Extent of dense native woodland and exotic weed infestation in the extensive grazing lands of the Upper Herbert and Upper Burdekin River Catchments of far north Queensland: results of a producer survey

The Mt Garnet Landcare Group commissioned a survey of landholders within the Upper Herbert and Upper Burdekin River Catchments to assess the density of native woodlands and to gauge the extent of exotic weed infestation. Twenty-four of 49 landholders responded, representing an area of nearly 500 000 ha or 47% of the total area. Dense native woodland covers 24% (>117 000 ha) of the area surveyed, while a further 30% (140 000 ha) supports moderately dense stands. The dense stands are largely confined to the highly fertile alluvial soils (26% dense woodland) and the lower fertility sandy-surfaced soils (33% or >96 000 ha). Moderate and dense infestations of exotic weeds, principally Lantana camara, occur on 54% (20 000 ha) of alluvial soils and on 13% of sandy-surfaced soils (39 000 ha), where praxelis (Praxelis clematidia) is the major weed. Basaltic soils have low levels of both dense woodland and exotic weed infestation. Some implications of the results are discussed.

Survey of Fusarium species associated with crown rot of wheat and barley in eastern Australia

Fusarium species associated with crown rot were isolated and identified from 409 wheat, barley or durum wheat crops from the eastern Australian grain belt between 1996 and 1999. Fusarium pseudograminearum was almost the only species isolated from crops in Queensland and New South Wales. F. pseudograminearum was also the most common species in Victoria and South Australia, but F. culmorum was frequently isolated in these states. F. culmorum accounted for more than 70% of isolates from the Victorian high-rainfall (> 500 mm) region and the South-East region of South Australia. F. culmorum comprised 18% of isolates from the Victorian medium-rainfall (350-500 mm) region, and 7% of isolates from each of the Victorian low-rainfall region and the Mid-North region of South Australia. F. avenaceum, F. crookwellense and F. graminearum were isolated very infrequently. The proportion of F. culmorum among isolates of Fusarium from districts in Victoria and South Australia was strongly correlated with climatic conditions around the end of the growing season, especially with rainfall in November.

Quantitative assessment of total and Gram-positive aerobic bacteria in fresh and ambient-temperature-stored sub-tropical marine fish

The current study was undertaken to enumerate Gram-positive bacteria in fresh sub-tropical marine fish and determine the effect of ambient storage (25°C) on the Gram-positive bacterial count. Total and Gram-positive bacteria were enumerated in the muscles, gills and gut of fresh and stored Pseudocaranx dentex, Pagrus auratus and Mugil cephalus on tryptone soya agar (TSA) and TSA with 0.25% phenylethyl alcohol (PEA), respectively. Initial studies indicated that PEA significantly reduced total aerobic bacterial count (TABC) whereas control Gram-positive bacteria were not affected by 0.25% PEA. TABC significantly increased in all fish body parts, whereas Gram-positive aerobic bacterial count (GABC) significantly increased only in the muscles and gills during ambient storage for 15 h. The TABC of the fish species increased from 4.00, 6.13 and 4.58 log cfu g-1, respectively in the muscles, gills, and gut to 6.31, 7.31 and 7.23 log cfu g-1 by the end of storage. GABC increased from 2.00, 3.52 and 2.20 log cfu g-1 to 4.70, 5.85 and 3.36 log cfu g-1. Within each species, TABC were significantly higher in the gills compared to that of muscles and gut; however, no significant differences were found in GABC between muscles and gills. This study demonstrated the potential importance of Gram-positive bacteria in sub-tropical marine fish and their spoilage.

