Genome-wide identification and analysis of Japonica and Indica cultivar-preferred transcripts in rice using 983 Affymetrix array data
文献类型：期刊论文
| 作者 | Jung KH[*]1; Gho HJ1; Giong HK1,2; Chandran AKN1; Nguyen QN1; Choi H1; Zhang T2; Wang W2; Kim JH3; Choi HK3 |
| 刊名 | RICE
 |
| 出版日期 | 2013 |
| 卷号 | 6期号:X页码:e19 |
| 关键词 | eQTL Indica Japonica Gene ontolgy enrichment Microarray meta-analysis |
| 通讯作者 | khjung2010@khu.ac.kr |
| 合作状况 | 其它 |
| 英文摘要 | 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. |
| 收录类别 | SCI |
| 资助信息 | This research was funded by the Next-Generation BioGreen 21 Program of South Korea (PJ008079 and PJ009514 to KHJ). |
| 语种 | 英语 |
| WOS记录号 | WOS:000329807100001 |
| 公开日期 | 2014-02-14 |
| 源URL | [http://159.226.149.42:8088/handle/152453/7803]  |
| 专题 | 昆明动物研究所_基因起源组 昆明动物研究所_遗传资源与进化国家重点实验室 |
| 作者单位 | 1.Department of Plant Molecular Systems Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin 446-701, Republic of Korea 2.CAS-Max Planck Junior Research Group on Evolutionary Genomics, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, China. 3.Department of Medical Bioscience, Dong-A University, Busan, Republic of Korea |
| 推荐引用方式 GB/T 7714 | Jung KH[*],Gho HJ,Giong HK,et al. Genome-wide identification and analysis of Japonica and Indica cultivar-preferred transcripts in rice using 983 Affymetrix array data[J]. RICE,2013,6(X):e19. |
| APA | Jung KH[*].,Gho HJ.,Giong HK.,Chandran AKN.,Nguyen QN.,...&An G.(2013).Genome-wide identification and analysis of Japonica and Indica cultivar-preferred transcripts in rice using 983 Affymetrix array data.RICE,6(X),e19. |
| MLA | Jung KH[*],et al."Genome-wide identification and analysis of Japonica and Indica cultivar-preferred transcripts in rice using 983 Affymetrix array data".RICE 6.X(2013):e19. |
入库方式： OAI收割
来源：昆明动物研究所
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