Construction and Application of Fine-Tuned Evo2-Based Models for Genomic Sequence Generation Models in Major Staple Crops

To construct genomic functional-element sequence generation models for major staple crops and evaluate their cross-species generalization ability, this study investigates fine-tuning and performance assessment of the Evo2 genomic language model for conditional sequence generation. Six representative crop genomes, including potato, peanut, indica rice cultivars (MH63 and ZS97), japonica rice, and wheat, are selected. A unified conditional generation and evaluation framework is established for six core genomic functional elements, including coding sequences (CDS), exons, introns, mRNA, 5′ untranslated regions (5′ UTR), and 3′ untranslated regions (3′ UTR). Based on this framework, Evo2 models are fine-tuned on crop-specific genomic data, while the pretrained Evo2 model without fine-tuning is retained as a zero-shot baseline. Experimental results show that fine-tuning consistently improves generation performance across all functional elements and crop species, an average absolute gain of about 0.49 percentage points, corresponding to a relative gain of approximately 0.79%. Cross-species evaluation further demonstrates that the fine-tuned models maintain good generalization ability when applied to unseen crop species, and the cross-species generalization gap remains below 1 percentage point for all six functional elements. Among them, coding-related elements such as CDS and mRNA show the most stable generation performance across species, whereas 5′ UTR is more sensitive to species differences. Additional bioinformatics analyses indicate that the generated sequences exhibit some degree of biological plausibility in ORF continuity, but still show limitations in codon preference, regulatory motifs in UTRs, and splice-site rules in introns. Overall, the results verify the effectiveness and cross-species applicability of Evo2-based fine-tuned genomic language models for functional-element sequence generation in major staple crops, providing a potential technical basis for genome-assisted breeding and crop improvement.