Construction of microsatellite linkage maps for Corymbia

The genus Corymbia is closely related to the genus Eucalyptus, and like Eucalyptus contains tree species that are important for sub-tropical forestry. Corymbia's close relationship with Eucalyptus suggests genetic studies in Corymbia should benefit from transfer of genetic information from its more intensively studied relatives. Here we report a genetic map for Corymbia spp. based on microsatellite markers identified de novo in Corymbia sp or transferred from Eucalyptus. A framework consensus map was generated from an outbred F 2 population (n = 90) created by crossing two unrelated Corymbia torelliana x C. citriodora subsp. variegata F1 trees. The map had a total length of 367 cM (Kosambi) and was composed of 46 microsatellite markers distributed across 13 linkage groups (LOD 3). A high proportion of Eucalyptus microsatellites (90%) transferred to Corymbia. Comparative analysis between the Corymbia map and a published Eucalyptus map identified eight homeologous linkage groups in Corymbia with 13 markers mapping on one or both maps. Further comparative analysis was limited by low power to detect linkage due to low genome coverage in Corymbia, however, there was no convincing evidence for chromosomal structural differences because instances of non-synteny were associated with large distances on the Eucalyptus map. Segregation distortion was primarily restricted to a single linkage group and due to a deficit of hybrid genotypes, suggesting that hybrid inviability was one factor shaping the genetic composition of the F2 population in this inter-subgeneric hybrid. The conservation of microsatellite loci and synteny between Corymbia and Eucalyptus suggests there will be substantial value in exchanging information between the two groups.

Using morphological traits to identify persistent lucernes for dryland agriculture in NSW, Australia

This paper reports on several studies conducted to better understand the variability between lucerne cultivars and lines, and use this to predict persistence in dryland grazing pastures in eastern Australia. Morphological traits of 20 cultivars/lines were measured in irrigated and dryland spaced plant experiments. Studies were also conducted to describe variation among lucernes in their utilisation of starch and responses to water deficit, pests and diseases. Multiple regression analyses were used to develop simple models where the measured traits could be used to predict persistence of lucerne lines in dryland evaluation experiments. Although there was significant variation among cultivars/lines in most measured traits, no single trait reliably predicted persistence of cultivars/lines in dryland evaluation experiments. However, variation in persistence at both sites could be explained by models developed by multiple regression using differences in the mean lengths of the longest stems at 10% flower in summer and winter. Persistent lucernes were those that had relatively long stems in summer and short stems in winter. Water use efficiencies, starch utilisation patterns and resistances to pests and diseases of different lucernes provided some improvement to this simple model, but these improvements were not consistent.

New annual and short-lived perennial pasture legumes for Australian agriculture--15 years of revolution

