In silico approach to investigate the potential HKT gene responsive to salt stress in rice

Abstract

AbstractRice is frequently subjected to various environmental stresses, resulting in significant production losses, with drought and salinity are the leading causes of plant damage globally. This study aims to characterize and understand the function of rice high-affinity potassium transporters (HKTs) genes in response to salinity stress. Initially, the genome-wide analysis was undertaken to reveal the evolutionarily conserved function of the OsHKT in higher plants. To investigate the transcription level of OsHKT during the vegetative and reproductive stages, two microarray datasets (GSE19024 and GSE3053) were analyzed, and salt-treated samples were subsequently evaluated using real-time PCR. Differentially expressed genes (DEGs) were identified from microarray datasets (GSE41650 and GSE14403), followed by constructing a DEG network that highlighted interaction partners of the OsHKTs. Genome mining of rice revealed 9 HKT genes, namely OsHKT1;1–1;5 and OsHKT2;1–2;4. These genes exhibited a well-conserved domain structure called TrkH. Comprehensive phylogenetic and motif analyses clustered genes encoding HKT proteins into seven monophyletic groups, and the motifs were relatively conserved. Ka/Ks ratios indicated a high degree of purifying selection during evolutionary time. Gene ontology findings suggested the involvement of OsHKT in stress response. Besides, several CRE motifs in the promoter regions of OsHKT have demonstrated their potential roles in abiotic stress responses. Furthermore, we analyzed the top 250 significant DEGs from the two datasets (p-value < 0.05; fold two change ≥ 1 or ≤  − 1) to evaluate the relationship among the DEGs and HKTs. Three co-expressed OsHKT genes were discovered to be upregulated in seedlings under salinity treatment, including OsP5CS2, OsHAK1, and OsNHX2, whereas OsP5CS1 and OsHAK27 were downregulated. The transcripts of OsHKT were found to be differentially expressed in a tissue-specific manner. Analysis of microarray datasets validated by real-time PCR shows that OsHKT1;5 had a higher expression level, followed by OsHKT1;1, OsHKT1;3, and OsHKT2;1 after salinity treatment. In addition, several micro-RNA targets in rice HKT genes regulate their expression in response to stress. This study paves the way for future investigation on genes and miRNA-target interaction in plants under environmental stresses, offering potential strategies to enhance stress tolerance in crops via targeted ion transport modification.