MtCro: multi-task deep learning framework improves multi-trait genomic prediction of crops

文献类型： 外文期刊

第一作者： Chao, Dian

作者： Chao, Dian;Wan, Fengqiang;Yang, Yang;Wang, Hao;Yan, Shen;Fang, Wei

作者机构：

关键词： Deep learning; Genomic prediction; Multi-task learning; Crop breeding

期刊名称：PLANT METHODS （ 影响因子：4.4； 五年影响因子：5.7 ）

ISSN：

年卷期： 2025 年 21 卷 1 期

页码：

收录情况： SCI

摘要： Genomic Selection (GS) predicts traits using genome-wide markers, speeding up genetic progress and enhancing breeding efficiency. Recent emphasis has been placed on deep learning models to enhance prediction accuracy. However, current deep learning models focus on learning specific phenotypes for the given task, overlooking the inter-correlations among different phenotypes. In response, we introduce MtCro, a multi-task learning approach that simultaneously captures diverse plant phenotypes within a shared parameter space. Extensive experiments reveal that MtCro outperforms mainstream models, including DNNGP and SoyDNGP, with performance gains of 1-9% on the Wheat2000 dataset, 1-8% on Wheat599, and 1-3% on Maize8652. Furthermore, comparative analysis shows a consistent 2-3% improvement in multi-phenotype predictions, emphasizing the impact of inter-phenotype correlations on accuracy. By leveraging multi-task learning, MtCro efficiently captures diverse plant phenotypes, enhancing both model training efficiency and prediction accuracy, ultimately accelerating the progress of plant genetic breeding. Our code is available on https://github.com/chaodian12/mtcro.

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