Quantitative assessment of total phenol contents of European oak (Quercus petraea and Quercus robur) by diffuse reflectance NIR spectroscopy on solid wood surfaces

Near infrared spectroscopy (NIRS) combined with multivariate analysis techniques was applied to assess phenol content of European oak. NIRS data were firstly collected directly from solid heartwood surfaces: in doing so, the spectra were recorded separately from the longitudinal radial and the transverse section surfaces by diffuse reflectance. The spectral data were then pretreated by several pre-processing procedures, such as multiplicative scatter correction, first derivative, second derivative and standard normal variate. The tannin contents of sawmill collected from the longitudinal radial and transverse section surfaces were determined by quantitative extraction with water/methanol (1:4, by vol). Then, total phenol contents in tannin extracts were measured by the Folin-Ciocalteu method. The NIR data were correlated against the Folin-Ciocalteu results. Calibration models built with partial least squares regression displayed strong correlation - as expressed by high determination correlation coefficient (r2) and high ratio of performance to deviation (RPD) - between measured and predicted total phenols content, and weak calibration and prediction errors (RMSEC, RMSEP). The best calibration was provided with second derivative spectra (r2 value of 0.93 for the longitudinal radial plane and of 0.91 for the transverse section plane). This study illustrates that the NIRS technique when used in conjunction with multivariate analysis could provide reliable, quick and non-destructive assessment of European oak heartwood extractives.

Detecting quantitative trait loci affecting beef tenderness on bovine chromosome 7 near calpastatin and lysyl oxidase

From a study of 3 large half-sib families of cattle, we describe linkage between DNA polymorphisms on bovine chromosome 7 and meat tenderness. Quantitative trait loci (QTL) for Longissimus lumborum peak force (LLPF) and Semitendonosis adhesion (STADH) were located to this map of DNA markers, which includes the calpastatin ( CAST) and lysyl oxidase (LOX) genes. The LLPF QTL has a maximum lodscore of 4.9 and allele substitution of approximately 0.80 of a phenotypic standard deviation, and the peak is located over the CAST gene. The STADH QTL has a maximum lodscore of 3.5 and an allele substitution of approximately 0.37 of a phenotypic standard deviation, and the peak is located over the LOX gene. This suggests 2 separate likelihood peaks on the chromosome. Further analyses of meat tenderness measures in the Longissimus lumborum, LLPF and LL compression (LLC), in which outlier individuals or kill groups are removed, demonstrate large shifts in the location of LLPF QTL, as well as confirming that there are indeed 2 QTL on bovine chromosome 7. We found that both QTL are reflected in both LLPF and LLC measurements, suggesting that both these components of tenderness, myofibrillar and connective tissue, are detected by both measurements in this muscle.

Mapping quantitative trait loci for resistance to Pratylenchus thornei from synthetic hexaploid wheat in the International Triticeae Mapping Initiative (ITMI) population

Root-lesion nematode (Pratylenchus thornei) is a serious pathogen of wheat in many countries. The International Triticeae Mapping Initiative (ITMI) population of recombinant inbred lines (RILs) was assessed for resistance to P. thornei to determine the chromosome locations of the resistance genes. The ITMI population is derived from a cross between the resistant synthetic hexaploid wheat W-7984 and a susceptible bread wheat cultivar Opata 85. Two years of phenotypic data for resistance to P. thornei were obtained in replicated glasshouse trials. Quantitative trait locus (QTL) analysis was performed using available segregation and map data for 114 RILs. A QTL on chromosome 6DS showed consistent effects for reduced nematode numbers (partial resistance) across years and accounted for 11% and 23% of the phenotypic variation. A second QTL for P. thornei resistance on chromosome 2BS accounted for an additional 19% and 5%. Restriction fragment length polymorphism (RFLP) and simple sequence repeat (SSR) markers associated with the QTLs are physically located in regions rich in major genes at the distal ends of the short chromosome arms of 6D and 2B. SSR markers with potential for marker-assisted selection of P. thornei resistance effective in different genetic backgrounds have been identified.

