Gene Expression Nebulas
A data portal of transcriptomic profiles analyzed by a unified pipeline across multiple species

Gene Expression Nebulas

A data portal of transcriptome profiles across multiple species
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PRJCA003821

PRJCA003821: Genomic basis of rice geographic adaptation to soil nitrogen

Source: NGDC / CRA003469
Submission Date: Nov 03 2020
Release Date: Nov 04 2020
Update Date: -

Summary: Intensive application of inorganic nitrogen underlies marked increase in crop production yet imposes detrimental impact on ecosystems, hence it is crucial for future sustainable agriculture to improve nitrogen-use efficiency (NUE). Here we report the identification of genetic basis of NUE associated with the local soil adaptation of cultivated rice. With a diverse rice germplasm panel collected from different ecogeographic regions, we performed genome-wide association study on tillering response to nitrogen (TRN), the most correlated trait to NUE of rice, and identified OsTCP19 as a modulator of TRN via transcriptionally responding to nitrogen.Using expression profiling by high throughput sequencing, we identified a number of target genes of OsTCP19 demonstrated its enormous potential for rice breeding and environment amelioration through reducing nitrogen application.

GEN Datasets:
GEND000319
Strategy:
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Protocol
Growth Protocol: -
Treatment Protocol: -
Extract Protocol: Poly (A) RNA from 1 mg total RNA was purified with OligodT beads and then used to generate the cDNA libraries.
Library Construction Protocol: -
Sequencing
Molecule Type: poly(A)+ RNA
Library Source:
Library Layout: PAIRED
Library Strand: -
Platform: BGISEQ
Instrument Model: BGISEQ-500
Strand-Specific: Unspecific
Samples
Basic Information:
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Sequencing:
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Analysis:
Data Resource GEN Sample ID GEN Dataset ID Project ID BioProject ID Sample ID Sample Name BioSample ID Sample Accession Experiment Accession Release Date Submission Date Update Date Species Race Ethnicity Age Age Unit Gender Source Name Tissue Cell Type Cell Subtype Cell Line Disease Disease State Development Stage Mutation Phenotype Case Detail Control Detail Growth Protocol Treatment Protocol Extract Protocol Library Construction Protocol Molecule Type Library Layout Strand-Specific Library Strand Spike-In Strategy Platform Instrument Model Cell Number Reads Number Gbases AvgSpotLen1 AvgSpotLen2 Uniq Mapping Rate Multiple Mapping Rate Coverage Rate
Publications
Genomic basis of geographical adaptation to soil nitrogen in rice.
Nature . 2021-01-06 [PMID: 33408412]