Browsing by Department "Agronomy and Soil Science"

Estimated breeding values for the selection of more profitable sheep for the sheep meat and wool industries are currently based on pedigree and phenotypic records. With the advent of a medium-density DNA marker array, which genotypes ~50 000 ovine single nucleotide polymorphisms, a third source of information has become available. The aim of this paper was to determine whether this genomic information can be used to predict estimated breeding values for wool and meat traits. The effects of all single nucleotide polymorphism markers in a multi-breed sheep reference population of 7180 individuals with phenotypic records were estimated to derive prediction equations for genomic estimated breeding values (GEBV) for greasy fleece weight, fibre diameter, staple strength, breech wrinkle score, weight at ultrasound scanning, scanned eye muscle depth and scanned fat depth. Five hundred and forty industry sires with very accurate Australian sheep breeding values were used as a validation population and the accuracies of GEBV were assessed according to correlations between GEBV and Australian sheep breeding values. The accuracies of GEBV ranged from 0.15 to 0.79 for wool traits in Merino sheep and from –0.07 to 0.57 for meat traits in all breeds studied. Merino industry sires tended to have more accurate GEBV than terminal and maternal breeds because the reference population consisted mainly of Merino haplotypes. The lower accuracy for terminal and maternal breeds suggests that the density of genetic markers used was not high enough for accurate across-breed prediction of marker effects. Our results indicate that an increase in the size of the reference population will increase the accuracy of GEBV.

Genome-wide association studies (GWAS) for quantitative traits in livestock are primarily focused on genomic selection and the prediction of genomic breeding values (GEBV). Genomic selection is a form of marker-assisted selection in which genetic markers covering the whole genome are used so that most QTL are in linkage disequilibrium with at least one marker (Meuwissen et al. 2001). As an alternative to gene discovery, which is genome research focused on mapping and characterising quantitative trait loci (QTL) (Gao et al. 2007) genome-wide association analysis allows prediction of breeding value or phenotype for traits of economic importance using all SNP across the whole genome simultaneously (Lee et al. 2008). Prediction of breeding vale is relevant for the stud sector, for genome assisted selection of breeding animals, whereas prediction of phenotype can be relevant in production systems, for early allocation of animals into specific cohorts. Phenotypic prediction of growth and composition aims to sort animals into homogeneous groups to increase uniformity and profitability (Tedeschi et al. 2004) and therefore helps to satisfy downstream consumers. Meat quality grade, yield grade and growth performance factors explain much of the variation in profit under grid pricing (Greer and Trapp 2000) and the cost penalties when specifications are missed can be large. Trials conducted by (Cox et al. 2006) showed 42% of product did not meet specification in the Australian food service industry. Using phenotypic prediction in the management of animals to increase the proportion that meet specification could increase profitability in sheep meat production by increasing the consistency in meeting consumer requirements. Better allocation of animals to cohorts allows better animal management and can be used to create a relationship between consumers and a product (Walker and Olson 1991) thereby increasing customer retention and satisfaction (Eriksson and Vaghult 2000). In this study we explore the accuracy of predicting phenotype for carcass and growth traits. We use data collected on animal phenotypes and genotypes based on a 50k SNP chip, using a subset of a data to estimate SNP effects and a remaining test set to evaluate the accuracy of genome based prediction of phenotype. Training and test sets were created either randomly; within sire families or across breeds.

A tiered approach to contamination exposure assessment is currently adopted in many countries. Increasing the site-specific information in exposure assessments is generally recommended when guideline values for contaminants in soil are exceeded. This work details a Bayesian Network (BN) approach to developing a site-specific environmental exposure assessment that focuses on the simple mapping and assessment of assumptions and the effect of new data on assessment outcomes. The BN approach was applied to a floodplain system in New South Wales, Australia, where site-specific information about elevated antimony (Sb) concentrations and distribution in soils was available. Guidelines for exposure assessment in Australia are used as a template for this site, although the approach is generic. The BN-based assessment used an iterative approach starting with limited soil Sb data (41 samples ranging from 0 to 18 mg kg⁻¹ Sb) and extending the model with more detailed Sb data (145 samples ranging from 0 to 40 mg kg⁻¹ Sb). The analyses identified dominant exposure pathways and assessed the sensitivity of these pathways to changes in assumptions and the level of site-specific information available. In particular, there was a 10.8% probability of exceeding the tolerable daily intake of Sb in the case study when the limited soil Sb data was used, which increased to 26.2% with the more detailed sampling regime. There was also a 47% decrease in the probability of overexposure to Sb when the dermal bioavailability of arsenic (a similar metalloid) was used as a surrogate measure instead of a default bioavailability of 100%. We conclude that the BN approach to soil exposure assessment has merit both in the context of Australian and international soil exposure assessments.

Bioaccumulation and uptake of antimony (Sb) were investigated in a highly contaminated stream, Bakers Creek, running adjacent to mining and processing of Sb–As ores at Hillgrove Mine, NSW, Australia. Comparisons with arsenic (As) were included owing to its co-occurrence at high concentrations. Mean metalloid creek rhizome sediment concentrations were 777±115μgg⁻¹ Sb and 60±6μgg⁻¹ As, with water concentrations at 381±23μgL⁻¹ Sb and 46±2μgL⁻¹ As. Antimony and As were significantly elevated in aquatic autotrophs (96–212μgg⁻¹ Sb and 32–245μgg⁻¹ As) but Sb had a lower uptake efficiency. Both metalloids were elevated in all macroinvertebrates sampled (94–316μgg⁻¹ Sb and 1.8–62μgg⁻¹ As) except Sb in gastropods. Metalloids were detected in upper trophic levels although biomagnification was not evident. Metalloid transfer to riparian vegetation leaves from roots and rhizome soil was low but rhizome soil to leaf As concentration ratios were up to 2–3 times greater than Sb concentration ratios. Direct exposure to the rhizosphere sediments and soils, water ingestion and consumption of aquatic autotrophs appear to be the major routes of Sb and As uptake for the fauna of Bakers Creek.

