Genome-wide identification and comprehensive analysis of the COI1 gene family in Medicago sativa

COI1 (CORONATINE INSENSITIVE) is a central regulator of plant defense against biotic stresses, yet its family members remain uncharacterized in the globally important forage crop alfalfa (<i>Medicago sativa</i> L.). Here, we identified 32 <i>MsCOI1</i> genes, which were phylogenetically classified into four subfamilies (I-IV). The four subfamilies each contain 5, 6, 9, and 12 <i>MsCOI1</i> genes, respectively. Structural analysis revealed conserved three-exon architecture and six critical motifs, with Motif 3 exclusively absent in Subfamily IV. Promoter cis-element profiling showed enrichment in stress-responsive elements: 93.8% contained ABRE (abscisic acid response), 68.8% harbored MeJA-responsive elements, and 50% possessed TC-rich repeats (defense/stress response). Expression dynamics demonstrated tissue specificity (e.g., <i>MsCOI1-24/25/26</i> in nodules/roots) and hormone responsiveness (40.6% induced by MeJA/ABA). Crucially, six of eight tested <i>MsCOI1s</i> were upregulated during <i>Alfamovirus</i> AMV (commonly known as Alfalfa mosaic virus, AMV) infection. However, <i>MsCOI1-8</i> was significantly inhibited at 5 dpi, indicating that the virus manipulates the COI1-mediated plant response. This study provides the first comprehensive resource of <i>MsCOI1</i> genes for enhancing viral resistance in alfalfa breeding.