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    Genomic dissection and expression analysis of stress-responsive genes in C4 panicoid models, Setaria italica and Setaria viridis
    (Elsevier B.V., 2020) Muthamilarasan, Mehanathan; Singh, Roshan Kumar; Suresh, Bonthala Venkata; Rana, Sumi; Dulani, Priya; Prasad, Manoj
    The study reports the identification and expression profiling of five major classes of C4 pathway-specific genes, namely, carbonic anhydrase (CaH), phosphoenolpyruvate carboxylase (PEPC), pyruvate orthophosphate dikinase (PPDK), NADP-dependent malate dehydrogenase (MDH) and NADP-dependent malic enzyme (NADP-ME), in the model species, Setaria italica and Setaria viridis. A total of 42 and 41 genes were identified in S. italica and S. viridis, respectively. Further analysis revealed that segmental and tandem duplications have contributed to the expansion of these gene families. RNA-Seq derived expression profiles of the gene family members showed their differential expression pattern in tissues and dehydration stress. Comparative genome mapping and Ks dating provided insights into their duplication and divergence in the course of evolution. Expression profiling of candidate genes in contrasting S. italica cultivars subjected to abiotic stresses and hormone treatments showed distinct stress-specific upregulation of SiαCaH1, SiβCaH5, SiPEPC2, SiPPDK2, SiMDH8, and SiNADP-ME5 in the tolerant cultivar. Overexpression of SiNADP-ME5 in heterologous yeast system enabled the transgenic cells to survive and grow in dehydration stress conditions, which highlights the putative role of SiNADP-ME5 in conferring tolerance to dehydration stress. Altogether, the study highlights key genes that could be potential candidates for elucidating their functional roles in abiotic stress response.
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    Study on aquaporins of Setaria italica suggests the involvement of SiPIP3;1 and SiSIP1;1 in abiotic stress response
    (Springer Nature, 2019) Singh, Roshan Kumar; Shweta, Shweta; Muthamilarasan, Mehanathan; Rani, Rekha; Prasad, Manoj
    Aquaporins are versatile proteins involved in several biological as well as molecular functions, and they have been extensively studied in various plant systems. Increasing evidences indicate their role in biotic and abiotic stresses, and therefore, studying these proteins in a naturally stress-tolerant crop would provide further insights into the roles of this important protein family. Given this, the present study was performed in foxtail millet (Setaria italica), a model plant for studying biofuel, stress tolerance, and C4 photosynthetic traits. The study identified 12 plasma membrane intrinsic proteins (PIPs), 11 tonoplast intrinsic proteins (TIPs), 13 NOD26-like intrinsic proteins (NIPs), and 3 small basic intrinsic proteins (SIPs) in foxtail millet. The identified proteins and their corresponding genes were characterized using in silico approaches such as chromosomal localization, analysis of gene and protein properties, phylogenetic analysis, promoter analysis, and RNA-seq-derived expression profiling. The candidate genes identified through these analyses were studied for their expression in response to abiotic stresses (dehydration, salinity, and heat) as well as hormone treatments (abscisic acid, methyl jasmonate, and salicylic acid) in two contrasting cultivars of foxtail millet. The study showed that SiPIP3;1 and SiSIP1;1 were differentially expressed in both the cultivars in response to stress and hormone treatments. Overexpression of these genes in a heterologous yeast system also demonstrated that the transgenic cells were able to tolerate dehydration as well as salt stress which suggests the involvement of these proteins in the tolerance mechanism. Overall, the present study provides insights into structure and organization of the aquaporin gene family in foxtail millet and highlights the potential candidate genes for further functional characterizations.
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    Genetic determinants of drought stress tolerance in Setaria
    (Springer, 2017) Muthamilarasan, Mehanathan; Prasad, Manoj
    Cultivated foxtail millet (Setaria italica) and its wild progenitor (S. viridis) have collectively been considered as tractable model species for studying C4 photosynthesis, stress biology, and biofuel traits. Being cultivated in arid and semiarid tropics of the world, these species are well adapted to harsh environments such as drought, heat, and salinity. This adaptation or acclimation potential of Setaria spp. has drawn research interest, and attempts have been made to dissect the molecular mechanisms of stress tolerance. Compared to other stresses, drought response has been studied extensively in S. italica and many drought-responsive genes encoding for transcription factors, signaling molecules, and enzymes have been identified and characterized. Several genome-wide studies have reported on identification of stress-responsive gene family members, and speculated on the potential for expansion and neofunctionalization of paralogs in these gene families. In this context, this chapter discusses the key genetic determinants identified for stress tolerance in S. italica and demonstrates their use in improving drought tolerance. In addition, strategies for identification of genes underlying stress tolerance are also described. Little effort has so far been made towards understanding the stress-tolerance characteristics of Setaria as compared to studies reported in other crops. Comprehensive functional studies along with the use of integrated -omics approaches are required to elucidate the genetics and genomics of stress tolerance in Setaria, as it is important to develop climate change resilient crops to meet the growing demand for food and feed.
