Transcriptomic analysis of wheat near-isogenic lines identifies PM19-A1 and A2 as candidates for a major dormancy QTL

BACKGROUND: Next-generation sequencing technologies provide new opportunities to identify the genetic components responsible for trait variation. However, in species with large polyploid genomes, such as bread wheat, the ability to rapidly identify genes underlying quantitative trait loci (QTL) remains non-trivial. To overcome this, we introduce a novel pipeline that analyses, by RNA-sequencing, multiple near-isogenic lines segregating for a targeted QTL. RESULTS: We use this approach to characterize a major and widely utilized seed dormancy QTL located on chromosome 4AL. It exploits the power and mapping resolution afforded by large multi-parent mapping populations, whilst reducing complexity by using multi-allelic contrasts at the targeted QTL region. Our approach identifies two adjacent candidate genes within the QTL region belonging to the ABA-induced Wheat Plasma Membrane 19 family. One of them, PM19-A1, is highly expressed during grain maturation in dormant genotypes. The second, PM19-A2, shows changes in sequence causing several amino acid alterations between dormant and non-dormant genotypes. We confirm that PM19 genes are positive regulators of seed dormancy. CONCLUSIONS: The efficient identification of these strong candidates demonstrates the utility of our transcriptomic pipeline for rapid QTL to gene mapping. By using this approach we are able to provide a comprehensive genetic analysis of the major source of grain dormancy in wheat. Further analysis across a diverse panel of bread and durum wheats indicates that this important dormancy QTL predates hexaploid wheat. The use of these genes by wheat breeders could assist in the elimination of pre-harvest sprouting in wheat.Jose M. Barrero, Colin Cavanagh, Klara L. Verbyla, Josquin F.G. Tibbits, Arunas P. Verbyla, B. Emma Huang, Garry M. Rosewarne, Stuart Stephen, Penghao Wang, Alex Whan, Philippe Rigault, Matthew J. Hayden, and Frank Guble

The influence of the accessory genome on bacterial pathogen evolution

Bacterial pathogens exhibit significant variation in their genomic content of virulence factors. This reflects the abundance of strategies pathogens evolved to infect host organisms by suppressing host immunity. Molecular arms-races have been a strong driving force for the evolution of pathogenicity, with pathogens often encoding overlapping or redundant functions, such as type III protein secretion effectors and hosts encoding ever more sophisticated immune systems. The pathogens’ frequent exposure to other microbes, either in their host or in the environment, provides opportunities for the acquisition or interchange of mobile genetic elements. These DNA elements accessorise the core genome and can play major roles in shaping genome structure and altering the complement of virulence factors. Here, we review the different mobile genetic elements focusing on the more recent discoveries and highlighting their role in shaping bacterial pathogen evolution

Metagenomics of the Svalbard Reindeer Rumen Microbiome Reveals Abundance of Polysaccharide Utilization Loci

Lignocellulosic biomass remains a largely untapped source of renewable energy predominantly due to its recalcitrance and an incomplete understanding of how this is overcome in nature. We present here a compositional and comparative analysis of metagenomic data pertaining to a natural biomass-converting ecosystem adapted to austere arctic nutritional conditions, namely the rumen microbiome of Svalbard reindeer (Rangifer tarandus platyrhynchus). Community analysis showed that deeply-branched cellulolytic lineages affiliated to the Bacteroidetes and Firmicutes are dominant, whilst sequence binning methods facilitated the assemblage of metagenomic sequence for a dominant and novel Bacteroidales clade (SRM-1). Analysis of unassembled metagenomic sequence as well as metabolic reconstruction of SRM-1 revealed the presence of multiple polysaccharide utilization loci-like systems (PULs) as well as members of more than 20 glycoside hydrolase and other carbohydrate-active enzyme families targeting various polysaccharides including cellulose, xylan and pectin. Functional screening of cloned metagenome fragments revealed high cellulolytic activity and an abundance of PULs that are rich in endoglucanases (GH5) but devoid of other common enzymes thought to be involved in cellulose degradation. Combining these results with known and partly re-evaluated metagenomic data strongly indicates that much like the human distal gut, the digestive system of herbivores harbours high numbers of deeply branched and as-yet uncultured members of the Bacteroidetes that depend on PUL-like systems for plant biomass degradation

Sensitivity of jarrah (Eucalyptus marginata) to phosphate, phosphite, and arsenate pulses as influenced by fungal symbiotic associations

