Functionally associated molecular genetic marker map construction in perennial ryegrass (Lolium perenne L.)

A molecular marker-based map of perennial ryegrass (Lolium perenne L.) has been constructed through the use of polymorphisms associated with expressed sequence tags (ESTs). A pair-cross between genotypes from a North African ecotype and the cultivar Aurora was used to generate a two-way pseudo-testcross population. A selection of 157 cDNAs assigned to eight different functional categories associated with agronomically important biological processes was used to detect polymorphic EST–RFLP loci in the F1(NA6 × AU6) population. A comprehensive set of EST–SSR markers was developed from the analysis of 14,767 unigenes, with 310 primer pairs showing efficient amplification and detecting 113 polymorphic loci. Two parental genetic maps were produced: the NA6 genetic map contains 88 EST–RFLP and 71 EST–SSR loci with a total map length of 963 cM, while the AU6 genetic map contains 67 EST–RFLP and 58 EST–SSR loci with a total map length of 757 cM. Bridging loci permitted the alignment of homologous chromosomes between the parental maps, and a sub-set of genomic DNA-derived SSRs was used to relate linkage groups to the perennial ryegrass reference map. Regions of segregation distortion were identified, in some instances in common with other perennial ryegrass maps. The EST-derived marker-based map provides the basis for in silico comparative genetic mapping, as well as the evaluation of co-location between QTLs and functionally associated genetic loci.

Genetic variability of Tomato spotted wilt virus in Australia and validation of real time RT-PCR for its detection in single and bulked leaf samples

The potential for large-scale use of a sensitive real time reverse transcription polymerase chain reaction (RT-PCR) assay was evaluated for the detection of Tomato spotted wilt virus (TSWV) in single and bulked leaf samples by comparing its sensitivity with that of DAS-ELISA. Using total RNA extracted with RNeasy® or leaf soak methods, real time RT-PCR detected TSWV in all infected samples collected from 16 horticultural crop species (including flowers, herbs and vegetables), two arable crop species, and four weed species by both assays. In samples in which DAS-ELISA had previously detected TSWV, real time RT-PCR was effective at detecting it in leaf tissues of all 22 plant species tested at a wide range of concentrations. Bulk samples required more robust and extensive extraction methods with real time RT-PCR, but it generally detected one infected sample in 1000 uninfected ones. By contrast, ELISA was less sensitive when used to test bulked samples, once detecting up to 1 infected in 800 samples with pepper but never detecting more than 1 infected in 200 samples in tomato and lettuce. It was also less reliable than real time RT-PCR when used to test samples from parts of the leaf where the virus concentration was low. The genetic variability among Australian isolates of TSWV was small. Direct sequencing of a 587 bp region of the nucleoprotein gene (S RNA) of 29 isolates from diverse crops and geographical locations yielded a maximum of only 4.3% nucleotide sequence difference. Phylogenetic analysis revealed no obvious groupings of isolates according to geographic origin or host species. TSWV isolates, that break TSWV resistance genes in tomato or pepper did not differ significantly in the N gene region studied, indicating that a different region of the virus genome is responsible for this trait.

Evolutionary relationships between bat coronaviruses and their hosts

Recent studies have suggested that bats are the natural reservoir of a range of coronaviruses (CoVs), and that rhinolophid bats harbor viruses closely related to the severe acute respiratory syndrome (SARS) CoV, which caused an outbreak of respiratory illness in humans during 2002-2003. We examined the evolutionary relationships between bat CoVs and their hosts by using sequence data of the virus RNA-dependent RNA polymerase gene and the bat cytochrome b gene. Phylogenetic analyses showed multiple incongruent associations between the phylogenies of rhinolophid bats and their CoVs, which suggested that host shifts have occurred in the recent evolutionary history of this group. These shifts may be due to either virus biologic traits or host behavioral traits. This finding has implications for the emergence of SARS and for the potential future emergence of SARS-CoVs or related viruses.

