Project description:A spatial resolved transcriptome for germinating barley grain was obtained for over 14,000 genes at 0, 1, 3 6 and 24 hours after imbibition. The spatial expression of a number of genes was validated using in-situ PCR, quantitative comparison to bulk RNA-seq reveal good correlations, despite the differences in the methodologies, and marker gene definition for tissues/clusters was consistent with previous gene specific studies. Targeted analysis of genes encoding aquaporins, crucial for water and ion movement during germination, revealed specific spatial expression patterns for gene members, and the tissue specific changes in gene members over time. Highly restricted spatial (and temporal) expression patterns were observed for genes encoding cell wall and transcription factors, e.g. one of the strongest expressed transcription factors was a bZIP family member that responds to germinating promoting Karrikin. It’s expression was restricted to the scutellum and the adjacent endosperm (0-3 HAI) and declined afterwards. Discovery-based bio-informatic approaches revealed thousands of genes displayed a spatially restricted pattern within tissues, with gene ontology revealing enriched categories such as auxin related functions of transport and response factors displaying distinct spatial expression patterns in tissues. This provides unprecedented spatial resolved cellular map for germination and specific genes to target for functional genomics to define cellular restricted processes in tissues during germination.
Project description:Analysis of barley grains/seedlings representing six well characterized and distinct germination stages over the course of seed germination and seedling growth.
Project description:Analysis of barley grains/seedlings representing six well characterized and distinct germination stages over the course of seed germination and seedling growth. Three biological replications, six developmental stages.
Project description:Plant seeds prepare for germination already during seed maturation. We performed a detailed transcriptome analysis of barley grain maturation, desiccation and germination in two tissue fractions (endosperm/aleurone = e/a and embryo = em) using the Affymetrix barley1 chip. Keywords: time course
Project description:Seeds germination is seriously sensitive to salt stress. The mechanism in response to salt stress during seed germination is still little known. In this study, two genotypes of hulless barley lk621 and lk53 were selected to investigate the molecular mechanism of seeds salinity response during germination stage through RNA-seq and iTRAQ technologies
Project description:Plant seeds prepare for germination already during seed maturation. We performed a detailed transcriptome analysis of barley grain maturation, desiccation and germination in two tissue fractions (endosperm/aleurone = e/a and embryo = em) using the Affymetrix barley1 chip. Experiment Overall Design: Barley developing and germinating seeds were harvested at different time points after flowering (developing) and imbibition (germinating). To further disseect the influence of different tissues, seeds were dissecte and tissues were analyzed individually.
Project description:The spatial transcriptomic analysis of barley embryos in response to 75 µM ABA was investigated using Visium Spatial Transcriptomics (10×Genomics) technology. Embryo sections were collected from wild-type 'Sebastian' and a double mutant hvcbp20.ab/hvcbp80.b impaired in both subunits of the Cap-Binding Complex (CBC): CBP20 and CBP80 at 1 day after imbibition (DAI) under control and 75 µM ABA conditions. Cryosectioned tissues were stained, mounted on Visium slides, and processed for spatial gene expression profiling. Sequencing was performed on an Illumina NovaSeq 6000 platform (paired-end, 151 bp). The data were aligned to the barley reference genome (cv. MorexV3) and used to identify differentially expressed genes (DEGs) across six distinguished embryonic regions: coleoptile, cotyledon, mesocotyl, plumule, scutellum, and radicle. The dataset provides insights into the spatial regulation of ABA-responsive genes in embryos during barley seed germination.
