Wheat dwarf virus (WDV) poses significant threats to gramineous crops, making it crucial to explore its codon usage patterns and evolutionary dynamics for effective disease control. This study analyzed ten WDV isolates, including two from triticale (WDVT_117 and WDVT_118), using metrics such as relative synonymous codon usage (RSCU), effective number of codons (ENC), codon adaptation index (CAI), and codon bias index (CBI). Neutrality plots, ENC-plots, and PR2-plots were employed to assess the role of mutation and selection. Results revealed weak codon preference in triticale-derived strains (CAI: 0.145–0.269; CBI: −0.042–0.111; ENC > 40), with hierarchical GC content. Neutrality analysis and ENC-plot distributions indicated natural selection as the dominant force, supported by T/C bias at the third codon position (PR2-plot). Shared optimal codons UUC and UAC in highly expressed genes may imply a potential significant role in virus adaptation. RSCU-based clustering and MP phylogenetic analysis revealed that WDVT strains form a distinct cluster with elevated genetic diversity, potentially driven by genomic recombination in the synthetic host. These findings demonstrate that WDVT balances mutational constraints and host adaptation through selective codon optimization. This study provides a foundation for codon-based antiviral research and the development of agricultural strategies to combat WDV infections.

Medicago ruthenica L., a superior forage crop within the genus Medicago (Fabaceae), is endowed with remarkable stress tolerance and an abundance of bioactive compounds, conferring significant ecological and forage value. Existing reviews primarily focus on a single research direction, and the most recent findings are dated, failing to cover breakthroughs at the molecular level. This paper systematically synthesizes the latest research progress in five key areas: genetic diversity and genomic studies, biotic stress responses, abiotic stress tolerance mechanisms (drought, salinity, and low temperature, etc.), utilization (including genetic breeding, ecological restoration, and forage development), and future research prospects. This review addresses critical gaps in existing literature, particularly regarding advances in genomic sequencing, biotic stresses, and research on stress-associated microorganisms. Research indicates that M. ruthenica exhibits extensive genetic diversity, and its genome contains numerous positive selection signals associated with stress resistance. It can tolerate multiple abiotic and biotic stresses through morphoplasticity, physiological metabolic regulation, and transcriptional regulation. Furthermore, its symbiosis with microorganisms such as rhizobia significantly enhances its stress tolerance. M. ruthenica demonstrates outstanding application potential in degraded grassland restoration and high-quality forage production. Future research should focus on mining stress-resistant genes, optimizing molecular breeding techniques, and integrating artificial intelligence into breeding practices. That will facilitate its transformation from a regional endemic resource to a commercially viable functional species, thereby providing robust support for ecological security and the sustainable development of grassland-based livestock husbandry in cold and arid regions.