Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1098056 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Pea (Pisum. sativum L.) is a traditional and important edible legume that can be sorted into grain pea and vegetable pea according to their harvested maturely or not. Vegetable pea by eating the fresh seed is becoming more and more popular in recent years. These two type peas display huge variations of the taste and nutrition, but how seed development and nutrition accumulation of grain pea and vegetable pea and their differences at the molecular level remains poorly understood. To understand the genes and gene networks regulate seed development in grain pea and vegetable pea, high throughput RNA-Seq and bioinformatics analysis were used to compare the transcriptomes of vegetable pea and grain pea developing seed. RNA-Seq generated 18.7 G raw data, which was then de novo assembled into 77,273 unigenes with a mean length of 930 bp. Functional annotation of the unigenes was carried out using the nr, Swiss-Prot, COG, GO and KEGG databases. There were 459 and 801 genes showing differentially expressed between vegetable pea and grain pea at early and late seed maturation phases, respectively. Sugar and starch metabolism related genes were dramatically activated during pea seed development. The up-regulated of starch biosynthesis genes could explain the increment of starch content in grain pea then vegetable pea; while up-regulation of sugar metabolism related genes in vegetable pea then grain pea should participate in sugar accumulation and associated with the increase in sweetness of vegetable pea then grain pea. Furthermore, transcription factors were implicated in the seed development regulation in grain pea and vegetable pea. Thus, our results constitute a foundation in support of future efforts for understanding the underlying mechanism that control pea seed development and also serve as a valuable resource for improved pea breeding.
2017-02-09 | GSE72573 | GEO
Project description:Inferring in humans biological responses to external cues such as drugs, chemicals, viruses and hormones, is an essential question in biomedicine and cannot be easily studied in humans. Thus, biomedical research has continuously relied on animal models for studying the impact of these compounds and attempted to M-^StranslateM-^T the results to humans. In this context, the Systems Biology Verification for Industrial Methodology for Process Verification in Research (SBV IMPROVER) initiative had run a Species Translation Challenge for the scientific community to explore and understand the limit of translatability from rodent to human using systems biology. Therefore, a multi-layer omics dataset was generated that comprised of phosphoproteomics, transcriptomics and cytokine data derived from normal human (NHBE) and rat (NRBE) bronchial epithelial cells exposed in parallel to more than 50 different stimuli under identical conditions. The present manuscript describes in detail the experimental settings, the generation, processing and quality control analysis of the multi-layer omics dataset. The datasets are accessible in public repositories could be leveraged for further translation studies.
2014-06-10 | E-MTAB-2091 | biostudies-arrayexpress
Project description:Background: Cowpea (Vigna unguiculata L. Walp) is an important food and fodder legume of the semiarid tropics and subtropics worldwide, especially in sub-Saharan Africa. High density genetic linkage maps are needed for marker assisted breeding but are not available for cowpea. A single feature polymorphism (SFP) is a microarray-based marker which can be used for high throughput genotyping and high density mapping. Results: Here we report detection and validation of SFPs in cowpea using a readily available soybean (Glycine max) genome array. Robustified projection pursuit (RPP) was used for statistical analysis using RNA as a surrogate for DNA. Using a 15% outlying score cut-off, 1058 potential SFPs were enumerated between two parents of a recombinant inbred line (RIL) population segregating for several important traits including drought tolerance, Fusarium and brown blotch resistance, grain size and photoperiod sensitivity. Sequencing of 25 putative polymorphism-containing amplicons yielded a SFP probe set validation rate of 68%. Conclusions: We conclude that the Affymetrix soybean genome array is a satisfactory platform for identification of some 1000's of SFPs for cowpea. This study provides an example of extension of genomic resources from a well supported species to an orphan crop. Presumably, other legume systems are similarly tractable to SFP marker development using existing legume array resources. Keywords: Polymorphism discovery, array based genotyping
2008-02-21 | GSE10284 | GEO
Project description:Crop reproduction is highly sensitive to water-deficit and heat stress. The molecular networks of stress adaptation and grain development in tetraploid wheat (T. turgidum durum) are not well understood. Small RNAs (sRNAs) are important epigenetic regulators connecting the transcriptional and post-transcriptional regulatory networks. This study presents the first multi-omics analysis of the sRNAome, transcriptome and degradome in T. turgidum developing grains, under single and combined water-deficit and heat stress. We identified 690 microRNAs (miRNAs), with 84 being novel, from 118 sRNA libraries. Complete profiles of differentially expressed miRNA (DEMs) specific to genotypes, stress types and different reproductive time-points are provided. The first degradome-seq report for developing durum grains discovered a significant number of new target genes regulated by miRNAs post-transcriptionally. Transcriptome-seq profiled 53,146 T. turgidum genes, with differentially expressed genes (DEGs) enriched in functional categories such as nutrient metabolism, cellular differentiation, transport, reproductive development and hormone transduction pathways. miRNA-mRNA networks that affect grain characteristics such as starch synthesis and protein metabolism were constructed, based on integrated analysis of the three omics. This study provides a substantial amount of novel information on the post-transcriptional networks in T. turgidum grains, which will facilitate innovations for breeding programs aiming to improve crop resilience and grain quality.
