Integrated Transcriptomic and Metabolomic Analyses Reveal Differential Responses of Two Alfalfa Cultivars with Contrasting Fall Dormancy Ratings During Germination and Early Seedling Development Under Simulated Autumn Conditions

Fall dormancy is an important adaptive trait that determines the regional adaptation of alfalfa (Medicago sativa L.); however, the responses of cultivars with contrasting fall dormancy ratings to fall-dormancy-associated cues during early development remain poorly understood. Seeds of two alfalfa cultivars with contrasting fall dormancy ratings, ‘Queen’ (fall dormancy rating 2) and ‘Eureka+’ (fall dormancy rating 8), were exposed to simulated autumn conditions (4 °C, 8 h light/16 h dark photoperiod, and reduced light intensity) for 5 days, then germinated at 25 °C. Germination traits were evaluated, and transcriptomic and metabolomic analyses were performed at the radicle protrusion stage. The simulated autumn treatment reduced germination vigor, induced red hypocotyl coloration, and increased fresh weight in ‘Queen’ but decreased it in ‘Eureka+’, and increased dry weight in both. Compared with the controls, 4838 differentially expressed genes and 637 differentially accumulated metabolites were identified in ‘Queen’, whereas 4636 genes and 965 metabolites were identified in ‘Eureka+’. ‘Queen’ showed enrichment in glutathione metabolism, flavonoid biosynthesis, and lipid-related metabolic pathways, whereas ‘Eureka+’ was associated with photosynthesis, the Calvin cycle, ribosome-related processes, and amino acid biosynthesis. These findings reveal different transcriptomic and metabolomic response patterns between the two tested cultivars under simulated autumn conditions.