Odour emissions from anaerobic piggery ponds. 1. Results of a three season, 14-month survey

Odour emission rates were measured for seven different anaerobic ponds treating piggery wastes at six to nine discrete locations across the surface of each pond on each sampling occasion over a 14-month period. Emission rate values varied between ponds, between seasons for the same pond and even for the same pond on different days of a sampling week. Average seasonal emission rates ranged from 7.9 to 46.5 OU/m2 s, while average emission rates ranged from 16.0 to 29.0 OU/m2 s. Factors potentially responsible for the variability in emission rates were investigated, including air and pond liquor temperatures, time of day of sample collection, season and the impact of a prolonged drought.

A survey of management and economic impact of weeds in dryland cotton cropping systems of subtropical Australia

In dryland cotton cropping systems, the main weeds and effectiveness of management practices were identified, and the economic impact of weeds was estimated using information collected in a postal and a field survey of Southern Queensland and northern New South Wales. Forty-eight completed questionnaires were returned, and 32 paddocks were monitored in early and late summer for weed species and density. The main problem weeds were bladder ketmia (Hibiscus trionum), common sowthistle (Sonchus oleraceus), barnyard grasses (Echinochloa spp.), liverseed grass (Urochloa panicoides) and black bindweed (Fallopia convolvulus), but the relative importance of these differed with crops, fallows and crop rotations. The weed flora was diverse with 54 genera identified in the field survey. Control of weed growth in rotational crops and fallows depended largely on herbicides, particularly glyphosate in fallow and atrazine in sorghum, although effective control was not consistently achieved. Weed control in dryland cotton involved numerous combinations of selective herbicides, several non-selective herbicides, inter-row cultivation and some manual chipping. Despite this, residual weeds were found at 38-59% of initial densities in about 3-quarters of the survey paddocks. The on-farm financial costs of weeds ranged from $148 to 224/ha.year depending on the rotation, resulting in an estimated annual economic cost of $19.6 million. The approach of managing weed populations across the whole cropping system needs wider adoption to reduce the weed pressure in dryland cotton and the economic impact of weeds in the long term. Strategies that optimise herbicide performance and minimise return of weed seed to the soil are needed. Data from the surveys provide direction for research to improve weed management in this cropping system. The economic framework provides a valuable measure of evaluating likely future returns from technologies or weed management improvements.

Identification of quantitative trait loci for resistance to two species of root-lesion nematode (Pratylenchus thornei and P. neglectus) in wheat

Pratylenchus thornei and P. neglectus are two species of root-lesion nematode that cause substantial yield losses in wheat. No commercially available wheat variety has resistance to both species. A doubled-haploid population developed from a cross between the synthetic hexaploid wheat line CPI133872 and the bread wheat Janz was used to locate and tag quantitative trait loci (QTLs) associated with resistance to both P. thornei and P. neglectus. Wheat plants were inoculated with both species of nematode in independent replicated glasshouse trials repeated over 2 years. Known locations of wheat microsatellite markers were used to construct a framework map. After an initial single-marker analysis to detect marker-trait linkages, chromosome regions associated with putative QTLs were targetted with microsatellite markers to increase map density in the chromosome regions of interest. In total, 148 wheat microsatellite markers and 21 amplified fragment length polymorphism markers were mapped. The codominant microsatellite marker Xbarc183 on the distal end of chromosome 6DS was allelic for resistance to both P. thornei and P. neglectus. The QTL were designated QRlnt.lrc-6D.1 and QRlnn.lrc-6D.1, for the 2 traits, respectively. The allele inherited from CPI133872 explained 22.0-24.2% of the phenotypic variation for P. thornei resistance, and the allele inherited from Janz accounted for 11.3-14.0% of the phenotypic variation for P. neglectus resistance. Composite interval mapping identified markers that flank a second major QTL on chromosome 6DL (QRlnt.lrc-6D.2) that explained 8.3-13.4% of the phenotypic variation for P. thornei resistance. An additional major QTL associated with P. neglectus resistance was detected on chromosome 4DS (QRlnn.lrc-4D.1) and explained a further 10.3-15.4% of the phenotypic variation. The identification and tagging of nematode resistance genes with molecular markers will allow appropriate allele combinations to be selected, which will aid the successful breeding of wheat with dual nematode resistance.

