Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan, Iran.
Department of Horticulture, College of Agriculture, Isfahan University of Technology, Isfahan, Iran.
BMC Genomics. 2021 Sep 30;22(1):704. doi: 10.1186/s12864-021-07989-1.
Spinach is a beneficial annual vegetable species and sensitive to the bolting or early flowering, which causes a large reduction in quality and productivity. Indeed, bolting is an event induced by the coordinated effects of various environmental factors and endogenous genetic components. Although some key flowering responsive genes have been identified in spinach, non-coding RNA molecules like long non-coding RNAs (lncRNAs) were not investigated yet. Herein, we used bioinformatic approaches to analyze the transcriptome datasets from two different accessions Viroflay and Kashan at two vegetative and reproductive stages to reveal novel lncRNAs and the construction of the lncRNA-mRNA co-expression network. Additionally, correlations among gene expression modules and phenotypic traits were investigated; day to flowering was chosen as our interesting trait.
In the present study, we identified a total of 1141 lncRNAs, of which 111 were differentially expressed between vegetative and reproductive stages. The GO and KEGG analyses carried out on the cis target gene of lncRNAs showed that the lncRNAs play an important role in the regulation of flowering spinach. Network analysis pinpointed several well-known flowering-related genes such as ELF, COL1, FLT, and FPF1 and also some putative TFs like MYB, WRKY, GATA, and MADS-box that are important regulators of flowering in spinach and could be potential targets for lncRNAs.
This study is the first report on identifying bolting and flowering-related lncRNAs based on transcriptome sequencing in spinach, which provides a useful resource for future functional genomics studies, genes expression researches, evaluating genes regulatory networks and molecular breeding programs in the regulation of the genetic mechanisms related to bolting in spinach.
菠菜是一种有益的一年生蔬菜，对抽薹或早期开花敏感，这会导致其质量和产量大幅下降。事实上，抽薹是由各种环境因素和内源性遗传成分协同作用引起的事件。虽然已经在菠菜中鉴定出一些关键的开花响应基因，但像长非编码 RNA（lncRNA）等非编码 RNA 分子尚未得到研究。在此，我们使用生物信息学方法分析了来自两个不同品系 Viroflay 和 Kashan 的两个营养和生殖阶段的转录组数据集，以揭示新的 lncRNA 并构建 lncRNA-mRNA 共表达网络。此外，还研究了基因表达模块与表型特征之间的相关性；选择开花日作为我们感兴趣的性状。
在本研究中，我们总共鉴定了 1141 个 lncRNA，其中 111 个在营养和生殖阶段之间差异表达。对 lncRNA 的顺式靶基因进行 GO 和 KEGG 分析表明，lncRNA 在调控菠菜开花中起着重要作用。网络分析确定了几个与开花相关的基因，如 ELF、COL1、FLT 和 FPF1，以及一些假定的 TF，如 MYB、WRKY、GATA 和 MADS-box，它们是菠菜开花的重要调节剂，可能是 lncRNA 的潜在靶标。
本研究是首次基于转录组测序鉴定菠菜抽薹和开花相关 lncRNA 的报告，为未来的功能基因组学研究、基因表达研究、评估与菠菜抽薹相关的遗传机制的基因调控网络和分子育种计划提供了有用的资源。