Remote sensing of nitrogen and water stress in wheat

Nitrogen (N) is the largest agricultural input in many Australian cropping systems and applying the right amount of N in the right place at the right physiological stage is a significant challenge for wheat growers. Optimizing N uptake could reduce input costs and minimize potential off-site movement. Since N uptake is dependent on soil and plant water status, ideally, N should be applied only to areas within paddocks with sufficient plant available water. To quantify N and water stress, spectral and thermal crop stress detection methods were explored using hyperspectral, multispectral and thermal remote sensing data collected at a research field site in Victoria, Australia. Wheat was grown over two seasons with two levels of water inputs (rainfall/irrigation) and either four levels (in 2004; 0, 17, 39 and 163 kg/ha) or two levels (in 2005; 0 and 39 kg/ha N) of nitrogen. The Canopy Chlorophyll Content Index (CCCI) and modified Spectral Ratio planar index (mSRpi), two indices designed to measure canopy-level N, were calculated from canopy-level hyperspectral data in 2005. They accounted for 76% and 74% of the variability of crop N status, respectively, just prior to stem elongation (Zadoks 24). The Normalised Difference Red Edge (NDRE) index and CCCI, calculated from airborne multispectral imagery, accounted for 41% and 37% of variability in crop N status, respectively. Greater scatter in the airborne data was attributable to the difference in scale of the ground and aerial measurements (i.e., small area plant samples against whole-plot means from imagery). Nevertheless, the analysis demonstrated that canopy-level theory can be transferred to airborne data, which could ultimately be of more use to growers. Thermal imagery showed that mean plot temperatures of rainfed treatments were 2.7 °C warmer than irrigated treatments (P < 0.001) at full cover. For partially vegetated fields, the two-Dimensional Crop Water Stress Index (2D CWSI) was calculated using the Vegetation Index-Temperature (VIT) trapezoid method to reduce the contribution of soil background to image temperature. Results showed rainfed plots were consistently more stressed than irrigated plots. Future work is needed to improve the ability of the CCCI and VIT methods to detect N and water stress and apply both indices simultaneously at the paddock scale to test whether N can be targeted based on water status. Use of these technologies has significant potential for maximising the spatial and temporal efficiency of N applications for wheat growers. ‘Ground–breaking Stuff’- Proceedings of the 13th Australian Society of Agronomy Conference, 10-14 September 2006, Perth, Western Australia.

High resolution genetic and physical mapping of the I-3 region of tomato chromosome 7 reveals almost continuous microsynteny with grape chromosome 12 but interspersed microsynteny with duplications on Arabidopsis chromosomes 1, 2 and 3

The tomato I-3 gene introgressed from the Lycopersicon pennellii accession LA716 confers resistance to race 3 of the fusarium wilt pathogen Fusarium oxysporum f. sp. lycopersici. We have improved the high-resolution map of the I-3 region of tomato chromosome 7 with the development and mapping of 31 new PCR-based markers. Recombinants recovered from L. esculentum cv. M82 × IL7-2 F2 and (IL7-2 × IL7-4) × M82 TC1F2 mapping populations, together with recombinants recovered from a previous M82 × IL7-3 F2 mapping population, were used to position these markers. A significantly higher recombination frequency was observed in the (IL7-2 × IL7-4) × M82 TC1F2 mapping population based on a reconstituted L. pennellii chromosome 7 compared to the other two mapping populations based on smaller segments of L. pennellii chromosome 7. A BAC contig consisting of L. esculentum cv. Heinz 1706 BACs covering the I-3 region has also been established. The new high-resolution map places the I-3 gene within a 0.38 cM interval between the molecular markers RGA332 and bP23/gPT with an estimated physical size of 50-60 kb. The I-3 region was found to display almost continuous microsynteny with grape chromosome 12 but interspersed microsynteny with Arabidopsis thaliana chromosomes 1, 2 and 3. An S-receptor-like kinase gene family present in the I-3 region of tomato chromosome 7 was found to be present in the microsyntenous region of grape chromosome 12 but was absent altogether from the A. thaliana genome.

