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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 j...

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Autores principales: 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
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Springer New York 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4883688/
https://www.ncbi.nlm.nih.gov/pubmed/24280533
http://dx.doi.org/10.1186/1939-8433-6-19
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author 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
author_facet 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
author_sort Jung, Ki-Hong
collection PubMed
description 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1939-8433-6-19) contains supplementary material, which is available to authorized users.
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spelling pubmed-48836882016-06-21 Genome-wide identification and analysis of Japonica and Indica cultivar-preferred transcripts in rice using 983 Affymetrix array data 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 Rice (N Y) Research 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1939-8433-6-19) contains supplementary material, which is available to authorized users. Springer New York 2013-08-10 /pmc/articles/PMC4883688/ /pubmed/24280533 http://dx.doi.org/10.1186/1939-8433-6-19 Text en © Jung et al.; licensee Springer. 2013 This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research
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
Genome-wide identification and analysis of Japonica and Indica cultivar-preferred transcripts in rice using 983 Affymetrix array data
title Genome-wide identification and analysis of Japonica and Indica cultivar-preferred transcripts in rice using 983 Affymetrix array data
title_full Genome-wide identification and analysis of Japonica and Indica cultivar-preferred transcripts in rice using 983 Affymetrix array data
title_fullStr Genome-wide identification and analysis of Japonica and Indica cultivar-preferred transcripts in rice using 983 Affymetrix array data
title_full_unstemmed Genome-wide identification and analysis of Japonica and Indica cultivar-preferred transcripts in rice using 983 Affymetrix array data
title_short Genome-wide identification and analysis of Japonica and Indica cultivar-preferred transcripts in rice using 983 Affymetrix array data
title_sort genome-wide identification and analysis of japonica and indica cultivar-preferred transcripts in rice using 983 affymetrix array data
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4883688/
https://www.ncbi.nlm.nih.gov/pubmed/24280533
http://dx.doi.org/10.1186/1939-8433-6-19
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