Transcriptome analysis of grain development in hexaploid wheat

Background: Hexaploid wheat is one of the most important cereal crops for human nutrition. Molecular understanding of the biology of the developing grain will assist the improvement of yield and quality traits for different environments. High quality transcriptomics is a powerful method to increase this understanding. Results: The transcriptome of developing caryopses from hexaploid wheat ( Triticum aestivum, cv. Hereward) was determined using Affymetrix wheat GeneChip (R) oligonucleotide arrays which have probes for 55,052 transcripts. Of these, 14,550 showed significant differential regulation in the period between 6 and 42 days after anthesis ( daa). Large changes in transcript abundance were observed which were categorised into distinct phases of differentiation ( 6 - 10 daa), grain fill ( 12 - 21 daa) and desiccation/maturation ( 28 - 42 daa) and were associated with specific tissues and processes. A similar experiment on developing caryopses grown with dry and/or hot environmental treatments was also analysed, using the profiles established in the first experiment to show that most environmental treatment effects on transcription were due to acceleration of development, but that a few transcripts were specifically affected. Transcript abundance profiles in both experiments for nine selected known and putative wheat transcription factors were independently confirmed by real time RT-PCR. These expression profiles confirm or extend our knowledge of the roles of the known transcription factors and suggest roles for the unknown ones. Conclusion: This transcriptome data will provide a valuable resource for molecular studies on wheat grain. It has been demonstrated how it can be used to distinguish general developmental shifts from specific effects of treatments on gene expression and to diagnose the probable tissue specificity and role of transcription factors

Secondary cell wall composition and candidate gene expression in developing willow (Salix purpurea) stems

The properties of the secondary cell wall (SCW) in willow largely determine the suitability of willow biomass feedstock for potential bioenergy and biofuel applications. SCW development has been little studied in willow and it is not known how willow compares with model species, particularly the closely related genus Populus. To address this and relate SCW synthesis to candidate genes in willow, a tractable bud culture-derived system was developed in Salix purpurea, and cell wall composition and RNA-Seq transcriptome were followed in stems during early development. A large increase in SCW deposition in the period 0–2 weeks after transfer to soil was characterised by a big increase in xylan content, but no change in the frequency of substitution of xylan with glucuronic acid, and increased abundance of putative transcripts for synthesis of SCW cellulose, xylan and lignin. Histochemical staining and immunolabeling revealed that increased deposition of lignin and xylan was associated with xylem, xylem fibre cells and phloem fibre cells. Transcripts orthologous to those encoding xylan synthase components IRX9 and IRX10 and xylan glucuronyl transferase GUX1 in Arabidopsis were co-expressed, and showed the same spatial pattern of expression revealed by in situ hybridisation at four developmental stages, with abundant expression in proto-xylem, xylem fibre and ray parenchyma cells and some expression in phloem fibre cells. The results show a close similarity with SCW development in Populus species, but also give novel information on the relationship between spatial and temporal variation in xylan-related transcripts and xylan composition

Localisation of iron and zinc in grain of biofortified wheat

The dietary contributions of iron (Fe) and zinc (Zn) from cereals are determined by concentrations, locations and chemical forms. A genetically biofortified wheat line showed higher concentrations of Zn and Fe than three control lines when grown over two years. The mineral distributions determined using imaging (histochemical staining and LA-ICP-MS), sequential pearling and hand dissection showed no consistent differences between the two lines. Fe was most abundant in the aleurone layer and the scutellum and Zn in the scutellar epithelium, the endosperm transfer cells and embryonic axis. Pearling fractions showed positive correlations between the concentration of P and those of Zn and Fe in all fractions except the outermost layer. This is consistent with Fe and Zn being concentrated in phytates. Developing grains showed decreasing gradients in concentration from the proximal to the distal ends. The concentrations of Fe and Zn were therefore higher in the biofortified line than the control lines but their locations did not differ

Temperature and nitrogen supply interact to determine protein distribution gradients in the wheat grain endosperm

Gradients exist in the distribution of storage proteins in the wheat (Triticum aestivum L.) endosperm and determine the milling properties and protein recovery rate of the grain. A novel image analysis technique was developed to quantify both the gradients in protein concentration, and the size distribution of protein bodies within the endosperm of wheat plants grown under two different (20 °C or 28 °C) post-anthesis temperatures, and supplied with a nutrient solution with either high or low nitrogen content. Under all treatment combinations protein concentration was greater in the endosperm cells closest to the aleurone layer, and decreased towards the centre of the two lobes of the grain, i.e. a negative gradient. This was accompanied by a decrease in size of protein bodies from the outer to the inner endosperm layers in all but one of the treatments. Elevated post-anthesis temperature had the effect of increasing the magnitude of the negative gradients in both protein concentration and protein body size, whilst limiting nitrogen supply decreased the gradients

