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.Electronic supplementary materialThe online version of this article (doi:10.1186/1939-8433-6-19) contains supplementary material, which is available to authorized users.
Highlights
Accumulation of genome-wide transcriptome data provides new insight on a genomic scale which cannot be gained by analyses of individual data
Using significant microarray analysis (SAM) in the TIGR multi experiment viewer (MEV) toolkit, we identified 104 genes with preferential expression in indica and 490 genes preferentially expressed in japonica
Japonica or indica Expression quantitative trait loci (eQTLs) identified from rice Affymetrix microarray data To identify eQTLs between japonica and indica, we collected Affymetrix microarray data from the NCBI gene expression omnibus (NCBI Gene expression omnibus (GEO), http://www.ncbi.nlm. nih.gov/geo/) or ArrayExpress (Barrett et al 2011; Parkinson et al 2011)
Summary
Accumulation 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. Kitaake) and an indica variety (IR64) revealed that about 10% of light-responsive rice genes differed between subspecies (Jung et al 2008b). The RiceXPro database in particular provides a large collection of expression data on japonica (Sato et al 2013). This database provides diverse views for expression analysis of rice genes in terms of anatomy, development, diurnal regulation, hormone response and laser-captured root cell types (Sato et al 2013)
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