Simple sequence repeat markers associated with three quantitative trait loci for black point resistance can be used to enrich selection populations in bread wheat

Black point in wheat has the potential to cost the Australian industry $A30.4 million a year. It is difficult and expensive to screen for resistance, so the aim of this study was to validate 3 previously identified quantitative trait loci (QTLs) for black point resistance on chromosomes 2B, 4A, and 3D of the wheat variety Sunco. Black point resistance data and simple sequence repeat (SSR) markers, linked to the resistance QTLs and suited to high-throughput assay, were analysed in the doubled haploid population, Batavia (susceptible) × Pelsart (resistant). Sunco and Pelsart both have Cook in their pedigree and both have the Triticum timopheevii translocation on 2B. SSR markers identified for the 3 genetic regions were gwm319 (2B, T. timopheevii translocation), wmc048 (4AS), and gwm341 (3DS). Gwm319 and wmc048 were associated with black point resistance in the validation population. Gwm341 may have an epistatic influence on the trait because when resistance alleles were present at both gwm319 and wmc048, the Batavia-derived allele at gwm341 was associated with a higher proportion of resistant lines. Data are presented showing the level of enrichment achieved for black point resistance, using 1, 2, or 3 of these molecular markers, and the number of associated discarded resistant lines. The level of population enrichment was found to be 1.83-fold with 6 of 17 resistant lines discarded when gwm319 and wmc048 were both used for selection. Interactions among the 3 QTLs appear complex and other genetic and epigenetic factors influence susceptibility to black point. Polymorphism was assessed for these markers within potential breeding material. This indicated that alternative markers to wmc048 may be required for some parental combinations. Based on these results, marker-assisted selection for the major black point resistance QTLs can increase the rate of genetic gain by improving the selection efficiency and may facilitate stacking of black point resistances from different sources.

Survey of weed flora and management relative to cropping practices in the north-eastern grain region of Australia

The main weeds and weed management practices undertaken in broad acre dryland cropping areas of north-eastern Australia have been identified. The information was collected in a comprehensive postal survey of both growers and agronomists from Dubbo in New South Wales (NSW) through to Clermont in central Queensland, where 237 surveys were returned. A very diverse weed flora of 105 weeds from 91 genera was identified for the three cropping zones within the region (central Queensland, southern Queensland and northern NSW). Twenty-three weeds were common to all cropping zones. The major common weeds were Sonchus oleraceus, Rapistrum rugosum, Echinochloa spp. and Urochloa panicoides. The main weeds were identified for both summer and winter fallows, and sorghum, wheat and chickpea crops for each of the zones, with some commonality as well as floral uniqueness recorded. More genera were recorded in the fallows than in crops, and those in summer fallows exceeded the number in winter. Across the region, weed management relied heavily on herbicides. In fallows, glyphosate and mixes with glyphosate were very common, although the importance of the glyphosate mix partner differed among the cropping zones. Use and importance of pre-emergence herbicides in-crop varied considerably among the zones. In wheat, more graminicides were used in northern NSW than in southern Queensland, and virtually none were used in central Queensland, reflecting the differences in winter grass weed flora across the region. Atrazine was the major herbicide used in sorghum, although metolachlor was also used predominantly in northern NSW. Fallow and inter-row cultivation were used more often in the southern areas of the region. Grazing of fallows was more prominent in northern NSW. High crop seeding rates were not commonly recorded indicating that growers are not using crop competition as a tool for weed management. Although many management practices were recorded overall, few growers were using integrated weed management, and herbicide resistance has been and continues to be an issue for the region.

A new semi-dwarfing gene identified by molecular mapping of quantitative trait loci in barley.

