Rice Sequence Variation
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB33930 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The SNP set of 94 rice representative species
| PRJEB33929 | ENA
Project description:Background and study aims
Colorectal cancer (CRC) is one of the most commoncancers among humans worldwide. Recent studies demonstrated that the composition of the bacterial community in the human gut, as well as inflammation occurring in the gut, are some of the factors that modify the risk of an individual to develop CRC. The human gut is home to more than 1000 bacterial species, including health-promoting species and disease-causing species.
The consumption of rice bran, a by-product of rice milling, was previously shown to positively modify bacterial composition in the gut among healthy adults. The protective effect of a long-term rice bran consumption against CRC among individuals known to have higher risk of CRC, such as older individuals who are regular smokers and having a family history of CRC, needs to be established.
This study aims to investigate whether the implementation of a 24-week dietary programme involving rice bran consumption among adults at high risk of CRC is feasible, and whether it has any effect in inducing a health-promoting modification of the bacterial community, as well as a reduction of inflammation, in the gut of these individuals.
Who can participate?
Chinese adults of either gender, who are aged 50 or above and are categorised to be in the high risk CRC group by the Asian-Pacific Colorectal Screening tool, in which classification is based on age, smoking status and family history of CRC.
What does the study involve?
After the recruited subjects were screened for eligibility of study participation and written informed consent had been obtained from them, they were randomly assigned into either Group A or Group B. Participants in Group A were given packets of rice bran and were asked to consume 30 grams of the rice bran at 24-hour intervals for 24 weeks. Participants in Group B were given packets of rice powder that has similar appearance and colour as the rice bran, and were asked to consume 30 grams of the rice powder, also at 24-hour intervals for 24 weeks. All participants were asked to provide a stool sample and blood sample at various time points during the study, namely just before rice bran consumption, as well as 6 weeks, 12 weeks and 24 weeks after the start of rice bran consumption. Laboratory tests were conducted on these samples. All participants were also instructed to complete a log book, detailing the date and time of rice bran or rice powder intake each day, and the amount consumed. The participants also completed a faecal diary where they documented the frequency of egestion, and the shape and amount of stool egested each day, as well as the occurrence of any abdominal discomfort or pain.
| 2415781 | ecrin-mdr-crc
Project description:A High Density Rice Array (HDRA) was developed as an Affymetrix Custom GeneChip Array by the McCouch Rice Lab at Cornell University. The HDRA assays 700,000 SNPs, or approximately one SNP every 0.54 Kb across the rice genome (genome size = 380 Mb). It was designed to capture most of the haplotype variation observed in a discovery panel consisting of 16M SNPs (generated by sequencing 125 rice genomes at ~7X genome coverage) and to maximize the inclusion of non-synonymous SNPs. Six probes per SNP target were designed as 3 A-allele and 3 B-allele probes at offsets from center ranging from -6 to +6. A small fraction of SNPs have only 4 probes (2-A, 2-B). For all SNPs, the “A” allele is the reference allele (Os-Nipponbare-Reference-IRGSP-1.0 assembly). Additionally, we designed 23,656 x 25-bp probes complimentary to invariant regions of the genome that were used to normalize systematic differences between samples. An estimated 45% of HDRA SNPs map within genes, hitting all 39,045 unique, non-TE rice gene models (MSUv7 rice genome annotation, GFF3 file, Feb. 7, 2012, http://rice.plantbiology.msu.edu/), while 55% of SNPs map to intergenic regions. Non-synonymous are found in 91% of unique, non-TE gene models, and 57% of genic SNPs are distributed within exons, 36% within introns, 5% within 5’ UTRs and 2% within 3’ UTRs. Of the intergenic SNPs, 40% are located in putative regulatory regions within 2 Kb of a transcriptional start site.
