MMGS: a novel genomic prediction framework to integrate genotype, environment and their interactions for multi-environment breeding trials. Zhu, M., Zheng, Z., Liu, W., Han, Y., Mou, W., Yin, T., Dai, X., Wu, H., Yang, Y., Zan, Y., & Liu, J. Horticulture Research, 13(5):uhag035, May, 2026. ![MMGS: a novel genomic prediction framework to integrate genotype, environment and their interactions for multi-environment breeding trials [link]](https://bibbase.org/img/filetypes/link.svg "link")
Paper doi abstract bibtex Accurately predicting the performance of trees and crops across diverse and changing climates is essential for matching genotypes to both current and future environments. Yet modelling the complex interplay among genotype, environment, and phenotype in multi-environment trials remains a major challenge. Here, we introduce a unified framework, polygenic environmental interaction (PEI), directly models genotype-by-environment interactions through integrating genotypes and environmental covariates. We implemented an ensemble of 15 estimators spanning parametric, non-parametric, and machine-learning approaches. We then benchmarked our framework against the classical reaction norm (RN) using three genetically distinct populations and three traits with variable genetic architectures. Furthermore, we released an open-source R package, Multiple-environments genomic selection (MMGS), on GitHub. Together, our study offers a flexible and computationally efficient approach for multi-environment genomic prediction, enhancing breeding efficiency, providing deeper insights into modelling the genotype-environment-phenotype continuum.
@article{zhu_mmgs_2026,
title = {{MMGS}: a novel genomic prediction framework to integrate genotype, environment and their interactions for multi-environment breeding trials},
volume = {13},
issn = {2662-6810},
shorttitle = {{MMGS}},
url = {https://doi.org/10.1093/hr/uhag035},
doi = {10.1093/hr/uhag035},
abstract = {Accurately predicting the performance of trees and crops across diverse and changing climates is essential for matching genotypes to both current and future environments. Yet modelling the complex interplay among genotype, environment, and phenotype in multi-environment trials remains a major challenge. Here, we introduce a unified framework, polygenic environmental interaction (PEI), directly models genotype-by-environment interactions through integrating genotypes and environmental covariates. We implemented an ensemble of 15 estimators spanning parametric, non-parametric, and machine-learning approaches. We then benchmarked our framework against the classical reaction norm (RN) using three genetically distinct populations and three traits with variable genetic architectures. Furthermore, we released an open-source R package, Multiple-environments genomic selection (MMGS), on GitHub. Together, our study offers a flexible and computationally efficient approach for multi-environment genomic prediction, enhancing breeding efficiency, providing deeper insights into modelling the genotype-environment-phenotype continuum.},
number = {5},
urldate = {2026-05-15},
journal = {Horticulture Research},
author = {Zhu, Mingjia and Zheng, Zeyu and Liu, Wei and Han, Yu and Mou, Wenjie and Yin, Tongming and Dai, Xiaogang and Wu, Huaitong and Yang, Yongzhi and Zan, Yanjun and Liu, Jianquan},
month = may,
year = {2026},
pages = {uhag035},
}
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