Soil acidity limits plant growth and has an adverse effect on crop production. As of now, there is very little information about acidic responsive genes in rice. This study aims to identify such genes, the results of which can be further applied to develop acidity tolerant cultivars of rice. Initially, publicly available microarray datasets of A. thaliana consisting of 22,810 genes were utilized to identify differentially expressed genes (DEGs) under varied pH conditions at different time durations. A total of 983 DEGs were found as pH responsive genes responding to acidic stress conditions (at pH 4.5 and 6.0) at different time durations (after 1 and 8 h). Thereafter, weighted gene co-expression network analysis (WGCNA) algorithm was applied to construct gene co-expression networks in A. thaliana. Gene co-expression network analysis classified the DEGs into six different modules. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were carried out to identify key biological processes and metabolic pathways related to acidity response. Hub genes were identified on the basis of highest intra modular connectivity in the modules of interest. These genes are genes with highest connectivity in the modules of interest. The novel candidate (hub) genes of A. thaliana were used to identify homolog genes in rice. These rice homolog genes were used to check their expression in traditional rice varieties of Jharkhand under acidic stress (at pH 6.5, pH 5.5 and pH 4.5) using Real Time-PCR. Subsequently, these rice homolog genes were analysed using STRING-database and MapMan 3.5.1R2 tool. This series of identified homolog genes in rice will prove to be beneficial in developing acidity tolerant varieties of rice.

土壤酸度限制植物生长并对作物生产产生不利影响。到目前为止，关于水稻中酸性响应基因的信息很少。本研究旨在鉴定这些基因，其结果可进一步应用于开发耐酸水稻品种。最初，利用由 22,810 个基因组成的拟南芥的公开微阵列数据集来鉴定不同 pH 条件下不同时间段的差异表达基因 (DEG)。总共发现 983 个 DEG 作为在不同持续时间（1 小时和 8 小时后）响应酸性胁迫条件（pH 4.5 和 6.0）的 pH 响应基因。此后，应用加权基因共表达网络分析（WGCNA）算法构建拟南芥基因共表达网络. 基因共表达网络分析将 DEG 分为六个不同的模块。进行了基因本体论 (GO) 和京都基因和基因组百科全书 (KEGG) 分析，以确定与酸度反应相关的关键生物过程和代谢途径。集线器基因是基于感兴趣模块中最高的模块内连接性来确定的。这些基因是在感兴趣的模块中具有最高连通性的基因。拟南芥的新型候选（枢纽）基因用于鉴定水稻中的同源基因。这些水稻同源基因用于使用实时 PCR 检测它们在酸性胁迫（pH 6.5、pH 5.5 和 pH 4.5）下的贾坎德邦传统水稻品种中的表达。随后，这些水稻同源基因使用 STRING 数据库和 MapMan 3.5.1R2 工具进行分析。这一系列在水稻中鉴定的同源基因将证明有利于培育耐酸水稻品种。