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    Identification, characterization and expression profiling of Dicer-like, Argonaute and RNA-dependent RNA polymerase gene families in foxtail millet
    (Springer, 2015) Yadav, Chandra Bhan; Muthamilarasan, Mehanathan; Pandey, Garima; Prasad, Manoj
    Post-transcriptional control of gene expression is achieved through RNA interference where the activities of Dicer-like (DCL), Argonautes (AGO) and RNA-dependent RNA polymerases (RDRs) are significant. Hence, considering the importance of DCL, AGO and RDRs, a comprehensive genome-wide analysis was performed in foxtail millet. The study identified 8 DCL, 19 AGO and 11 RDR genes. Phylogenetic and domain analysis provided interesting information on the evolutionary and structural aspects of these proteins. The orthologs of Setaria italica DCL (SiDCL), AGO (SiAGO) and RDRs (SiRDRs) were identified in sorghum, maize and rice, and the evolutionary relationships among the orthologous gene pairs were investigated. Promoter analysis of SiDCL, SiAGO and SiRDR genes revealed the presence of unique and common cis-acting elements at the upstream of respective gene sequences, which serves as binding sites for several developmental and stress-related transcription factors. In silico expression profiling using RNA-sequence data showed tissue-specific expression patterns of these genes in foxtail millet. Candidate genes representing each sub-family were chosen for expression analysis through quantitative real-time PCR (qRT-PCR) under salinity, dehydration and hormonal treatments. It revealed the differential expression pattern of candidate genes at different time points of stresses. This is the first report on genome-wide analysis of SiDCL, SiAGO and SiRDR gene families in foxtail millet, which provides basic genomic information and insights into the putative roles of these genes in abiotic stresses. The present study will serve as a base for further functional characterization of these gene families in foxtail millet and related grass species.
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    C2H2 type of zinc finger transcription factors in foxtail millet define response to abiotic stresses
    (Springer, 2014) Muthamilarasan, Mehanathan; Bonthala, Venkata Suresh; Mishra, Awdhesh Kumar; Khandelwal, Rohit; Khan, Yusuf; Roy, Riti; Prasad, Manoj
    C2H2 type of zinc finger transcription factors (TFs) play crucial roles in plant stress response and hormone signal transduction. Hence considering its importance, genome-wide investigation and characterization of C2H2 zinc finger proteins were performed in Arabidopsis, rice and poplar but no such study was conducted in foxtail millet which is a C4 Panicoid model crop well known for its abiotic stress tolerance. The present study identified 124 C2H2-type zinc finger TFs in foxtail millet (SiC2H2) and physically mapped them onto the genome. The gene duplication analysis revealed that SiC2H2s primarily expanded in the genome through tandem duplication. The phylogenetic tree classified these TFs into five groups (I-V). Further, miRNAs targeting SiC2H2 transcripts in foxtail millet were identified. Heat map demonstrated differential and tissue-specific expression patterns of these SiC2H2 genes. Comparative physical mapping between foxtail millet SiC2H2 genes and its orthologs of sorghum, maize and rice revealed the evolutionary relationships of C2H2 type of zinc finger TFs. The duplication and divergence data provided novel insight into the evolutionary aspects of these TFs in foxtail millet and related grass species. Expression profiling of candidate SiC2H2 genes in response to salinity, dehydration and cold stress showed differential expression pattern of these genes at different time points of stresses.
