GRE:与小麦产量相关的显著SNP识别框架利用GWAS-随机森林联合特征选择和可解释的机器学习基因组选择算法
Mei Song1, Shanghui Zhang1, Shijie Qiu1
1School of Mathematics and Statistics, Ludong University, Yantai 264025, China.
Genes
|October 29, 2025
概括
基因组选择 (GS) 模型使用新的框架 (GRE) 进行了改进,该框架结合了GWAS和随机森林,以准确预测小麦产量. 这种方法提高了育种效率,并有助于识别可持续农业的关键遗传标记.
科学领域:
- 农业科学 农业科学
- 遗传学 遗传学是一种遗传学.
- 生物信息学是一种生物信息学.
背景情况:
- 全球小麦生产面临环境退化和耕地减少的挑战,需要进行育种创新以提高产量.
- 基因组选择 (GS) 通过增加遗传收益来提高小麦育种的效率,但受到高维基因组数据的阻碍.
- 精确预测基因组估计育种值 (GEBV) 对于有效的育种计划至关重要.
研究的目的:
- 开发一种可解释的机器学习框架 (GRE),用于小麦的基因组选择.
- 将GWAS的生物学意义与RF的预测能力相结合,用于改进的GS模型.
- 提高小麦产量特征预测的准确性和可解释性.
主要方法:
- 拟议的GRE框架将GWAS和随机森林 (RF) 结合起来用于SNP选择和分析.
- 评估了六个GS算法,包括GBLUP和五个机器学习模型,使用预测准确性 (PCC) 和错误指标.
- 使用Shapley添加式解释 (SHAP) 进行模型解释,揭示SNP对小麦产量的影响.
主要成果:
- 在XGBoost和ElasticNet模型中,使用GRE.0.5识别的383个SNP实现了高预测准确度 (PCC>0.864) 和稳定性 (SD<0.005).
- SHAP分析有效地解释了显著SNP对小麦产量特征的主要影响和相互作用.
- 该研究确定了最佳的SNP子集和机器学习算法,以实现高效的小麦育种.
结论:
- GRE框架为推进小麦育种中的基因组选择提供了一个强大的,可解释的工具.
- 这种方法支持智能育种芯片设计和重要特征基因的挖掘.
- 这些发现有助于转化GS技术,以实现可持续的全球农业生产力.
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