Transcriptome analyses revealed differential gene expression patterns in contrasting rice landraces as a response to acidic or proton toxicity stress

Acidic soil is harmful for plants and limits its growth. Four different rice landraces of Jharkhand, India, i.e., Jhilli Dhan, Gora Dhan, Desi Lalat Dhan and Khijur Jhopa Dhan were screened physiologically to identify low pH (acid) -sensitive and -tolerant landraces. The contrasting pairs were taken for RNA sequencing and further the data was analysed to elucidate the differential gene expression in rice leaves under different acidic stress conditions (pH 6.5 and pH 4.5). Based on the screening, Jhilli Dhan was identified as the acid-sensitive and Khijur Jhopa Dhan as acid-tolerant variety. Total 149,017,664 raw paired-end reads were generated from four rice samples (two from each variety) with percentage annotation of 99.89 % with the reference genome from RNA sequencing. Total 3617 differentially expressed genes were identified as significantly expressed genes in both the rice landraces. Gene Ontology analysis indicated the enrichment of genes associated to a variety of stimulus and responses to acidic stress. Kyoto Encyclopedia of Genes and Genomes based pathway analysis revealed that studied genes were related primarily to phenylpropanoid biosynthesis and flavonoid biosynthesis. Total 58 transcription factor families were differentially expressed that includes AP2-EREBP, bHLH, NAC, MYB, FAR1, and WRKY. Furthermore, 15 significantly expressed genes were validated through qRT-PCR to confirm the expression of these genes under acidic stress. Interestingly, OsCDT3 (LOC_Os01g08300), metal cation transporter (LOC_Os03g46454), cysteine rich receptor- like protein kinase 10 precursor (LOC_Os01g38910), calcium transporting ATPase (LOC_Os03g42020), UDP-glucoronosyl and UDP-glucosyl transferase (LOC_Os02g14540), OsASR5 (LOC_Os11g06720) and C2H2 zinc finger family (LOC_Os01g39110) genes were up-regulated by 2.5, 5.2, 3.5, 3.7, 4.5, 2.5 and 4.7 fold, respectively. These genes will prove to be beneficial in developing low-pH (acidic) stress tolerant rice varieties.