Transcriptional multiomics reveals the mechanism of seed deterioration in Nicotiana tabacum L. and Oryza sativa L.,Journal of Advanced Research

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Transcriptional multiomics reveals the mechanism of seed deterioration in Nicotiana tabacum L. and Oryza sativa L.
Journal of Advanced Research ( IF 11.4 ) Pub Date : 2022-03-16 , DOI: 10.1016/j.jare.2022.03.009
Jianyu An ₁ , Yihan Liu ₂ , Jiajun Han ₁ , Can He ₁ , Min Chen ₁ , Xiaobo Zhu ₂ , Weimin Hu ₂ , Wenjian Song ₂ , Jin Hu ₂ , Yajing Guan ₂

Affiliation

Introduction

Mature seeds deteriorate gradually and die eventually during long-term storage. Controlled deterioration is often used to accelerate the seed deterioration rate to assess the seed vigor and physiological quality of seed lots.

Objectives

Although it is well known that the process of seed deterioration produced by controlled deterioration is distinct from that caused by long-term storage, the differences in transcriptional levels have not been reported. Clarifying the mechanism of seed deterioration is critical for identifying, conserving and utilizing germplasm resources.

Methods

Tobacco (Nicotiana tabacum L.) seeds were studied thoroughly using transcriptome, small RNA, and degradome sequencing after long-term storage (LS) and controlled deterioration (CD). Co-expression trend analysis identified transcripts involved in tobacco seed deterioration, while phylogenetic analysis helped to uncover comparable targets in rice (Oryza sativa L.) for further verification and utilization.

Results

In LS and CD, a total of 2,112 genes and 164 miRNAs were differentially expressed, including 20 interaction miRNA-mRNA pairs with contrasting expression. Transcriptional multiomics found that the main causes of LS were plant hormone signal transduction and protein processing in the endoplasmic reticulum, whereas the primary cause of CD was nucleotide excision repair dysfunction. The homeostatic balance of RNA degradation and the spliceosome occurred in both modes of seed deterioration. Additionally, co-expression trend analysis identified two coherent pairs, nta-miR160b-NtARF18 and nta-miR396c-NtMBD10, as being significant in LS and CD, respectively. For utilization, rice homologous targets OsARF18 and OsMBD707 were verified to play similar roles in LS and CD, respectively.

Conclusion

This study demonstrated the transcriptional mechanism of tobacco and key genes in seed deterioration. And the application of key genes in rice also verified the feasibility of the multiomics method, guiding the identification of candidate genes to precisely delay seed deterioration in other species of seed research.

中文翻译：

转录多组学揭示了烟草和稻种子恶化的机制。

介绍

成熟的种子在长期储存过程中逐渐变质并最终死亡。控制恶化通常用于加速种子恶化速度，以评估种子批的种子活力和生理质量。

目标

尽管众所周知，受控变质产生的种子变质过程与长期储存引起的种子变质过程不同，但转录水平的差异尚未见报道。阐明种子劣化机理对于种质资源的识别、保存和利用至关重要。

方法

在长期储存 (LS) 和控制变质 (CD) 后，使用转录组、小 RNA 和降解组测序对烟草 ( Nicotiana tabacum L.) 种子进行了彻底研究。共表达趋势分析确定了与烟草种子恶化有关的转录本，而系统发育分析有助于发现水稻（ Oryza sativa L.）中的类似目标，以供进一步验证和利用。

结果

在LS和CD中，共有2,112个基因和164个miRNA存在差异表达，其中包括20个具有对比表达的相互作用miRNA-mRNA对。转录多组学发现，LS的主要原因是植物激素信号转导和内质网蛋白质加工，而CD的主要原因是核苷酸切除修复功能障碍。 RNA 降解和剪接体的稳态平衡发生在种子劣化的两种模式中。此外，共表达趋势分析确定了两个相干对， nta-miR160b - NtARF18和nta-miR396c - NtMBD10 ，分别在 LS 和 CD 中显着。为了利用，水稻同源靶点OsARF18和OsMBD707被验证分别在 LS 和 CD 中发挥相似的作用。