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Author: search.filters.author.Khan, YusufSubject: search.filters.subject.Foxtail millet (Setaria italica)

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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.