Rice
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA659985 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:This experiment was designed to identify transcribed regions of both japonica and indica rice chromosome 10. A series of high-density oligonucleotide tiling arrays that represent sense and antisense strands of the entire nonrepetitive sequence of the chromosome were used to measure transcriptional activities. A total of 750,282 and 838,816 36mer oligonucleotide probes, positioned every 46 nt on average, were designed to interrogating the japonica and the indica chromosome, respectively. The probes were synthesized via maskless photolithography at a feature density of approximately 389,000 probes per slide. The arrays were hybridized with fluorescence-labeled cDNA reverse-transcribed from equal amounts of four selected poly(A)+ RNA populations, namely, seedling roots, seedling shoots, panicles, and suspension cultured cells of the respective rice subspecies. Keywords: other
2005-04-09 | GSE2500 | GEO
Project description:Purpose: The goal of this study is to compare the different genetic mechanisms between Indica and Japonica rice under cadmium stress.
2023-01-02 | GSE196229 | GEO
Project description:Cis-regulatory elements (CREs) fine-tune gene transcription during normal growth and development and environmental stress responses in eukaryotes. CREs with sequence variations play vital roles in driving plant or crop domestication. However, how global genomic sequence and structural variations causative for multi-level changes between Indica and Japonica are still less studied. To answer this question, we here conducted MH-seq (MNase hypersensitive sequencing) for global profiling of open chromatin (MNase hypersensitive sites, MHSs) between two typical Oryza sativa cultivars, Nipponbare (NIP) and 93-11. We found that differential MHSs exhibited some distinct intrinsic genomic sequence features between NIP and 93-11. Moreover, MHSs can coordinate with DNA sequence or genomic structural variations in the regulation of differential gene expression between NIP and 93-11. Importantly, by applying MHS-GWAS association analyses, we found that CREs with sequence variations may act as the key determinant for controlling expression of genes responsible for some biological relevance in NIP and 93-11. Therefore, this study provides new insights into how sequence and genomic structural variations function in differential biological relevance and key crop agronomic traits between Indica and Japonica. It also provides some promising genomic editing targets for molecular breeding to improve favorable agronomic trait.
2023-09-02 | GSE196604 | GEO
Project description:Expression Data of Rice Crown and Growing Point Tissue Under Salt Stress imposed during the Panicle Initiation Stage Experiment Overall Design: Rice Genotypes a sensitive japonica, m103, tolerant japonica agami, sensitive indica ir29 and tolerant indica ir63731 were used for expression anlaysis using the tissue from crown and growing point under control and salt stressed conditions at the sensitive early reproductive stage (panicel initiation).
2008-11-05 | E-GEOD-4438 | biostudies-arrayexpress
Project description:Morus alba L. Raw protein sequence reads and sequence
2024-02-08 | PXD049451 |
Project description:Comparative transcriptional profiling of two contrasting rice genotypes,IRAT109 (drought-resistant japonica cultivar) and ZS97 (drought-sensitive indica cultivar), under drought stress during the reproductive stage
2011-11-05 | GSE25176 | GEO
Project description:rice flag leaves at heading stage from three chromosome substitution line populations, which were respectively constructed by introducing genomic segments from japonica cultivar Niponbare, indica cultivar Minghui 63 and wild accession ACC10, to an indica cultivar Zhenshan 97, were collected. Metabolomics profile was conducted to generate quantitative trait loci that may affect contents of metabolites, and candidate genes were assigned.
2018-08-06 | ST001031 | MetabolomicsWorkbench
Project description:Rice is the most salt sensitive cereal crop and its cultivation is particularly threatened by salt stress. This study reports the development of salt tolerant introgressed lines (ILs) derived from crosses between the salt tolerant indica rice variety FL478, which harbors the Saltol QTL, and the salt-sensitive japonica elite cultivar PL12. Although the introgression of the Saltol QTL has been widely used to improve salinity tolerance, the molecular basis underlying the salinity tolerance conferred by Saltol remains poorly understood. Equally, the impact of introgressions from a Saltol donor parent on the global transcriptome of ILs is largely unknown. Here, genotyping-by-sequencing (GBS) and Kompetitive allele specific PCR (KASP) genotyping, in combination with step-wise phenotypic selection in hydroponic culture, were used for the identification of salt-tolerant ILs. Transcriptome-based genotyping allowed the fine mapping of indica genetic introgressions in the best performing IL line (IL22). A total of 1,595 genes were identified in indica regions in IL22, which mainly located in large introgressions at Chromosomes 1 and 3. In addition to OsHKT1;5, an important number of genes potentially contributing to salt stress tolerance were identified in indica segments of IL22. Comparative transcript profiling also revealed important transcriptional reprograming in IL22 plants both under non-stress and salt-stress conditions, indicating an impact on the transcriptome of the japonica background by the indica introgressed genes and vice versa. Interactions among indica and japonica genes would provide novel regulatory networks contributing to salt stress tolerance in introgression rice lines.
2021-12-20 | GSE167342 | GEO
Project description:We used RNA-Seq to perform a whole transcriptome analysis in roots of Azucena (tropical japonica), IR64 (indica), and the near-isogenic lines AZU[IR64121] and IR64[AZU12.1] in control conditions and treated with 80 μM Al3+ activity for 4 hours
2017-09-01 | GSE89494 | GEO
Project description:Here, we performed deep transcriptome sequencing for the aerial-tissues and the roots of S. japonica, generating over 2 billion raw reads with an average length of 101 nt by using an Illumina paired-end sequencing by HiSeq2000 platform. Using a combined approach of three popular assemblers, de novo transcriptome assembly for S. japonica was obtained, yielding in 81,729 unigenes with an average length as 884bps and N50-value as 1,452bps, with 46,963 unigenes being annotated based on the sequence similarity against NCBI-nr protein database.
2016-07-01 | GSE80057 | GEO