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通过机器学习和差异基因相关性分析,揭示黄瓜中对浸水反应的基因

Zahra Zinati¹, Leyla Nazari², Ali Niazi³

¹Department of Agroecology, College of Agriculture and Natural Resources of Darab, Shiraz University, Shiraz, Iran.

Botanical studies

|August 14, 2024

概括

气候变化增加了水浸,使黄瓜面临压力. 这项研究使用先进的生物信息学确定了关键的黄瓜基因 (LOC101209599,LOC101217277,LOC101216320),这些基因对水浸耐受性至关重要,有助于培育更有弹性的品种.

科学领域:

植物科学植物科学
基因组学就是基因组学.
生物信息学是一种生物信息学.

背景情况:

气候变化正在增加淹水事件,对黄瓜生产构成重大威胁.
了解黄瓜对淹水的遗传反应对于开发有弹性的作物品种至关重要.

研究的目的:

为了确定参与黄瓜对积水压力的反应的关键基因.
用多种特征选择和分类方法验证已识别的基因的可靠性.
提供关于黄瓜浸水耐受性的基础分子机制的见解.

主要方法:

使用各种特征选择算法 (不确定性,缓解,SVM,相关性,LASSO) 对三个公开的RNA-seq数据集 (36个样本) 的分析.
差异基因相关性分析 (DGCA) 用于在压力下识别基因相互作用网络的变化.
使用随机森林 (RF) 分类器和夏普利添加式扩展 (SHAP) 值对选定基因的验证.
与Boruta算法进行交叉验证,以确认基因选择的稳定性.

主要成果:

多种特征选择方法确定了与积水压力相关的重要基因.
DGCA 发现了 13 个基因在水浸层下相关性的显著变化.
随机森林模型实现了100%的准确性,LOC101209599,LOC101217277和LOC101216320被确定为具有高度影响力的.
在多个特征选择算法中一致识别了8个基因,包括LASSO,DGCA和Boruta.

结论:

关键基因 (例如,LOC101209599,LOC101217277,LOC101216320) 对黄瓜浸水耐受性至关重要.
这些基因涉及至关重要的途径,包括耐压力,根部发育和信号传递.
已识别的基因和通路为培育具有增强水浸耐药性的黄瓜品种提供了有价值的目标.

关键词:

无生物应激应激是一种非生物应激.属性权重算法属性权重算法黄瓜 - 黄瓜是一种基因表达基因表达基因表达

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