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.

Application of a model to assess aflatoxin risk in peanuts.

When exposed to hot (22-35 degrees C) and dry climatic conditions in the field during the final 4-6 weeks of pod filling, peanuts (Arachis hypogaea L.) can accumulate highly carcinogenic and immuno-suppressing aflatoxins. Forecasting of the risk posed by these conditions can assist in minimizing pre-harvest contamination. A model was therefore developed as part of the Agricultural Production Systems Simulator (APSIM) peanut module, which calculated an aflatoxin risk index (ARI) using four temperature response functions when fractional available soil water was <0.20 and the crop was in the last 0.40 of the pod-filling phase. ARI explained 0.95 (P <= 0.05) of the variation in aflatoxin contamination, which varied from 0 to c. 800 mu g/kg in 17 large-scale sowings in tropical and four sowings in sub-tropical environments carried out in Australia between 13 November and 16 December 2007. ARI also explained 0.96 (P <= 0.01) of the variation in the proportion of aflatoxin-contaminated loads (>15 mu g/kg) of peanuts in the Kingaroy region of Australia during the period between the 1998/99 and 2007/08 seasons. Simulation of ARI using historical climatic data from 1890 to 2007 indicated a three-fold increase in its value since 1980 compared to the entire previous period. The increase was associated with increases in ambient temperature and decreases in rainfall. To facilitate routine monitoring of aflatoxin risk by growers in near real time, a web interface of the model was also developed. The ARI predicted using this interface for eight growers correlated significantly with the level of contamination in crops (r=095, P <= 0.01). These results suggest that ARI simulated by the model is a reliable indicator of aflatoxin contamination that can be used in aflatoxin research as well as a decision-support tool to monitor pre-harvest aflatoxin risk in peanuts.

Germination, emergence, and persistence of Sonchus oleraceus, a major crop weed in subtropical Australia.

Sonchus oleraceus (common sowthistle) is a dominant weed and has increased in prevalence in conservation cropping systems of the subtropical grain region of Australia. Four experiments were undertaken to define the environmental factors that favor its germination, emergence, and seed persistence. Seeds were germinated at constant temperatures between 5 and 35C and water potentials between 0 and -1.4 MPa. The maximum germination rate of 86-100% occurred at 0 and -0.2 MPa, irrespective of the temperature when exposed to light (12 h photoperiod light/dark), but the germination rate was reduced by 72% without light. At water potentials of -0.6 to -0.8 MPa, the germination rate was reduced substantially by higher temperatures; no seed germinated at a water potential >-1.0 MPa. Emergence and seed persistence were measured over 30 months following seed burial at 0 (surface), 1, 2, 5, and 10 cm depths in large pots that were buried in a south-eastern Queensland field. Seedlings emerged readily from the surface and 1 cm depth, with no emergence from below the 2 cm depth. The seedlings emerged during any season following rain but, predominantly, within 6 months of planting. Seed persistence was short-term on the soil surface, with 2% of seeds remaining after 6 months, but it increased with the burial depth, with 12% remaining after 30 months at 10 cm. Thus, a minimal seed burial depth with reduced tillage and increased surface soil water with stubble retention has favored the proliferation of this weed in any season in a subtropical environment. However, diligent management without seed replenishment will greatly reduce this weed problem within a short period.

Emergence and seed persistence of Echinochloa colona, Urochloa panicoides and Hibiscus trionum in the sub-tropical environment of north-eastern Australia.

Better understanding of seed-bank dynamics of Echinochloa colona, Urochloa panicoides and Hibiscus trionum, major crop weeds in sub-tropical Australia, was needed to improve weed control. Emergence patterns and seed persistence were investigated, with viable seeds sown at different depths in large in-ground pots. Seedlings of all species emerged between October and March when mean soil temperatures were 21-23C. However, E. colona emerged as a series of flushes predominantly in the first year, with most seedlings emerging from 0-2 cm. Urochloa panicoides emerged mostly as a single large flush in the first two years, with most seedlings emerging from 5 cm. Hibiscus trionum emerged as a series of flushes over three seasons, initially with majority from 5 cm and then 0-2 cm in the later seasons. Longevity of the grass seed was short, with <5% remaining after burial at 0-2 cm for 24 months. In contrast, 38% of H. trionum seeds remained viable after the same period. Persistence of all species increased significantly with burial depth. These data highlight that management strategies need to be tailored for each species, particularly relating to the need for monitoring, application times for control tactics, impact of tillage, and time needed to reduce the seed-bank to low numbers.

Detection of Polymyxa graminis in a barley crop in Australia.