Tan spot: A new disease of pyrethrum caused by Microsphaeropsis tanaceti sp. nov

The isolation frequency of Microsphaeropsis sp. in spring in association with necrotic lesions on leaves in Tasmanian pyrethrum (Tanacetum cinerariifolium) fields has increased substantially since first identification in 2001. Examination of morphological features and sequencing of the internal transcribed spacer region (ITS) resulted in the identification of a new species, herein described as Microsphaeropsis tanaceti sp. nov. The pathogenicity of three M. tanaceti isolates to two pyrethrum cultivars was confirmed by inoculating glasshouse-grown plants in three experiments. No significant differences in the susceptibility of the two cultivars to infection by M. tanaceti were found. Symptoms were tan-coloured spots which coalesced around the margins of the leaves. Therefore, the name 'tan spot' is proposed for this new disease of pyrethrum. The sensitivity of seven M. tanaceti isolates to difenoconazole and azoxystrobin, commonly used fungicides for the management of foliar diseases in spring, was assessed under in vitro conditions. Sensitivity testing for difenoconazole was conducted using a mycelial growth assay on potato dextrose agar, whilst testing for sensitivity to azoxystrobin used a conidial germination assay on water agar. Microsphaeropsis tanaceti was found to be more sensitive to azoxystrobin than difenoconazole, with complete inhibition of conidial germination at concentrations above 0.625 µg a.i. mL-1. By comparison, concentrations of 50 µg a.i. difenoconazole mL-1 or greater were required for significant inhibition of mycelial growth. It therefore appears likely that there is currently some control of tan spot as a result of the use of azoxystrobin and to a lesser extent, difenoconazole, for the control of other diseases.

Response of tropical turfgrasses to recycled water in southern Queensland

The effects of recycled water (effluent) on 8 tropical grasses growing in 100-L bags of sand were studied in Murrumba Downs, just north of Brisbane in southern Queensland (27.4°S, 153.1°E). The species used were: Axonopus compressus (broad-leaf carpetgrass), Cynodon dactylon (bermudagrass 'Winter Green') and C. dactylon x C. transvaalensis hybrid ('Tifgreen'), Digitaria didactyla (Queensland blue couch), Paspalum notatum (bahiagrass '38824'), Stenotaphrum secundatum (buffalograss 'Palmetto'), Eremochloa ophiuroides (centipedegrass 'Centec') and Zoysia japonica (zoysiagrass 'ZT-11'). From May 2002 to June 2003, control plots were irrigated with potable water and fertilised monthly. Plots irrigated with effluent received no fertiliser from May to August 2002 (deficient phase), complete fertilisers at control rates from September to December 2002 (recovery phase) and nitrogen (N) only at control rates from January to June 2003 (supplementary phase). In October 2002, the average shoot weight of plants from the effluent plots was 4% of that from potable plots, with centipedegrass less affected than the other species (relative growth of 20%). Shoot N concentrations declined by 40% in the effluent plots from May to August 2002 (1.8 ± 0.1%) along with phosphorus (P, 0.46 ± 0.02%), potassium (K, 1.6 ± 0.2%), sulfur (S, 0.28 ± 0.02%) and manganese (Mn, 19 ± 2 mg/kg) concentrations. Only the N and Mn concentrations were below the optimum for grasses. The grasses grew satisfactorily when irrigated with effluent if it was supplemented with N. Between January and June 2003 the average weight of shoots from the effluent plots was 116% of the weight of shoots from the control plots. Shoot nutrient concentrations were also similar in the 2 regimes at this time. The recycled water supplied 23% of the N required for maximum shoot growth, 80-100% of the P and K, and 500-880% of the S, calcium and magnesium. The use of recycled water represents savings in irrigation and fertiliser costs, and reductions in the discharge of N and P to local waterways. Effluent is currently about 50% of the cost of potable water with a saving of about AU$8000/ha.year for a typical sporting field.

Evaluation of partial replacement of live and fresh feeds with a formulated diet and the influence of weaning Panulirus ornatus phyllosomata onto a formulated diet during early ontogeny

We have evaluated the potential of a formulated diet as a replacement for live and fresh feeds for 7-day post-hatch Panulirus ornatus phyllosomata and also investigated the effect of conditioning phyllosomata for 14-21 days on live feeds prior to weaning onto a 100% formulated diet. In the first trial, the highest survival (>55%) was consistently shown by phyllosomata fed a diet consisting of a 50% combination of Artemia nauplii and 50% Greenshell mussel, followed by phyllosomata fed 50% Artemia nauplii and 50% formulated diet and, thirdly, by those receiving 100% Artemia nauplii. The second trial assessed the replacement of on-grown Artemia with proportions of formulated diet and Greenshell mussel that differed from those used in trial 1. Phyllosomata fed a 75% combination of formulated diet and 25% on-grown Artemia and 50% on-grown Artemia and 50% Greenshell mussel consistently showed the highest survival (>75%). Combinations of Greenshell mussel and formulated diet resulted in significantly (P < 0.05) reduced survival. In trial 3, phyllosomata were conditioned for 14, 18 or 21 days on Artemia nauplii prior to weaning onto a 100% formulated diet, which resulted in survival rates that were negatively related to the duration of feeding Artemia nauplii. In the final trial, phyllosomata were conditioned for 14 days on live on-grown Artemia prior to weaning onto one of three formulated diets (one diet with 44% CP and two diets with 50%). Phyllosomata fed a 44% CP diet consistently showed the highest survival (>35%) among all treatments, while those fed a 50%-squid CP diet showed a significant (P < 0.05) increase in mortality at day 24. The results of these trials demonstrate that hatcheries can potentially replace 75% of live on-grown Artemia with a formulated diet 7 days after hatch. The poor performance associated with feeding combinations of Greenshell mussel and formulated diet, and 100% formulated diet as well as conditioning phyllosomata for 14-21 days on live feeds prior to weaning onto a formulated diet highlights the importance of providing Artemia to stimulate feeding.

