ArticleRice (New York, N.Y.)2013
Genome-wide identification and analysis of Japonica and Indica cultivar-preferred transcripts in rice using 983 Affymetrix array data.
Article in Rice (New York, N.Y.), 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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14 citing papers in PubMed, 38 citations in OpenAlex.
- Field-crop transcriptome models are enhanced by measurements in systematically controlled environments.Genome biology · 2025Article
- Comparison of the Phenotypic Performance, Molecular Diversity, and Proteomics in Transgenic Rice.Plants (Basel, Switzerland) · 2022Article
- Comparative analysis of the transcriptomes of two rice subspecies during domestication.Scientific reports · 2021Article
- Weighted Gene Co-Expression Network Coupled with a Critical-Time-Point Analysis during Pathogenesis for Predicting the Molecular Mechanism Underlying Blast Resistance in Rice.Rice (New York, N.Y.) · 2020Article
- Plant breeding involving genetic engineering does not result in unacceptable unintended effects in rice relative to conventional cross-breeding.The Plant journal : for cell and molecular biology · 2020Article
- Characterization of the transcriptional divergence between the subspecies of cultivated rice (Oryza sativa).BMC genomics · 2020Article
- Over-Expression ofFrontiers in bioengineering and biotechnology · 2020Article
- Meta-expression analysis of unannotated genes in rice and approaches for network construction to suggest the probable roles.Plant molecular biology · 2018Article
- Evolutionary relationships and expression analysis of EUL domain proteins in rice (Oryza sativa).Rice (New York, N.Y.) · 2017Article
- QTL mapping and candidate gene analysis of ferrous iron and zinc toxicity tolerance at seedling stage in rice by genome-wide association study.BMC genomics · 2017Article
- Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes.BMC genomics · 2015Article
- Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism.Nature genetics · 2014Article
- Quantitative trait locus mapping and candidate gene analysis for plant architecture traits using whole genome re-sequencing in rice.Molecules and cells · 2014Article
- RNA-Seq using two populations reveals genes and alleles controlling wood traits and growth in Eucalyptus nitens.PloS one · 2014Article
Corrections and comments
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Authors and funding
11 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundAccumulation of genome-wide transcriptome data provides new insight on a genomic scale which cannot be gained by analyses of individual data. The majority of rice (O. sativa) species are japonica and indica cultivars. Genome-wide identification of genes differentially expressed between japonica and indica cultivars will be very useful in understanding the domestication and evolution of rice species.
resultsIn this study, we analyzed 983 of the 1866 entries in the Affymetrix array data in the public database: 595 generated from indica and 388 from japonica rice cultivars. To discover differentially expressed genes in each cultivar, we performed significance analysis of microarrays for normalized data, and identified 490 genes preferentially expressed in japonica and 104 genes in indica. Gene Ontology analyses revealed that defense response-related genes are significantly enriched in both cultivars, indicating that japonica and indica might be under strong selection pressure for these traits during domestication. In addition, 36 (34.6%) of 104 genes preferentially expressed in indica and 256 (52.2%) of 490 genes preferentially expressed in japonica were annotated as genes of unknown function. Biotic stress overview in the MapMan toolkit revealed key elements of the signaling pathway for defense response in japonica or indica eQTLs.
conclusionsThe percentage of screened genes preferentially expressed in indica was 4-fold higher (34.6%) and that in japonica was 5-fold (52.2%) higher than expected (11.1%), suggesting that genes of unknown function are responsible for the novel traits that distinguish japonica and indica cultivars. The identification of 10 functionally characterized genes expressed preferentially in either japonica or indica highlights the significance of our candidate genes during the domestication of rice species. Functional analysis of the roles of individual components of stress-mediated signaling pathways will shed light on potential molecular mechanisms to improve disease resistance in rice.
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