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.

Background: Soil salinization and alkalization are major constraints to global crop production. Fenugreek ( Trigonella foenum-graecum L.) is considered a potential salt-alkali-tolerant crop; however, the molecular mechanisms underlying its tolerance remain poorly understood. Methods: Four fenugreek provenances were evaluated under saline-alkali stress at the seedling stage. Growth and physiological traits were measured to assess stress tolerance. Based on these results, the most tolerant provenance was selected for transcriptome analysis. Saline-alkali treatments of 0 (control), 100 mmol/L (moderate stress), and 200 mmol/L (severe stress) were applied according to preliminary physiological experiments to induce measurable but non-lethal stress responses suitable for transcriptomic investigation. Results: The tolerance of the four provenances followed the order: Qinghai > Anhui > Yunnan > Gansu, with the Qinghai provenance showing the strongest tolerance. Transcriptome sequencing generated 47,757 unigenes, of which 27,300 were successfully annotated. A total of 2,041 differentially expressed genes (DEGs) were identified among treatments. Functional enrichment analysis indicated that these DEGs were mainly involved in metabolic processes, stress responses, and key pathways such as flavonoid biosynthesis, plant hormone signal transduction, and starch and sucrose metabolism. In addition, 24 transcription factors associated with abiotic stress were identified, primarily belonging to the AP2/ERF, bHLH, MYB, and NAC families. The reliability of the RNA-Seq results was confirmed by qRT-PCR analysis of nine selected DEGs using β-actin as the reference gene. Conclusions: These findings provide new insights into the molecular mechanisms underlying saline-alkali tolerance in fenugreek and offer valuable genetic resources for the breeding of stress-tolerant cultivars.

Soil salinization and alkalization severely limit agricultural sustainability in alpine regions. The integrated responses of oats to complex saline–alkali stress, covering phenotypic, physiological, and metabolomic alterations, remain poorly elucidated. This study aimed to clarify the synergistic adaptive mechanisms of oats with differential saline–alkali tolerance. Three oat varieties with distinct tolerance levels, including the tolerant cultivar Meida, the moderately tolerant cultivar Qingtian No. 2, and the sensitive cultivar Qinghai Sweet Oat, were treated with a 150 mmol·L⁻¹ mixed saline–alkali solution (Na₂SO₄:NaCl:NaHCO₃ = 2:1:1, pH 8.65) to simulate the natural alpine soil environment of Qinghai Province. Compound saline–alkali stress markedly inhibited oat growth and aggravated cellular oxidative damage. The tolerant cultivar effectively alleviated stress injury by improving antioxidant enzyme activities and accumulating osmoprotectants. A total of 396 core differential metabolites were screened in this study, and flavonoid biosynthesis was identified as a conserved core pathway for oat stress resistance. Tolerant oat varieties simultaneously activated defense responses and energy metabolism to adapt to stress conditions. In contrast, sensitive varieties only depended on basal metabolic adjustments to cope with stress. These findings clarify the differential adaptive strategies of oats under saline–alkali stress. They provide key metabolic marker resources and a solid theoretical basis for the breeding and cultivation of salt–alkali-tolerant oats in alpine saline–alkali land.