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Responses to Salt Stress

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Salt Stress Adaptations in Soybean Involve Alterations in Pre-mRNA Processing.

Shoudong Zhang^1,2,3, Zhixia Xiao^2,3, Ailin Liu^2,3

¹School of Agriculture, Yunnan University, Kunming, China.

Plant, Cell & Environment

|April 3, 2025

Summary

This summary is machine-generated.

Soybean plants adapt to salt stress by altering gene expression and RNA processing. Direct RNA sequencing revealed novel transcripts and changes in poly(A) tails and m6A modifications, crucial for salt tolerance.

Keywords:

N6‐methyladenosine (m6A) modification Oxford Nanopore Technology Direct RNA sequencing (ONT DRS)alternative splicing fusion transcript novel transcripts poly(A) tail length salt stress soybean

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Area of Science:

Plant Biology
Molecular Biology
Genomics

Background:

Salt stress significantly impacts plant survival and development.
Plant adaptation to abiotic stress involves complex gene expression and RNA processing alterations.
Traditional sequencing methods have limitations in comprehensively profiling pre-mRNA processing patterns.

Purpose of the Study:

To comprehensively profile salt stress-responsive pre-mRNA processing patterns in soybean using Oxford Nanopore Technologies Direct RNA Sequencing (ONT DRS).
To investigate the impact of salt stress on transcript isoforms, alternative mRNA processing, and fusion transcripts.
To analyze changes in poly(A) tail lengths and N6-methyladenosine (m6A) modifications in response to salt stress.

Main Methods:

Utilized Oxford Nanopore Technologies Direct RNA Sequencing (ONT DRS) for direct, full-length native RNA sequencing without reverse transcription or amplification.
Analyzed soybean leaves and roots subjected to short-term salt stress.
Identified novel transcript isoforms, alternative mRNA processing events, and fusion transcripts.
Quantified poly(A) tail lengths and m6A modification levels.

Main Results:

Discovered over 89,586 novel transcript isoforms and 44,877 annotated ones in soybean under salt stress.
Identified 102,191 alternative mRNA processing events and 1216 fusion transcripts.
Observed significant alterations in poly(A) tail lengths and m6A modification ratios in upregulated and downregulated genes in roots under salt stress.
Found that m6A modification levels changed with prolonged salt stress and correlated with the expression of m6A erasers.

Conclusions:

ONT DRS provides unprecedented accuracy in profiling pre-mRNA processing at the single-molecule level.
Salt stress reshapes mRNA traits, including poly(A) tail length and m6A modification, contributing to soybean adaptation.
These findings offer novel insights into the molecular mechanisms underlying plant salt tolerance.