Genome-wide expression analysis of HSP70 family genes in rice and identification of a cytosolic HSP70 gene highly induced under heat stress.

The heat shock protein 70 (HSP70) gene family plays a key role in protecting plant cells or tissues from thermal or oxidative stress. Although many studies have elucidated the molecular functions of individual family members, genome-wide analysis of this family is still limited, especially for crop species. Our objective was to integrate various meta-profiling data into the context of a phylogenetic tree, which would enable us to perform fine evaluation of functional dominancy or redundancy within this family. Our data indicated that a loss-of-function mutant of a rice cytosolic HSP70 gene (OsctHSP70-1) did not show a clear defective phenotype in response to high temperature because of the existence of another gene family member that was closely clustered with OsctHSP70-1 and had similar expression patterns. Moreover, the second gene showed much stronger anatomical expression. We indirectly analyzed the function of OsctHSP70-1 by studying GUS activity under the control of the endogenous promoter. We also designed a probable interaction network mediated by OsctHSP70-1 and used co-expression analysis among its components to refine the network, suggesting more probable model to explain the function of OsctHSP70-1.

A systematic view of rice heat shock transcription factor family using phylogenomic analysis.

The heat shock transcription factor (Hsf) family includes key regulators of the physiological response to heat stress. Here, we present a systematic analysis of the Hsf family in rice using a phylogenomics-based approach that integrates multi-omics data into the context of a phylogenetic tree. For 25 previously identified Hsfs, we integrated anatomical meta-profiling data from 983 Affymetrix arrays into a phylogenetic tree, revealing a global view of the functional redundancy within this family. Interestingly, most of the Hsfs showed significant fluctuation in gene expression patterns, suggesting that they have condition- or stress-dependent roles. Therefore, we further analyzed the abiotic stress responses of the Hsfs using log(2-)fold change data in response to heat, cold, drought and salt stresses. Subsequently, we identified 19 Hsfs that are positively associated with heat stress, 11 with drought, 9 with salt, and 7 with cold stress, as indicated by at least a 2-fold change and coefficient of variation less than 1. The Hsf subfamily A2 was conserved in the heat stress response. The Hsf subfamily C showed a strong positive association with drought, salt and cold stresses. Downregulation of three members in the Hsf subfamily B in response to cold stress is characteristic. More interestingly, half of the Hsf subfamily B genes were upregulated by heat, drought and salt stresses, while one gene in the other half was downregulated by drought, salt, and cold stresses. Finally, we developed a hypothetical functional gene network mediated by OsHsfA2e/OsHsf-12 that is involved in thermotolerance as well as upregulated in response to heat. We expect that our data will help researchers design more efficient strategies to study the rice Hsf family with information about probable functional redundancy.

Genome-wide identification and analysis of Japonica and Indica cultivar-preferred transcripts in rice using 983 Affymetrix array data.

BACKGROUND: 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. RESULTS: In 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. CONCLUSIONS: The 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.