Fifteen years ago subterranean clover (Trifolium subterraneum) and annual medics (Medicago spp.) dominated annual pasture legume sowings in southern Australia, while limited pasture legume options existed for cropping areas of subtropical Australia. Since then a number of sustainability and economic challenges to existing farming systems have emerged, exposing shortcomings in these species and the lack of legume biodiversity. Public breeding institutions have responded to these challenges by developing 58 new annual and short-lived perennial pasture legumes with adaptation to both existing and new farming systems. This has involved commercialisation of new species and overcoming deficiencies in traditional species. Traits incorporated in legumes of Mediterranean Basin origin for the Mediterranean, temperate and southern subtropical climates of Australia include deeper root systems, protection from false breaks (germination-inducing rainfall events followed by death from drought), a range of hardseed levels, acid-soil tolerant root nodule symbioses, tolerance to pests and diseases and provision of lower cost seed through ease of seed harvesting and processing. Ten new species, French serradella (Ornithopus sativus), biserrula (Biserrula pelecinus), sulla (Hedysarum coronarium), gland (Trifolium glanduliferum), arrowleaf (Trifolium vesiculosum), eastern star (Trifolium dasyurum) and crimson (Trifolium incarnatum) clovers and sphere (Medicago sphaerocarpos), button (Medicago orbicularis) and hybrid disc (Medicago tornata x Medicago littoralis) medics have been commercialised. Improved cultivars have also been developed of subterranean (T. subterraneum), balansa (Trifolium michelianum), rose (Trifolium hirtum), Persian (Trifolium resupinatum) and purple (Trifolium purpureum) clovers, burr (Medicago polymorpha), strand (M. littoralis), snail (Medicago scutellata) and barrel (Medicago truncatula) medics and yellow serradella (Ornithopus compressus). New tropical legumes for pasture phases in subtropical cropping areas include butterfly pea (Clitoria ternatea), burgundy bean (Macroptilium bracteatum) and perennial lablab (Lablab purpureus). Other species and cultivars of Mediterranean species are likely to be released soon. The contributions of genetic resources, rhizobiology, pasture ecology and agronomy, plant pathology, entomology, plant chemistry and animal science have been paramount to this success. A farmer survey in Western Australia has shown widespread adoption of the new pasture legumes, while adoption of new tropical legumes has also been high in cropping areas of the subtropics. This trend is likely to increase due to the increasing cost of inorganic nitrogen, the need to combat herbicide-resistant crop weeds and improved livestock prices. Mixtures of these legumes allows for more robust pastures buffered against variable seasons, soils, pests, diseases and management decisions. This paper discusses development of the new pasture legumes, their potential use and deficiencies in the current suite. 'Ground–breaking Stuff’- Proceedings of the 13th Australian Society of Agronomy Conference, 10-14 September 2006, Perth, Western Australia.

Needs for applied climate education in agriculture

This paper reports on a purposive survey study which aimed to identify needs for the development, delivery and evaluation of applied climate education for targeted groups, to improve knowledge and skills to better manage under variable climatic conditions. The survey sample consisted of 80 producers and other industry stakeholders in Australia (including representatives from consulting, agricultural extension and agricultural education sectors), with a 58% response rate to the survey. The survey included an assessment of (i) knowledge levels of the Southern Oscillation Index and sea surface temperatures, and (ii) skill and ability in interpreting weather and climate parameters. Results showed that despite many of the respondents having more than 20 years experience in their industry, the only formal climate education or training undertaken by most was a 1-day workshop. Over 80% of the applied climate skills listed in the survey were regarded by respondents as essential or important, but only 42% of educators, 30% of consultants and 28% of producers rated themselves as competent in applying such skills. Essential skills were deemed as those that would enable respondents or their clients to be better prepared for the next extended wet or dry meteorological event, and improved capability in identifying and capitalising on key decision points from climate information and a seasonal climate outlook. The complex issue of forecast accuracy is a confounding obstacle for many in the application of climate information and forecasts in management. Addressing this problem by describing forecast 'limitations and skill' can help to overcome this problem. The survey also highlighted specific climatic tactical and strategic information collated from grazing, cropping and agribusiness enterprises, and showed the value of such information from a users perspective.

Stakeholder expectations for environmental assurance in agriculture: Lessons from the pastoral industry

This paper outlines the expectations of a wide range of stakeholders for environmental assurance in the pastoral industries and agriculture generally. Stakeholders consulted were domestic consumers, rangeland graziers, members of environmental groups, companies within meat and wool supply chains, and agricultural industry, environmental and consumer groups. Most stakeholders were in favour of the application of environmental assurance to agriculture, although supply chains and consumers had less enthusiasm for this than environmental and consumer groups. General public good benefits were more important to environmental and consumer groups, while private benefits were more important to consumers and supply chains. The 'ideal' form of environmental assurance appears to be a management system that provides for continuous improvement in environmental, quality and food safety outcomes, combined with elements of ISO 14024 eco-labelling such as life-cycle assessment, environmental performance criteria, third-party certification, labelling and multi-stakeholder involvement. However, market failure prevents this from being implemented and will continue to do so for the foreseeable future. In the short term, members of supply chains (the people that must implement and fund environmental assurance) want this to be kept simple and low cost, to be built into their existing industry standards and to add value to their businesses. As a starting point, several agricultural industry organisations favour the use of a basic management system, combining continuous improvement, risk assessment and industry best management practice programs, which can be built on over time to meet regulator, market and community expectations.

