Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium.
VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium.
Plant Physiol. 2022 Nov 28;190(4):2350-2365. doi: 10.1093/plphys/kiac374.
With the need to increase plant productivity, one of the challenges plant scientists are facing is to identify genes that play a role in beneficial plant traits. Moreover, even when such genes are found, it is generally not trivial to transfer this knowledge about gene function across species to identify functional orthologs. Here, we focused on the leaf to study plant growth. First, we built leaf growth transcriptional networks in Arabidopsis (Arabidopsis thaliana), maize (Zea mays), and aspen (Populus tremula). Next, known growth regulators, here defined as genes that when mutated or ectopically expressed alter plant growth, together with cross-species conserved networks, were used as guides to predict novel Arabidopsis growth regulators. Using an in-depth literature screening, 34 out of 100 top predicted growth regulators were confirmed to affect leaf phenotype when mutated or overexpressed and thus represent novel potential growth regulators. Globally, these growth regulators were involved in cell cycle, plant defense responses, gibberellin, auxin, and brassinosteroid signaling. Phenotypic characterization of loss-of-function lines confirmed two predicted growth regulators to be involved in leaf growth (NPF6.4 and LATE MERISTEM IDENTITY2). In conclusion, the presented network approach offers an integrative cross-species strategy to identify genes involved in plant growth and development.
随着提高植物生产力的需求，植物科学家面临的挑战之一是鉴定在有益植物性状中发挥作用的基因。此外，即使发现了这些基因，通常也不容易将有关基因功能的知识从一个物种转移到另一个物种，以鉴定功能同源物。在这里，我们专注于叶片来研究植物生长。首先，我们构建了拟南芥（Arabidopsis thaliana）、玉米（Zea mays）和白杨（Populus tremula）中的叶片生长转录网络。接下来，使用已知的生长调节剂（在这里定义为当突变或异位表达时改变植物生长的基因）以及跨物种保守网络作为指导，来预测新的拟南芥生长调节剂。通过深入的文献筛选，在 100 个预测的生长调节剂中，有 34 个在突变或过表达时被证实会影响叶片表型，因此它们代表了新的潜在生长调节剂。总体而言，这些生长调节剂参与细胞周期、植物防御反应、赤霉素、生长素和油菜素内酯信号转导。功能丧失系的表型特征分析证实了两个预测的生长调节剂参与叶片生长（NPF6.4 和 LATE MERISTEM IDENTITY2）。总之，所提出的网络方法提供了一种综合的跨物种策略，用于鉴定参与植物生长和发育的基因。
