Oilseed rape seed microbiota
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB51924 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Many crop species have polyploid genomes that are unlikely to be sequenced to a high standard in the near future, representing a barrier to genomics-based breeding. As an exemplar, we sequenced the leaf transcriptome to analyse both sequence variation1 and transcript abundance across a mapping population of oilseed rape (Brassica napus), together with representatives of ancestors of the parents of the population. Twin SNP linkage maps were constructed, comprising 23,037 markers in all. These were used to analyse the genome for alignment to that of a related species, Arabidopsis thaliana, and to genome sequence assemblies of the progenitor species of B. napus. Methods were developed that enabled us to detect genome rearrangements and track inheritance of genomic segments, including the outcome of an inter-specific cross. This transformative advance, enabling economical high-resolution dissection of the genomes of most, if not all, crop species, will enable us to understand the genetic consequences of breeding and domestication, and will underpin the development of efficient predictive breeding strategies.
2011-06-23 | E-MTAB-4284 | biostudies-arrayexpress
Project description:Seed germination is a complex trait determined by the interaction of hormonal, metabolic, genetic, and environmental components. Variability of this trait in crops has a big impact on seedling establishment and yield in the field. Classical studies of this trait in crops have focused mainly on the analyses of one level of regulation in the cascade of events leading to seed germination. We have carried out an integrative and extensive approach to deepen our understanding of seed germination in Brassica napus by generating transcriptomic, metabolic and hormonal data at different stages upon seed imbibition. Deep phenotyping of different seed germination associated traits in six winter-type B. napus accessions has revealed that seed germination kinetics, in particular seed germination speed, are major contributors to the variability of this trait. Metabolic profiling of these accessions has allowed us to describe a common pattern of metabolic change and to identify the levels of malate and aspartate metabolites as putative metabolic markers to estimate germination performance. Additionally, analysis of seed content of different hormones suggests that hormonal balance between ABA, GA and IAA at crucial time points during this process might underlie seed germination differences in these accessions. In this study, we have also defined the major transcriptome changes accompanying the germination process in B. napus. Furthermore, we have observed that earlier activation of key germination regulatory genes seems to generate the differences in germination speed observed between accessions in B. napus. Finally, we have found that protein-protein interactions between some of these key regulators are conserved in B. napus suggesting a shared regulatory network with other plants species. Altogether, our results provide a comprehensive and detailed picture of seed germination dynamics in oilseed rape. This new framework will be extremely valuable, not only to evaluate germination performance of B. napus accessions, but also to identify key targets for crop improvement in this important process.
2019-09-11 | GSE137230 | GEO
Project description:mRNA expression profiling of the embryo, endosperm (micropylar, peripheral, chalazal), and seed coat (outer, inner, chalazal, chalazal proliferating tissue) of the developing Brassica napus seed. Tissues were isolated using laser microdissection (LMD) from Brassica napus seeds at the globular, heart, and mature green stages of seed development.
2024-07-15 | GSE271809 | GEO
Project description:Time course of gene expression profiles during seed development and maturation in Brassica napus were studied using Combimatrix Brassica microarray.
2013-03-01 | GSE43918 | GEO
Project description:Time course of gene expression profiles during seed development and maturation in Brassica napus were studied using Combimatrix Brassica microarray. The time course expression of 90K Brassica napus EST contigs were measured at 8 developing seed stages of 10, 15, 20, 25, 30, 35, 40 and 45 DAF (days after flowering) using single color microarray
2013-03-01 | E-GEOD-43918 | biostudies-arrayexpress
Project description:Epigenome bias in the seed of the allopolyploid Brassica napus
2021-08-31 | GSE157372 | GEO
Project description:The transcriptome of Leptosphaeria maculans was analyzed in mycelium and during oilseed rape (Brassica napus) leaf infection. The array probes were designed from gene models from the L. maculans whole genome annotation. One aim of this study was to verify the expression of the automatically annotated gene models in various conditions. Another goal was to monitor gene expression profiles during oilseed rape leaf infection and to highlight tissue-specific transcripts, e.g. in plant up-regulated transcripts, for further analyses.
2011-02-09 | GSE27152 | GEO
Project description:The transcriptome of Leptosphaeria maculans was analyzed in mycelium and during oilseed rape (Brassica napus) leaf infection. The array probes were designed from gene models from the L. maculans whole genome annotation. One aim of this study was to verify the expression of the automatically annotated gene models in various conditions. Another goal was to monitor gene expression profiles during oilseed rape leaf infection and to highlight tissue-specific transcripts, e.g. in plant up-regulated transcripts, for further analyses. We performed 9 hybridizations (NimbleGen) with samples derived from mycelium and infected oilseed rape leaves. Samples from infected oilseed rape leaves were harvested 7 and 14 days post infection. Three replicates each. All samples were labeled with Cy3.
2011-02-09 | E-GEOD-27152 | biostudies-arrayexpress
Project description:We profiled the gene regulatory landscape of Brassica napus reproductive development using RNA sequencing. Comparative analysis of this nascent allotetraploid across the plant lifecycle revealed the contribution of each subgenome to plant reproduction. Global mRNA profiling across reproductive development revealed lower accumulation of C subgenome transcripts relative to the A subgenome. Subgenome-specific transcriptional networks identified distinct transcription factor families enriched in each of the A and C subgenome in early seed development. Analysis of a tissue specific transcriptome of early seed development revealed transcription factors predicted to be regulators encoded by the A subgenome are expressed primarily in the seed coat whereas regulators encoded by the C subgenome were expressed primarily in the embryo. Whole genome transcription factor networks identified BZIP11 as an essential regulator of early B. napus seed development. Knockdown of BZIP11 using RNA interference resulted in knockdown of predicted target genes, and a reproductive-lethal phenotype. Our data indicate that subgenome bias are characteristic features of the B. napus seed throughout its development, and that such bias might not be universal across the embryo, endosperm, and seed coat of the developing seed. We also find that examining transcriptional networks spanning both the A and C genomes of the whole B. napus seed can identify valuable targets for seed development research. We suggest that-omics level approaches to studying gene regulation in B. napus can benefit from both broad and high-resolution analyses.
2021-08-31 | GSE144771 | GEO
Project description:Crop establishment practices are a driver of the plant microbiota in winter oilseed rape (Brassica napus)
| PRJEB14407 | ENA