2016-02-25 | GSE71553 | GEO
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:The studies of rice nitrogen concentration on the expression of miRNA so far are mostly limited to the exogenous nitrogen, leaving the effect of endogenous nitrogen largely unexplored. OsNAR2.1 is a high-affinity nitrate transporter partner protein which plays a central role in nitrate absorption and translocation in rice. The expression of OsNAR2.1 could influence the concentration of the endogenous nitrogen in rice. We showed that the expression and production of miRNA in rice can be influenced by manipulating the endogenous nitrogen concentration via OsNAR2.1 transgenic lines. The small RNA expressed differently in two transgenic rice lines (nitrogen efficient line with overexpression of OsNAR2.1 (Ov199), nitrogen-inefficient line with knockdown OsNAR2.1 by RNAi (RNAi)) compared to the wild-type (NP). Comparative hierarchical clustering expression pattern analysis revealed that the expression profiles of mature miRNA in both transgenic lines were different from NP.
2023-06-23 | GSE224933 | GEO
Project description:Changes in patterns of gene expression are believed to be responsible for the phenotypic differences within and between species. Although the evolutionary significance of functional mutations has been emphasized in rice domestication, little is known about the differences in gene regulation underlying the phenotypic diversification among rice varieties. MicroRNAs (miRNAs) are small regulatory RNAs that play crucial roles in regulating post-transcriptional gene expression. Here, we studied the variation in the expression of both miRNAs and mRNA transcripts in three indica and three japonica rice varieties using RNA sequencing (RNA-seq) to examine the miRNA regulatory effect on target gene expression in rice. In total, 71.0%, 9.2%, and 1.5% of the expressed mature miRNAs showed tissue, subspecies, and tissue-subspecies interaction-biased expression. Most of these differentially expressed miRNAs are evolutionarily weakly conserved. To examine the miRNA regulatory effect on global gene expression under endogenous conditions, we performed pair-wise correlation coefficient analyses on the expression levels of 240 mature miRNAs and 1178 messenger RNAs (mRNAs) both globally and for each specific miRNA-mRNA pair. We found that the deeply conserved miRNAs can significantly decrease the target mRNA abundance. In addition, a total of 109 miRNA-mRNA pairs were identified as significantly correlated pairs (Adjusted p<0.01). Of those, 41 pairs showed positive correlations, while 68 pairs showed negative correlations. Functional analysis elucidated that these mRNAs belonged to different biological pathways that could regulate the stress response, metabolic processes, and rice development. In conclusion, the joint interrogation of miRNA and mRNA expression profiles in this study proved useful for the study of the role of miRNA expression and regulation in the plant transcriptome.
2017-02-09 | GSE71925 | GEO
Project description:The aim of this study is to assess natural variation in transcriptional responses to salt stress in rice. We utilized a diversity panel (RDP1) described in Zhao et al 2011. Eight day old rice seedlings were subjected to a gradual 6 dS·m-1 salt stress for a period of 24h. RNA seqeuncing was performed on shoot tissue using Illumina HiSeq 2500.
2018-01-01 | GSE98455 | GEO
Project description:The lack of MIRNA set and genome sequence of O. rufipogon (the ancestor of the cultivated rice) has limited to answer the role of MIRNA genes in rice domestication. In this study, a genome, three small RNA populations and a degradome of O.rufipogon were sequenced by Illumina platform and miRNA expression were investigated by miRNA chips. A de novo genome was assembled using ~55x coverage of raw sequencing data and a total of 387 MIRNAs were identified in the O. rufipogon genome based on ~5.2 million unique small RNA reads from three different tissues of O. rufipogon. Of these O. rufipogon MIRNAs, 259 were not found in the cultivated rice, suggesting loss of these MIRNAs in the cultivated rice. We also found that 48 MIRNAs were novel in the cultivated rice, suggesting that they were potential targets of domestication selection. Some miRNAs showed significant expression difference in the wild and cultivated rice, suggesting that expression of miRNA could also be a target of domestication, as demonstrated for the miR164 family. Our results illustrated MIRNA genes, like protein-coding genes, were significantly shaped during rice domestication and could be one of the driven forces contributed to rice domestication.
2012-08-10 | GSE39308 | GEO