The title of this article is deliberately provocative. Pupae busting has been an icon of resistance management for the cotton industry, since the first Insecticide Resistance Management Scheme (IRMS) for pyrethroid insecticides in 1984. Combined with windows for application of specific chemical groups, it has formed the basis of these schemes ever since. It provides an effective means of killing overwintering pupae which have been exposed to selection pressure towards the end of the season. Pupae busting has been carried forward into RMPs for Bt cotton, beginning with Ingard in 1996, and then Bollgard II. Many in the industry might consider it almost sacrilegious to suggest removing it. Yet many growers dislike pupae busting. It costs money - Cotton CRC economists have estimated a cost of $26 per hectare in fuel, labour and depreciation. More significantly, it interferes with farming systems. It is incompatible with minimum tillage, which is widely adopted in dryland farming systems and brings many benefits in reducing soil erosion, conserving soil moisture and improving carbon sequestration. These issues are most pressing for dryland cotton growers, since irrigated growers often have to perform operations in normal ground preparation which serve the purpose of pupae busting, especially for back-to-back cotton crops. Yet even for irrigated growers, the need to pupae bust can often restrict rotation crop options, and prolonged wet weather can expose growers to the risk of being non-compliant with RMPs, triggering impositions such as additional refuge planting in the next season.

In Australia, the surface and subsurface soils of the majority of cotton ('Gossypium hirsutum' L.)-growing regions are sodic. Application of organic amendments can be an option to stabilize the structure of sodic Vertisols due to their potential positive effect on soil physical properties. An incubation experiment was conducted for 4 wk in a temperature-controlled (30°C) growth chamber to study the effect of organic amendments on the properties of two Vertisols with different sodicity levels. The exchangeable Na percentages (ESPs) in these Vertisol soils collected from the Australian Cotton Research Institute (ACRI) near Narrabri, New South Wales, and a commercial cotton farm near Dalby, Queensland, were modified such that three different sodicity levels resulted, i.e., nonsodic (ESP<6), moderately sodic (ESP 6-15), and strongly sodic (ESP>15). The organic amendments used were cotton gin trash (60 Mg ha⁻¹), cattle manure (60 Mg ha⁻¹), and composted chicken manure (18 Mg ha⁻¹), as well as an unamended control. The organic amendments improved the physical properties of both Vertisols by decreasing clay dispersion. In the Dalby soil, cotton gin trash produced the largest decrease (29%) in the dispersion index over the control at the moderate sodicity level, whereas in the strongly sodic soil, the lowest dispersion index resulted from the application of chicken manure. Nutrient availability (N, P, and K) was also increased significantly at higher sodicity levels for both the ACRI and Dalby soils by using organic amendments. These results indicate that using organic amendments can be beneficial for the amelioration of sodic vertisols and also to sustain soil quality.

Background: Knowing the phase of marker genotype data can be useful in genome-wide association studies, because it makes it possible to use analysis frameworks that account for identity by descent or parent of origin of alleles and it can lead to a large increase in data quantities via genotype or sequence imputation. Long-range phasing and haplotype library imputation constitute a fast and accurate method to impute phase for SNP data. Methods: A long-range phasing and haplotype library imputation algorithm was developed. It combines information from surrogate parents and long haplotypes to resolve phase in a manner that is not dependent on the family structure of a dataset or on the presence of pedigree information. Results: The algorithm performed well in both simulated and real livestock and human datasets in terms of both phasing accuracy and computation efficiency. The percentage of alleles that could be phased in both simulated and real datasets of varying size generally exceeded 98% while the percentage of alleles incorrectly phased in simulated data was generally less than 0.5%. The accuracy of phasing was affected by dataset size, with lower accuracy for dataset sizes less than 1000, but was not affected by effective population size, family data structure, presence or absence of pedigree information, and SNP density. The method was computationally fast. In comparison to a commonly used statistical method (fastPHASE), the current method made about 8% less phasing mistakes and ran about 26 times faster for a small dataset. For larger datasets, the differences in computational time are expected to be even greater. A computer program implementing these methods has been made available. Conclusions: The algorithm and software developed in this study make feasible the routine phasing of high-density SNP chips in large datasets.

Background: Two-spotted spider mites ('Tetranychus urticae' Koch) oviposit near leaf veins or in leaf folds on the undersides of cotton ('Gossypium hirsutum' L.) leaves where the humid boundary layer offers protection from desiccation. The authors predicted that the boundary layer of glabrous cotton leaves should be shallower than that of hairy leaves, providing some resistance to mites. The dynamics of mite populations, leaf damage, leaf gas exchange and crop yield on two leaf hair isolines (smooth versus hairy) in two genetic backgrounds was assessed. Results: Mite colonies developed faster on the hairy leaf isolines, but leaf damage per mite was higher in smooth leaf isolines, indicating more intense damage. A 50% reduction in photosynthesis on the hairy isolines required 1.8 times more mites than smooth leaves. The yield of cotton was reduced in + mite treatments, but the magnitude of reduction was similar for hairy and smooth isolines. Conclusion: Paradoxically, the relative inhospitality of glabrous leaves may have induced mites to concentrate in protected leaf sections, causing more localised and more severe damage, negating the yield benefits from fewer mites. These results highlight interactions between leaf microenvironment, pest behaviour and plant productivity that may have implications for other instances of plant resistance.

Low responsiveness of cotton to P fertilizer application on soils with low soil-test P values indicates that cotton might take up P from stable P pools. The ability of cotton to acquire P from sparingly soluble P sources was examined by comparing with wheat and white lupin. The plants were grown in washed river sand, with P sources applied at a rate of 40 mg P kg⁻¹, as sparingly soluble AlPO₄, FePO₄, or hydroxyapatite. Cotton was inefficient in accessing P from any of the sparingly soluble P sources. Thus, the low responsiveness of cotton to P fertilizers could be attributed to factors other than efficient P acquisition from the stable P pool in the soil. In contrast to white lupin which accessed little P from the sparingly soluble P sources in this study, wheat showed an outstanding ability in utilizing AlPO₄. When compared with the control, total uptake of P from AlPO₄ by wheat was approximately 9 times higher than cotton and 7 times higher than white lupin, which was possibly related to its high root Al concentration and high root:shoot ratio. The study concludes that the three species differed substantially in P acquisition from the sparingly soluble AlPO₄, with cotton being least efficient and wheat most efficient.

