Homologues of the maize rust resistance gene Rp1-D are genetically associated with a major rust resistance QTL in sorghum

As part of a comparative mapping study between sugarcane and sorghum, a sugarcane cDNA clone with homology to the maize Rp1-D rust resistance gene was mapped in sorghum. The cDNA probe hybridised to multiple loci, including one on sorghum linkage group (LG) E in a region where a major rust resistance QTL had been previously mapped. Partial sorghum Rp1-D homologues were isolated from genomic DNA of rust-resistant and -susceptible progeny selected from a sorghum mapping population. Sequencing of the Rp1-D homologues revealed five discrete sequence classes: three from resistant progeny and two from susceptible progeny. PCR primers specific to each sequence class were used to amplify products from the progeny and confirmed that the five sequence classes mapped to the same locus on LG E. Cluster analysis of these sorghum sequences and available sugarcane, maize and sorghum Rp1-D homologue sequences showed that the maize Rp1-D sequence and the partial sugarcane Rp1-D homologue were clustered with one of the sorghum resistant progeny sequence classes, while previously published sorghum Rp1-D homologue sequences clustered with the susceptible progeny sequence classes. Full-length sequence information was obtained for one member of a resistant progeny sequence class ( Rp1-SO) and compared with the maize Rp1-D sequence and a previously identified sorghum Rp1 homologue ( Rph1-2). There was considerable similarity between the two sorghum sequences and less similarity between the sorghum and maize sequences. These results suggest a conservation of function and gene sequence homology at the Rp1 loci of maize and sorghum and provide a basis for convenient PCR-based screening tools for putative rust resistance alleles in sorghum.

Australian and Thai isolates of Burkholderia pseudomallei are distinct by multilocus sequence typing: Revision of a case of mistaken identity

A recent study using multilocus sequence typing (MLST) of Burkholderia pseudomallei isolates found a sequence type (ST60) to be common to both Thailand and Australia, contradicting earlier studies showing complete distinction between isolates from these regions. The ST60 isolates reportedly from Australia had been obtained for MLST from United Kingdom and U.S. collections. We have located and characterized the original Australian isolates; they were collected in 1983, and they are neither ST60 nor B. pseudomallei isolates. The B. pseudomallei MLST database has been corrected, and there is no ST common to isolates verified as obtained from Australia or from Thailand.

Phosphorus concentrations in the leaves of cotton in tropical Australia are determined by temperature.

Previous research on P leaf analysis for detecting deficiencies in cotton (Gossypium hirsutum L.) has not considered temperature as a determining factor. This is despite correlations between leaf P content and temperature being observed in other crops. As part of research into a new cotton farming system for the semi-arid tropics of Australia, we conducted two P fertiliser rate experiments on recently cleared un-cropped (bicarbonate P < 5 mg kg- 1) and previously cropped (bicarbonate P 26 mg kg- 1) soil. They aimed to develop P requirements and more importantly to determine if temperature affects the leaf P concentrations used to diagnose P deficiencies. In 2002, optimal yield on un-cropped, low P soil was achieved with a 60 kg P ha- 1 rate. In 2003, residual P from the 40 kg P ha- 1 treatment produced optimal yield. On cropped, high P soil there was no yield response to treatments up to 100 kg P ha- 1. On low P soil, a positive correlation was observed between P concentration in the youngest fully-unfurled leaf (YFUL), fertiliser rate, and mean diurnal temperature in the seven days prior to sampling. On high P soil, a positive correlation was observed between the YFUL and mean diurnal temperature however there was no correlation with fertiliser rate. These results show that YFUL analysis can be used to diagnose P deficiencies in cotton, provided the temperature prior to sampling is considered.

How effective are broad-scale nutrient mass balances for determining the sustainability of lot-feed manure application?

Nutrient mass balances have been used to assess a variety of land resource scenarios, at various scales. They are widely used as a simple basis for policy, planning, and regulatory decisions but it is not clear how accurately they reflect reality. This study provides a critique of broad-scale nutrient mass balances, with particular application to the fertiliser use of beef lot-feeding manure in Queensland. Mass balances completed at the district and farm scale were found to misrepresent actual manure management behaviour and potentially the risk of nutrient contamination of water resources. The difficulties of handling stockpile manure and concerns about soil compaction mean that manure is spread thickly over a few paddocks at a time and not evenly across a whole farm. Consequently, higher nutrient loads were applied to a single paddock less frequently than annually. This resulted in years with excess nitrogen, phosphorus, and potassium remaining in the soil profile. This conclusion was supported by evidence of significant nutrient movement in several of the soil profiles studied. Spreading manure is profitable, but maximum returns can be associated with increased risk of nutrient leaching relative to conventional inorganic fertiliser practices. Bio-economic simulations found this increased risk where manure was applied to supply crop nitrogen requirements (the practice of the case study farms, 200-5000 head lot-feeders). Thus, the use of broad-scale mass balances can be misleading because paddock management is spatially heterogeneous and this leads to increased local potential for nutrient loss. In response to the effect of spatial heterogeneity policy makers who intend to use mass balance techniques to estimate potential for nutrient contamination should apply these techniques conservatively.

