title: Salinity induced differential methylation patterns in contrasting cultivars of foxtail millet (Setaria italica L.).
abstract: Genome-wide methylation analysis of foxtail millet cultivars contrastingly differing in salinity tolerance revealed DNA demethylation events occurring in tolerant cultivar under salinity stress, eventually modulating the expression of stress-responsive genes. Reduced productivity and significant yield loss are the adverse effects of environmental conditions on physiological and biochemical pathways in crop plants. In this context, understanding the epigenetic machinery underlying the tolerance traits in a naturally stress tolerant crop is imperative. Foxtail millet (Setaria italica) is known for its better tolerance to abiotic stresses compared to other cereal crops. In the present study, methylation-sensitive amplified polymorphism (MSAP) technique was used to quantify the salt-induced methylation changes in two foxtail millet cultivars contrastingly differing in their tolerance levels to salt stress. The study highlighted that the DNA methylation level was significantly reduced in tolerant cultivar compared to sensitive cultivar. A total of 86 polymorphic MSAP fragments were identified, sequenced and functionally annotated. These fragments showed sequence similarity to several genes including ABC transporter, WRKY transcription factor, serine threonine-protein phosphatase, disease resistance, oxidoreductases, cell wall-related enzymes and retrotransposon and transposase like proteins, suggesting salt stress-induced methylation in these genes. Among these, four genes were chosen for expression profiling which showed differential expression pattern between both cultivars of foxtail millet. Altogether, the study infers that salinity stress induces genome-wide DNA demethylation, which in turn, modulates expression of corresponding genes.
authors.affiliation: National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110 067, India.
authors.forename: Garima
authors.initials: G
authors.lastname: Pandey
authors.affiliation: National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110 067, India.
authors.forename: Chandra Bhan
authors.initials: CB
authors.lastname: Yadav
authors.affiliation: National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110 067, India.
authors.forename: Pranav Pankaj
authors.initials: PP
authors.lastname: Sahu
authors.affiliation: National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110 067, India.
authors.forename: Mehanathan
authors.initials: M
authors.lastname: Muthamilarasan
authors.affiliation: National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110 067, India. manoj_prasad@nipgr.ac.in.
authors.forename: Manoj
authors.identifier: http://orcid.org/0000-0003-0691-0163
authors.initials: M
authors.lastname: Prasad
mesh_terms: D019175:DNA Methylation / Q000187:drug effects / Q000235:genetics; D018506:Gene Expression Regulation, Plant / Q000187:drug effects / Q000235:genetics; D008745:Methylation / Q000187:drug effects; D010940:Plant Proteins / Q000235:genetics*; D054712:Salinity; D055049:Salt Tolerance; D032983:Setaria Plant / Q000187:drug effects* / Q000235:genetics*; D012965:Sodium Chloride / Q000494:pharmacology
chemical_list: D010940:Plant Proteins; D012965:Sodium Chloride
keywords: Abiotic stress; Epigenetics; Foxtail millet; Methylation; Methylation-sensitive amplified polymorphism (MSAP); Salt stress