Resources for genome of rice
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ABSTRACT:
PROVIDER: PRJEB81107 | ENA |
REPOSITORIES: ENA
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Project description:<p>Pigmented rice (<em>Oryza sativa L.</em>) is a rich source of nutrients, but pigmented lines typically have long life cycles and limited productivity. Here we generated genome assemblies of 5 pigmented rice varieties and evaluated the genetic variation among 51 pigmented rice varieties by resequencing an additional 46 varieties. Phylogenetic analyses divided the pigmented varieties into four varietal groups: Geng-japonica, Xian-indica, circum-Aus and circum-Basmati. Metabolomics and ionomics profiling revealed that black rice varieties are rich in aromatic secondary metabolites. We established a regeneration and transformation system and used CRISPR-Cas9 to knock out three flowering time repressors (Hd2, Hd4 and Hd5) in the black Indonesian rice Cempo Ireng, resulting in an early maturing variety with shorter stature. Our study thus provides a multi-omics resource for understanding and improving Asian pigmented rice.</p>
2023-03-27 | MTBLS3320 | MetaboLights
Project description:Abstract We have re-analysed publicly available mass spectrometry (MS) data sets enriched for phosphopeptides from Asian rice (Oryza sativa). In total we have identified, 15522 phosphosites on Serine, Threonine and Tyrosine residues on rice proteins. The data has been loaded into UniProtKB, enabling researchers to visualise the sites alongside other stored data on rice proteins, including structural models from AlphaFold2, and into PeptideAtlas, enabling visualisation of the source evidence for each site, including scores and source mass spectra. We identified sequence motifs for phosphosites, and link motifs to enrichment of different biological processes, indicating different downstream regulation caused by different kinase groups. We cross-referenced phosphosites against single amino acid variation (SAAV) data sourced from the rice 3000 genomes data, to identify SAAVs within or proximal to phosphosites that could cause loss of a particular site in a given rice variety. The data was further clustered to identify groups of sites with similar patterns across rice family groups, allowing us to identify sites highly conserved in Japonica, but mostly absent in, for example, Aus type rice varieties - known to have different responses to drought. These resources can assist rice researchers to discover alleles with significantly different functional effects across rice varieties.
2023-11-08 | PXD046188 | Pride
Project description:In the present investigation, the genetic diversity architecture of 96 deep-water rice genotypes of Assam and association mapping strategy was, for the first time, applied to determine the significant SNPsand genes for deep-water rice. These genotypes are known for their unique elongation ability under deep-water condition.The internode elongation under water related genes will be identified here can provide affluent resources for rice breeding especially in flood-prone areas. We investigated the genome-wide association studies (GWAS) using 50 K rice genic SNPchip across 96 deep-water rice genotypes collected from different flood-prone districts/villages of Assam.
2025-05-01 | GSE231797 | GEO
Project description:[Oryza sativa Genome Oligo Set Version 1.0 was designed by Beijing Genomics Institute (BGI) and contain 60,727 70mer oligos representing both indica and japonica genomes. All oligos were designed from cDNAs, expreseed sequence tag (EST) sequences, predicted genes of BGI rice genome build and other public resources. Mapping to TIGR rice genome pseudommolecues release 2 is based on the BLAST results, if a oligo has greater than 97% identity to a gene sequence from TIGR pseudomolecules, the oligo represents that gene. Rice 30K Operon Version 1.0 -70 mer oligos. The array is in 48 pin conformation. It has 25 columns and 25 rows in each of 4 x 12 subarrays. This is the slideA of the two slide sets. Platform_catalog_number: XDEN-A Platform_coating: poly L lysine Platform_manufacture_protocol: Omnigrid 100 contact printer; TeleChem Stealth SMP3 split pins; See http://keck.med.yale.edu/dnaarrays/printing Platform_manufacturer: Keck Biotechnology Resource Lab at Yale Platform_support: glass slide Platform_technology: spotted oligonucleotide ] Series_sample_order: Sample 1-15 Slide A; Sample 16-30 Slide B Keywords: other
2005-05-24 | GSE2691 | GEO
Project description:Rice, the world’s most important food crop, is attacked by multiple herbivores and pathogens.the rice striped stem borer (SSB) Chilo suppressalis is one of another most important rice insect pests. Here, we use Affymetrix Whole-Genome rice arrays to detect SSB infestation responsive genes.
2011-03-18 | GSE28012 | GEO
Project description:In this study, we provide a global overview of genome-wide OsHOX24 binding sites in rice under control and desiccation stress conditions in wild-type and OsHOx24 overexpressing rice plants (H49 line) via chromatin immunoprecipitation sequencing (ChIP-sequencing) approach. We identified numerous downstream targets of OsHOX24 under desiccation stress and control by analyzing the comprehensive binding site map of OsHOX24 at whole genome level in rice.
2021-04-04 | GSE144419 | GEO
Project description:We explores the effects of K+ and Na+ on global G4 formation in vitro, thereby providing valuable resources for functional G4 studies in rice. It will provide certain G4 loci for the biotechnological engineering of rice in the future.
2022-08-01 | GSE209990 | GEO
Project description:[Oryza sativa Genome Oligo Set Version 1.0 was designed by Beijing Genomics Institute (BGI) and contain 60,727 70mer oligos representing both indica and japonica genomes. All oligos were designed from cDNAs, expreseed sequence tag (EST) sequences, predicted genes of BGI rice genome build and other public resources. Mapping to TIGR rice genome pseudommolecues release 2 is based on the BLAST results, if a oligo has greater than 97% identity to a gene sequence from TIGR pseudomolecules, the oligo represents that gene. Rice 30K Operon Version 1.0 -70 mer oligos. The array is in 48 pin conformation. It has 25 columns and 25 rows in each of 4 x 12 subarrays. This is the slideA of the two slide sets. Platform_catalog_number: XDEN-A Platform_coating: poly L lysine Platform_manufacture_protocol: Omnigrid 100 contact printer; TeleChem Stealth SMP3 split pins; See http://keck.med.yale.edu/dnaarrays/printing Platform_manufacturer: Keck Biotechnology Resource Lab at Yale Platform_support: glass slide Platform_technology: spotted oligonucleotide ] Series_sample_order: Sample 1-15 Slide A; Sample 16-30 Slide B
2010-06-10 | E-GEOD-2691 | biostudies-arrayexpress
Project description:This experiment was designed to identify transcribed regions of indica rice genome. 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 838,816 36mer oligonucleotide probes, positioned every 46 nt on average, were designed to interrogate the indica genome, 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: genome tiling experiments
2005-10-15 | GSE3452 | GEO
Project description:Rice is one of important crop and, the genome has been already completely sequenced. Moreover we collected more than 30K rice FL-cDNA clones as transcriptome resources. However, the cDNA collection did not reveal the transcription activity and specificity of expression. So, we designed 60-mer oligo array based on the array system of Agilent Technologies (GPL477) as custom array. For validation of the array, we tested the reproducibility of labeling and hybridization. After this validation, 22K rice oligo array was supplied from Agilent Technologies (GPL892). 2: reproducibility of hybridization-1: We made a dye-swap experiment to validate dye-effect and data reproducibility between arrays. We hybridized shoot (as control) and other developmental stage tissues. This data also indicated the diversity of gene expression profile among developmental stages. Keywords: variety among tissues
2008-04-01 | GSE7531 | GEO