A field plot experiment was established on a sandy loam Typic Natrustalf, duplex soil in Northern NSW, Australia in 1997, to determine crop response, nutrient recovery, and impacts on surface and subsurface water flow following the application of feedlot manure and effluent. Over the three year study, treatments included a control, (nil manure), moderate annual manure applications (20-25t DM/ha applied every year), a high initial application (60 t DM/ha applied in year 1 only) and an inorganic fertiliser treatment (N, P, K applied every year). Both the moderate annual and high initial manure treatments received supplementary inorganic N fertiliser in years 2 and 3. Successive forage crops of sorghum ('Sorghum bicolour' cv. Super-Dan) and triticale ('Triticosecale spp'.cv. Madonna) were grown with highest total dry matter yields recorded by the manure and inorganic treatments. The highest recovery of N, P and S was in the inorganic treatment (63%, 48% & 32%) and K from the high initial manure treatment (269%). Supplemental N applied to the moderate annual manure treatment tended to increase nutrient recovery mainly through increased yield. Total cumulative surface runoff ranked in descending order was control>inorganic>moderate annual>high initial manure treatment. The high initial manure treatment also recorded the lowest total cumulative subsurface flow (95mm) compared to all other treatments (mean 150mm).

'Hyparrhenia hirta' is a pasture grass that has become highly invasive in several parts of the world, including Australia where it has become a serious environmental weed in recent decades. Knowledge of the likely potential distribution and relative abundance of this invasive species, under current and future climate scenarios, will help biosecurity and weed control authorities to plan better strategies to manage the invasion. The CLIMEX modelling package was used to investigate the impacts of climate change on the potential global distribution of 'H. hirta', based on eco-physiological data. The worldwide potential distribution of 'H. hirta' under current climatic conditions is vast and far greater than the current distribution, with suitable climate conditions extending over much of the tropics and subtropics. Under future climate scenarios, the range of 'H. hirta' is likely to expand into areas currently too cold for its survival and contract from areas that are projected to become hotter and drier under climate change. The effects of likely climatic scenarios on the global potential distribution of 'H. hirta' are sufficiently great that they should be considered routinely in strategic control plans for biotic invasions. Changes in the potential range of an invasive species such as 'H. hirta', under global warming scenarios, will mean that it could invade new jurisdictions. Knowledge of this emerging threat could help to formulate effective prevention, surveillance and response measures in these presently marginally unsuitable regions.

We investigated the efficacy of insecticides combined with a plant volatile-based attractant for 'Helicoverpa armigera' moths, under laboratory and field conditions. In the laboratory, 16 insecticides were assessed by the level of mortality and time to incapacitate and kill moths. The proboscis extension reflex technique was used for dosing moths. The pyrethroids, bifenthrin (only when synergised by the addition of piperonyl butoxide (PBO) but not without it) and cyfluthrin (with or without PBO), endosulfan, the carbamates methomyl and thiodicarb, and spinosad killed all moths tested at rates equivalent to, or less than, those which would be applied in cover sprays targeting larvae. The shortest time to moth incapacitation and death was observed with methomyl and thiodicarb. Spinosad produced very high mortality but moths took much longer to die. The two pyrethroids gave relatively slow kills, as did endosulfan. In a field trial, four insecticides were combined with the attractant and dead moths were collected daily from 1 to 4 days after application of the attracticide on 50 m rows of cotton. Significantly more dead moths ('H. armigera', 'H. punctigera' and other noctuids) were found near the rows treated with attracticide containing methomyl compared with spinosad, fipronil and deltamethrin. For determining the impact of attracticides by recovering dead moths, quick acting insecticides are required to prevent moths flying away from the treated area to locations where they cannot be found. Methomyl and thiodicarb are suitable for this, but other insecticides especially spinosad could be used where quick action is not needed. Large numbers of moths were killed in the field trial, suggesting that attracticides for female 'Helicoverpa' spp. moths could have significant impacts on local populations of these pests.

Background: The theory of genomic selection is based on the prediction of the effects of quantitative trait loci (QTL) in linkage disequilibrium (LD) with markers. However, there is increasing evidence that genomic selection also relies on "relationships" between individuals to accurately predict genetic values. Therefore, a better understanding of what genomic selection actually predicts is relevant so that appropriate methods of analysis are used in genomic evaluations. Methods: Simulation was used to compare the performance of estimates of breeding values based on pedigree relationships (Best Linear Unbiased Prediction, BLUP), genomic relationships (gBLUP), and based on a Bayesian variable selection model (Bayes B) to estimate breeding values under a range of different underlying models of genetic variation. The effects of different marker densities and varying animal relationships were also examined. Results: This study shows that genomic selection methods can predict a proportion of the additive genetic value when genetic variation is controlled by common quantitative trait loci (QTL model), rare loci (rare variant model), all loci (infinitesimal model) and a random association (a polygenic model). The Bayes B method was able to estimate breeding values more accurately than gBLUP under the QTL and rare variant models, for the alternative marker densities and reference populations. The Bayes B and gBLUP methods had similar accuracies under the infinitesimal model. Conclusions: Our results suggest that Bayes B is superior to gBLUP to estimate breeding values from genomic data. The underlying model of genetic variation greatly affects the predictive ability of genomic selection methods, and the superiority of Bayes B over gBLUP is highly dependent on the presence of large QTL effects. The use of SNP sequence data will outperform the less dense marker panels. However, the size and distribution of QTL effects and the size of reference populations still greatly influence the effectiveness of using sequence data for genomic prediction.