Semi-dwarfing genes have been widely used in spring barley (Hordeum vulgare L.) breeding programs in many parts of the world, but the success in developing barley cultivars with semi-dwarfing genes has been limited in North America. Exploiting new semi-dwarfing genes may help in solving this dilemma. A recombinant inbred line population was developed by crossing ZAU 7, a semi-dwarf cultivar from China, to ND16092, a tall breeding line from North Dakota. To identify quantitative trait loci (QTL) controlling plant height, a linkage map comprised of 111 molecular markers was constructed. Simple interval mapping was performed for each of the eight environments. A consistent QTL for plant height was found on chromosome 7HL. This QTL is not associated with maturity and rachis internode length. We suggest the provisional name Qph-7H for this QTL. Qph-7H from ZAU 7 reduced plant height to about 3/4 of normal; thus, Qph-7H is considered a semi-dwarfing gene. Other QTLs for plant height were found, but their expression was variable across the eight environments tested.

Quantitative trait loci and epistatic interactions in barley conferring resistance to net type net blotch (Pyrenophora teres f. teres) isolates.

Net type net blotch (NTNB) is an important barley disease in Australia and elsewhere, with significant yield reduction. This trait is important in selection along with other traits of quality and agronomic value. Two-hundred doubled-haploid lines were generated through anther culture from a cross between 'Pompadour' and 'Stirling'. Quantitative trait loci (QTL) were identified against five isolates of Pyrenophora teres f. teres, which represent virulences across Australia. QTL were mapped on chromosomes 3H and 6H using simple sequence repeat (SSR) markers. The resistance locus on 6H was detected with all isolates while the 3H locus was detected with two isolates. The 6H QTL from 'Pompadour' contributed resistance to isolates 97NB1, 95NB100 and NB81, whereas 6H QTL from 'Stirling' contributed resistance to isolates NB50 and NB52B. The 3H QTL from 'Pompadour' contributed resistance to NB50 and NB52B. Significant epistatic interactions were detected between QTL on 3H and 6H. These resistance QTL are a useful resource and identifying closely linked SSR markers with allelic combinations will facilitate in marker-assisted selection to develop NTNB resistant breeding lines.

Quantitative and molecular genetics of juvenile wood traits in radiata and slash/Caribbean pines.

