Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A dynamic co-expression map of early inflorescence development in Setaria viridis provides a resource for gene discovery and comparative genomics

ABSTRACT: A dynamic co-expression map of early inflorescence development in Setaria viridis provides a resource for gene discovery and comparative genomics

PROVIDER: PRJNA486397 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR7704030_1.fastq.gz	Fastqsanger.gz
	SRR7704030_2.fastq.gz	Fastqsanger.gz
	SRR7704040.fastq.gz	Fastqsanger.gz
	SRR7704031_1.fastq.gz	Fastqsanger.gz
	SRR7704031_2.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 34

Similar Datasets

A dynamic co-expression map of early inflorescence development in Setaria viridis provides a resource for gene discovery and comparative genomics

Project description:Setaria viridis is a small, rapidly growing grass species in the subfamily Panicoideae, a group that includes economically important cereal crops such as maize and sorghum. The S. viridis inflorescence displays complex branching patterns, but its early development is similar to that of other panicoid grasses, and thus is an ideal model for studying inflorescence architecture. Here we report detailed transcriptional resource that captures dynamic transitions across six sequential stages of S. viridis inflorescence development, from reproductive onset to floral organ differentiation. Co-expression analyses identified stage-specific signatures of development, which include homologs of previously known developmental genes from maize and rice, suites of transcription factors and gene family members, and genes of unknown function. This spatiotemporal co-expression map and associated analyses provide a foundation for gene discovery in S. viridis inflorescence development, and a comparative model for exploring related architectural features in agronomically important cereals.

2018-08-17 | GSE118673 | GEO

A Dynamic Co-expression Map of Early Inflorescence Development in <i>Setaria viridis</i> Provides a Resource for Gene Discovery and Comparative Genomics.

Project description:The morphological and functional diversity of plant form is governed by dynamic gene regulatory networks. In cereal crops, grain and/or pollen-bearing inflorescences exhibit vast architectural diversity and developmental complexity, yet the underlying genetic framework is only partly known. Setaria viridis is a small, rapidly growing grass species in the subfamily Panicoideae, a group that includes economically important cereal crops such as maize and sorghum. The S. viridis inflorescence displays complex branching patterns, but its early development is similar to that of other panicoid grasses, and thus is an ideal model for studying inflorescence architecture. Here we report a detailed transcriptional resource that captures dynamic transitions across six sequential stages of S. viridis inflorescence development, from reproductive onset to floral organ differentiation. Co-expression analyses identified stage-specific signatures of development, which include homologs of previously known developmental genes from maize and rice, suites of transcription factors and gene family members, and genes of unknown function. This spatiotemporal co-expression map and associated analyses provide a foundation for gene discovery in S. viridis inflorescence development, and a comparative model for exploring related architectural features in agronomically important cereals.

| S-EPMC6143762 | biostudies-literature

Brassinosteroids modulate meristem fate and differentiation of unique inflorescence morphology in Setaria viridis

Project description:RNA-seq was performed to profile the transcriptomes of inflorescence primordia hand-dissected from the bristleless1-1 (bsl1-1)mutant in Setaria viridis compared to wild-type controls sampled under the same conditions. Bsl1 encodes a rate limiting enzyme in BR biosynthesis, which is the ortholog of D11 from rice. Mutants are characterized by a homeotic conversion of sterile bristles to spikelets in the inflorescence.

2017-12-23 | GSE100423 | GEO

The SvFUL2 transcription factor is required for inflorescence determinacy and timely flowering in Setaria viridis

Project description:Inflorescence architecture in cereal crops directly impacts yield potential through regulation of seed number and harvesting ability. Extensive architectural diversity found in inflorescences of grass species is due to spatial and temporal activity and determinacy of meristems, which control the number and arrangement of branches and flowers, and underlie plasticity. Timing of the floral transition is also intimately associated with inflorescence development and architecture. Here, we show that a single mutation in a gene encoding an AP1 A-class MADS-box transcription factor significantly delays flowering time and disrupts multiple levels of meristem determinacy in panicles of the C4 model panicoid grass, Setaria viridis.

2021-04-02 | GSE156047 | GEO

A rice single cell transcriptomic atlas defines the developmental trajectories of rice floret and inflorescence meristems

Project description:We have used high-throughput single-cell RNA sequencing to profile rice inflorescence cells, and construct a genome-scale gene expression resource covering the inflorescence-to-floret transition during early reproductive development.

2022-02-25 | GSE185068 | GEO

Ancient DNA provides insights into 4,000 years of resource economy across Greenland

Project description:Ancient DNA provides insights into 4,000 years of resource economy across Greenland

| PRJEB55117 | ENA

The regulatory landscape of early maize inflorescence development

Project description:The functional genome of agronomically important plant species remains largely unexplored, yet presents a virtually untapped resource for targeted crop improvement. Functional elements and regulatory DNA revealed through chromatin accessibility maps can be harnessed for manipulating gene expression to subtle phenotypic outputs that enhance productivity in specific environments. Here, we present a genome-wide view of accessible chromatin and nucleosome occupancy at a very early stage in the development of both pollen- and grain-bearing inflorescences of the important cereal crop maize (Zea mays), using an assay for differential sensitivity of chromatin to micrococcal nuclease (MNase) digestion. Results showed that in these largely undifferentiated tissues, approximately 1.5-4 percent of the genome is accessible, with the majority of MNase hypersensitive sites marking proximal promoters but also 3’ flanks of maize genes. This approach mapped regulatory elements to footprint-level resolution, and through integration of complementary transcriptome and transcription factor occupancy data, we annotated regulatory factors such as combinatorial motifs and long non-coding RNAs that potentially contribute to organogenesis in maize inflorescence development, including tissue-specific regulation between male and female structures. Finally, genome-wide association studies for inflorescence architecture traits based only on functional regions delineated by MNase hypersensitivity, revealed new SNP-trait associations in known regulators of inflorescence development. These analyses provide a first look into the cis-regulatory landscape during inflorescence differentiation in a major cereal crop, which ultimately shapes architecture and influences yield potential.

2020-06-05 | GSE136685 | GEO

The Arabidopsis transcription factor TCP5 during petal and inflorescence development

Project description:RNA-sequencing performed on petals and inflorescence of Arabidopsis plants. The study provides insight into the role of the TCP5 transcription factor and its molecular mechanism underlying petal growth, using knock-out, overexpression and induction lines on which RNA-sequencing was performed.

2018-03-14 | GSE103762 | GEO

Transcriptomic dataset for early inflorescence stages of oil palm in response to defoliation stress

Project description:Oil palm breeding and seed development have been hindered due to the male parent's incapacity to produce male inflorescence as a source of pollen under normal conditions. On the other hand, a young oil palm plantation has a low pollination rate due to a lack of male flowers. These are the common problem of sex ratio in the oil palm industry. Nevertheless, the regulation of sex ratio in oil palm plants is a complex mechanism and remains an open question until now. Researchers have previously used complete defoliation to induce male inflorescences, but the biological and molecular mechanisms underlying this morphological change have yet to be discovered. Here, we present an RNA-seq dataset from three early stages of an oil palm inflorescence under normal conditions and complete defoliation stress. This transcriptomic dataset is a valuable resource to improve our understanding of sex determination mechanisms in oil palm inflorescence.

2021-10-23 | GSE186394 | GEO

Inflorescence apices: rtr-2 versus wild type samples

Project description:Transcriptional profiling of inflorescence apices from wild type and rtr-2 mutant plants . Goal was to determine the differentially expressed genes between wild type and mutant plants in inflorescence apices.

2014-12-31 | GSE60169 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data