He Bing, Meng Lin, Tang Lina, Qi Weicong, Hu Fengqin, Lv Yuanda, Song Wenjing
Key Laboratory of Tobacco Biology and Processing, Ministry of Agriculture, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China.
Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, China.
Front Plant Sci. 2021 Nov 8;12:774829. doi: 10.3389/fpls.2021.774829. eCollection 2021.
Alternative splicing (AS) occurs extensively in eukaryotes as an essential mechanism for regulating transcriptome complexity and diversity, but the AS landscape regulating potassium (K) use efficiency in plants is unclear. In this study, we performed high-throughput transcriptome sequencing of roots and shoots from allopolyploid under K deficiency. Preliminary physiological analysis showed that root system architecture was dramatically changed due to potassium deficiency and that IAA content was significantly reduced in root and shoot. AS analysis showed that a total of 28,179 genes exhibited 54,457 AS events, and 1,510 and 1,732 differentially alternatively spliced (DAS) events were identified in shoots and roots under low K stress. Nevertheless, only 120 DAS events occurred in both shoots and roots, implying that most DAS events were tissue-specific. Both in shoot and the root, the proportion of DAS genes in differentially expressed (DE) genes equaled that in non-DE genes, which indicated that AS might play a unique regulatory role in response to low potassium. Gene ontology analysis further indicated that transcription regulation and AS modulation worked independently in response to low K stress in tobacco, as their target biological processes were different. Totally 45 DAS transcription factors (TFs) were found, which were involved in 18 TF families. Five Auxin response factor (ARF) TFs were significantly DAS in root, suggesting that response to auxin was probably subject to AS regulation in the tobacco root. Our study shows that AS variation occurs extensively and has a particular regulatory mechanism under K deficiency in tobacco. The study also links changes in root system architecture with the changes in AS of ARF TFs, which implied the functional significance of these AS events for root growth and architecture.
可变剪接（AS）在真核生物中广泛存在，是调节转录组复杂性和多样性的重要机制，但植物中调节钾（K）利用效率的AS图谱尚不清楚。在本研究中，我们对低钾条件下异源多倍体的根和地上部进行了高通量转录组测序。初步生理分析表明，缺钾导致根系结构发生显著变化，根和地上部的生长素（IAA）含量显著降低。AS分析表明，共有28179个基因发生了54457个AS事件，在低钾胁迫下，地上部和根部分别鉴定出1510个和1732个差异可变剪接（DAS）事件。然而，只有120个DAS事件在地上部和根部均发生，这意味着大多数DAS事件具有组织特异性。在地上部和根部，DAS基因在差异表达（DE）基因中的比例与在非DE基因中的比例相等，这表明AS可能在响应低钾时发挥独特的调节作用。基因本体分析进一步表明，转录调控和AS调节在烟草响应低钾胁迫时独立发挥作用，因为它们的目标生物学过程不同。共发现45个DAS转录因子（TF），它们涉及18个TF家族。五个生长素响应因子（ARF）TF在根中显著发生DAS，表明烟草根中对生长素的响应可能受AS调控。我们的研究表明，AS变异广泛存在，并且在烟草低钾条件下具有特定的调节机制。该研究还将根系结构的变化与ARF TF的AS变化联系起来，这暗示了这些AS事件对根生长和结构的功能意义。