Improving surface charge characteristics of geric Ferralsols may increase nutrient retention in highly weathered tropical soils of Vietnam. Application of increasing amounts of fused magnesium phosphate (FMP) increased soil pH by one unit and cation exchange capacity (CEC) 10-fold following 7 days incubation near field capacity at 40°C. Similarly, calcium and magnesium silicate amendments at rates designed to apply the same amount of silicon as a high FMP application also increased pH and CEC. In contrast pH₀ remained relatively unchanged except following high silicon application. It is recommended that strategies that increase pH are more likely to increase CEC in geric soils than amendments that aim to lower the pH₀.

Biochar is reputed to improve the water holding capacity and the availability of nutrients in soil as well as the biomass of crops. Biochar combined with nitrogen fertiliser has been reported to have positive effects for the soil and the plant. A glasshouse pot experiment was undertaken to investigate the effect of rice husk biochar on the growth and macronutrient content of corn. The experiment was a factorial arranged in randomised blocks with three replicates. The factors included were; with and without biochar (10t/ha); with and without leaching, and single and split applications of either urea or a urea containing a nitrification inhibiter (Entec). There were zero N controls for each biochar and leaching combination. The application of 10t/ha rice husk biochar increased the tops dry matter yield in the single urea and Entec treatments both in the presence and absence of leaching. Biochar also increased the tops content of K and P and decreased the tops content of Ca and Mg in both the presence and absence of leaching. There was no significant effect of biochar on tops S and N content.

The Jiangxi Academy of Agricultural Sciences (JAAS) has conducted five experiments to compare elemental S and sulphate S containing fertilizers. The elemental S containing fertilizer used was a sulphur enhanced diammonium phosphate (SEF12) and the sulphate S was supplied from single superphosphate (SSP). A diammonium phosphate (DAP) control was used. In a cabbage experiment conducted in 2003 there was a significant response to S and a lower incidence of soft rot where SEF12 was applied (18-19% reduction compared to DAP, c.f. 5% with SSP) and leaf disease (20-31% reduction, c.f. 19% with SSP) where elemental S was applied. In two rice experiments there was a greater response to SEF12 compared to SSP and this was associated with a lower incidence of disease and insects (rice leaf roller and brown plant hopper) where SEF12 was applied. Incidences of rice leaf blight and rice blast were also observed on the DAP and SSP treatments. Two plot trials with rapeseed were established in 2006 in which the fertilizers were applied either at rates to deliver the same rate of P as applied in DAP at Maying Shishan or with the same rate of S as applied in SSP at Maying Sequ. At the Maying Shishan site there was a significant response to S in SSP and SEF12 when applied at the same P application rate. At the Maying Sequ site SEF12 out yielded SSP when applied at the same S rate. These trials are the first to report soil applied elemental S having an effect on protecting crops against insects and disease and indicate that the mechanism involved requires further investigation in both upland and flooded crops.

Best practice management (BPM) guides are a commonly used form of extension to improve private landholder management of invasive pest species in Australia. However, relatively little is known about the quantifiable benefits of these guides as a standalone extension technique. Extension is effective in delivering messages to target audiences, and fostering adoption of best management practices. However, none of the literature quantifies the impact of extension programs on practice change. While BPM guides are amongst the most highly regarded written information sources on pest species management amongst landholders, face to face approaches are more highly regarded. Ideally then, BPM guides can play an important role in supporting these interpersonal forms of extension as part of an integrated and complementary extension strategy which accounts for diversity of opinions, experiences, capabilities and interest amongst target audiences, and increases the potential for success. Preparing a successful BPM guide will commence with an assessment of the actual need for extension. The guide development process will involve a 'continuum' of information gathering and consultation to ensure it is as relevant as possible to the target audience.

The effects of nutrient and lime additions on antimony (Sb) and arsenic (As) accumulation by native Australian and naturalised plants growing in two contaminated mine site soils (2735 mg kg⁻¹ and 4517 mg kg⁻¹ Sb; 826 mg kg⁻¹ and 1606 As mg kg⁻¹) was investigated using a glasshouse pot experiment. The results indicated an increase in soil solution concentrations with nutrient addition in both soils and also with nutrient + lime addition for Sb in one soil. Metalloid concentrations in plant roots were significantly greater than concentrations in above ground plant parts. The metalloid transfer to above ground plant parts from the roots and from the soil was, however, low (ratio of leaf concentration/soil concentration <<1) for all species studied. 'Eucalyptus michaeliana' was the most successful at colonisation with lowest metalloid transfer to above ground plant parts. Addition of nutrients and nutrients + lime to soils, in general, increased plant metalloid accumulation. Relative As accumulation was greater than that of Sb. All the plant species studied were suitable for consideration in the mine soil phytostabilisation strategies but lime additions should be limited and longer term trials also recommended.

A 36-hectare demonstration site at Armidale on the Northern Tablelands of New South Wales has been established to give livestock producers a practical insight into the magnitude of carbon fluxes, especially methane (CH4), associated with crossbred lamb production. The site contains soil and topographical diversity typical of the region (pH 4.8–5.1 (1:5 CaCl₂); soil organic carbon 1.2–3.8%; cation exchange capacity 3–41 meq/100g). The replicated study over two years will compare animal productivity and emissions of low stocking rate enterprises on a low fertility (hill) section of the site (3.7 DSE/ha) with those of high soil fertility enterprises on the more fertile alluvial flats (6.7 DSE/ha). An EM38 soil map and seven soil samples were used to characterise the soil diversity within the two landscapes and to block each landscape into three classes (A, B, C), with three paddocks/class. Monthly pasture (green and dead DM availability) and regular production data (liveweight gain, fat score, fecundity, wool and lamb carcass weights at slaughter) will be collected. These measures will be used in decision support tools to estimate total on-farm CH₄ emissions, emission per unit product, and to conduct a life cycle analysis of the contrasting enterprises. It is intended to use the site as a regional reference point for effective integration of farm carbon, productivity and economic understandings.

