N6-methyladenosine (m6A) is a widespread RNA modification in eukaryotes, yet its contribution to growth and metabolic regulation in perennial leguminous forage crops remains poorly understood. Here, we identify MsMTA, a nuclear-localized m6A methyltransferase in alfalfa (Medicago sativa), as a key regulator of the global m6A landscape, plant architecture, and forage nutritional composition. Suppression of MsMTA expression reduced overall m6A levels and caused a pronounced dwarf phenotype. At the metabolic level, MsMTA knockdown lines showed a strong increase in soluble sugar content, accompanied by only a modest reduction in crude protein and decreased fiber, reflecting a reprogramming of carbon–nitrogen allocation that enhances agronomic quality in alfalfa. Integrated m6A sequencing and transcriptome profiling showed that m6A sites are preferentially enriched in the 3′UTR and that the expression of 549 genes is significantly altered; these genes are mainly involved in oxidation–reduction processes, small-molecule metabolic processes, and organonitrogen compound biosynthesis. Representative metabolic genes, such as GS2 and SDR1, exhibited reduced m6A modification and decreased mRNA stability, directly linking MsMTA-dependent methylation to transcript turnover. Together, these findings establish MsMTA as a central node connecting the m6A epitranscriptome with carbon–nitrogen metabolic homeostasis in alfalfa, and indicate that targeted manipulation of MsMTA-dependent m6A methylation offers a potential route to develop alfalfa cultivars that maintain high protein content while substantially elevating soluble sugars, thereby improving forage yield and quality in leguminous crops.

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