Are we focussing wild dog control the wrong time of the year and going about it the wrong way?

Our evaluation of the predation of calves by wild dogs in the 1990s found that the number of calves killed and frequency of years that calf losses occurred, is higher in baited areas compared to adjoining, non-baited areas of similar size. Calf losses were highest with poor seasonal conditions, low prey numbers and where baited areas were re-colonised by wild dogs soon after baiting. We monitored wild dog “activity” before and after 35 baiting programs in southwest, central west and far north Queensland between 1994 and 2006 and found change in activity depends on the timing of the baiting. Baiting programs conducted between October and April show an increase in dog activity post-baiting (average increase of 219.1%, SEM 100.9, n=9, for programs conducted in October and November; an increase of 82.5%, SEM 54.5, n=7 for programs conducted in March and April; and a decrease in activity of 46.5%, SEM 10.2, n=19 for programs conducted between May and September). We monitored the seasonal activity and dispersal of wild dogs fitted with satellite transmitters 2006 to present. We have found that: • Activity of breeding males and females, whilst rearing and nurturing pups, is focussed around the den between July to September and away from areas of human activity. Activity of breeding groups appears to avoid locations of human activity until juveniles become independent (around late November). • While independent and solitary yearlings often have unstable, elliptically-shaped territories in less favourable areas, members of breeding groups have territories that appear seasonally stable and circular located in more favourable habitats. • Extra-territorial forays of solitary yearlings can be huge, in excess of 200 km. The largest forays we have monitored have occurred when the activity of pack members is focussed around rearing pups and juveniles (August to November). • Where wild dogs have dispersed or had significant territorial expansion, it has occurred within days of baiting programs and onto recently baited properties. • The wild dogs we have tracked have followed netting barrier fences for hundreds of kilometres and lived adjacent to or bypassed numerous grids in the barrier. Based on these studies, we conclude that a proportion of the perceived decline in dog activity between May and September, post baiting, is due to a decline in dog activity in areas associated with human activity. The increase in dog activity post-baiting between October and May (and increased calf predation on baited properties) is likely caused by wild dogs dispersing (juveniles and yearlings) or expanding (adults) their territory into baited, now ‘vacant’, areas. We hypothesise that baiting programs should be focussed in summer and autumn commencing late November as soon as juveniles become independent of adults. We also hypothesise that instead of large, annual or semi-annual baiting programs, laying the same number of baits over 4-6 weeks may be more effective. These hypotheses need to be tested through an adaptive management project.

How accurate are the marker orders in crop linkage maps generated from large marker datasets?

Marker ordering during linkage map construction is a critical component of QTL mapping research. In recent years, high-throughput genotyping methods have become widely used, and these methods may generate hundreds of markers for a single mapping population. This poses problems for linkage analysis software because the number of possible marker orders increases exponentially as the number of markers increases. In this paper, we tested the accuracy of linkage analyses on simulated recombinant inbred line data using the commonly used Map Manager QTX (Manly et al. 2001: Mammalian Genome 12, 930-932) software and RECORD (Van Os et al. 2005: Theoretical and Applied Genetics 112, 30-40). Accuracy was measured by calculating two scores: % correct marker positions, and a novel, weighted rank-based score derived from the sum of absolute values of true minus observed marker ranks divided by the total number of markers. The accuracy of maps generated using Map Manager QTX was considerably lower than those generated using RECORD. Differences in linkage maps were often observed when marker ordering was performed several times using the identical dataset. In order to test the effect of reducing marker numbers on the stability of marker order, we pruned marker datasets focusing on regions consisting of tightly linked clusters of markers, which included redundant markers. Marker pruning improved the accuracy and stability of linkage maps because a single unambiguous marker order was produced that was consistent across replications of analysis. Marker pruning was also applied to a real barley mapping population and QTL analysis was performed using different map versions produced by the different programs. While some QTLs were identified with both map versions, there were large differences in QTL mapping results. Differences included maximum LOD and R-2 values at QTL peaks and map positions, thus highlighting the importance of marker order for QTL mapping