Woodlots ranging in area from 0.18 to 0.5 ha were established within the Cicerone Project farmlet trial on the Northern Tablelands of New South Wales, Australia, due to a lack of physical protection in most paddocks across the farmlets. Two percent of each farmlet was planted to trees to examine the commercial and environmental potential of seven species to provide shade and shelter for livestock, increase biodiversity or contribute to cash flow through farm forestry diversification. 'Eucalyptus caliginosa' (timber), 'E. nitens' (timber, pulp wood), 'E. radiata '(essential oil) and 'Pinus radiata'(timber) were planted in four upslope plots (1059– 1062ma.s.l.) in different paddocks. 'Casuarina cunninghamiana' (timber,shelter), 'E. acaciiformis' (shade, shelter and biodiversity), 'E. dalrympleana' (timber, biodiversity), 'E. nitens' (timber, pulp wood), 'E. radiata' (essential oil) and 'P. radiata' (timber) were planted in four low-lying plots (1046–1050ma.s.l.) in separate paddocks, 400–1200 m distant. The pines and natives were planted in August and October 2003, respectively, into a well prepared, weed-free, mounded, planting bed. After 5 years, 'P. radiata' (98% survival) and 'E. nitens' (83%) survived best in upslope plots, reaching maximum heights of 7.8 and 8.8mand exhibiting no or only modest insect damage, respectively. In low-lying plots, 'E. acaciiformis' (75% survival) and 'E. dalrympleana' (80%) survived best, reaching maximum heights of 5.5 and 4.5 m, and exhibiting little or only moderate insect damage, respectively. 'P. radiata' exhibited 17–69%survival in the two lowest-lying plots but 100% survival in the other two lowland plots. On average, <50% of C. 'cunninghamiana, E. nitens' and 'E. radiata' survived in low-lying plots and survivors grew poorly. Early frosts in March 2004 were the primary cause of losses in low-lying plots, and frost, waterlogging, insect attack and some inadvertent livestock browsing explain the slower growth of species in low-lying plots compared with their performance upslope. P. radiata and perhaps E. nitens have commercial promise for timber production on Northern Tablelands farms, but only in higher (well drained, less frost-prone) parts of the landscape. 'E. acaciiformis' can withstand the stressful growing conditions in open pasture in low-lying plots, and should be planted more widely for on-farm shade and shelter. 'E. dalrympleana' can also be considered for amenity and biodiversity plantings in lower parts of the landscape.

Fireweed ('Senecio madagascariensis') continues to spread in coastal pastures in south eastern Australia, as well as onto the Northern and Southern Tablelands of NSW and in far north Queensland on the Atherton Tablelands. Wherever it spreads it is causing considerable angst amongst farming communities. Recognising the impact and spread of fireweed, and as a result of landholder lobbying, particularly by the Bega Valley Fireweed Association, the Australian Government funded a 2 year research project through the University of New England and CSIRO in 2010 to examine ways to better control this weed and fully assess prospects for biological control. Field sites were established at Dorrigo and Armidale in northern NSW to collect data on survival of fireweed seeds in the soil, impact of fireweed on pasture production and availability, and fireweed seedling emergence times. Initial results indicate that pasture availability to livestock is reduced where fireweed plants are growing close to one another but that seed longevity can be relatively short in the soil seed bank under high rainfall conditions. Where pasture growth is weakened e.g. through herbicide application, fireweed seedlings may germinate in large numbers out of season. An application was submitted to the Australian Weeds Committee (AWC) in September 2010 on behalf of the Australian Government to have fireweed listed as a Weed of National Significance (WoNS), but this application is still under consideration. Twelve natural enemies have been identified in initial surveys across five populations of fireweed in the Kwa-Zulu Natal Province of South Africa, including three stem borers, four flower feeders, two sap suckers, and three plant pathogens. A postdoctoral research fellow and Masters student at the University of Kwa-Zulu Natal will examine what factors keep fireweed in check in South Africa and continue quantitative studies of the weed's natural enemies including attempts to rear the species and make more specific identification.

Sturt's desert pea ('Swainsona formosa') is an Australian native legume used as an ornamental pot plant and is also suitable for hanging baskets and as a cut flower. One of the impediments to the commercialisation of S. 'formosa' as a pot plant is its inability to produce flower under low light conditions. The work reported here investigated the effect of high light intensity (800 ± 50 μmol m⁻²s⁻¹) and low light intensity (150 ± 10 μmol m⁻²s⁻¹) on the flowering of 'S. formosa' with particular emphasis on the changes of glucose concentration in shoot apices from the vegetative to floral stages. Plants grown under high light initiated flowers within 45 days from seed germination, while plants grown under low light intensity remained vegetative and produced no flowers during the 60 days of experimental period. Using HPLC, trace amounts (0.52 mg g⁻​¹) of glucose were detected under high light intensity at the beginning of transition from vegetative to floral stage (40 days after germination) which increased to 2.70 mg g⁻​¹ with progressive floral development. No glucose was detected in shoot apices of plants grown under low light during the experimental period. Results indicate that adequate glucose production may be required for floral initiation and development in 'S. formosa'.

Recent studies report low and variable phosphorus (P) fertiliser use efficiency (PUE) for cotton in the northern grains region (NGR) of eastern Australia. This may be due to cotton accessing P pools that are not currently tested for in the subsoil (10-30 cm) or variation in response to P source and placement strategy. Two glasshouse studies were used to investigate this, incorporating two soil P tests to assess readily and slowly available P pools (Colwell, and a dilute acid colloquially referred to as the BSES extractant), and five different P fertiliser placement strategies in the subsoil. Eighteen Vertosols were collected across southern to central Queensland in the NGR, and then used to grow faba bean ('Vicia faba' L.) and cotton ('Gossypium hirsutum' L.) sequentially in the same 28-L pot. Readily available P pools assessed by Colwell-P were of major importance for faba bean and cotton dry matter, as well as for tissue P concentrations. Cotton was less responsive to extractable subsoil P concentrations than faba bean, suggesting either greater internal PUE or improved ability to accumulate P under conditions of limited availability. We recommend that subsoil P fertilisation should occur before sowing faba bean to maximise PUE in a cotton-faba bean rotation. Faba bean and cotton both recovered more P when the subsoil was fertilised, but no individual P fertiliser placement strategy was superior. Phosphorus extracted using the BSES method was not correlated with faba bean or cotton dry matter or tissue P concentration over the single crop cycle. We also recommend that Colwell-P be measured in the topsoil and subsoil to understand the quantity of plant-available P in Vertosols of the NGR, and that further research is needed to describe the resupply of the readily available P pool from slowly available P pools during a single crop cycle.