Subcellular dynamics studies of iron reveal how tissue‐specific distribution patterns are established in developing wheat grains

Understanding the mechanisms of iron trafficking in plants is key to enhancing the nutritional quality of crops. Because it is difficult to image iron in transit, we currently have an incomplete picture of the route(s) of iron translocation in developing seeds and how the tissue-specific distribution is established. We have used a novel approach, combining iron-57 ( 57Fe) isotope labelling and nanoscale secondary ion mass spectrometry (NanoSIMS), to visualize iron translocation between tissues and within cells in immature wheat grain, Triticum aestivum. This enabled us to track the main route of iron transport from maternal tissues to the embryo through the different cell types. Further evidence for this route was provided by genetically diverting iron into storage vacuoles, with confirmation provided by histological staining and transmission electron microscopy energy dispersive X-ray spectroscopy (TEM-EDS). Almost all iron in both control and transgenic grains was found in intracellular bodies, indicating symplastic rather than apoplastic transport. Furthermore, a new type of iron body, highly enriched in 57Fe, was observed in aleurone cells and may represent iron being delivered to phytate globoids. Correlation of the 57Fe enrichment profiles obtained by NanoSIMS with tissue-specific gene expression provides an updated model of iron homeostasis in cereal grains with relevance for future biofortification strategies

Harnessing Knowledge from Plant Functional Genomics and Multi-Omics for Genetic Improvement

Plant biology research has currently entered the post-genomics era with the advances in genomic technologies [...

The composition and geochemical significance of organic matters in surface sediments from the Southwest Sub-basin of the South China Sea

Information about ocean evolution and material-energy exchange between the ocean and surrounding continents can be preserved in marine sediments. The Southwest Sub-basin, located among the Xisha Islands, the Zhongsha Islands, and the Nansha Islands, is an ideal tectonic unit to analyze the sedimentary environments of the South China Sea. In this paper, the distribution patterns of lipid biomarkers and their compound-specific stable carbon isotopes in surface sediments from the Southwest Sub-basin of the South China Sea were analyzed. Lipid biomarkers are composed of different proportions of aliphatic hydrocarbons, carboxylic acids, alcohols and series of sterols, indicating that the organic matter of the Southwest Sub-basin was derived from marine bacteria, algae and terrestrial higher plants. The average concentration of total organic carbon (TOC) in the study samples was 0.5 +/- 0.16%. TOC, total n-alkanes, and total carboxylic acids (TFA) decreased gradually from the margins to the center of the sub-basin, whereas the content of total n-alkanols increased. The spatial distribution trends resulted from varying water depths and the contribution of terrestrial organic matter. The concentration of TFA and the TFA/TOC revealed that the accumulation of organic matter in this area was generally low. The strong correlation between TOC and TFA of surface sediments in the study area may be related to a balance between the ocean production and ocean deposition rates

Identification of unique transcriptomic signatures and key genes through RNA sequencing and integrated WGCNA and PPI network analysis in HIV infected lung cancer

Abstract With the widespread use of highly active antiretroviral therapy (HARRT), the survival time of AIDS patients has been greatly extended. However, the incidence of lung cancer in HIV‐infected patients is increasing and has become a major problem threatening the survival of AIDS patients. The aim of this study is to use Weighted Gene Co‐expression Network Analysis (WGCNA) and differential gene analysis to find possible key genes involved in HIV‐infected lung cancer. In this study, using lung tissue samples from five pairs of HIV‐infected lung cancer patients, second‐generation sequencing was performed and transcriptomic data were obtained. A total of 132 HIV‐infected lung cancer‐related genes were screened out by WGCNA and differential gene expression analysis methods. Based on gene annotation analysis, these genes were mainly enriched in mitosis‐related functions and pathways. In addition, in protein–protein interaction (PPI) analysis, a total of 39 hub genes were identified. Among them, five genes (ASPM, CDCA8, CENPF, CEP55, and PLK1) were present in both three hub gene lists (intersection gene, DEGs, and WCGNA module) suggesting that these five genes may become key genes involved in HIV‐infected lung cancer