De novo RNA-Seq analysis in sensitive rice cultivar and comparative transcript profiling in contrasting genotypes reveal genetic biomarkers for fluoride-stress response. (December 2020)

• Record Type: Journal Article
• Authors: Banerjee, Aditya; Singh, Ankur; Roychoudhury, Aryadeep
• Is Part Of: Environmental pollution. Volume 267(2020)
• Publication Date: 2020-12
• Subjects: RNA-Seq -- de novo assembly -- Fluoride toxicity -- Differentially expressed genes -- IR-64 and Khitish -- Statistical modelling; Pollution -- Periodicals; Pollution -- Environmental aspects -- Periodicals; Environmental Pollution -- Periodicals; Pollution -- Périodiques; Pollution -- Aspect de l'environnement -- Périodiques; Pollution -- Effets physiologiques -- Périodiques; Pollution; Pollution -- Environmental aspects; Periodicals; Electronic journals; 363.73
• DOI: 10.1016/j.envpol.2020.115378
• Languages: English
• ISSNs: 0269-7491

Abstract

Abstract: The fluoride-sensitive indica rice cultivar, IR-64 was subjected to NaF-treatment for 25 days, following which RNA-Seq analysis identified significant up and down regulation of 1, 303 and 93 transcripts respectively. Gene ontology (GO) enrichment analysis classified transcripts into groups related to 'cellular part', 'membrane', 'catalytic activity', 'transporter activity', 'binding', 'metabolic processes' and 'cellular processes'. Analysis of differentially expressed genes (DEGs) revealed fluoride-mediated suppression of abscisic acid (ABA) biosynthesis and signaling. Instead, the gibberellin-dependent pathway and signaling via ABA-independent transcription factors (TFs) was activated. Comparative profiling of selected DEGs in IR-64 and fluoride-tolerant variety, Khitish revealed significant cytoskeletal and nucleosomal remodelling, accompanied with escalated levels of autophagy in stressed IR-64 (unlike that in stressed Khitish). Genes associated with ion, solute and xenobiotic transport were strongly up regulated in stressed IR-64, indicating potential fluoride entry through these channels. On the contrary, genes associated with xenobiotic mobility were suppressed in the tolerant cultivar, which restricted bioaccumulation and translocation of fluoride. Pairwise expression profile analysis between stressed IR-64 and Khitish, supported by extensive statistical modelling predicted that fluoride susceptibility was associated with high expression of genes like amino acid transporter, ABC transporter2, CLCd, MFS monosaccharide transporter, SulfT2.1 and PotT2 while fluoride tolerance with high expression of Sweet11 . Graphical abstract: Image 1 Highlights: Fluoride toxicity extensively altered the transcriptome in susceptible rice variety, IR-64. Fluoride response was mediated in abscisic acid-independent and gibberellic acid-dependent pathway. Cytoskeletal, nucleosomal assembly along with molecular transport was affected. These processes were least affected in the tolerant cultivar Khitish. Genetic biomarkers were identified through statistical modelling.