Genomic selection (GS) is a method to predict breeding values in livestock; however the underlying mechanism by which it predicts is not fully clear. Initially it was thought that GS predicted effects of quantitative trait loci (QTL), in linkage disequilibrium (LD) with markers (Meuwissen et al. 2001). Increasingly, there has been a realization that GS predicts 'relationships' between animals (Habier et al., 2010). Literature suggests that a very small part of the additive genetic variance is explained by variation at known QTL (Maher, 2008). Fearnhead et al, (2004) noted that this is often inconsistent with high estimates of heritability and they proposed that a rare variant model might explain this "missing heritability". Given this debate, it is relevant to obtain greater understanding into what GS is actually predicting for several reasons. Firstly, the LD paradigm predicts that GS can estimate breeding values with higher accuracies as long as marker densities are increasing, possibly even allowing prediction of breeding value across breeds (Goddard et al., 2006). Moreover, accurate prediction would persist for several generations into the future. In contrast, if the relationship paradigm is true, then our predictive ability based on genomic data would remain for only one or two generations ahead. Consequently continuous measurement of phenotypes of individuals that are at least somewhat related to selection candidates would be needed.

An evaluation of three novel elemental sulfur (S°) coated mono-ammonium phosphate (MAP) products ((MAP with coarse (75-100μm) S° coating (MAP75), MAP with fine (17-24μm) S° coating (MAP17), and MAP with 1/3 coarse S°, 1/3 fine S°, and 1/3 sulfate coating (MAPM)) was undertaken in an intact core pot trial using red clover ('Trifolium pratense') and compared with single superphosphate (SSP). Sulfur (S) uptake from coated S sources was not significantly different (p<0.05) from SSP after 120 days of growth. Between 34% and 53% plant S was derived from the fertiliser sources. There was no significant difference in % fertiliser recovery between MAPM and SSP at either harvest and at both harvests fertiliser S recovery was in the order MAP < MAP75 < MAP17 < MAPM < SSP. The key finding was that a MAP coated with 1/3 sulfate and 2/3 S° was able to supply clover with the same amount of S, at the same rate, as SSP over 120 days. Under leaching conditions, this availability may result in slower, longer release of S as the coarser fraction slowly meets plant demands and protects added S from leaching.

In all systems, phosphorus (P), particularly phosphate, is inexorably drawn to sorption surfaces or precipitated, and is removed from the readily plant-available P pools. Mobilising this less-available P is a significant challenge in organic and low-input agro-ecosystems where readily available P sources may not be applied regularly. Although good-quality inputs, with low C : P ratio, and rotations may be effective in managing organic P cycles in pasture and forestry systems, extensive cropping systems will remain problematic. Two conceptual models are proposed to use organic matter additions to transfer this recalcitrant P into the biocycle, one involving highly labile organic matter and the other involving less-labile organic additions. Current literature provides some evidence for the efficacy of both models, but further work is necessary to clarify which is optimal for agro-ecosystems relying on either low inputs of P or forms of P that are allowed in organic agricultural systems, such as manures or rock phosphate. The microbial biomass is integral to P biocycling in organic systems, but further work is necessary to clarify the role of fungal and bacterial decomposers in decomposition processes. Identifying P-efficient cultivars with low translocation from roots to shoots to provide an 'organic' P source for following crops, essentially optimal rotation sequences for mobilising P using plants, is an avenue of promising research potential. Enzyme activation of recalcitrant organic P sources is unlikely to be effective if applied to bulk soils; however, further research on enzyme activities in the rhizosphere holds promise. We strongly recommend that further research be directed toward understanding and limiting reactions of inorganic P with soil colloids and minerals, either through chemical means (pH change, competitive sorption) or introduction and manipulation of organic materials. The research issues identified above overlap considerably with conventional agricultural concerns and benefits will accrue to both conventional and organic producers where further research is promoted.

An evaluation of a Sulfur Enhanced Fertilizer (Thiogro) fertilizer (MAP12) was undertaken on a native pasture oversown with clover near Armidale, NSW, Australia from August 2007 to November 2008. Fertilizers (Single superphosphate (SSP), mono-ammonium phosphate (MAP), pastille DAPS (pastille) and Sulfur enhanced mono-ammonium phosphate 12 (MAP12)) were top dressed onto the sward and four harvests taken over the period. SSP and MAP12 produced higher clover yields than MAP and pastille DAPS. MAP12 was superior to SSP, particularly at the later harvests. This is an important result as clover growth is essential in the pasture both to contribute fixed N and for animal protein. Addition of S fertilizers increased the uptake of S in all treatments, except pastille DAPS. Highest uptake was with MAP12. Calculation of apparent fertilizer recovery (S uptake in S treatment - S uptake in MAP treatment)/ S applied) showed a recovery of 16% from SSP, 32% from MAP12 and no recovery from DAP pastille. The increased yield resulting from S application resulted in an increase in the apparent recovery of fertilizer P.

A Long Range Haplotype Imputation algorithm was developed and combined with a Recursive Long Range Phasing algorithm. These were tested on simulated SNP data sets which had structures possibly similar to those found in sheep and dairy cattle. Performance, measured by accuracy of phasing (>97.6%) and computing time, was competitive in comparison to industry standard software.

This paper provides a review of P acquisition strategies by cotton plants. Except for excretion of phosphatase enzymes, the cotton plant lacks the ability to manipulate its rhizosphere chemistry, and to mobilize nonlabile inorganic P sources. Phosphorus acquisition by cotton plants mainly depends on root exploration of relatively labile inorganic P and organic P sources from the surface and subsurface soil layers. Root morphological traits, such as increased root to shoot ratio or AM associations, would result in a high root absorbing surface area. Subsoil P sources could be accessed by cotton plant over time possibly due to the water stress encountered at the topsoil, and the presence of roots in the subsoil. The role that mycorrhizae play with cotton plants in Vertosol soils is worthy of future investigation.