Pitfalls and benefits of involving industry in fisheries research: A case study of the live reef fish industry in Queensland, Australia

Including collaboration with industry members as an integral part of research activities is a relatively new approach to fisheries research. Earlier approaches to involving fishers in research usually involved compulsory accommodations of research, such as through compulsory observer programs, in which fishers were seen as subjects of rather than participants in research. This new approach brings with it significant potential benefits but also some unique issues both for the researchers and the participating industry members. In this paper we describe a research project involving the Queensland Coral Reef Finfish Fishery that originated from industry and community concerns about changes in marketing practices in an established commercial line fishery. A key aspect of this project was industry collaboration in all stages of the research, from formulation of objectives to assistance with interpretation of results. We discuss this research as a case study of some of the issues raised by collaboration between industry and research groups in fisheries research and the potential pitfalls and benefits of such collaborations for all parties. A dedicated liaison and extension strategy was a key element in the project to develop and maintain the relationships between fishers and researchers that were fundamental to the success of the collaboration. A major research benefit of the approach was the provision of information not available from other sources: 300 days of direct and unimpeded observation of commercial fishing by researchers; detailed catch and effort records from a further 126 fishing trips; and 53 interviews completed with fishers. Fishers also provided extensive operational information about the fishery as well as ongoing support for subsequent research projects. The time and resources required to complete the research in this consultative framework were greater than for more traditional, researcher-centric fisheries research, but the benefits gained far outweighed the costs.

Annual forecasting of the Australian macadamia crop - integrating tree census data with statistical climate-adjustment models

To facilitate marketing and export, the Australian macadamia industry requires accurate crop forecasts. Each year, two levels of crop predictions are produced for this industry. The first is an overall longer-term forecast based on tree census data of growers in the Australian Macadamia Society (AMS). This data set currently accounts for around 70% of total production, and is supplemented by our best estimates of non-AMS orchards. Given these total tree numbers, average yields per tree are needed to complete the long-term forecasts. Yields from regional variety trials were initially used, but were found to be consistently higher than the average yields that growers were obtaining. Hence, a statistical model was developed using growers' historical yields, also taken from the AMS database. This model accounted for the effects of tree age, variety, year, region and tree spacing, and explained 65% of the total variation in the yield per tree data. The second level of crop prediction is an annual climate adjustment of these overall long-term estimates, taking into account the expected effects on production of the previous year's climate. This adjustment is based on relative historical yields, measured as the percentage deviance between expected and actual production. The dominant climatic variables are observed temperature, evaporation, solar radiation and modelled water stress. Initially, a number of alternate statistical models showed good agreement within the historical data, with jack-knife cross-validation R2 values of 96% or better. However, forecasts varied quite widely between these alternate models. Exploratory multivariate analyses and nearest-neighbour methods were used to investigate these differences. For 2001-2003, the overall forecasts were in the right direction (when compared with the long-term expected values), but were over-estimates. In 2004 the forecast was well under the observed production, and in 2005 the revised models produced a forecast within 5.1% of the actual production. Over the first five years of forecasting, the absolute deviance for the climate-adjustment models averaged 10.1%, just outside the targeted objective of 10%.

Capsicum chlorosis virus infecting Capsicum annuum in the East Kimberley region of Western Australia

Capsicum chlorosis virus (CaCV) was detected in field grown Capsicum annuum from Kununurra in northeast Western Australia. Identification of the Kununurra isolate (WA-99) was confirmed using sap transmission to indicator hosts, positive reactions with tospovirus serogroup IV-specific antibodies and CaCV-specific primers, and amino acid sequence comparisons that showed >97% identity with published CaCV nucleocapsid gene sequences. The reactions of indicator hosts to infection with WA-99 often differed from those of the type isolate from Queensland. The virus multiplied best when test plants were grown at warm temperatures. CaCV was not detected in samples collected in a survey of C. annuum crops planted in the Perth Metropolitan area.