The Juvenile Wood Initiative (JWI) project has been running successfully since July 2003 under a Research Agreement with FWPA and Letters of Association with the consortium partners STBA (Southern Tree Breeding Association), ArborGen and FPQ (Forestry Plantations Queensland). Over the last five and half years, JWI scientists in CSIRO, FPQ, and STBA have completed all 12 major milestones and 28 component milestones according to the project schedule. We have made benchmark progress in understanding the genetic control of wood formation and interrelationships among wood traits. The project has made 15 primary scientific findings and several results have been adopted by industry as summarized below. This progress was detailed in 10 technical reports to funding organizations and industry clients. Team scientists produced 16 scientific manuscripts (8 published, 1 in press, 2 submitted, and several others in the process of submission) and 15 conference papers or presentations. Primary Scientific Findings. The 15 major scientific findings related to wood science, inheritance and the genetic basis of juvenile wood traits are: 1. An optimal method to predict stiffness of standing trees in slash/Caribbean pine is to combine gravimetric basic density from 12 mm increment cores with a standing tree prediction of MoE using a time of flight acoustic tool. This was the most accurate and cheapest way to rank trees for breeding selection for slash/Caribbean hybrid pine. This method was also recommended for radiata pine. 2. Wood density breeding values were predicted for the first time in the STBA breeding population using a large sample of 7,078 trees (increment cores) and it was estimated that selection of the best 250 trees for deployment will produce wood density gains of 12.4%. 3. Large genetic variation for a suite of wood quality traits including density, MFA, spiral grain, shrinkage, acoustic and non-acoustic stiffness (MoE) for clear wood and standing trees were observed. Genetic gains of between 8 and 49% were predicted for these wood quality traits with selection intensity between 1 to 10% for radiata pine. 4. Site had a major effect on juvenile-mature wood transition age and the effect of selective breeding for a shorter juvenile wood formation phase was only moderate (about 10% genetic gain with 10% selection intensity, equivalent to about 2 years reduction of juvenile wood). 5. The study found no usable site by genotype interactions for the wood quality traits of density, MFA and MoE for both radiata and slash/Caribbean pines, suggesting that assessment of wood properties on one or two sites will provide reliable estimates of the genetic worth of individuals for use in future breeding. 6. There were significant and sizable genotype by environment interactions between the mainland and Tasmanian regions and within Tasmania for DBH and branch size. 7. Strong genetic correlations between rings for density, MFA and MoE for both radiata and slash/Caribbean pines were observed. This suggests that selection for improved wood properties in the innermost rings would also result in improvement of wood properties in the subsequent rings, as well as improved average performance of the entire core. 8. Strong genetic correlations between pure species and hybrid performance for each of the wood quality traits were observed in the hybrid pines. Parental performance can be used to identify the hybrid families which are most likely to have superior juvenile wood properties of the slash/Caribbean F1 hybrid in southeast Queensland. 9. Large unfavourable genetic correlations between growth and wood quality traits were a prominent feature in radiata pine, indicating that overcoming this unfavourable genetic correlation will be a major technical issue in progressing radiata pine breeding. 10. The project created the first radiata pine 18 k cDNA microarray and generated 5,952 radiata pine xylogenesis expressed sequence tags (ESTs) which assembled into 3,304 unigenes. 11. A total of 348 genes were identified as preferentially expressed genes in earlywood or latewood while a total of 168 genes were identified as preferentially expressed genes in either juvenile or mature wood. 12. Juvenile earlywood has a distinct transcriptome relative to other stages of wood development. 13. Discovered rapid decay of linkage disequilibrium (LD) in radiata pine with LD decaying to approximately 50% within 1,700 base pairs (within a typical gene). A total of 913 SNPS from sequencing 177,380 base pairs were identified for association genetic studies. 14. 149 SNPs from 44 genes and 255 SNPs from a further 51 genes (total 95 genes) were selected for association analysis with 62 wood traits, and 30 SNPs were shortlisted for their significant association with variation of wood quality traits (density, MFA and MoE) with individual significant SNPs accounting for between 1.9 and 9.7% of the total genetic variation in traits. 15. Index selection using breeding objectives was the most profitable selection method for radiata pine, but in the long term it may not be the most effective in dealing with negative genetic correlations between wood volume and quality traits. A combination of economic and biological approaches may be needed to deal with the strong adverse correlation.

Salmonella Virchow and Salmonella Weltevreden in a Random Survey of the Asian House Gecko, Hemidactylus frenatus, in Houses in Northern Australia.

Background: Salmonella enterica serotype Virchow is the most common cause of invasive nontyphoid salmonellosis in North Queensland, particularly in infants, but the zoonotic source is unknown. This study aimed at determining (i) the prevalence of the introduced Asian house gecko, Hemidactylus frenatus, in houses in North Queensland and (ii) whether they were a potential source of Salmonella Virchow. Methods: Asian house geckos were collected in a random survey of houses in Townsville, North Queensland. Gut contents underwent microbiological analysis within 2 h of removal using both direct plating and enrichment broth methods. Any organism found to be a presumptive Salmonella spp. was then sent to a reference lab for confirmation of genus/species, serotyping, and phage typing if indicated. Results: One hundred Asian house geckos were collected from 57 houses. Geckos were present in 100% of houses surveyed, and prevalence of Salmonella in large intestinal contents was 7% (95% confidence interval 2, 12%). Three serotypes were found: Virchow (phage type 8), Weltevreden, and an untypable subspecies 1 serotype 11:-:1,7. Conclusion: Since Salmonella Virchow (phage type 8) is associated with invasive disease, the introduced Asian house gecko may play a significant role in the epidemiology of sporadic salmonellosis in places invaded by these peridomestic reptiles. These results justify more detailed epidemiological studies on the role of the Asian house gecko in sporadic salmonellosis and development of evidence-based strategies to decrease this potential zoonotic hazard.