Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea.
Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea.
J Plant Physiol. 2018 Jan;220:11-23. doi: 10.1016/j.jplph.2017.10.003. Epub 2017 Oct 26.
Plant root systems play essential roles in developmental processes, such as the absorption of water and inorganic nutrients, and structural support. Gene expression is affected by growth conditions and the genetic background of plants. To identify highly conserved root-preferred genes in rice across diverse growth conditions and varieties, we used two independent meta-anatomical expression profiles based on a large collection of Affymetrix and Agilent 44K microarray data sets available for public use. We then identified 684 loci with root-preferred expression, which were validated with in silico analysis using both meta-expression profiles. The expression patterns of four candidate genes were confirmed in vivo by monitoring expression of β-glucuronidase under control of the candidate-gene promoters, providing new tools to manipulate agronomic traits associated with roots. We also utilized real-time PCR to examine the root-preferential expression of 14 genes across four rice varieties, including japonica and indica cultivars. Using a database of rice genes with known functions, we identified the reported functions of 39 out of the 684 candidate genes. Sixteen genes are directly involved in root development, while the remaining are involved in processes indirectly related to root development (i.e., soil-stress tolerance or growth retardation). This indicates the importance of our candidate genes for studies on root development and function. Gene ontology enrichment analysis in the 'biological processes' category revealed that root-preferred genes in rice are closely associated with nutrient transport-related genes, indicating that the primary role of roots is the uptake of nutrients from soil. In addition, predicted protein-protein interaction analysis suggested a molecular network for root development composed of 215 interactions associated with 44 root-preferred or root development-related genes. Taken together, our data provide an important foundation for future research on root development in rice.
植物根系在发育过程中发挥着重要作用，例如吸收水分和无机养分以及提供结构支撑。基因表达受生长条件和植物遗传背景的影响。为了在不同的生长条件和品种中鉴定水稻中高度保守的根偏好基因，我们使用了两个独立的基于大量公共可用的 Affymetrix 和 Agilent 44K 微阵列数据集的元解剖表达谱。然后，我们鉴定了 684 个具有根偏好表达的基因座，并用两个元表达谱的计算机分析进行了验证。四个候选基因的表达模式通过监测候选基因启动子控制下β-葡糖苷酸酶的表达在体内得到了证实，为操纵与根相关的农艺性状提供了新的工具。我们还利用实时 PCR 检查了四个水稻品种（包括粳稻和籼稻品种）中 14 个基因的根偏好表达。使用具有已知功能的水稻基因数据库，我们鉴定了 684 个候选基因中的 39 个的报告功能。16 个基因直接参与根发育，而其余基因则间接参与与根发育相关的过程（即耐土壤胁迫或生长迟缓）。这表明我们的候选基因对于根发育和功能的研究非常重要。在“生物过程”类别中的基因本体富集分析表明，水稻中的根偏好基因与与养分运输相关的基因密切相关，这表明根的主要作用是从土壤中吸收养分。此外，预测的蛋白质-蛋白质相互作用分析表明，由与 44 个根偏好或根发育相关基因相关的 215 个相互作用组成的根发育分子网络。总之，我们的数据为水稻根发育的未来研究提供了重要的基础。
