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

• Published in: Rice (New York, N.Y.) Vol. 6; no. 1; p. 19
• Main Authors: Jung, Ki-Hong, Gho, Hyun-Jung, Giong, Hoi-Khoanh, Chandran, Anil Kumar Nalini, Nguyen, Quynh-Nga, Choi, HeeBak, Zhang, Tian, Wang, Wen, Kim, Jin-Hyun, Choi, Hong-Kyu, An, Gynheung
• Format: Journal Article
• Language: English
• Published: New York Springer New York 10-08-2013; BioMed Central Ltd
• Subjects: Agriculture; Biomedical and Life Sciences; Life Sciences; Plant Breeding/Biotechnology; Plant Ecology; Plant Genetics and Genomics; Plant Sciences; Selected articles from the 10th International Symposium of Rice Functional Genomics; Microarray meta-analysis; eQTL; Gene ontolgy enrichment
• ISSN: 1939-8425; 1939-8433; 1939-8433
• DOI: 10.1186/1939-8433-6-19

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.