Polymyxa graminis was detected in the roots of barley plants from a field near Wondai, Queensland, in 2009. P. graminis was identified by characteristic sporosori in roots stained with trypan blue. The presence of P. graminis f. sp. tepida (which is hosted by wheat and oats as well as barley) in the roots was confirmed by specific PCR tests based on nuclear ribosomal DNA. P. graminis is the vector of several damaging soil-borne virus diseases of cereals in the genera Furovirus, Bymovirus and Pecluvirus. No virus particles were detected in sap extracts from leaves of stunted barley plants with leaf chlorosis and increased tillering. Further work is required to determine the distribution of P. graminis in Australian grain crops and the potential for establishment and spread of the exotic soil-borne viruses that it vectors.

Impact of tillage and residues from rotation crops on the nematode community in soil and surface mulch during the following sugarcane crop.

The impact of three cropping histories (sugarcane, maize and soybean) and two tillage practices (conventional tillage and direct drill) on plant-parasitic and free-living nematodes in the following sugarcane crop was examined in a field trial at Bundaberg. Soybean reduced populations of lesion nematode (Pratylenchus zeae) and root-knot nematode (Meloidogyne javanica) in comparison to previous crops of sugarcane or maize but increased populations of spiral nematode (Helicotylenchus dihystera) and maintained populations of dagger nematode (Xiphinema elongatum). However the effect of soybean on P zeae and M. javanica was no longer apparent 15 weeks after planting sugarcane, while later in the season, populations of these nematodes following soybean were as high as or higher than maize or sugarcane. Populations of P zeae were initially reduced by cultivation but due to strong resurgence tended to be higher in conventionally tilled than direct drill plots at the end of the plant crop. Even greater tillage effects were observed with M. javanica and X. elongatum, as nematode populations were significantly higher in conventionally tilled than direct drill plots late in the season. Populations of free-living nematodes in the upper 10 cm of soil were initially highest following soybean, but after 15, 35 and 59 weeks were lower than after sugarcane and contained fewer omnivorous and predatory nematodes. Conventional tillage increased populations of free-living nematodes in soil in comparison to direct drill and was also detrimental to omnivorous and predatory nematodes. These results suggest that crop rotation and tillage not only affect plant-parasitic nematodes directly, but also have indirect effects by impacting on natural enemies that regulate nematode populations. More than 2 million nematodes/m(2) were often present in crop residues on the surface of direct drill plots. Bacterial-feeding nematodes were predominant in residues early in the decomposition process but fungal-feeding nematodes predominated after 15 weeks. This indicates that fungi become an increasingly important component of the detritus food web as decomposition proceeds, and that that the rate of nutrient cycling decreases with time. Correlations between total numbers of free-living nematodes and mineral N concentrations in crop residues and surface soil suggested that the free-living nematode community may provide an indication of the rate of mineralisation of N from organic matter.

Sustaining productivity of tropical red snappers using new monitoring and reference points

OBJECTIVES: 1. Analyse current monitoring and logbook data sets, as well as survey and other information,to establish whether these data provide sufficient power to develop critical indicators of fishery performance. 2. Provide a risk analysis that examines the use of age structure and catch rate information for development of critical indicators, and response rules for those criteria, in the absence of other fishery information. 3. Develop a monitoring program that uses commercial vessels from the fishery to provide independent data.

Development of a Gulf community based natural resource monitoring program.

Development of a Gulf community based natural resource monitoring program, with sawfish as an initial focus.

Ground Cover Monitoring in the Fitzroy Basin

Ground Cover Monitoring in the Fitzroy Basin.

Monitoring darkling beetle populations for resistance to spinosad

Management of insecticide resistance.

Better Macadamia crop forecasting

Better Macadamia crop forecasting.

Integrated crop management for brassica production

Early season beneficials in brassica crops.

Better Macadamia Crop Forecasting - Part 2

The continually expanding macadamia industry needs an accurate crop forecasting system to allow it to develop effective crop handling and marketing strategies, particularly when the industry faces recurring cycles of unsustainably high and low commodity prices. This project aims to provide the AMS with a robust, reliable predictive model of national crop volume within 10% of the actual crop by 1 April each year by factoring known seasonal, environmental, cultural, climatic, management and biological constraints, together with the existing AMS database which includes data on tree numbers, tree age, variety, location and previous season's production.

Relocation of intensive crop production systems to northern Australia

To adapt to climate variability and a lack of irrigation water, businesses and growers in southern Australia, northern New South Wales and southern Queensland are, or are considering, migrating their businesses to northern Australia.