Vegetable soil health systems for overcoming limitations causing soil borne diseases

The purpose of the report is to summarise progress in developing vegetable production systems with improved soil health that overcome soil limitations with the potential to suppress soil borne diseases. Management approaches to soil health improvement were regionally specific to overcome regional soil limitations in different production environments.

ACIAR Improving soil health in support of sustainable development in the Pacific

The proposed project focuses on developing research-based indicators that growers and extensionists can use to assess soil health status (including key chemical, physical and biological variables), as well as extension approaches to communicate soil health.

Defining critical soil nutrient concentrations in soils supporting grains and cotton in Northern NSW and Queensland

This project focussed on the phosphorus (P) and potassium (K) status of northern cropping soils. Stores of P and K have been depleted by crop removal and limited fertiliser application, with depletion most significant in the subsoil. Soil testing strategies are confounded by slowly available mineral reserves with uncertain availability. The utility of new soil tests was assessed to measure these reserves, their availability to plants quantified and a regional sampling strategy undertaken to identify areas of greatest P and K deficit. Fertiliser application strategies for P and K have been tested and the interactions between these and other nutrients have been determined in a large field program.

Soil Micro Testing

Soil Micro Testing for nematodes on grain farms.

Soil C stocks in grains and sugar farming systems

Quantify soil C stocks in grains and sugarcane cropping systems of Queensland, including impacts of management practices.

Innovative management of herbicide resistant weeds - seed banks and soil biology

The project will evaluate seed bank depletion of key northern herbicide resistant weeds under different environments, cropping systems, crop agronomies and non-chemical control tactics. The project will also evaluate soil biology and seed bank relationships to explain differences in seed bank persistence.

Crop sequences to manage soil pathogens and increase northern grain production

This is part of a GRDC funded project led by Dr Jeremy Whish of CSIRO Ecosystem Sciences. The project aims to build a root-lesion nematode module into the crop growth simulation program APSIM (Agricultural Production Systems Simulator). This will utilise existing nematode and crop data from field, glasshouse and laboratory research led by Dr John Thompson. New data will be collected to validate and extend the model.

National soil health consortium

Work with Land and Water Australia to coordinate soil health work across Queensland and Australia.

Declining soil phosphorus reserves on sustainable agricultural production systems

PhD scholarship investigating the relative sensitivity of nitrogen fixation in adapted grain and ley legume species to low soil phosphorus.

DAQ00049 Farming Systems for Central Queensalnd Soil Research and Monitoring

Sustainable Farming Systems for Central Queensland.

QPI64 Sustainable Soil Health Management Workshop Northern Broadacre Cropping Industries

Workshops to increase participants understanding and knowledge by farm businesses and healthy catchments farmers about the role of soil health in supporting sustainable through variable circumstances, farm businesses and healthy catchments.

A versatile gene-based test for genome-wide association studies

We have derived a versatile gene-based test for genome-wide association studies (GWAS). Our approach, called VEGAS (versatile gene-based association study), is applicable to all GWAS designs, including family-based GWAS, meta-analyses of GWAS on the basis of summary data, and DNA-pooling-based GWAS, where existing approaches based on permutation are not possible, as well as singleton data, where they are. The test incorporates information from a full set of markers (or a defined subset) within a gene and accounts for linkage disequilibrium between markers by using simulations from the multivariate normal distribution. We show that for an association study using singletons, our approach produces results equivalent to those obtained via permutation in a fraction of the computation time. We demonstrate proof-of-principle by using the gene-based test to replicate several genes known to be associated on the basis of results from a family-based GWAS for height in 11,536 individuals and a DNA-pooling-based GWAS for melanoma in approximately 1300 cases and controls. Our method has the potential to identify novel associated genes; provide a basis for selecting SNPs for replication; and be directly used in network (pathway) approaches that require per-gene association test statistics. We have implemented the approach in both an easy-to-use web interface, which only requires the uploading of markers with their association p-values, and a separate downloadable application.

