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.

Recent advances in the molecular biology of Leifsonia xyli subsp. xyli, causal organism of ratoon stunting disease

Twelve years ago our understanding of ratoon stunting disease (RSD) was confined almost exclusively to diagnosis of the disease and control via farm hygiene, with little understanding of the biology of the interaction between the causal agent (Leifsonia xyli subsp. xyli) and the host plant sugarcane (Saccharum spp. hybrids). Since then, research has focused on developing the molecular tools to dissect L. xyli subsp. xyli, so that better control strategies can be developed to prevent losses from RSD. Within this review, we give a brief overview of the progression in research on L. xyli subsp. xyli and highlight future challenges. After a brief historical background on RSD, we discuss the development of molecular tools such as transformation and transposon mutagenesis and discuss the apparent lack of genetic diversity within the L. xyli subsp. xyli world population. We go on to discuss the sequencing of the genome of L. xyli subsp. xyli, describe the key findings and suggest some future research based on known deficiencies that will capitalise on this tremendous knowledge base to which we now have access.

Speciation of Gram-positive bacteria in fresh and ambient-stored sub-tropical marine fish.

This study identified Gram-positive bacteria in three sub-tropical marine fish species: Pseudocaranx dentex (silver trevally), Pagrus auratus (snapper) and Mugil cephalus (sea mullet). It further elucidated the role played by fish habitat, fish body part and ambient storage on the composition of the Gram-positive bacteria. A total of 266 isolates of Gram-positive bacteria were identified by conventional biochemical methods, VITEK, PCR using genus- and species-specific primers and/or 16S rRNA gene sequencing. The isolates were found to fall into 13 genera and 30 species. In fresh fish, Staphylococcus epidermidis and Micrococcus luteus were the most frequent isolates. After ambient storage, S. epidermidis, S. xylosus and Bacillus megaterium were no longer present whereas S. warned, B. sphaericus, Brevibacillus borstelensis, Enterococcus faecium and Streptococcus uberis increased in frequency. Micrococcus luteus and S. warned were the most prevalent isolates from P. dentex, while E. faecium and Strep. uberis were the most frequent isolates from P. auratus and M. cephalus. With respect to different parts of the fish body. E. faecium, Strep. uberis and B. sphaericus were the most frequent isolates from the muscles, E. faecium, Strep. uberis from the gills and M. luteus from the gut. This study showed a diversity of Gram-positive bacteria in sub-tropical marine fish; however, their abundance was affected by fish habitat, fish body part and ambient storage.

Comparative seed and dispersal ecology of three exotic subtropical Asparagus species

The genus Asparagus includes at least six invasive species in Australia. Asparagus aethiopicus and A. africanus are invasive in subtropical Australia, and a third species, A. virgatus is naturalized and demonstrates localized spread in south east Queensland. To better understand how the attributes of these species contribute to their invasiveness, we compared fruit and seed traits, germination, seedling emergence, seed survival, and time-to-maturity. We further investigated dispersal ecology of A. africanus, examining the diet of a local frugivore, the figbird (Sphecotheres viridis) and the effect of gut passage on seedling emergence. Overall, A. aethiopicus was superior in germination and emergence, with the highest mean germination (98.8%) and emergence (94.5%) under optimal conditions and higher emergence (mean of 73.3%) across all treatments. In contrast, A. africanus had the lowest germination under optimal conditions (71.7%) and low mean seedling emergence (49.5%), but had fruits with the highest relative yield (ratio of dry pulp to fruit fresh weight) that were favored by a local frugivore. Figbirds consumed large numbers of A. africanus fruits (~30% of all non-Ficus fruits), and seedling germination was not significantly affected by gut passage compared to unprocessed fruits. Asparagus virgatus germinated poorly under cool, light conditions (1.4%) despite a high optimum mean (95.0%) and had low mean performance across emergence treatments (36.3%). The species also had fruits with a low pulp return for frugivores. For all species, seed survival declined rapidly in the first 12 mo and fell to < 3.2% viability at 36 mo. On the basis of the traits considered, A. virgatus is unlikely to have the invasive potential of its congeners. Uniformly short seed survival times suggest that weed managers do not have to contend with a substantial persistent soil-stored seed bank, but frugivore-mediated dispersal beyond existing infestations will present a considerable management challenge.

The conservation status of the world’s reptiles

Effective and targeted conservation action requires detailed information about species, their distribution, systematics and ecology as well as the distribution of threat processes which affect them. Knowledge of reptilian diversity remains surprisingly disparate, and innovative means of gaining rapid insight into the status of reptiles are needed in order to highlight urgent conservation cases and inform environmental policy with appropriate biodiversity information in a timely manner. We present the first ever global analysis of extinction risk in reptiles, based on a random representative sample of 1500 species (16% of all currently known species). To our knowledge, our results provide the first analysis of the global conservation status and distribution patterns of reptiles and the threats affecting them, highlighting conservation priorities and knowledge gaps which need to be addressed urgently to ensure the continued survival of the world’s reptiles. Nearly one in five reptilian species are threatened with extinction, with another one in five species classed as Data Deficient. The proportion of threatened reptile species is highest in freshwater environments, tropical regions and on oceanic islands, while data deficiency was highest in tropical areas, such as Central Africa and Southeast Asia, and among fossorial reptiles. Our results emphasise the need for research attention to be focussed on tropical areas which are experiencing the most dramatic rates of habitat loss, on fossorial reptiles for which there is a chronic lack of data, and on certain taxa such as snakes for which extinction risk may currently be underestimated due to lack of population information. Conservation actions specifically need to mitigate the effects of human-induced habitat loss and harvesting, which are the predominant threats to reptiles.

Bacterial and fungal community composition over time in chicken litter with high or low moisture content

1. Changes in bacterial and fungal communities in chicken litter with high and low moisture content over a five week period during a single chicken grow out cycle in a poultry shed in subtropical Australia were investigated to study the association between specific microbes and odour production. 2. Microbial biomass, as indicated by DNA yields, was higher and community composition was more dynamic over time in moist compared with dry chicken litter. 3. Bacillus, Atopostipes and Aspergillus species increased in relative abundance in moist chicken litter samples over time reflecting the relatively high fitness and hence activity of these specific bacteria and this specific fungus in this environment.

The Relationship Between the Stay-Green Trait and Grain Yield in Elite Sorghum Hybrids Grown in a Range of Environments

The stay-green drought adaptation mechanism has been widely promoted as a way of improving grain yield and lodging resistance in sorghum [Sorghum bicolor (L.) Moench] and as a result has been the subject of many physiological and genetic studies. The relevance of these studies to elite sorghum hybrids is not clear given that they sample a limited number of environments and were conducted using inbred lines or relatively small numbers of experimental F-1 hybrids. In this study we investigated the relationship between stay-green and yield using data from breeding trials that sampled 1668 unique hybrid combinations and 23 environments whose mean yields varied from 2.3 to 10.5 t ha(-1). The strength and direction of the association between stay-green and grain yield varied with both environment and genetic background (male tester). The majority of associations were positive, particularly in environments with yields below 6 t ha(-1). As trial mean yield increased above 6 t ha(-1) there was a trend toward an increased number of negative associations; however, the number and magnitude of the positive associations were larger. Given that post-flowering drought is very commonly experienced by sorghum crops world wide and average yields are 1.2 and 2.5 t ha(-1) for the world and Australia, respectively, our results indicate that selection for stay-green in elite sorghum hybrids may be broadly beneficial for increasing yield in a wide range of environments.