Low soil phosphorus (P) availability commonly limits yield in Australian broadacre organic production systems where superphosphate fertiliser is not permitted, and alternative P nutrition strategies are sought. Glasshouse experiments were conducted to investigate the potential of faba beans (Vicia faba L.) (FB), or field peas (Pisum sativum L.) (FP), grown in acidic sandy loam or alkaline clay, to accumulate P, which could then be supplied to a subsequent crop as part of a green manure rotation or after harvest. Another experiment investigated differences in growth and P acquisition between corn (Zea mays L.) cultivars: Hycorn 424 (a modern hybrid), and four traditional cultivars used in organic production. The experiments were carried out under conditions of P stress and had rock phosphate (RP), poultry manure (PM), or single superphosphate (SP) applied at 50 kg P/ha. For FP, maximum P input to the soil from incorporation would occur at or after pod initiation. However, P uptake by both legumes in both soils from sparingly soluble RP was low, with fertiliser P-use efficiencies of 0–1.3% compared with 1.8–12.7% for PM and 6.1–9.9% for SP. In the corn experiment, P fertiliser source had much larger effects than cultivar on plant biomass and P uptake, with responses generally ranked SP >PM>> RP > Control. Hycorn 424 generally produced higher dry matter and P uptake than the traditional cultivars under all P treatments. The implications of these preliminary investigations for Australian broadacre organic agriculture are discussed.

'Polymeria longifolia' Lindl., of the Convolvulace, is a native Australian species commonly known as either clumped or erect bindweed (Cunningham et al. 1981), polymeria, Peak Downs curse (Stanley and Ross 1986, Auld and Medd 1987) or polymeria take-all (Johnson et al 2003). Wilson et al. (1995) make a distinction between two species commonly known as Peak Downs curse, 'P. longifolia' and 'Teucrium integrifolium' Benth., a member of the Lamiaceae. 'P. longifolia' is known as one of the 'take-all' weeds, because of its perennial rhizomatous habit, its ability to form dense competitive infestations that smother the ground and its ability to extract soil water and nutrients (Johnson 2002).

An evaluation of the predictive capacity of resin sulfur (S) and phosphorus (P) extraction was undertaken on 18 soils from the New England Tablelands in northern NSW, Australia. Maize ('Zea mays') plants were grown for 40 days in a glasshouse in the presence or absence of sulfur and/or phosphorus fertiliser, and relative yield was determined. Comparison of the relative yield response against resin extractable S, monocalcium phosphate (MCP) S and KCl40 S using a Cate-Nelson plot revealed little difference between the three S extraction methods when soil test values were below the identified critical levels. However, values above the critical value were better able to identify where fertiliser was not required in the resin and MCP tests. The inability of the KCl40 test to correctly identify when fertiliser would not be needed was related to the short time frame of the trial where the longer term reserves that it identifies are not able to be exploited by potted plants. Evaluation of P responses was not possible due to the responsiveness of all soils to applied P, despite critical values being above previously determined threshold values for more than one third of the soils examined. It remains unclear why all soils responded to P, however tissue P concentrations match with increasing response to soil P test values. In conclusion, there is no benefit in terms of predicting S response to move to a resin extraction method, and we were unable to determine if benefits would accrue with respect to P resin tests.

Genomic Selection (GS: Meuwissen et al, 2001) aims to provide genomic estimated breeding values (gEBVs) as criteria for selection by exploiting associations between genetic markers and phenotypes. This process generally assumes additive genetic merit, implicitly regressing individual phenotype on the number of specific alleles carried, separately for each locus. gEBVs are thus based on estimated allele substitution effects at QTL or at linked marker loci. This paper aims to give proof of concept that genomic selection can be used to breed for dominance effects as well as additive effects, without having to fit both these effects in statistical models. This leads to increasing heterosis in crossbred animals though genomic selection within the contributing parental lines. Should this work under real conditions, the benefits could be substantial, particularly in the pig and poultry industries. In this paper the target is genetic merit in crossbred individuals. This has been well addressed by Ibánẽz-Escriche et al. (2009), but without consideration of non-additive QTL effects. This paper aims to exploit within-locus dominance deviations as well as additive effects while selecting within purebred parental lines. This can be done by estimating allele substitution effects on crossbred phenotypes, separately for each parental line. Consider the average effect of an allele substitution in gametes of line A, evaluated on its phenotypic impact in the AxB crossbred genotype. This depends on allele frequency in gametes contributed from line B, and is thus the same as the average effect of an allele substitution within line B, assuming no epistatic effects.

High density genotyping of individuals does not by itself yield information on phase: linkage of alleles between loci in the contributing gametes. This additional information is important, because it helps to determine which segments of chromosome are identical by descent across the population, and thereby improve inference about segregation of quantitative trait loci (QTL). This paper presents a recursive algorithm to give efficient implementation of long range phasing, a recently-published strategy that infers IBD between distant relatives from long strings of SNP genotypes that show no opposing homozygotes (i.e. no evidence of lack of IBS). These relatives can be both distant and unknown to the analysis. Successful implementation of this strategy gives opportunity to use haplotype and/or combined linkage-linkage disequilibrium analysis for QTL mapping or genomic selection.

