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Evaluating Evo 2 for plant variant effect prediction

Kato, Y.; Takayama, S.; Fujii, S.

2026-03-26 plant biology
10.64898/2026.03.24.714098 bioRxiv
Show abstract

The genomic foundation model Evo 2 enables zero-shot variant effect prediction. Here, we evaluate its performance using Arabidopsis thaliana reproductive barrier genes with experimentally confirmed gain- and loss-of-function variants, and show that Evo 2 distinguishes functionally impactful variants. Together with a sign-reversal amplitude metric that recovers a variant missed by standard scoring, these results highlight the potential of Evo 2 for causal variant prioritization in plant GWAS and QTL mapping.

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