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.

Optimization of Phenotyping Assays for the Model Monocot Setaria viridis

“…Several exogenous factors affect seed germination, and germination in the presence of different hormones or stressors has been widely used for screening of mutant seeds, identification of abiotic stress sensitivity of plants, or to study the effect of plant hormones such as ABA, which is well-known to inhibit seed germination ( Leon-Kloosterziel et al, 1996 ; Garciarrubio et al, 1997 ; Finkelstein et al, 2002 , 2008 ; Brocard-Gifford et al, 2003 ). Similarly, the effect of different abiotic stresses have been studied on different aspects of Setaria growth and development ( Dekker and Hargrove, 2002 ; Doust and Kellogg, 2006 ; Yue et al, 2014 ; Amini et al, 2015b ; Muthamilarasan et al, 2015 ; Feng et al, 2016 ; Li et al, 2016 ; Pan et al, 2016 ; Saha et al, 2016 ; Singh et al, 2016 ; Feldman et al, 2017 ; Pandey et al, 2017 ). We evaluated the effect of different ABA concentrations ranging from 0.5 to 10 μM on Setaria seed germination.…”

“…Salinity stress negatively affects seed germination. NaCl is commonly used as an agent to study the effect of salt stress on seed germination, growth and other physiological processes ( Saleki et al, 1993 ; Yue et al, 2014 ; Duan et al, 2015 ; Muthamilarasan et al, 2015 ; Liu et al, 2017 ; Pandey et al, 2017 ). To assess the effect of salinity on Setaria seed germination, seeds were plated on media containing 50, 100, 150, and 200 mM NaCl and compared with control media with no added NaCl.…”

“…Together with its close relative S. italica , with which it is interfertile, S. viridis also serves as a good model system to study crop domestication ( Li and Brutnell, 2011 ). Furthermore, extensive genomics and transcriptomics resources are currently available and are being constantly developed for this species ( Xu J. et al, 2013 ; Huang et al, 2016 ; Singh et al, 2016 ; Pandey et al, 2017 ). A number of studies, many already harnessing these resources, have recently been published corroborating its considerable potential as a model system for gene discovery, physiological and developmental analyses, stress responses and nutrient use efficiency ( Yue et al, 2014 ; Li et al, 2016 ; Mauro-Herrera and Doust, 2016 ; Pan et al, 2016 ; Bandyopadhyay et al, 2017 ; Huang et al, 2017 ).…”

Metabolomics, biomass and lignocellulosic total sugars analysis in foxtail millet (Setaria italica) inoculated with different combinations of plant growth promoting bacteria and mycorrhiza

“…Foxtail millet is an annual grass that is widely used for both food and livestock feed and grown in arid and semi-arid regions of the world (Pandey et al 2017). Being a close relative of an important biofuel crop switchgrass, it is also a potential biofuel source.…”

Systems biology of seeds: deciphering the molecular mechanisms of seed storage, dormancy and onset of germination

“…Results of comparative proteomics studies for instance showed that the accumulation of vicilin during the pre-treatment of two defense elicitors β-amino butyric acid and γ-amino butyric acid in citrus seed germination under salt stress conditions reversed salt stress impediment and improved germination vigor (Ziogas et al 2017). Two additional studies unraveled the salt tolerance mechanisms through epigenetics (Pandey et al 2016) and proteomics (Parveda et al 2017).…”