Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Oryza sativa Indica Group x Oryza sativa Japonica Group

ABSTRACT: Genetic analysis of QTLs conferring resistance in rice to brown planthopper by genotyping-by-sequencing

PROVIDER: PRJDB12062 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Oryza sativa Japonica Group transcriptome sequencing

Project description:Phosphate starvation/sufficient rice seedling, root or shoot Pi-starvation or Pi-sufficient stresses responsible rice genes, including previously unannotated genes were identified by Illumina mRNA-seq technology. 53 million reads from Pi-starvation or Pi-sufficient root or shoot tissues were uniquely mapped to the rice genome, and these included 40574 RAP3 transcripts in root and 39748 RAP3 transcripts in shoot. We compared our mRNA-seq expression data with that from Rice 44K oligomicroarray, and about 95.5% (root) and 95.4% (shoot) transcripts supported by the array were confirmed expression both by the array and by mRNA-seq, Moreover, 11888 (root) and 11098 (shoot) RAP genes which were not supported by array, were evidenced expression with mRNA-seq. Furthermore, we discovered 8590 (root) and 8193 (shoot) previously unannotated transcripts upon Pi-starvation and/or Pi-sufficient.

2012-01-06 | E-MTAB-4302 | biostudies-arrayexpress

Oryza sativa Indica Group

Project description:A global analysis of QTLs for expression variations in rice shoot at early seedling stage

| PRJNA128427 | ENA

Characterisation of Indica Special Protein (ISP), a marker protein for the differentiation of Oryza sativa subspecies indica and japonica.

Project description:Based on both morphological and physiological traits, Asian cultivated rice (Oryza sativa L.) can be classified into two distinct subspecies, indica and japonica. To better understand the differences between the two subspecies, a proteomic approach was used to profile proteins present in the yellow seedling stage of 10 indica and 10 japonica rice varieties. We report the discovery of a new protein, Indica Special Protein (ISP), which was only detected in yellow seedlings of indica varieties, and was absent from japonica varieties. Hence, ISP may represent a key gene for the differentiation of indica and japonica subspecies.

| S-EPMC4057675 | biostudies-literature

Classifying Oryza sativa accessions into Indica and Japonica using logistic regression model with phenotypic data.

Project description:In Oryza sativa, indica and japonica are pivotal subpopulations, and other subpopulations such as aus and aromatic are considered to be derived from indica or japonica. In this regard, Oryza sativa accessions are frequently viewed from the indica/japonica perspective. This study introduces a computational method for indica/japonica classification by applying phenotypic variables to the logistic regression model (LRM). The population used in this study included 413 Oryza sativa accessions, of which 280 accessions were indica or japonica. Out of 24 phenotypic variables, a set of seven phenotypic variables was identified to collectively generate the fully accurate indica/japonica separation power of the LRM. The resulting parameters were used to define the customized LRM. Given the 280 indica/japonica accessions, the classification accuracy of the customized LRM along with the set of seven phenotypic variables was estimated by 100 iterations of ten-fold cross-validations. As a result, the classification accuracy of 100% was achieved. This suggests that the LRM can be an effective tool to analyze the indica/japonica classification with phenotypic variables in Oryza sativa.

| S-EPMC6842562 | biostudies-literature

Salt stress in salt sensitive Oryza sativa Indica group IR29

Project description:Oryza sativa Indica group IR29 (salt sensitive) seedlings were subjected to salt stress or control conditions and sampled at five time points over the course of 24 hours. RNA samples extracted were assayed using the Illumina HiSeq 2000 platform.

2017-10-02 | E-MTAB-1913 | biostudies-arrayexpress

Genetic analysis of heterotic loci detected in a cross between indica and japonica rice (Oryza sativa L.).

Project description:The study on the genetic basis of heterosis has received significant attention in recent years. In this study, using a set of introgression lines (ILs) and corresponding testcross F(1) populations, we investigated heterotic loci (HL) associated with six yield-related traits in both Oryza sativa L. subsp. indica and japonica. A total of 41 HL were detected on the basis of mid-parent heterosis values with single-point analysis. The F(1) test-cross population showed superiority in most yield-related traits and was characterized by a high frequency of overdominant HL. Thirty-eight of the 41 HL were overdominant, and in the absence of epistasis, three HL were dominant, suggesting that heterotic effects at the single-locus level mainly appeared to be overdominant in rice. Twenty-four HL had a real positive effect, suggesting that they are viable candidates for the improvement of rice yield potential. Compared with the quantitative trait loci (QTLs) detected in the ILs, only six out of the 41 (14.6%) HL were detected in QTL analysis under the same statistical threshold, indicating that heterosis and trait performance may be conditioned by different sets of loci.

| S-EPMC3406766 | biostudies-literature

Oryza sativa

Project description:Expression data from rice after brown planthopper attack

| PRJNA140845 | ENA

Oryza sativa

Project description:Genome sequence of brown planthopper resistant rice cultivar

| PRJDB9518 | ENA

Oryza sativa Indica Group cultivar:NLR-33892

Project description:Rapid Mapping of QTLs associated with Grain Number in NLR-33892

| PRJNA484092 | ENA

Oryza sativa Indica Group x Oryza sativa Japonica Group

Project description:Oryza sativa Indica Group x Oryza sativa Japonica Group Genome sequencing and assembly