Soil type does not affect seed ageing when soil water potential and temperature are controlled

To investigate the effects of soil type on seed persistence in a manner that controlled for location and climate variables, three weed species—Gomphocarpus physocarpus (swan plant), Avena sterilis ssp. ludoviciana (wild oat) and Ligustrum lucidum (broadleaf privet)—were buried for 21 months in three contrasting soils at a single location. Soil type had a significant effect on seed persistence and seedling vigour, but soil water content and temperature varied between soils due to differences in physical and chemical properties. Warmer, wetter conditions favoured shorter persistence. A laboratory-based test was developed to accelerate the rate of seed ageing within soils, using controlled superoptimal temperature and moisture conditions (the soil-specific accelerated ageing test, SSAAT). The SSAAT demonstrated that soil type per se did not influence seed longevity. Moreover, the order in which seeds aged was the same whether aged in the field or SSAAT, with L. lucidum being shortest-lived and A. sterilis being longest-lived of the three species.

Two sympatric spotted gum species are molecularly homogeneous.

Large fruited spotted gum eucalypt Corymbia henryi occurs sympatrically with small fruited spotted gum Corymbia citriodora subspecies variegata over a large portion of its range on the east coast of Australia. The two taxa are interfertile, have overlapping flowering times and share a common set of insect and vertebrate pollinators. Previous genetic analysis of both taxa from two geographically remote sites suggested that the two were morphotypes rather than genetically distinct species. In this study we further explore this hypothesis of genic species by expanding sampling broadly through their sympatric locations and examine local-scale spatial genetic structure in stands that differ in species and age composition. Delineation of populations at five microsatellite loci, using an individual-based approach and Bayesian modelling, as well as clustering of individuals based on allele frequencies showed the two species to be molecularly homogeneous. Genetic structure aligned largely with geographic areas of origin, and followed an isolation-by-distance model, where proximal populations were generally less differentiated than more distant ones. At the stand level, spotted gums also generally showed little structure consistent with the high levels of gene flow inferred across the species range. Disturbances in the uniformity of structuring were detected, however, and attributed to localised events giving rise to even aged stands, probably due to regeneration from a few individuals following fire.

Radish leaves and radish roots: are we eating the right part for cancer prevention?

Radishes are most commonly consumed as a root vegetable, although radish leaves are occasionally used in salads and cooking. While both the radish root and shoot contain glucosinolates with anti-cancer potential, the glucosinolate profile of the root and the shoot are very different. Whereas the root contains mainly glucodehydroerucin (2.8 mol/gFW) (also known as glucoraphasatin), the main glucosinolate components of the shoot are glucoraphanin (2.8 mol/gFW) and glucoraphenin (2.1 mol/gFW). Upon hydrolysis, the latter glucosinolates produce sulforaphane and sulforaphene respectively, both potent inducers of mammalian phase 2 enzymes. Previously, radishes have been dismissed as having minimal anti-cancer potential based on studies with radish roots. However, depending on the cultivar, radish shoots can have up to 45 times the capacity of roots to induce phase 2 enzymes. In fact, shoots of a number of radish cultivars (eg. 'Black Spanish') have similar or greater anti-cancer potential than broccoli florets, a vegetable that has received considerable interest in this area.

Indicator traits in bulls that are predictive of female fertility in cattle

Indicator traits in bulls that are predictive of female fertility in cattle.

Beyond fecundity control: which weeds are most containable?

1. Eradication is often the preferred strategy in the management of new weed invasions, but recent research has shown that the circumstances under which eradication can be achieved are highly constrained. Containment is a component of an eradication strategy and also a management objective in its own right. Just as for eradication, containment of a weed invasion should be attempted only if it is considered feasible. However, very little guidance exists for the assessment of containment feasibility for weeds. 2. Numerous factors have been proposed as influencing feasibility of containment, but those that relate to the potential for management of dispersal pathways and timely detection of new foci of infestation appear to be critical. Theory suggests that the rate of spread is largely driven by long-distance dispersal (LDD). However, LDD is generally unpredictable and often occurs for species that do not appear to be adapted for it. Furthermore, many (if not most) LDD events fail to give rise to new infestations. 3. As the probability of colonisation is related to the numbers of propagules immigrating ('propagule pressure') at a point in the landscape, dispersal pathways that move relatively large numbers of propagules simultaneously and/or repeatedly should most enhance weed spread. It is these pathways whose potential for management has the greatest bearing upon containment feasibility. A key impediment to containment is undetected spread; this need not occur through LDD and is more likely to occur through dispersal to lesser distances. 4. Synthesis and applications. Feasibility of containment should be viewed in terms of the effort required to reduce weed spread rate, as well as the effectiveness of relevant management actions. Where dispersal vectors are not readily manageable and the probability of detection via structured and/or unstructured surveillance is low, a much greater reliance upon fecundity control will be needed to contain a weed. A combination of empirical and theoretical approaches should be used to develop and refine estimates of containment feasibility. Such estimates will aid decision-making with regard to whether to attempt to reduce weed spread and assist in prioritisation of different weeds for containment.

