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Manoj Prasad - One of the best experts on this subject based on the ideXlab platform.
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Foxtail Millet: An Introduction
Compendium of Plant Genomes, 2017Co-Authors: Roshan Kumar Singh, Mehanathan Muthamilarasan, Manoj PrasadAbstract:Foxtail Millet (Setaria italica L.) is a versatile crop known for being genetically closely related to biofuel grasses, for its C4 photosynthesis, and for its tolerance to abiotic stresses. These attributes have made this crop a model system and, in view of this, the genome of Foxtail Millet has been sequenced. Among Millets, Foxtail Millet is the only crop possessing rich genetic and genomic resources, and globally it is the second most cultivated Millet next to pearl Millet. In the context of its importance in agronomic and research terms, the present chapter summarizes the origin, domestication, phylogeny, and agroeconomic importance of Foxtail Millet.
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Exploiting Genome Sequence Information to Develop Genomic Resources for Foxtail Millet Improvement
Compendium of Plant Genomes, 2017Co-Authors: Mehanathan Muthamilarasan, Manoj PrasadAbstract:Foxtail Millet is an excellent model crop for studying the biology of C4 photosynthesis, abiotic stress tolerance, and biofuel traits. In addition, grains of Foxtail Millet are rich in proteins, micro- and macro-nutrients, and other bioactive compounds. Being an old domesticated crop, Foxtail Millet has contributed to the development of human civilization and is still grown as a staple food, particularly in India and China. India is the largest producer of Millets. However, the breeding technology used for Foxtail Millet is far behind that of major Millets such as pearl Millet and finger Millet, and major cereals such as rice and wheat. Development of genomic resources is the first step toward improving the breeding strategies, which subsequently lead to the development of elite cultivars with higher yield and desirable agronomic traits. Much national and international effort has been invested in this regard to develop genetic and genomic resources and these have produced significant outcomes. In this context, the present chapter enumerates the genetic and genomic resources available for Foxtail Millet improvement. In particular, the chapter discusses the development of novel molecular markers, their application in genomics-assisted breeding, and the construction of integrated databases. In addition, the genes and families identified in Foxtail Millet which have relevance to growth, development, and stress response have also been summarized.
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development of novel microrna based genetic markers in Foxtail Millet for genotyping applications in related grass species
Molecular Breeding, 2014Co-Authors: Chandra Bhan Yadav, Mehanathan Muthamilarasan, Yusuf Khan, Garima Pandey, Manoj PrasadAbstract:DNA markers are important in molecular breeding, and, hence, considering its prominence, a variety of DNA-based molecular markers have been explored and developed for expediting crop improvement programs. microRNA (miRNA)-based molecular marker is a type of functional markers exploited predominantly in animal sciences, but reported in very few plants. Considering the efficacy, stability and transferability potential of the miRNA-based markers, the present study was conducted to develop these markers in the model crop Foxtail Millet. The pre-miRNA sequences of Foxtail Millet and other related grasses including rice, maize, wheat, sorghum and Brachypodium were retrieved and aligned for identifying the conserved regions. One hundred and seventy-six primer pairs were designed for these consensus sequences, and all these 176 miRNA-based markers were mapped onto Foxtail Millet genome. Of the 176 markers, 66 were chosen for further experimentations based on representing the nine chromosomes of Foxtail Millet and presence of highly conserved regions. All the 66 markers showed 100 % amplification in five cultivars of Foxtail Millet. Moreover, all the markers showed a higher level of cross-genera transferability potential with an average of ~67 % in Millets and non-Millet species. This is the first report on the development of novel miRNA-based markers in Foxtail Millet. Promisingly, these markers would serve as novel genotyping tool for various molecular breeding approaches aiming at crop improvement in Millets and non-Millet species.
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c2h2 type of zinc finger transcription factors in Foxtail Millet define response to abiotic stresses
Functional & Integrative Genomics, 2014Co-Authors: Mehanathan Muthamilarasan, Venkata Suresh Bonthala, Awdhesh Kumar Mishra, Rohit Khandelwal, Yusuf Khan, Manoj PrasadAbstract: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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development of 5123 intron length polymorphic markers for large scale genotyping applications in Foxtail Millet
DNA Research, 2014Co-Authors: Mehanathan Muthamilarasan, Garima Pandey, Venkata B Suresh, Kajal Kumari, Swarup K Parida, Manoj PrasadAbstract:Generating genomic resources in terms ofmolecularmarkers is imperative in molecularbreeding forcrop improvement.Thoughdevelopment and application ofmicrosatellite markers inlarge-scalewas reported in the model crop Foxtail Millet, no such large-scale study was conducted for intron-length polymorphic (ILP) markers. Considering this, we developed 5123 ILP markers, of which 4049 were physically mapped onto 9 chromosomesofFoxtailMillet.BLASTanalysisof5123expressedsequencetags(ESTs)suggestedthefunction for ∼71.5% ESTs and grouped them into 5 different functional categories. About 440 selected primer pairs representingtheFoxtailMilletgenomeandthedifferentfunctionalgroupsshowedhigh-levelofcross-genera amplification at an average of ∼85% in eight Millets and five non-Millet species. The efficacy of the ILP markers for distinguishing the Foxtail Millet is demonstrated by observed heterozygosity (0.20) and Nei’s averagegenediversity(0.22).InsilicocomparativemappingofphysicallymappedILPmarkersdemonstrated substantial percentage of sequence-based orthology and syntenic relationship between Foxtail Millet chromosomes and sorghum (∼50%), maize (∼46%), rice (∼21%) and Brachypodium (∼21%) chromosomes. Hence, for the first time, we developed large-scale ILP markers in Foxtail Millet and demonstrated their utility in germplasm characterization, transferability, phylogenetics and comparative mapping studies in Millets and bioenergy grass species.
