Department of Agricultural Biology, Faculty of Agriculture, University of Peradeniya, Peradeniya 20400, Sri Lanka.
Comput Biol Chem. 2019 Oct;82:1-8. doi: 10.1016/j.compbiolchem.2019.06.004. Epub 2019 Jun 5.
Grain number, plant height and heading date 7 (GhD7) is considered to be one of the key yield-related genes in the production of high-yielding and climate-ready super rice varieties. GhD7 delays the plant's flowering under long-day conditions, which ultimately results in increased yield. Recent findings indicate that GhD7 also plays a major role in the abiotic stress response; however, the fine regulatory mechanisms controlling Ghd7 expression have yet to be uncovered. This study was carried out to explore the transcription factor binding site (TFBS) architecture of the GhD7 promoter to identify the regulatory dynamics of GhD7 transcription. The promoter sequence (-2000 to +200 base pairs from the transcription start site) was retrieved from the PlantPAN 2.0 database. Ab initio promoter analysis, DNase I hypersensitive site (DHS) analysis, and methylation analysis were carried out to identify TFBSs. The TFBS diversity among rice varieties was also assessed. In addition to the previously identified 8 cis-elements, 448 novel cis-elements were identified in the GhD7 promoter that provide binding sites for 25 transcription factor families. Furthermore, a DNase I hypersensitive site and a CpG island were also identified. The identified transcription factor families include key transcription factors involved in both development and abiotic stress responses, revealing the regulatory dynamics of GhD7. Comparative analysis of multiple GhD7 promoters identified 31 single-nucleotide polymorphisms that result in TFBS variations among rice accessions. These variations are mostly found in relation to flowering and abiotic stress responsive TFBSs on the promoter. This study supports the model that GhD7 acts as a central regulator of rice growth, development, and the abiotic stress response.
粒数、株高和抽穗期 7（GhD7）被认为是高产和适应气候变化的超级稻品种产量相关的关键基因之一。GhD7 在长日照条件下延迟植物开花，最终导致产量增加。最近的研究结果表明，GhD7 还在非生物胁迫响应中起主要作用；然而，控制 Ghd7 表达的精细调控机制仍有待揭示。本研究旨在探索 GhD7 启动子的转录因子结合位点（TFBS）结构，以确定 GhD7 转录的调控动态。从 PlantPAN 2.0 数据库中检索到 GhD7 启动子序列（转录起始位点前 2000 至+200 个碱基对）。进行了从头预测启动子分析、DNase I 超敏位点（DHS）分析和甲基化分析，以鉴定 TFBS。还评估了水稻品种之间的 TFBS 多样性。除了先前鉴定的 8 个顺式元件外，在 GhD7 启动子中还鉴定出 448 个新的顺式元件，为 25 个转录因子家族提供了结合位点。此外，还鉴定出一个 DNase I 超敏位点和一个 CpG 岛。鉴定出的转录因子家族包括参与发育和非生物胁迫响应的关键转录因子，揭示了 GhD7 的调控动态。对多个 GhD7 启动子的比较分析确定了 31 个单核苷酸多态性，导致水稻品种之间的 TFBS 变异。这些变异主要与启动子上的开花和非生物胁迫响应 TFBS 有关。本研究支持 GhD7 作为水稻生长、发育和非生物胁迫响应的中央调控因子的模型。