Predicting Additive and Non-additive Genetic Effects from Trials Where Traits Are Affected by Interplot Competition

There are two key types of selection in a plant breeding program, namely selection of hybrids for potential commercial use and the selection of parents for use in future breeding. Oakey et al. (in Theoretical and Applied Genetics 113, 809-819, 2006) showed how both of these aims could be achieved using pedigree information in a mixed model analysis in order to partition genetic effects into additive and non-additive effects. Their approach was developed for field trial data subject to spatial variation. In this paper we extend the approach for data from trials subject to interplot competition. We show how the approach may be used to obtain predictions of pure stand additive and non-additive effects. We develop the methodology in the context of a single field trial using an example from an Australian sorghum breeding program.

Rabbit haemorrhagic disease: are Australian rabbits (Oryctolagus cuniculus) evolving resistance to infection with Czech CAPM 351 RHDV?

Rabbit haemorrhagic disease is a major tool for the management of introduced, wild rabbits in Australia. However, new evidence suggests that rabbits may be developing resistance to the disease. Rabbits sourced from wild populations in central and southeastern Australia, and domestic rabbits for comparison, were experimentally challenged with a low 60 ID50 oral dose of commercially available Czech CAPM 351 virus - the original strain released in Australia. Levels of resistance to infection were generally higher than for unselected domestic rabbits and also differed (0-73% infection rates) between wild populations. Resistance was lower in populations from cooler, wetter regions and also low in arid regions with the highest resistance seen within zones of moderate rainfall. These findings suggest the external influences of non-pathogenic calicivirus in cooler, wetter areas and poor recruitment in arid populations may influence the development rate of resistance in Australia.

Soral synapomorphies are significant for the systematics of the Ustilago-Sporisorium-Macalpinomyces complex (Ustilaginaceae)

The genera Ustilago, Sporisorium and Macalpinomyces are a polyphyletic complex of plant pathogenic fungi. The four main morphological characters used to define these genera have been considered homoplasious and not useful for resolving the complex. This study re-evaluates character homology and discusses the use of these characters for defining monophyletic groups recovered from a reconstructed phylogeny using four nuclear loci. Generic delimitation of smut fungi based on their hosts is also discussed as a means for identifying genera within this group. Morphological characters and host specificity can be used to circumscribe genera within the Ustilago-Sporisorium-Macalpinomyces complex.

Diploid and tetraploid progenitors of wheat are valuable sources of resistance to the root lesion nematode Pratylenchus thornei

The root lesion nematode Pratylenchus thornei is widely distributed in Australian wheat (Triticum aestivum) producing regions and can reduce yield by more than 50%, costing the industry AU$50 M/year. Genetic resistance is the most effective form of management but no commercial cultivars are resistant (R) and the best parental lines are only moderately R. The wild relatives of wheat have evolved in P. thornei-infested soil for millennia and may have superior levels of resistance that can be transferred to commercial wheats. To evaluate this hypothesis, a collection of 251 accessions of wheat and related species was tested for resistance to P. thornei under controlled conditions in glasshouse pot experiments over two consecutive years. Diploid accessions were more R than tetraploid accessions which proved more R than hexaploid accessions. Of the diploid accessions, 11 (52%) Aegilops speltoides (S-[B]-genome), 10 (43%) Triticum monococcum (A (m) -genome) and 5 (24%) Triticum urartu (A (u) -genome) accessions were R. One tetraploid accession (Triticum dicoccoides) was R. This establishes for the first time that P. thornei resistance is located on the A-genome and confirms resistance on the B-genome. Since previous research has shown that the moderate levels of P. thornei resistance in hexaploid wheat are dose-dependent, additive and located on the B and D-genomes, it would seem efficient to target A-genome resistance for introduction to hexaploid lines through direct crossing, using durum wheat as a bridging species and/or through the development of amphiploids. This would allow resistances from each genome to be combined to generate a higher level of resistance than is currently available in hexaploid wheat.