FSBLUP: a novel strategy of fusion similarity matrix construction via optimally integrating intermediate omics data to enhance genomic prediction.

The increasing availability of multi-omics data is promising in enhancing genomic prediction in breeding and human genetics. However, integrating multi-omics data into genomic prediction models remains challenging due to complex relationships between omics layers and phenotypic outcomes. We propose Fusion Similarity Best Linear Unbiased Prediction (FSBLUP), a novel strategy that integrates genomic and intermediate omics data using a unified similarity matrix approach. FSBLUP systematically estimates how different omics layers contribute to phenotypic variation via machine-learning-optimized parameters that capture underlying genetic architecture of complex traits. FSBLUP demonstrates greater predictive accuracy than existing methods, as validated through theoretical and practical evaluations.