Transcription profiling of developing field grown barley grain in response different nitrogen fertilizer regime
ABSTRACT: Gene expression was investigated in response to nitrogen fertilizer in developing grains of field grown barley (Hordeum vulgare L. cv. Barke) at four different time points: 10, 15, 18 and 25 days after pollination (DAP).
The aim of the study was to describe the molecular and biochemical interactions associated with amino acid biosynthesis and storage protein accumulation in the developing grains of field-grown barley. Our strategy was to analyse the transcription of genes associated with the biosynthesis of storage products during the development of field-grown barley grains using a grain-specific microarray assembled in our laboratory. To identify co-regulated genes, a distance matrix was constructed which enab ...[more]
Project description:Grain development in the Poaceae defines important end-use properties such as yield, quality and nutritive value. Microarray analyses have been performed on barley grain endosperm extracts from three to eight days after pollination (DAP), when cellularization of the syncytium occurs through the growth of cell walls around individual nuclei. Profiling of transcripts differentially expressed over time reveal 56 specific modules of genes that cluster into 15 groups. Expression patterns have been superimposed upon microscopy data, which identify the timing of key stages in grain development. Thus, cellularization is complete at six DAP, aleurone-related genes can be detected at seven to eight DAP, and starch synthase and hordein genes increase dramatically at seven and eight DAP, respectively. Genes known to be involved in cell wall metabolism are found predominantly in a single module, but analysis using a gene ontology approach splits these genes into four modules, which remain in a single cluster. Transcript levels of the cell wall-related genes peak at seven DAP and the developmental patterns of genes involved in arabinoxylan and (1,3;1,4)-β-glucan synthesis are defined. The transcript data are publicly available (www.etc.) and can be used to interrogate co-expression and differential expression patterns for other groups of genes. In addition, the examination of transcription factor genes that are co-expressed in modules of genes involved in specific processes, such as aleurone differentiation, can be used to identify candidate genes for the control of those particular processes during barley grain development.
Project description:Comparison of the transcriptome profiles of a widely commercialized MON810 maize variety (HelenBt) at two levels of nitrogen fertilization. Variety Helen Bt; obtained by Advanta; authorized the 11/08/2005; now commercialized by Limagrain Iberica. Conventional nitrogen fertilization compared to not nitrogen fertilization during the season.
Project description:Comparison of the transcriptome profiles of a widely commercialized maize variety (Helen) at two levels of nitrogen fertilization. Conventional nitrogen fertilization compared to not nitrogen fertilization during the season.
Project description:Comparison of the transcriptome profiles of a widely commercialized maize MON810 variety and its non-GM near-isogenic counterpart grown in agricultural fields. The Helen variety was commercialized by Limagrain Iberica. Variety Helen B was obtained by Advanta; authorized the 11/08/2005; now commercialized by Limagrain Iberica. The insert integrated into the maize genome contains: Cauliflower Mosaic Virus 35S promoter + maize HSP70 intron (partial) + synthetic sequence coding for the Bacillus thuringensis CRYIA(b) insecticidal protein (truncated).
Project description:Microarray analysis was performed on a well-defined set of potato tuber samples grown under different, well-recorded environmental conditions. The data were analysed to assess the potential of transcriptomics to detect differences in gene expression as a result of these environmental conditions. Differences were found for both factors, both in PCA and in ANOVA analysis. Factorial design; 1 potato cultivar (Sante); 2 fertilizers (organic, conventional); 2 crop protection treatments (organic, conventional), 4 biological replicates, 16 samples. Raw data files: columns 1 - 11 is Cy3, 12 - 21 is Cy5
Project description:Microarray analysis was performed on a well-defined set of potato tuber samples grown under different, well-recorded environmental conditions. The data were analysed to assess the potential of transcriptomics to detect differences in gene expression as a result of these environmental conditions. Differences were found for both factors, both in PCA and in ANOVA analysis.
Project description:In angiosperms, endosperm plays a crucial role in coordinating seed development through genetic balance and molecular interaction, and is the primary tissue where genomic imprinting occurs. To identify small interfering RNA (siRNA) “imprintome” and its paternal transcriptome activation in early developing maize endosperms, we performed high-throughput small RNA sequencing of whole kernels at 0, 3 and 5 days after pollination (DAP) and endosperms at 7, 10 and 15 DAP, using B73 by Mo17 reciprocal crosses. We observed gradually increased expression of paternal siRNAs in 3- and 5-DAP kernels and balanced contribution of parental siRNA transcriptome in 7-DAP endosperm, followed by identification 460 imprinted siRNA loci with majority (456/460, 99.1%) being maternally expressed that occurred at 10 DAP. Genome-wide scanning found 13 imprinted genes harboring imprinted siRNA loci within their 2-Kb flanking regions, which was significantly different from random probability based on simulation analysis. Finally, gene ontology categories of “response to auxin stimulus”, “response to brassinosteroid stimulus” and “regulation of gene expression” for genes harboring 10-DAP specific siRNAs and “nutrient reservoir activity”, “protein localization to vacuole” and “secondary metabolite biosynthetic process” for genes harboring 15-DAP specific siRNAs indicated that siRNAs could be involved in influencing specific cellular or biochemical processes that are essential for endosperm development, e.g. nutrient uptake and allocation. Although the mechanism of how these siRNAs regulating endosperm key events remains unclear, this study provided us an alternative perspective of siRNA function in plant. The unpollinated kernels (0 DAP), the kernels of 3, 5 DAP and endosperms of 7 10, 15 DAP from the B73 and Mo17 reciprocal crosses were used to perform high-throughput sequencing using the Illumina HiSeq2000 platform
Project description:Transcriptional profiling of seeds of Medicago truncatula during maturation. To identify genes that are regulated during seed maturation in the model legume Medicago truncatula, plants at flowering stage were grown at controlled temperature of 21-19°C, 16h light. Seeds were then collected at different stages of development. Using the Medicago NimbleGen chip, a transcriptomic analysis was performed to follow the differential expression of genes during seed maturation. Seeds of Medicago truncatula grown at 21-19°C were collected at different developmental stages, 15 developmental stages were analysed. Two replicates from each developmental stage were used for dye switch, each time the control was considered as the earlier developmental stage vs the treatment, corresponding to the later developmental stage. For each repetition 8 hybridisation were made: 8DAP vs 11DAP, 14DAP vs 17DAP, 20DAP vs 23DAP, 26DAP vs 29DAP,32DAP vs 35DAP, 38DAP vs 41DAP, 44DAP vs Abs, DS (Rep1 and Rep2) vs 8DAP (Rep3 and Rep4). For each biological replicates, RNA was extracted from 50 seeds collected from 5 different plants, grown in the same conditions. One replicate per array.