Department of Plant Molecular Systems Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin 446-701, Republic of Korea.
Rice (N Y). 2013 Aug 10;6(1):19. doi: 10.1186/1939-8433-6-19.
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.
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.
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.
全基因组转录组数据的积累提供了在基因组范围内的新见解，而这是通过对单个数据的分析无法获得的。大多数水稻（Oryza sativa）物种是粳稻和籼稻品种。鉴定粳稻和籼稻品种之间差异表达的基因将非常有助于理解水稻物种的驯化和进化。
在这项研究中，我们分析了公共数据库中 Affymetrix 芯片数据的 1866 个条目中的 983 个：595 个来自籼稻，388 个来自粳稻品种。为了发现每个品种中差异表达的基因，我们对归一化数据进行了微阵列显著性分析，鉴定出 490 个在粳稻中优先表达的基因和 104 个在籼稻中优先表达的基因。GO 分析表明，与防御反应相关的基因在两个品种中都显著富集，表明在驯化过程中，粳稻和籼稻可能受到这些性状的强烈选择压力。此外，104 个在籼稻中优先表达的基因中有 36 个（34.6%）和 490 个在粳稻中优先表达的基因中有 256 个（52.2%）被注释为未知功能的基因。MapMan 工具包中的生物胁迫概述揭示了粳稻或籼稻 eQTL 中防御反应信号通路的关键元素。
在籼稻中优先表达的筛选基因的百分比（34.6%）是预期值（11.1%）的 4 倍，在粳稻中优先表达的基因的百分比（52.2%）是预期值的 5 倍，这表明未知功能的基因负责区分粳稻和籼稻品种的新性状。鉴定出 10 个在粳稻或籼稻中优先表达的功能特征基因，突出了这些候选基因在水稻物种驯化过程中的重要性。对胁迫介导的信号通路中单个成分的功能分析将揭示提高水稻抗病性的潜在分子机制。