2020-10-19 | GSE153932 | GEO
Project description:Floral organ shape and size in cereal crops can affect grain size and yield, so genes that regulate their development are promising breeding targets. The lemma, which protects inner floral organs, can physically constrain grain growth; while the awn, a needle-like extension of the lemma, creates photosynthates to promote grain fill. Although several genes and modules controlling grain size and awn/lemma growth in rice have been characterized, these processes, and the relationships between them, are not well understood for barley and wheat. Here, we demonstrate that the barley E-class gene HvMADS1 positively regulates awn length and lemma width, leading to increased grain size and weight. Cytological data indicated that MADS1 promotes grain growth by promoting cell proliferation, while multi-omics data revealed MADS1 target genes associated with cell cycle, phytohormone signaling, and developmental processes. We defined two direct targets of MADS1 regulation, HvSHI and HvDL, whose knockout mutants mimic awn and/or lemma phenotypes of mads1 mutants; and demonstrated that MADS1 interacts APETALA2 (A-class) to synergistically activate downstream genes in awn/lemma development. Notably, we found that MADS1 function remains conserved in wheat, promoting cell proliferation to increase awn length. These findings extend our understanding of MADS1 function in floral organ development to inform strategies for Triticeae crop improvement. Three replicates of barley tissues were collected for RNA extraction: lemma and awn from the central part of lemma and awn from WT and mads1 mutants for RNA-seq and RT-qPCR
2023-09-01 | GSE228410 | GEO
Project description:This experiment employed ATAC-seq (Assay for Transposase Accessible Chromatin with sequencing) to explore the mechanism of how different concentrations of VFAs regulate ruminal epithelial chromatin accessibility under the Grain-diet and Hay-diet patterns in both am and pm. Cells from Grain-am, Grain-pm, Hay-am, and Hay-pm treatment groups were havest for ATAC-seq experiments, n=3 pooled biological replicates per library.
2025-01-08 | GSE286160 | GEO
Project description:Micronutrient stress impacts growth, biomass production, and grain yield in crops. Multi-omics studies are valuable resources for identifying genes for functional studies for trait improvement such as accumulation of Fe or Zn under deficient or excess conditions for bioenergy or grain agriculture. We conducted transcriptomics and ionomics analyses on Sorghum bicolor BTx623, grown under Fe and Zn limiting and excess conditions over a 21-day time-period. To identify early and late transcriptional response in roots and leaves, 180 RNAseq libraries were sequenced for differential expression and coexpression network analyses. Fe and Zn accumulation was measured using ICP-MS at each time point and a fluorometer was used to estimate chlorophyll content in leaves. Among the four treatments, Fe limiting and Zn excess resulted in the largest phenotypic effects and transcriptional response in roots and leaves.
2025-03-26 | GSE292584 | GEO
Project description:Development of wheat (Triticum aestivum L.) grain mainly depends on the processes of starch synthesis and storage protein accumulation, which are critical for grain yield and quality. However, the regulatory network underlying the transcriptional and physiological changes of grain development is still not clear. Here, we combined ATAC-seq and RNA-seq to discover the chromatin accessibility and gene expression dynamics during these processes. We found that the chromatin accessibility changes are tightly associated with differential expressions and the proportion of distal ACRs were increased gradually during grain development. Specific transcription factor (TF) binding sites were enriched at different stages, and were diversified among the 3 subgenomes. We further predicted the potential interactions between key TFs and genes related with starch and storage protein biosynthesis and found different copies of some key TFs played diversified roles. Overall, our findings have provided numerous resources and illustrated the regulatory network during wheat grain development, which would shed lights on the improvement of wheat yields and qualities.
2023-02-15 | GSE214737 | GEO