The leaf-tying moth Hypocosmia pyrochroma (Lep., Pyralidae), a host-specific biological control agent for cat's claw creeper Macfadyena unguis-cati (Bignoniaceae) in Australia

Cat's claw creeper, Macfadyena unguis-cati, a major environmental weed in coastal and sub-coastal areas of Queensland and New South Wales, Australia is a target for classical biological control. Host specificity of Hypocosmia pyrochroma Jones (Lep., Pyralidae), as a potential biological control agent was evaluated on the basis of no-choice and choice larval feeding and survival, and adult oviposition preference tests, involving 38 plant species in 10 families. In no-choice tests, larval feeding and development occurred only on cat's claw creeper. In choice tests, oviposition and larval development was evident only on cat's claw creeper. The results support the host-specificity tests conducted in South Africa, and suggest that H. pyrochroma is a highly specific biological control agent that does not pose any risk to non-target plants tested in Australia. This agent has been approved for field release by relevant regulatory authorities in Australia.

Advances in the culture of lobsters.

Commercial aquaculture of marine lobsters is an attractive proposition, as most species are high value with established market demand, and fishery production is static or diminishing. Nevertheless, achievement of commercial success will necessitate resolution of technical difficulties associated with on-growing of aggressive species (clawed lobsters) or with rearing the larvae, which for spiny and slipper lobsters is generally a painstaking and protracted process. Notwithstanding these technical challenges, increasing market demand for the product is driving a substantial research and development effort around the world to develop commercial lobster farming technology. This chapter reports on the status of that effort, the successes and obstacles.

Global banana disease management - getting serious with sustainability and food security

Much research in understanding plant diseases has been undertaken, but there has been insufficient attention given to dealing with coordinated approaches to preventing and managing diseases. A global management approach is essential to the long-term sustainability of banana production. This approach would involve coordinated surveys, capacity building in developing countries, development of disease outbreak contingency plans and coordinated quarantine awareness, including on-line training in impact risk assessment and web-based diagnostic software. Free movement of banana plants and products between some banana-producing countries is causing significant pressure on the ability to manage diseases in banana. The rapid spread of Fusarium oxysporum f. sp. cubense 'tropical race 4' in Asia, bacterial wilts in Africa and Asia and black leaf streak [Mycosphaerella fijiensis] in Brazil and elsewhere are cases in point. The impact of these diseases is devastating, severely cutting family incomes and jeopardising food security around the globe. Agreements urgently need to be reached between governments to halt the movement of banana plants and products between banana-producing countries before it is too late and global food security is irreparably harmed. Black leaf streak, arguably the most serious banana disease, has become extremely difficult to control in commercial plantations in various parts of the world. Sometimes in excess of 50 fungicide sprays have to be applied each year. Disease eradication and effective disease control is not possible because there is no control of disease inoculum in non-commercial plantings in these locations. Additionally, there have been enormous sums of money invested in international banana breeding programmes over many years only to see the value of hybrid products lost too soon. 'Goldfinger' (AAAB, syn. 'FHIA-01'), for example, has recently been observed severely affected by black leaf streak in Samoa. Resistant cultivars alone cannot be relied upon in the fight against this disease. Real progress in control may only come when the local communities are engaged and become actively involved in regional programmes. Global recommendations are long overdue and urgently needed to help ensure the long-term sustainable utilisation of the products of the breeding programmes.

The distribution of badnavirus-infected Musa germplasm from the International Transit Centre, Katholieke Universiteit Leuven, Belgium

Bioversity International is reviewing its moratorium on the distribution of virus-infected Musa germplasm from the International Transit Centre (ITC), and the ProMusa Crop Protection Working Group has been invited to comment on policy changes. This paper was written to form a basis of discussion among the working group members during the ISHS/ProMusa symposium. It argues that the distribution of Musa germplasm should be guided by the International Plant Protection Convention, which states that it is the responsibility of the importing country, not the exporter, to impose the phytosanitary measures. There may be special circumstances where the release of badnavirus-infected germplasm from the ITC could be justified.