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    Comprehensive genome-wide identification and expression profiling of foxtail millet [Setaria italica (L.)] miRNAs in response to abiotic stress and development of miRNA database
    (Springer, 2014) Khan, Yusuf; Yadav, Amita; Bonthala, Venkata Suresh; Muthamilarasan, Mehanathan; Yadav, Chandra Bhan; Prasad, Manoj
    MicroRNA (miRNA)-guided post-transcriptional regulation is an important mechanism of gene regulation during multiple biological processes including response to abiotic stresses. Foxtail millet is a model crop, which is genetically closely related to several bioenergy grasses and also known for its potential abiotic stress tolerance. Hence deciphering the role of miRNAs in regulating stress-responsive mechanism would enable imparting durable stress tolerance in both millets and bioenergy grasses. Considering this, a comprehensive genome-wide in silico analysis was performed in foxtail millet which identified 355 mature miRNAs along with their secondary structure as well as corresponding targets. Predicted miRNA targets were found to encode various DNA binding proteins, transcription factors or important functional enzymes, which could be the crucial regulators in plant abiotic stress responses. All the 355 miRNAs were physically mapped onto the foxtail millet genome and in silico tissue-specific expression for these miRNAs were studied. Comparative mapping of the 355 miRNAs between foxtail millet and other related grass species would assist miRNA studies in these genetically closely-related plants. Expression profiling was performed for eight candidate miRNAs under diverse abiotic stresses in foxtail millet, which unravelled the putative involvement of these miRNAs in stress tolerance. With an aim of providing the generated miRNA marker information to the global scientific community, a foxtail millet MiRNA Database (FmMiRNADb: http://​59.​163.​192.​91/​FmMiRNADb/​index.​html) has also been constructed. Overall, the present study provides novel insights onto the role of miRNAs in abiotic stress tolerance and would promisingly expedite research on post-transcriptional regulation of stress-related genes in millets and bioenergy grasses.
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    Population structure and association mapping of yield contributing agronomic traits in foxtail millet
    (Springer, 2014) Gupta, Sarika; Kumari, Kajal; Muthamilarasan, Mehanathan; Parida, Swarup K.; Prasad, Manoj
    Association analyses accounting for population structure and relative kinship identified eight SSR markers ( p < 0.01) showing significant association ( R (2) = 18 %) with nine agronomic traits in foxtail millet. Association mapping is an efficient tool for identifying genes regulating complex traits. Although association mapping using genomic simple sequence repeat (SSR) markers has been successfully demonstrated in many agronomically important crops, very few reports are available on marker-trait association analysis in foxtail millet. In the present study, 184 foxtail millet accessions from diverse geographical locations were genotyped using 50 SSR markers representing the nine chromosomes of foxtail millet. The genetic diversity within these accessions was examined using a genetic distance-based and a general model-based clustering method. The model-based analysis using 50 SSR markers identified an underlying population structure comprising five sub-populations which corresponded well with distance-based groupings. The phenotyping of plants was carried out in the field for three consecutive years for 20 yield contributing agronomic traits. The linkage disequilibrium analysis considering population structure and relative kinship identified eight SSR markers (p < 0.01) on different chromosomes showing significant association (R (2) = 18 %) with nine agronomic traits. Four of these markers were associated with multiple traits. The integration of genetic and physical map information of eight SSR markers with their functional annotation revealed strong association of two markers encoding for phospholipid acyltransferase and ubiquitin carboxyl-terminal hydrolase located on the same chromosome (5) with flag leaf width and grain yield, respectively. Our findings on association mapping is the first report on Indian foxtail millet germplasm and this could be effectively applied in foxtail millet breeding to further uncover marker-trait associations with a large number of markers.
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    FmTFDb: a foxtail millet transcription factors database for expediting functional genomics in millets
    (Springer, 2014) Bonthala, Venkata Suresh; Muthamilarasan, Mehanathan; Roy, Riti; Prasad, Manoj
    Foxtail millet has recently been regarded as a model crop for studying the systems biology of millets and bioenergy grass species. For expediting the functional genomic studies in this model crop as well as in the related millets and bioenergy grasses, we have developed a comprehensive transcription factor database. Our foxtail millet transcription factors database (FmTFDb: http://59.163.192.91/FmTFDb/index.html ) encompasses 2,297 putative TFs in 55 families along with its sequence features, chromosomal locations, tissue-specific gene expression data, gene ontology (GO) assignment, and phylogeny. FmTFDb is intended to provide the users an unrestricted public access in retrieving and visualizing the individual members of a TF family through a set of query interfaces and analysis tools, including the BLAST search, annotation query interfaces, and tools to identify enriched GO terms and to visualize physical maps. This FmTFDb will serve as a promising central resource for researchers as well as breeders who are dedicated towards crop improvement of millets and bioenergy grasses.