Functional annotation of the transcriptome of Sorghum bicolor in response to osmotic stress and abscisic acid

<p>Abstract</p> <p>Background</p> <p>Higher plants exhibit remarkable phenotypic plasticity allowing them to adapt to an extensive range of environmental conditions. Sorghum is a cereal crop that exhibits exceptional tolerance to adverse conditions, in particular, water-limiting environments. This study utilized next generation sequencing (NGS) technology to examine the transcriptome of sorghum plants challenged with osmotic stress and exogenous abscisic acid (ABA) in order to elucidate genes and gene networks that contribute to sorghum's tolerance to water-limiting environments with a long-term aim of developing strategies to improve plant productivity under drought.</p> <p>Results</p> <p>RNA-Seq results revealed transcriptional activity of 28,335 unique genes from sorghum root and shoot tissues subjected to polyethylene glycol (PEG)-induced osmotic stress or exogenous ABA. Differential gene expression analyses in response to osmotic stress and ABA revealed a strong interplay among various metabolic pathways including abscisic acid and 13-lipoxygenase, salicylic acid, jasmonic acid, and plant defense pathways. Transcription factor analysis indicated that groups of genes may be co-regulated by similar regulatory sequences to which the expressed transcription factors bind. We successfully exploited the data presented here in conjunction with published transcriptome analyses for rice, maize, and Arabidopsis to discover more than 50 differentially expressed, drought-responsive gene orthologs for which no function had been previously ascribed.</p> <p>Conclusions</p> <p>The present study provides an initial assemblage of sorghum genes and gene networks regulated by osmotic stress and hormonal treatment. We are providing an RNA-Seq data set and an initial collection of transcription factors, which offer a preliminary look into the cascade of global gene expression patterns that arise in a drought tolerant crop subjected to abiotic stress. These resources will allow scientists to query gene expression and functional annotation in response to drought.</p

Methane emissions and production potentials of forest swamp wetlands in the eastern Great Xing'An Mountains, Northeast China

Measurements of methane flux at a few inundated sites in China have been extrapolated to obtain estimates on a national scale. To enable those national estimates to be refined and to compare flux from geographically separated sites comprising the same wetland types, we used a closed chamber method to measure methane flux in uninundated Betula platyphylla-and Larix gmelinii-dominated peatlands in the Northeast China. Our measurements were taken from both vegetated and bare soil surfaces, and we compared flux with environmental measures including vegetation biomass, soil temperature and soil characteristics. We found that methane flux was low, and that there were no significant differences between wetland types, indicating that environmental influences were dominant. We found that flux was positively correlated to temperature in the surface layers of the soil, the above-ground biomass of the shrub and herb layers, total soil carbon and total soil nitrogen; and we suggest that emissions may be due to anaerobic microcosms in the surface layers. The methane production potentials of the soils were low and similar between both sites but inconsistent with the differences between fluxes, and inconsistent with production potentials and fluxes reported from the same wetland types elsewhere, indicating that there were subtle environmental differences between wetlands classed as being of the same type. Differences between fluxes in vegetated chambers with bare soil chambers were insignificant, indicating that no methane emission through aerenchyma occurred at our sites. We concluded that wetland type was not an accurate predictor of methane flux.Bing Yu, Philip Stott, Hongxian Yu, Xiaoyu L