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Deciphering the ceRNA Network in Alfalfa: Insights into Cold Stress Tolerance Mechanisms
Lin Zhu1, Yujie Zhao1,2, Maowei Guo1,3
1Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot 010010, China.
Biomolecules
|February 27, 2026
Summary
Cold stress limits alfalfa production. This study identifies key genes and regulatory networks, including messenger RNAs (mRNAs) and non-coding RNAs (ncRNAs), involved in cold tolerance, offering resources for improving crop resilience.
Area of Science:
- Plant Science
- Molecular Biology
- Genetics
Background:
- Cold stress is a major factor limiting alfalfa (Medicago sativa) production.
- Non-coding RNAs (ncRNAs) are known to play roles in plant abiotic stress responses, but their specific involvement in alfalfa's low-temperature tolerance, particularly through competing endogenous RNA (ceRNA) networks, is not well understood.
Purpose of the Study:
- To investigate the molecular mechanisms underlying alfalfa's response to cold stress.
- To identify differentially expressed messenger RNAs (mRNAs), microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs) under cold conditions.
- To construct a ceRNA regulatory network involved in cold stress response in alfalfa.
Main Methods:
- Integrated whole-transcriptome RNA-sequencing (RNA-seq) and genome-wide association studies (GWASs).
- Utilized degradome sequencing to validate the ceRNA network.
- Analyzed differentially expressed genes and RNAs, and performed functional enrichment analyses (KEGG and GO).
Main Results:
- Identified 46,936 differentially expressed mRNAs, with top KEGG pathways including ribosome, amino sugar and nucleotide sugar metabolism, and starch and sucrose metabolism.
- Discovered 223 DEmiRNAs, 1852 DElncRNAs, and 13 DEcircRNAs, associated with functions like leaf development, transcription factor activity, and response to auxin.
- Constructed a ceRNA network involving 28 lncRNAs, 8 circRNAs, 11 miRNAs, and 23 mRNAs, with MS.gene53818 (MsUAM1) identified as a critical candidate gene.
Conclusions:
- This study elucidates the roles of various RNAs in alfalfa's cold stress response.
- A comprehensive ceRNA network related to cold stress tolerance in alfalfa was established.
- The identified genes and regulatory networks provide valuable genetic resources for enhancing alfalfa's cold tolerance.
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