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Genomic language model-based genomic prediction in plant breeding
Journal article   Peer reviewed

Genomic language model-based genomic prediction in plant breeding

Ganesan Alagarasan, Huihui Li, Yunbi Xu, José Crossa and Rajeev K Varshney
Trends in plant science, Vol.31(9), pp.1164-1176
2026
PMID: 42097899

Abstract

DNA sequence grammar genomic prediction genomic language model molecular marker
Genomic prediction based on molecular markers has substantially advanced genomic selection; however, prediction accuracy often plateaus despite continued increases in marker density and methodological refinement. This saturation limits the effective use of available genomic information. The emergence of genomic language models (GLMs) offers a new framework for incorporating richer sequence-based information into genomic prediction, potentially capturing biologically meaningful DNA sequence grammar that is poorly represented by traditional marker-based approaches. We conclude that the future of genomic prediction will be shaped not primarily by algorithmic refinement but by the biological expressivity of genomic representations, and that GLMs offer a principled path toward expanding this representational frontier.

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