A Long Noncoding RNA Derived from lncRNA-mRNA Networks Modulates Seed Vigor

Area of Science:

• Plant Molecular Biology
• Genomics
• Transcriptomics

Background:

• Long noncoding RNAs (lncRNAs) are crucial regulators of gene expression, particularly in plant stress responses.
• Systematic analysis of lncRNAs in rice seeds under cold stress germination is lacking.

Purpose of the Study:

• To identify and characterize lncRNAs in rice seeds during cold stress germination.
• To investigate the role of lncRNAs in regulating rice seed vigor under cold stress.

Main Methods:

• Strand-specific whole transcriptome sequencing of rice seeds under cold and normal temperatures.
• Identification and analysis of differentially expressed lncRNAs and their target genes.
• CRISPR/Cas9 gene editing to study the function of a specific lncRNA (SVR).

Main Results:

• 6258 putative lncRNAs were identified, showing stage-specific expression patterns.
• The auxin-activated signaling pathway was significantly enriched among targets of differentially expressed lncRNAs.
• A seed vigor-related lncRNA, SVR, was identified, interacting in cis with SAUR family genes; SVR mutations delayed germination.

Conclusions:

• lncRNAs play a significant role in rice seed germination and vigor under cold stress.
• SVR is a key lncRNA involved in regulating seed vigor through interaction with the auxin signaling pathway.
• These findings offer new insights into lncRNA-mediated gene regulation in plants.