and litter into farmer agronomic practise and specific site issues. One focus has been on the fertilizer replacement value of the organic wastes when used in combination with chemical fertilizers for N, P and micronutrients Zn, Mn and Cu. A second focus has been on the effects that supplementary chicken litter or manure application may have to rectify productivity and nutrient deficiencies in newly developed land formed fields where ‘cuts’ can have a significant effect on productivity for several years.

Replicated cotton field trials on two soil types, red and grey chromosols with a range of chicken manure and litter amendment rates, have been established to evaluate productivity, nitrogen efficiency and macro and micro-nutrient uptake. The trials have been used to assess crop responses, examine the contributions and availability of important nutrients other than nitrogen (P, K, S, Zn, Cu) water stable aggregates and any negative or inconsequential impacts according to manure rate treatments. The work has provided regionally specific information which can be used to refine existing general manure management guidelines developed for broad acre cereals. These may assist cotton growers in the Murrumbidgee Valley to better estimate how manure may be applied to reduce synthetic fertilizer inputs without compromising yield and quality outcomes.

The potential economic gains for the Australian farm sector and associated supply chains arising from the adoption of decision agriculture will be estimated and recommendations made for business models and strategies to deliver decision agriculture products and services.

Decision agriculture is the analysis of digitally collected farm data along with other relevant digital datasets such as soils and environmental data to inform decision making associated with the production and supply of farm goods. The potential economic gain of decision agriculture will be estimated by determining the improvements to productivity and profitability that will be possible under a fully technologically enabled farm sector. The Centre for International Economics CIE-REGIONS general equilibrium model of the Australian economy will then be used to estimate the gains to the economy that could be achieved because of the increased productivity and profitability.

Decision agriculture will be enabled by access to appropriate data and data analytics, connectivity, clear value propositions and rules and procedures for data ownership and sharing. The contribution of these enabling functions to the economic gain achieved through decision agriculture will be measured through close consultation with other Precision to Decision (P2D) projects.

The provision of decision agriculture products and services to farmers will occur through private businesses, research agencies and government. Business models and strategies to deliver decision agriculture will differ depending on sector size, availability of commercial options and extent of integration with the processing sector amongst many other factors. A situation analysis will be performed to determine the structural factors for each farm sector involved in the P2D project that is relevant to the delivery of decision agriculture and appropriate recommendations made for suitable business models and strategies. Input will be obtained from an International consulting firm on the likely impact of the global development of digital agriculture technologies and associated business models.

This Travel sponsorship suuported Dr Sharwood to travel to Lubbock Texas USA to meet with Dr Paxton Payton and Dr James Mahan at the USDA-ARS to begin collaborative research to determine the interactive effects of water deficit and elevated temperature with elevated [COi) on cotton growth and physiology, and attend the Plant Biology 2015 meeting taking place at Minneapolis, Minnesota United States. Dr Sharwood presented project research results arising from the Science and Innovation Award project, along with subsequent follow up experiments.

Resistance to insecticides has repeatedly developed in Helicoverpa armigera around the world and is of major concern to the cotton industry in Australia. CYP337B3, the gene responsible for fenvalerate resistance was identified in 2012 (Joußen et al.) Different alleles of this resistance gene have been identified at different frequencies in different regions of the world. Identifying the variants present in Northern Australia gives us an insight into movement of H. armigera from Asia in Australia. A total of 91 samples from N. Australia, were tested. In this data set, the majority of individuals collected from the field in Northern Australia (80%) were positive for CYP337B3, either as a homozygote or a heterozygote. Almost half (47%) of the alleles sequenced from Northern Australia were found to be the allele predominantly found in Asia (CYP337B3v2) as compared to 20% of alleles from the cotton growing regions identified as Asian. The major implication from this work is that there is gene flow between Asian populations and Australia. F2 testing of an individual collected from the Ord River showed that this CYP337B3v2 gene was associated with survival of a discriminating dose of fenvalerate. Further work is required to examine connectivity between these populations and the potential risk of other resistance alleles arriving from Asia.

The Cotton export market is highly competitive and when it comes to quality Australia needs to be the world's best. To realise this goal, the whole of the Australian Cotton supply chain must continuously improve its supply of premium upland cotton. Cotton spinning mills already recognise that Australian cotton has desirable fibre characteristics and low contamination. These attributes increase efficiency for spinners and they actively seek Australian cotton and are sometimes prepared to pay a premium. To maintain this reputation continuous improvement across the whole supply chain is essential. The Australian cotton industry and CSIRO have expanded investment in post-harvest cotton processing research. The aim is to discover ways of maintaining and enhancing the quality of cotton produced by Australian growers. In July 2008 Rene van der SIuijs and the CSIRO team in Geelong opened the doors of their facility and hosted the 7th 'Cotton Field to Fabric Course'. This was the 8th course run in Geelong and it has been attended by participants from the length and breadth of the supply chain. They have included Agronomists, Growers, Researchers, Ginners and even students studying design. The course provided participants with an opportunity to see firsthand how cotton is processed from a bale into fabric. At Geelong they have both full scale and miniature versions of the equipment used in cotton processing factories used overseas including drawing and carding machines, spinning frame, weaving machines, and dyeing facilities. Understanding how these processes occur helps participants understand the importance quality standards and how our actions impact on the chain. The Australian cotton industry will benefit from a focus on its customer's needs and a desire to exceed their expectations. The' field to fabric 'course is one activity that the industry is undertaking to increase knowledge of cotton quality. It comes highly recommended by all who have participated.