The Zinc-Finger Protein MsCCCH20 Is Predicted to Regulate Salt-Stress Response in Alfalfa (Medicago sativa L.) by Binding to Conserved 3′UTR Motifs

Le résumé fourni par la source

Soil salinization is a source of major abiotic stress that severely limits the production of alfalfa (Medicago sativa L.), a globally critical forage legume for sustainable livestock production. Its complex autotetraploid genome and self-incompatibility greatly hinder salt tolerance genetic improvement, while the post-transcriptional regulatory mechanism of alfalfa salt stress response remains largely uncharacterized. This study aimed to narrow the gap between genome-wide genetic signals and causal regulatory mechanisms and identify core post-transcriptional regulators of alfalfa salt tolerance via a multi-layered integrative analysis pipeline. We performed a genome-wide association study (GWAS) using 220 globally collected alfalfa accessions, combined with public transcriptome integration, co-expression network analysis, 3′ untranslated region (3′UTR) motif discovery, and AlphaFold2-based protein-RNA docking simulation. We identified 20 significant salt tolerance-associated loci and prioritized the CCCH-type zinc-finger RNA-binding protein (RBP) MsCCCH20 as the core candidate regulator. We further screened 35 high-confidence target genes of MsCCCH20, detected conserved AU/AG-rich 3′UTR motifs, and provided structural predictions consistent with potential sequence-specific interactions (ipTM 0.70–0.79). Our findings establish a robust framework linking genetic association signals to post-transcriptional regulatory networks and provide high-confidence candidate genes and functional markers for the molecular breeding of salt-tolerant alfalfa.

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