How accurate are the marker orders in crop linkage maps generated from large marker datasets?

Marker ordering during linkage map construction is a critical component of QTL mapping research. In recent years, high-throughput genotyping methods have become widely used, and these methods may generate hundreds of markers for a single mapping population. This poses problems for linkage analysis software because the number of possible marker orders increases exponentially as the number of markers increases. In this paper, we tested the accuracy of linkage analyses on simulated recombinant inbred line data using the commonly used Map Manager QTX (Manly et al. 2001: Mammalian Genome 12, 930-932) software and RECORD (Van Os et al. 2005: Theoretical and Applied Genetics 112, 30-40). Accuracy was measured by calculating two scores: % correct marker positions, and a novel, weighted rank-based score derived from the sum of absolute values of true minus observed marker ranks divided by the total number of markers. The accuracy of maps generated using Map Manager QTX was considerably lower than those generated using RECORD. Differences in linkage maps were often observed when marker ordering was performed several times using the identical dataset. In order to test the effect of reducing marker numbers on the stability of marker order, we pruned marker datasets focusing on regions consisting of tightly linked clusters of markers, which included redundant markers. Marker pruning improved the accuracy and stability of linkage maps because a single unambiguous marker order was produced that was consistent across replications of analysis. Marker pruning was also applied to a real barley mapping population and QTL analysis was performed using different map versions produced by the different programs. While some QTLs were identified with both map versions, there were large differences in QTL mapping results. Differences included maximum LOD and R-2 values at QTL peaks and map positions, thus highlighting the importance of marker order for QTL mapping

Land condition monitoring information for reef catchments: a new era

Land condition monitoring information is required for the strategic management of grazing land and for a better understanding of ecosystem processes. Yet, for policy makers and those land managers whose properties are situated within north-eastern Australia's vast Great Barrier Reef catchments, there has been a general lack of geospatial land condition monitoring information. This paper provides an overview of integrated land monitoring activity in rangeland areas of two major Reef catchments in Queensland: the Burdekin and Fitzroy regions. The project aims were to assemble land condition monitoring datasets that would assist grazing land management and support decision-makers investing public funds; and deliver these data to natural resource management(NRM) community groups, which had been given increased responsibility for delivering local environmental outcomes. We describe the rationale and processes used to produce new land condition monitoring datasets derived from remotely sensed Landsat thematic mapper (TM) and high resolution SPOT 5 satellite imagery and from rapid land condition ground assessment. Specific products include subcatchment groundcover change maps, regional mapping of indicative very poor land condition, and stratified land condition site summaries. Their application, integration, and limitations are discussed. The major innovation is a better understanding of NRM issues with respect to land condition across vast regional areas, and the effective transfer of decision-making capacity to the local level. Likewise, with an increased ability to address policy questions from an evidence-based position, combined with increased cooperation between community, industry and all levels of government, a new era has emerged for decision-makers in rangeland management.

A consensus genetic map of sorghum that integrates multiple component maps and high-throughput Diversity Array Technology (DArT) markers