A simple and fast two-locus quality control test to detect false positives due to batch effects in genome-wide association studies

The impact of erroneous genotypes having passed standard quality control (QC) can be severe in genome-wide association studies, genotype imputation, and estimation of heritability and prediction of genetic risk based on single nucleotide polymorphisms (SNP). To detect such genotyping errors, a simple two-locus QC method, based on the difference in test statistic of association between single SNPs and pairs of SNPs, was developed and applied. The proposed approach could detect many problematic SNPs with statistical significance even when standard single SNP QC analyses fail to detect them in real data. Depending on the data set used, the number of erroneous SNPs that were not filtered out by standard single SNP QC but detected by the proposed approach varied from a few hundred to thousands. Using simulated data, it was shown that the proposed method was powerful and performed better than other tested existing methods. The power of the proposed approach to detect erroneous genotypes was approximately 80% for a 3% error rate per SNP. This novel QC approach is easy to implement and computationally efficient, and can lead to a better quality of genotypes for subsequent genotype-phenotype investigations.

Influence of soil organic amendments on suppression of the burrowing nematode, Radopholus similis, on the growth of bananas.

Radopholus similis is a major constraint to banana production in Australia and growers have relied on nematicides to manage production losses. The use of organic amendments is one method that may reduce the need for nematicides, but there is limited knowledge of the influence of organic amendments on endo-migratory nematodes, such as R. similis. Nine different amendments, namely, mill mud, mill ash, biosolids, municipal waste compost, banana residue, grass hay, legume hay, molasses and calcium silicate were applied to the three major soil types of the wet tropics region used for banana production. The nutrient content of the amendments was also determined. Banana plants were inoculated with R. similis and grown in the soil-amendment mix for 12-weeks in a glasshouse experiment. Assessments of plant growth, plant-parasitic nematodes and soil nematode community characteristics were made at the termination of the experiment. Significant suppression of plant-parasitic nematodes occurred in soils amended with legume hay, grass hay, banana residue and mill mud relative to untreated soil. These amendments were found to have the highest N and C content. The application of banana residue and mill mud significantly increased shoot dry weight at the termination of the experiment relative to untreated soil. Furthermore, the applications of banana residue, grass hay, mill mud and municipal waste compost increased the potential for suppression of plant-parasitic nematodes through antagonistic activity. The application of amendments that are high in C and N appeared to be able to induce suppression of plant-parasitic nematodes in bananas, by developing a more favourable environment for antagonistic organisms.

Nutrient loss and water quality under extensive grazing in the upper Burdekin river catchment, North Queensland

Increased sediment and nutrient losses resulting from unsustainable grazing management in the Burdekin River catchment are major threats to water quality in the Great Barrier Reef Lagoon. To test the effects of grazing management on soil and nutrient loss, five 1 ha mini-catchments were established in 1999 under different grazing strategies on a sedimentary landscape near Charters Towers. Reference samples were also collected from watercourses in the Burdekin catchment during major flow events.Soil and nutrient loss were relatively low across all grazing strategies due to a combination of good cover, low slope and low rainfall intensities. Total soil loss varied from 3 to 20 kg haˉ¹ per event while losses of N and P ranged from 10 to 1900 g haˉ¹ and from 1 to 71 g haˉ¹ per event respectively. Water quality of runoff was considered moderate across all strategies with relatively low levels of total suspended sediment (range: 8-1409 mg lˉ¹), total N (range: 101-4000 ug lˉ¹) and total P (range: 14-609 ug lˉ¹). However, treatment differences are likely to emerge with time as the impacts of the different grazing strategies on land condition become more apparent.Samples collected opportunistically from rivers and creeks during flow events displayed significantly higher levels of total suspended sediment (range: 10-6010 mg lˉ¹), total N (range: 650-6350 ug lˉ¹) and total P (range: 50-1500 ug lˉ¹) than those collected at the grazing trial. These differences can largely be attributed to variation in slope, geology and cover between the grazing trial and different catchments. In particular, watercourses draining hillier, grano-diorite landscapes with low cover had markedly higher sediment and nutrient loads compared to those draining flatter, sedimentary landscapes.These preliminary data suggest that on relatively flat, sedimentary landscapes, extensive cattle grazing is compatible with achieving water quality targets, provided high levels of ground cover are maintained. In contrast, sediment and nutrient loss under grazing on more erodable land types is cause for serious concern. Long-term empirical research and monitoring will be essential to quantify the impacts of changed land management on water quality in the spatially and temporally variable Burdekin River catchment.