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Item Histone deacetylase 9 interacts with SiHAT3.1 and SiHDA19 to repress dehydration responses through H3K9 deacetylation in foxtail millet(Oxford University Press, 2024) Kumar, Verandra; Singh, Babita; Singh, Roshan Kumar; Sharma, Namisha; Muthamilarasan, Mehanathan; Sawant, Samir V; Prasad, ManojClimate change inflicts several stresses on plants, of which dehydration stress severely affects growth and productivity. C4 plants possess better adaptability to dehydration stress; however, the role of epigenetic modifications underlying this trait is unclear. Particularly, the molecular links between histone modifiers and their regulation remain elusive. In this study, genome-wide H3K9 acetylation (H3K9ac) enrichment using ChIP-seq was performed in two foxtail millet cultivars contrastingly differing in dehydration tolerance (IC403579; cv. IC4 – tolerant, and IC480117; cv. IC41 – sensitive). It revealed that a histone deacetylase, SiHDA9, was significantly up-regulated in the sensitive cultivar. Further characterization indicated that SiHDA9 interacts with SiHAT3.1 and SiHDA19 to form a repressor complex. SiHDA9 might be recruited through the SiHAT3.1 recognition sequence onto the upstream of dehydration-responsive genes to decrease H3K9 acetylation levels. The silencing of SiHDA9 resulted in the up-regulation of crucial genes, namely, SiRAB18, SiRAP2.4, SiP5CS2, SiRD22, SiPIP1;4 and SiLHCB2.3, which imparted dehydration tolerance in the sensitive cultivar (IC41). Overall, the study provides mechanistic insights into SiHDA9-mediated regulation of dehydration stress response in foxtail millet.Item Millets for next generation climate-smart agriculture(Frontiers Media S.A., 2017) Bandyopadhyay, Tirthankar; Muthamilarasan, Mehanathan; Prasad, ManojPanicoids (subfamily: panicoideae) are a group of C4 grasses, which include agronomically important crops such as sorghum and maize, bioenergy feedstocks including sugarcane and miscanthus, nutri-cereals such as millets, and biofuel crops including switchgrass, napier grass and guinea grass. Among these, millets are known for their climate-resilient features including adaptation to a wide range of ecological conditions, less irrigational requirements, better growth and productivity in low nutrient input conditions, less reliance on synthetic fertilizers, and minimum vulnerability to environmental stresses (Kole et al., 2015). Also, millets are nutritionally superior to other major cereals as they are rich in dietary fibers, resistant starches, vitamins, essential amino acids, storage proteins and other bioactive compounds (Amadou et al., 2013). These attributes have made millets a crop of choice for cultivation in arid and semi-arid regions of the world; however, the less attempt has been made to study the climate-resilient features of millets compared to other major cereals. Among millets, foxtail millet (Setaria italica) and its wild progenitor, green foxtail (S. viridis) are extensively studied since they are considered as models for studying the traits related to C4 photosynthesis, stress biology, and bioenergy characteristics (Muthamilarasan and Prasad, 2015). The availability of genome sequence information of these two species (Bennetzen et al., 2012; Zhang et al., 2012) has unlocked the wealth of information pertaining to stress tolerance and biofuel characteristics. It has also expedited the development of large-scale genomic resources for crop improvement. On the other hand, studies on other millets are still in their infancy. The challenge to feed the ever-growing population with a healthy balanced diet and the threats faced by agricultural crops due to changing climate highlight the immediate requirement to exploit the beneficial attributes of millets. This could be utilized for the improvement of millets per se as well as other related grass species. The extensive gene-level synteny shared between the grass genomes would facilitate the transfer and introgression of useful genes, alleles and quantitative trait loci (QTL) of agronomic importance identified in millets to other major cereals. In the above context, this article advocates for initiating extensive research on millets to dissect their agronomic, nutritional as well as stress tolerance traits and develop strategies to transfer the useful traits to cultivated major cereals such as rice, wheat, maize, and sorghum.Item Comprehensive analysis of SET domain gene family in foxtail millet identifies the putative role of SiSET14 in abiotic stress tolerance(Nature Publishing Group, 2016) Yadav, Chandra Bhan; Muthamilarasan, Mehanathan; Dangi, Anand; Shweta, Shweta; Prasad, ManojSET domain-containing genes catalyse histone lysine methylation, which alters chromatin structure and regulates the transcription of genes that are involved in various developmental and physiological processes. The present study identified 53 SET domain-containing genes in C4 panicoid model, foxtail millet (Setaria italica) and the genes were physically mapped onto nine chromosomes. Phylogenetic and structural analyses classified SiSET proteins into five classes (I–V). RNA-seq derived expression profiling showed that SiSET genes were differentially expressed in four tissues namely, leaf, root, stem and spica. Expression analyses using qRT-PCR was performed for 21 SiSET genes under different abiotic stress and hormonal treatments, which showed differential expression of these genes during late phase of stress and hormonal treatments. Significant upregulation of SiSET gene was observed during cold stress, which has been confirmed by over-expressing a candidate gene, SiSET14 in yeast. Interestingly, hypermethylation was observed in gene body of highly differentially expressed genes, whereas methylation event was completely absent in their transcription start sites. This suggested the occurrence of demethylation events during various abiotic stresses, which enhance the gene expression. Altogether, the present study would serve as a base for further functional characterization of SiSET genes towards understanding their molecular roles in conferring stress tolerance.Item Genome-wide analysis of heat shock proteins in C4 model, foxtail millet identifies potential candidates for crop improvement under abiotic stress(Nature Publishing Group, 2016) Singh, Roshan Kumar; Jaishankar, Jananee; Muthamilarasan, Mehanathan; Shweta, Shweta; Dangi, Anand; Prasad, ManojHeat shock proteins (HSPs) perform significant roles in conferring abiotic stress tolerance to crop plants. In view of this, HSPs and their encoding genes were extensively characterized in several plant species; however, understanding their structure, organization, evolution and expression profiling in a naturally stress tolerant crop is necessary to delineate their precise roles in stress-responsive molecular machinery. In this context, the present study has been performed in C4 panicoid model, foxtail millet, which resulted in identification of 20, 9, 27, 20 and 37 genes belonging to SiHSP100, SiHSP90, SiHSP70, SiHSP60 and SisHSP families, respectively. Comprehensive in silico characterization of these genes followed by their expression profiling in response to dehydration, heat, salinity and cold stresses in foxtail millet cultivars contrastingly differing in stress tolerance revealed significant upregulation of several genes in tolerant cultivar. SisHSP-27 showed substantial higher expression in response to heat stress in tolerant cultivar, and its over-expression in yeast system conferred tolerance to several abiotic stresses. Methylation analysis of SiHSP genes suggested that, in susceptible cultivar, higher levels of methylation might be the reason for reduced expression of these genes during stress. Altogether, the study provides novel clues on the role of HSPs in conferring stress tolerance.