Reciprocal BLUP: A Predictability-Guided Multi-Omics Framework for Plant Phenotype Prediction

Abstract

Sustainable improvement of crop performance requires integrative approaches that link genomic variation to phenotypic expression through intermediate molecular layers. Here, we present Reciprocal Best Linear Unbiased Prediction (Reciprocal BLUP), a predictability-guided multi-omics framework that quantifies cross-layer relationships among the genome, metabolome, and microbiome to enhance phenotype prediction. Using a panel of 198 soybean accessions grown under well-watered and drought conditions, we first evaluated four direction-specific prediction models (genome[->]microbiome, genome[->]metabolome, metabolome[->]microbiome, and microbiome[->]metabolome) to estimate the predictability of individual omics features. Then, we evaluated whether subsets of features with high cross-omics predictability improve phenotype prediction. These cross-layer models identify features that play physiologically meaningful roles within multi-omics systems, enabling us to prioritize variables that capture coherent biological signals enriched for phenotype-relevant information. As a result, metabolome features were highly predictable from microbiome data, whereas microbiome predictability from metabolomic data was weaker and more environment-dependent, revealing an asymmetric relationship between these layers. In the subsequent phenotype prediction analysis, the model incorporating predictability-based feature selection substantially outperformed models using randomly selected features and also achieved prediction accuracies comparable to those of the full-feature model. Under drought, phenotype prediction models based on metabolomic or microbiomic kernels (MetBLUP or MicroBLUP) outperformed the genomic baseline (GBLUP) for several biomass-related traits, indicating that environment-responsive omics layers captured phenotypic variation not explained by additive genetic effects. Our results highlight hierarchical interactions among genomic, metabolic, and microbial systems, with the metabolome functioning as an integrative mediator linking genotype, environment, and microbiome composition. The Reciprocal BLUP framework provides a biologically interpretable and practical approach for integrating multi-omics data, improving phenotype prediction, and guiding omics-based feature selection in plant breeding.