MsMTA regulates growth and metabolism in alfalfa (Medicago sativa) through m⁶A-mediated stabilization of metabolic...

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.