Long range phasing (LRP) is a fast and accurate rule based method which uses information from both related and unrelated individuals by invoking the concepts of surrogate parents and Erdös numbers (Kong et al., 2008). Recursive long range phasing and long haplotype imputation (RLRPLHI; Hickey et al., 2009) is an extended LRP algorithm with increased robustness partially due to the extra long haplotype imputation step (LHI) which is based on a the construction of a library of long haplotypes (e.g. 10cM) for a dataset. The LHI part of the algorithm is computationally much less intensive and less error prone compared to the LRP part, and it can easily incorporate prior information from other phasing methods, both laboratory and in silico. After building the initial haplotype library it may be possible to phase other genotyped individuals from the same population simply via the LHI step. The application of such an approach may be useful where small numbers of extra individuals are regularly added to a data set of previously phased individuals, especially where very many animals are genotyped making even a fast phasing method feasible for only small subsets of the data. It may also be useful through incorporation into the LRP part of RLRPLHI in order to improve the accuracy and speed of RLRPLHI. Another application of a long haplotype library could be to use it in combination with segregation analysis (Kerr and Kinghorn, 1996) to impute dense genotype or sequence data in ungenotyped individuals in a sparsely genotyped pedigree. The objectives of this research were to evaluate LHI for phasing genotyped individuals, and segregation analysis and long haplotype imputation (SALHI) for imputing genotypes in ungenotyped individuals, using simulated genotypic data in a national and global Holstein pedigree.

In 2009 we registered a formulation of plant volatile compounds, sucrose (feeding stimulant), and various excipients including antioxidants, thickeners, emulsifiers and dyes, for use against the adult stages of the noctuid moths 'Helicoverpa armigera' and 'H. punctigera' in cotton, corn and beans. We believe it is the world's first such product approved for application to crops. The volatiles are nature-equivalent, but synthetically produced. This meant it could not be registered as a biological product, but was potentially eligible under a category including "commonly used household or industrial chemicals with a history of safe use", for which the registration requirements were less stringent than for novel active ingredients. The Australian Pesticides and Veterinary Medicines Authority (APVMA) determined that, for plant volatiles, the primary criterion or a history of safe use was inclusion in the Generally Recognised as Safe (GRAS) list of the Flavour and Extract Manufacturer's Association of the USA (FEMA). Excipient ingredients had to be food-grade. Farmers can add insecticides (methomyl, thiodicarb or spinosad) to make the product lethal to the target insects. These insecticides were already approved as conventional larvicides, and were efficacious for moths at concentrations below those resulting in registered active ingredient loads in the relevant crops. The impact of these requirements on the commercialisation of the product, and implications for developing similar plant volatile blends for pest management, were reviewed in 2010 and published in Australian Journal of Entomology.

The theory of genomic selection is based on the prediction of the effects of genetic markers in linkage disequilibrium (LD) with quantitative trait loci (QTL). However, there is increasing evidence that genomic selection also relies on relationships between individuals or the patterns of LD associated with these relationships to accurately predict genetic value. This study aimed to examine the relative importance of information on essentially unrelated individuals on the estimation of breeding value when using gBLUP and BLUP. Analysis was undertaken using a simulated population of 2000 animals. Two reference populations were formed from 1750 animals and the accuracy of prediction was assessed for the remaining 250 animals that formed the test population. Two test populations were constructed such that one included 10 families that had no family members in the reference population and the other included 5 half siblings from 50 families. The gBLUP method more accurately predicted breeding value than BLUP in both test populations. The highest accuracy was achieved when gBLUP was used to predict the breeding value of closely related animals. However, gBLUP was still able to predict breeding value accurately even when animals were distantly related.

Reductions in atmospheric inputs of S in rainfall, and the world's reliance on non-, or low-S containing TSP, DAP, MAP and urea has resulted in a widening gap in the S input/output balance, and an increasing incidence of S deficiency in agriculture. A technology to incorporate elemental S, with or without sulphate S, into ammonium phosphate fertilizers has been developed and patented by Shell. The fertilizers produced by this process are generically called "Sulphur Enhanced Fertilizer" (SEF or Thiogro). A wide range of experimental N, P, S formulations have been made, with elemental S concentrations up to 15% or greater. Agronomic testing of several of these products has been undertaken in a wide range of crops in temperate and tropical environments in China, generating a weighted mean crop yield increase to Thiogro of 13%, compared to the zero S control, in S responsive sites. Soil analyses from 82 of the 101 field trials were used to establish the utility of the mono-calcium phosphate extract to estimate the potential S response at each site. The accepted critical soil S test value for the MCP extract is 10 mg/kg. Predictability of an S response was low (47% correct) at low soil test values and acceptable (72%correct) on non-responsive sites. These data indicate that MCP extraction is not a good way to identify potentially S responsive sites.

Soils of Cambodia are low in fertility and conventional rice cultivation destroys any structure that they have. Usage of inorganic fertilizers is low and farmers are encouraged to use animal manure. Much of the research conducted on crop responses to manure is based on trials where unrealistically high application rates have been used so the farmers are given false hopes as to what they might achieve through its use. Little response curve data exists on which to base fertilizer rate recommendations and general recommendations have been formulated for the different soil groups. An economic analysis comparing the general recommendation with site specific nutrient management (SSNM) recommendations has been made on the results of a published experiment and shown substantial increases in both profitability and benefit/cost ratio in using the SSNM recommendations on four soil types. Cambodian farmers, like many in the developing world, have to be careful with their limited cash resources in purchasing plant nutrients and more attention needs to be paid to producing profitable and reliable fertilizer and manure recommendations.

We have recently registered a product called Magnet®, for attract-and-kill of adults of Helicoverpa armigera and H. punctigera in Australian cotton. It consists of a mixture of six synthetic (nature-equivalent) plant volatile chemicals, with sucrose as a feeding stimulant. Farmers can add any one of three insecticides. When applied to cotton crops, Magnet® with insecticide is capable of attracting and killing large numbers of moths. It was developed as a component for IPM in conventional (non-Bt) cotton, but this now occupies a very small proportion of Australian cotton acreage, which is dominated by transgenic Bt (Bollgard II ®) cotton. Recent trends in the frequency of resistant alleles for the two Cry toxins in Bollgard II ® suggest that additional tools may be needed for inclusion in future Resistance Management Plans, either to supplement existing measures or to replace onerous requirements such as cultivation to destroy overwintering pupae. In this presentation we will describe experiments aimed at enhancing the productivity of refuges which are used to generate unselected moths by application of Magnet® without insecticide, or (by including insecticide) killing moths emerging from late season cotton, or emerging in spring from fields which grew cotton in the previous summer.