基于多平台基因表达数据的水稻干旱和盐胁迫相关基因预测  

Prediction of drought and salt stress-related genes in rice based on multi-platform gene expression data

作　　者：刘亚文 张红燕[1,2] 曹丹[2] 李兰芝[2] LIU Ya-Wen;ZHANG Hong-Yan;CAO Dan;LI Lan-Zhi(College of Information and Intelligence,Hunan Agricultural University,Changsha 410128,Hunan,China;Hunan Engineering and Technology Research Centre for Agricultural Big Data Analysis and Decision-making,Hunan Agricultural University,Changsha 410128,Hunan,China)

机构地区：[1]湖南农业大学信息与智能科学技术学院,湖南长沙410128 [2]湖南农业大学/湖南省农业大数据分析与决策工程技术研究中心,湖南长沙410128

出　　处：《作物学报》2021年第12期2423-2439,共17页Acta Agronomica Sinica

基　　金：湖南省教育厅科学研究重点项目(18A105);长沙市工业科技特派员项目(201845);湖南农业大学“双一流”建设项目(SYL2019075)资助。

摘　　要：基于多平台基因表达数据挖掘水稻胁迫相关基因,可增加关键基因预测的可靠性,获得更具普适意义的结果。本研究从NCBI数据库中收集了与水稻非生物胁迫相关的94份affymetrix基因芯片数据和42份RNA-seq转录组数据。首先对同一类型同一胁迫相关的多个数据集以数据转换法融合,得到干旱胁迫相关的affymetrix数据集D_affy和RNA-seq数据集D_rnaseq,盐胁迫相关的affymetrix数据集S_affy和RNA-seq数据集S_rnaseq;接着对4个数据集分别基于Pearson线性相关系数的经典WGCNA法和基于MIC非线性相关系数的改进WGCNA法进行基因共表达网络分析,共获取胁迫相关的8个Hub基因集;进一步,对同一胁迫相关的Hub基因进行整合分析,得到最终的水稻干旱胁迫相关Hub基因1936个、盐胁迫相关的Hub基因1504个。最后,从预测性能、富集分析、文献报道、STRING在线互作分析和Cytoscape可视化分析等多角度解析Hub基因的生物学意义。结果显示:Hub基因整体预测性能较优,且大多富集到了与干旱/盐胁迫相关的通路上,其中有文献已报道的干旱胁迫响应基因31个和盐胁迫响应基因22个。此外,通过对Hub基因的互作分析,预测得到11个干旱胁迫候选基因和5个盐胁迫候选基因。本研究为“高维度、小样本”的农作物基因测序数据的有效分析提供了新思路,实验结果为抗逆水稻品种研究提供了参考。Mining stress-related genes based on multi-platform gene expression data in rice can increase the reliability of key genes prediction and obtain more universally meaningful results.In this study,94 affymetrix microarray data and 42 RNA-seq transcriptome data related to rice abiotic stress were collected from NCBI databases.First,multiple datasets related to the same stress on the same type were fused by data conversion method to obtain the affymetrix data set D_affy and RNA-seq data set D_rnaseq related to drought stress,and the affymetrix data set S_affy and the RNA-seq data set S_rnaseq related to salt stress.Then,the four datasets were analyzed by the classical WGCNA method based on Pearson's linear correlation coefficient and the improved WGCNA method based on the MIC nonlinear correlation coefficient respectively,and the eight Hub gene sets related to stress were obtained.Further,the integration analysis of stress-related Hub genes yielded the final 1936 drought stress-related Hub genes and 1504 salt stress-related Hub genes.Finally,the biological significance of Hub gene was analyzed from multiple per-spectives,including prediction performance,enrichment analysis,literature report,STRING online interaction analysis,and Cytoscape visualization analysis.The results revealed that the overall prediction performance of Hub genes was better,and most of them were enriched in the pathways related to drought/salt stress.Among them,there were 31 drought stress response genes and 22 salt stress response genes reported in the literatures.In addition,11 drought stress candidate genes and 5 salt stress candidate genes were predicted using the interaction analysis of Hub genes.In conclusion,This study provides a new idea for the effective analysis of“high-dimensional,small-sample”crop gene sequencing data,and the experimental results provide a reference for the study of stress-resistant rice varieties.

关 键 词：水稻 多平台 干旱胁迫 盐胁迫 WGCNA-MIC 

分 类 号：S511[农业科学—作物学]