Mul‐PheG2P: decoupled learning and prediction–space fusion enables robust and interpretable multi‐phenotype genomic prediction

Abstract

Genomic prediction of multiple phenotypes is crucial in modern plant breeding; however, existing methods struggle with negative transfer and lack interpretability, particularly across high‐dimensional small‐sample data and diverse species. To address this, we propose Mul‐PheG2P, a novel paradigm based on decoupled learning and predictive space fusion. It employs a two‐stage design: first training phenotype‐specific encoders using genetic data, then decoupling phenotype‐specific learning from cross‐phenotype aggregation via an interpretable prediction layer. Mul‐PheG2P outperforms existing methods across diverse crop datasets, including maize (Zea mays), wheat (Triticum aestivum), and tomato (Solanum lycopersicum). It provides a multi‐scale interpretability chain: at the macro level, it quantifies phenotypic contributions via attention‐based weighting; at the micro level, Integrated Gradients reveal the genetic basis of predictions. Notably, the model successfully identified the CCT (CONSTANS, CO‐like, and TOC) motif regulating photoperiodism and the SQUAMOSA (SQUAMOSA promoter binding protein) promoter for inflorescence development, confirming its ability to capture functional biological mechanisms. These results highlight the high performance and interpretability of Mul‐PheG2P, showcasing its value for low‐cost, large‐scale screening to advance precision breeding.