MTMEGPS:使用深度学习进行多特征和多环境的基因组和现象选择的R包
Freddy Mora-Poblete1, Javiera Valenzuela-Herrera2, Matías Balach2
1Institute of Biological Sciences, University of Talca, Talca, Chile.
Frontiers in plant science
|January 21, 2026
概括
一个新的R包,MTMEGPS,通过深度学习增强了基因组和现象选择. 它提供了一个用户友好的工作流程,用于在多个特征和环境中预测复杂的特征,提高育种计划的效率.
科学领域:
- 植物育种和遗传学
- 计算生物学是一种计算生物学.
- 机器学习在农业中的应用.
背景情况:
- 在现代育种中,基因组和现象选择 (GPS) 对于数据驱动的复杂特征预测至关重要.
- 深度学习 (DL) 通过建模非线性模式,提供了增强的预测能力,而非线性模式通常被传统方法遗漏.
- 在繁殖中DL的有限采用源于计算成本和缺乏非程序员可访问的工具.
研究的目的:
- 介绍MTMEGPS (多路径和多环境的基因组和现象选择),这是一个R包,旨在简化基因组和现象选择.
- 提供一个端到端的工作流程,用于使用DL进行单一和多路径 (UT/MT) 和单一和多环境 (UE/ME) 预测.
- 通过为没有广泛编程经验的用户提供可访问的工具,促进DL在育种计划中的采用.
主要方法:
- 开发了MTMEGPS,一个R包,包括数据准备,超参数优化,模型训练和基于DL的评估.
- 将MTMEGPS应用于玉米 (基因组) 和树 (NIR现象) 数据集,以及一个独立的多环境数据集.
- 对各种UT/MT和UE/ME场景的基准模型进行评估的包装性能.
主要成果:
- 与基准模型相比,MTMEGPS在大多数场景中表现出优越的预测能力,特别是内部数据集的UT和独立多环境数据集的MT.
- 平均平方误差 (MSE) 值在所有模型中都是可比的,并且保持在适度范围内.
- 该套件在基因组和现象选择方面都被证明是有效的,即使预测错误也很小.
结论:
- 通过深度学习,MTMEGPS为先进的基因组和现象选择提供了实用和高效的解决方案.
- R包使DL在育种中的使用民主化,支持跨多种条件的复杂特征预测.
- 通过提供可访问的,数据驱动的预测工具,MTMEGPS增强了育种计划的能力.
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