Background: Sorghum genome mapping based on DNA markers began in the early 1990s and numerous genetic linkage maps of sorghum have been published in the last decade, based initially on RFLP markers with more recent maps including AFLPs and SSRs and very recently, Diversity Array Technology (DArT) markers. It is essential to integrate the rapidly growing body of genetic linkage data produced through DArT with the multiple genetic linkage maps for sorghum generated through other marker technologies. Here, we report on the colinearity of six independent sorghum component maps and on the integration of these component maps into a single reference resource that contains commonly utilized SSRs, AFLPs, and high-throughput DArT markers. Results: The six component maps were constructed using the MultiPoint software. The lengths of the resulting maps varied between 910 and 1528 cM. The order of the 498 markers that segregated in more than one population was highly consistent between the six individual mapping data sets. The framework consensus map was constructed using a "Neighbours" approach and contained 251 integrated bridge markers on the 10 sorghum chromosomes spanning 1355.4 cM with an average density of one marker every 5.4 cM, and were used for the projection of the remaining markers. In total, the sorghum consensus map consisted of a total of 1997 markers mapped to 2029 unique loci ( 1190 DArT loci and 839 other loci) spanning 1603.5 cM and with an average marker density of 1 marker/0.79 cM. In addition, 35 multicopy markers were identified. On average, each chromosome on the consensus map contained 203 markers of which 58.6% were DArT markers. Non-random patterns of DNA marker distribution were observed, with some clear marker-dense regions and some marker-rare regions. Conclusion: The final consensus map has allowed us to map a larger number of markers than possible in any individual map, to obtain a more complete coverage of the sorghum genome and to fill a number of gaps on individual maps. In addition to overall general consistency of marker order across individual component maps, good agreement in overall distances between common marker pairs across the component maps used in this study was determined, using a difference ratio calculation. The obtained consensus map can be used as a reference resource for genetic studies in different genetic backgrounds, in addition to providing a framework for transferring genetic information between different marker technologies and for integrating DArT markers with other genomic resources. DArT markers represent an affordable, high throughput marker system with great utility in molecular breeding programs, especially in crops such as sorghum where SNP arrays are not publicly available.

Remote Sensing - based precision agriculture tool for the sugar industry

The project will produce practical and relevant benchmarks, protocols and recommendations for the adoption of remote sensing technologies for improved in season management and therefore production within the Australian sugar cane industry.

Precision Agriculture and Remote Sensing Technologies in Central Queensland agricultural production systems

Demonstrate potential benefits of various Precision Agricultural technologies to Central Queensland farming community.

Relocation of Intensive Agriculture to Northern Australia: The Case of the Rice Industry

Development of new agricultural industries in northern Australia is seen as a way to provide food security in the face of reduced water availability in existing regions in the south. This report aims to identify some of the possible economic consequences of developing a rice industry in the Burdekin region, while there is a reduction of output in the Riverina. Annual rice production in the Riverina peaked at 1.7 M tonnes, but the long-term outlook, given climate change impacts on that region and government water buy-backs, is more likely to be less than 800,000 tonnes. Growers are highly efficient water users by international standards, but the ability to offset an anticipated reduction in water availability through further efficiency gains is limited. In recent years growers in the Riverina have diversified their farms to a greater extent and secondary production systems include beef, sheep and wheat. Production in north Queensland is in its infancy, but a potentially suitable farming system has been developed by including rice within the sugarcane system without competition and in fact contributing to the production of sugar by increasing yields and controlling weeds. The economic outcomes are estimated a large scale, dynamic, computable general equilibrium (CGE) model of the world economy (Tasman Global), scaled down to regional level. CGE models mimic the workings of the economy through a system of interdependent behavioural and accounting equations which are linked to an input-output database. When an economic shock or change is applied to a model, each of the markets adjusts according to the set of behavioural parameters which are underpinned by economic theory. In this study the model is driven by reducing production in the Riverina in accordance with relationships found between water availability and the production of rice and replacement by other crops and by increasing ride production in the Burdekin. Three scenarios were considered: • Scenario 1: Rice is grown using the fallow period between the last ratoon crop of sugarcane and the new planting. In this scenario there is no competition between rice and sugarcane • Scenario 2: Rice displaces sugarcane production • Scenario 3: Rice is grown on additional land and does not compete with sugarcane. Two time periods were used, 2030 and 2070, which are the conventional time points to consider climate change impacts. Under scenario 1, real economic output declines in the Riverina by $45 million in 2030 and by $139 million in 2070. This is only partially offset by the increased real economic output in the Burdekin of $35 million and $131 million respectively.

