title: Genome-wide identification and analysis of Japonica and Indica cultivar-preferred transcripts in rice using 983 Affymetrix array data.
abstract: 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.
authors.affiliation: Department of Plant Molecular Systems Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin 446-701, Republic of Korea. khjung2010@khu.ac.kr.
authors.forename: Ki-Hong
authors.initials: KH
authors.lastname: Jung
authors.forename: Hyun-Jung
authors.initials: HJ
authors.lastname: Gho
authors.forename: Hoi-Khoanh
authors.initials: HK
authors.lastname: Giong
authors.forename: Anil Kumar Nalini
authors.initials: AK
authors.lastname: Chandran
authors.forename: Quynh-Nga
authors.initials: QN
authors.lastname: Nguyen
authors.forename: Heebak
authors.initials: H
authors.lastname: Choi
authors.forename: Tian
authors.initials: T
authors.lastname: Zhang
authors.forename: Wen
authors.initials: W
authors.lastname: Wang
authors.forename: Jin-Hyun
authors.initials: JH
authors.lastname: Kim
authors.forename: Hong-Kyu
authors.initials: HK
authors.lastname: Choi
authors.forename: Gynheung
authors.initials: G
authors.lastname: An