Many plant species adapted to P-impoverished soils, including jarrah (Eucalyptus marginata), develop toxicity symptoms when exposed to high doses of phosphate (Pi) and its analogs such as phosphite (Phi) and arsenate (AsV). The present study was undertaken to investigate the effects of fungal symbionts Scutellospora calospora, Scleroderma sp., and Austroboletus occidentalis on the response of jarrah to highly toxic pulses (1.5 mmol kg−1 soil) of Pi, Phi, and AsV. S. calospora formed an arbuscular mycorrhizal (AM) symbiosis while both Scleroderma sp. and A. occidentalis established a non-colonizing symbiosis with jarrah plants. All these interactions significantly improved jarrah growth and Pi uptake under P-limiting conditions. The AM fungal colonization naturally declines in AM-eucalypt symbioses after 2–3 months; however, in the present study, the high Pi pulse inhibited the decline of AM fungal colonization in jarrah. Four weeks after exposure to the Pi pulse, plants inoculated with S. calospora had significantly lower toxicity symptoms compared to non-mycorrhizal (NM) plants, and all fungal treatments induced tolerance against Phi toxicity in jarrah. However, no tolerance was observed for AsV-treated plants even though all inoculated plants had significantly lower shoot As concentrations than the NM plants. The transcript profile of five jarrah high-affinity phosphate transporter (PHT1 family) genes in roots was not altered in response to any of the fungal species tested. Interestingly, plants exposed to high Pi supplies for 1 day did not have reduced transcript levels for any of the five PHT1 genes in roots, and transcript abundance of four PHT1 genes actually increased. It is therefore suggested that jarrah, and perhaps other P-sensitive perennial species, respond positively to Pi available in the soil solution through increasing rather than decreasing the expression of selected PHT1 genes. Furthermore, Scleroderma sp. can be considered as a fungus with dual functional capacity capable of forming both ectomycorrhizal and non-colonizing associations, where both pathways are always accompanied by evident growth and nutritional benefits

Mainstreams of Horizontal Gene Exchange in Enterobacteria: Consideration of the Outbreak of Enterohemorrhagic E. coli O104:H4 in Germany in 2011

Escherichia coli O104:H4 caused a severe outbreak in Europe in 2011. The strain TY-2482 sequenced from this outbreak allowed the discovery of its closest relatives but failed to resolve ways in which it originated and evolved. On account of the previous statement, may we expect similar upcoming outbreaks to occur recurrently or spontaneously in the future? The inability to answer these questions shows limitations of the current comparative and evolutionary genomics methods.status: publishe

Coal and Climate Change

This overview adopts a critical social science perspective to examine the state of play and potential futures for coal in the context of climate change. It introduces key trends in coal consumption, production and trade, before appraising the relevant literature. Finding surprisingly little literature directly focussed on coal and climate change compared with related fields, it appraises existing work and highlights key areas for future work. In addition to established bodies of work on the situated politics of coal and the political economy of coal, new work calling for demand side policies to be supplemented with supply side policies highlights the increasing importance of how normative contestations drive debates over coal, suggesting that future work needs to engage not only much more directly with climate change as an issue, but particularly with the place of coal in a just transition. Because of coal’s mammoth contribution to climate change and the complex political economy which drives its production and consumption, it is likely that coal will remain at the centre of difficult questions about the relationship between climate action and development for some time

The ‘Pritchard Trap’: A novel quantitative survey method for crayfish

1. As crayfish invasions continue to threaten native freshwater biota, a detailed understanding of crayfish distribution and population structure becomes imperative. Nonetheless, most current survey methods provide inadequate demographic data. The quantitative ‘Triple Drawdown’ (TDD) dewatering method has highlighted the importance of such data, yet practical constraints prevent its large-scale application. 2. Here, we introduce the ‘Pritchard Trap’, a novel passive sampling method that reliably generates quantitative crayfish population data while requiring substantially lower sampling effort than TDDs. This quadrat-style sampler was extensively tested in headwater streams of North Yorkshire, England, along an invasion gradient for signal crayfish (Pacifastacus leniusculus) from well-established sites to mixed populations of signal crayfish and native white-clawed crayfish (Austropotamobius pallipes). 3. The Pritchard Trap was trialled over several time intervals to determine the minimum required trap deployment time. TDDs at the same sites allowed for a robust evaluation of Pritchard Trap sampling accuracy in representing crayfish densities and population structure. 4. The Pritchard Trap successfully sampled both invasive and native crayfish (8–42 mm carapace length). A minimum passive deployment time of 4 days was required. At low crayfish densities (0.5 individuals m−2), increased trapping effort was necessary to achieve accurate population density and size class distribution estimates. The Pritchard Trap required substantially less sampling effort (working hours) and resources than the TDD, whilst also posing less risk to non-target species. 5. The Pritchard Trap, for the first time, affords logistically simple, truly quantitative investigations of crayfish population demographics for headwater systems. It could be integrated into crayfish research and management, for example to explore density-dependent ecological impacts of invasive crayfish and their management responses or to monitor populations and recruitment in native crayfish conservation initiatives