Relocation of Intensive Agriculture to Northern Queensland The Cotton Industry

Development of new agricultural industries in northern Australia is often perceived as a solution to changes in water availability that have occurred within southern Australia as a result of changes to government policy in response to and exacerbated by climate change. This report examines the likely private, social and community costs and benefits associated with the establishment of a cotton industry in the Burdekin. The research undertaken covers three spatial scales by modelling the response of cotton and to climate change at the crop and farm scale and linking this to regional scale modelling of the economy. Modelling crop growth as either a standalone crop or as part of a farm enterprise provides the clearest picture of how yields and water use will be affected under climate change. The alternative to this is to undertake very costly trials in environmental chambers. For this reason it is critical that funding for model development especially for crops being crop in novel environments be seen as a high priority for climate change and adaptation studies. Crop level simulations not only provide information on how the crop responds to climate change, they also illustrate that that these responses are the result of complex interactions and cannot necessarily be derived from the climate information alone. These simulations showed that climate change would lead to decreased cotton yields in 2030 and 2050 without the affect of CO2 fertilisation. Without CO2 fertilisation, yields would be decreased by 3.2% and 17.8%. Including CO2 fertilisation increased yields initially by 5.9%, but these were reduced by 3.6% in 2050. This still represents a major offset and at least ameliorates the impact of climate change on yield. To cope with the decreased in-crop rainfall (4.5% by 2030 and 15.8% in 2050) and an initial increase in evapotranspiration of 2% in 2030 and

Performance of Pinus elliottii, Pinus caribaea, their F-1, F-2 and backcross hybrids and Pinus taeda to 10 years in the Mesopotamia region, Argentina

Performances of Pinus taxa were studied to 10 years of age in two trials in each of Misiones and Entre Rios provinces across the Mesopotamia region of Argentina. Taxa comprised 22 populations from sources in Argentina, Australia, Brazil and Zimbabwe including Pinus elliottii var. elliottii (Pee), Pinus caribaea var. hondurensis (Pch), their four, inter-specific hybrids (F-1, F-2 and backcrosses from F-1 to Pch and to Pee-all as broadly based bulks); other Pee and Pinus taeda (Pt) comprised narrower or unspecified bulks. Variable numbers of taxa were missing at each site. Mean survival across sites at age 10 years ranged 53.2-91.3% averaging 74.2%. Analysis of variance of plot means indicated population effect was statistically significant (p < 0.05) for all or most growth and quality traits at all sites. However, significant differences from the nominated check seedlot at the Entre Rios sites (Pee, Australia) were extremely rare, while quite common at the northern, Misiones sites (check seedlot a Pt population). In the Misiones trials, F-1, F-2 and both backcross hybrids showed better stem straightness than Pee and Pt from Argentina, generally with statistically significant differences (p < 0.05). Pt showed lowest forking scores (desirable). Taxon x environment interaction was statistically significant (p < 0.01) for growth traits only (p > 0.05). However, this interaction contributed an average of only 34.1% of the taxon variance suggesting a lack of practical importance. Taxa most suitable for deployment in the Mesopotamia region, Argentina are suggested.

Methane in Australian agriculture: current emissions, sources and sinks, and potential mitigation strategies

Methane is a potent greenhouse gas with a global warming potential ∼28 times that of carbon dioxide. Consequently, sources and sinks that influence the concentration of methane in the atmosphere are of great interest. In Australia, agriculture is the primary source of anthropogenic methane emissions (60.4% of national emissions, or 3260kt-1methaneyear-1, between 1990 and 2011), and cropping and grazing soils represent Australia's largest potential terrestrial methane sink. As of 2011, the expansion of agricultural soils, which are ∼70% less efficient at consuming methane than undisturbed soils, to 59% of Australia's land mass (456Mha) and increasing livestock densities in northern Australia suggest negative implications for national methane flux. Plant biomass burning does not appear to have long-term negative effects on methane flux unless soils are converted for agricultural purposes. Rice cultivation contributes marginally to national methane emissions and this fluctuates depending on water availability. Significant available research into biological, geochemical and agronomic factors has been pertinent for developing effective methane mitigation strategies. We discuss methane-flux feedback mechanisms in relation to climate change drivers such as temperature, atmospheric carbon dioxide and methane concentrations, precipitation and extreme weather events. Future research should focus on quantifying the role of Australian cropping and grazing soils as methane sinks in the national methane budget, linking biodiversity and activity of methane-cycling microbes to environmental factors, and quantifying how a combination of climate change drivers will affect total methane flux in these systems.