Xianmin Diao - One of the best experts on this subject based on the ideXlab platform.
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A whole Foxtail Millet diet reduces blood pressure in subjects with mild hypertension
Journal of Cereal Science, 2018Co-Authors: Jing Chen, Xianmin Diao, Chao Wang, Xiaosong Hu, Yumei Zhang, Qun ShenAbstract:Abstract The potential anti-hypertensive effect of Foxtail Millet was investigated. Participants were recruited to a 12 wk open-label and self-controlled trial, considering the appearance and flavor of whole Foxtail Millet products. After screening, 45 subjects with untreated mild hypertension received a daily average of approximately 50 g of whole Foxtail Millet, replacing their partial regular staple food for the clinical intervention, and were included in the analyses. Measurements included blood pressure, renin–angiotensin–aldosterone system, blood lipids, fasting blood glucose, anthropometric indices, body composition and bone density. After 12 wk of whole Foxtail Millet diet intervention, significant reductions in the participants' SBP (4.13 mmHg, P = 0.022) and DBP (3.49 mmHg, P = 0.002) were observed. In addition, the body mass index, body fat percentage, and fat mass significantly decreased (p
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The Glucose-Lowering Effect of Foxtail Millet in Subjects with Impaired Glucose Tolerance: A Self-Controlled Clinical Trial.
Nutrients, 2018Co-Authors: Min Zhang, Xianmin Diao, Yumei Zhang, Jihong Wu, Jinrong Hu, Xiaosong HuAbstract:Foxtail Millet has relatively low starch digestibility and moderate glycemic index compared to other grains. Since there are still no clinical researches regarding its long-term effect on blood glucose, this self-controlled study was conducted to investigate the glucose-lowering effect of Foxtail Millet in free-living subjects with impaired glucose tolerance (IGT). Fifty g/day of Foxtail Millet was provided to enrolled subjects throughout 12 weeks and the related clinical parameters were investigated at week 0, 6 and 12, respectively. After 12 weeks of Foxtail Millet intervention, the mean fasting blood glucose of the subjects decreased from 5.7 ± 0.9 mmol/L to 5.3 ± 0.7 mmol/L (p < 0.001) and the mean 2 h-glucose decreased from 10.2 ± 2.6 mmol/L to 9.4 ± 2.3 mmol/L (p = 0.003). The intake of Foxtail Millet caused a significant increase of serum leptin (p = 0.012), decrease of insulin resistance (p = 0.007), and marginal reduction of inflammation. Furthermore, a sex-dependent difference in glucose-lowering effect of Foxtail Millet was observed in this study. Foxtail Millet could improve the glycemic control in free-living subjects with IGT, suggesting that increasing the consumption of Foxtail Millet might be beneficial to individuals suffering from type 2 diabetes mellitus.
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Foxtail Millet Breeding in China
Genetics and Genomics of Setaria, 2016Co-Authors: Xianmin DiaoAbstract:Although there is a long history of Foxtail Millet cultivation in China, modern Foxtail Millet breeding was only initiated in China in the 1950s and 1960s, with significant progress being made since the 1980s. Most of the research on Foxtail Millet breeding has been conducted in China, where it is an important regional cereal. The main research activities from the 1950s to 1970s were comparisons among landraces and individual selection, followed by cross-based pedigree selection in the 1970s. These comparisons and cross-based pedigree selections contributed greatly to Foxtail Millet improvement in China, including the development of the super cultivars ‘Yugu 1’ and ‘Zhaogu 1’ in the 1980s. Radiation and chemical-induced mutations have also been used in Foxtail Millet breeding to create novel types, such as dwarf lines. Although different types of male sterile lines have been developed over the past 50 years in China, only partial genetic male sterile lines (PAGMS) have been used successfully in hybrid seed production, allowing the use of heterosis to become a reality in recent years. The Foxtail Millet eco-regions, breeding phases, breeding methodology, and main cultivars grown at different times since the 1950s in China are reviewed in this chapter. With the rapid advances in Foxtail Millet genomic sciences, mining and elucidation of quantitative trait loci related to important traits will accelerate Foxtail Millet breeding in the near future.
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Origin and Domestication of Foxtail Millet
Genetics and Genomics of Setaria, 2016Co-Authors: Xianmin DiaoAbstract:Among the more than 100 species in Setaria, S. macrostachya, S. pumila, and Foxtail Millet (S. italica) cereals were domesticated by human beings. However, only Foxtail Millet became a worldwide crop, contributing greatly to the development of Chinese civilization and remaining as a staple cereal in arid and semi-arid regions. Green Foxtail is the ancestor of cultivated Foxtail Millet and both can be regarded as the same species. Archeological evidence indicates that the domestication of Foxtail Millet from green Foxtail probably began around 16,000 YBP, was a recognized crop around 9000–10,000 YBP, and became popular in Northern China at about 5000–6000 YBP, then spread to other parts of the world. Although there has been some controversies over whether the domestication of Foxtail Millet has occurred more than once, recent molecular data and archeological evidence suggest a single domestication event.
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Foxtail Millet Germplasm and Inheritance of Morphological Characteristics
Genetics and Genomics of Setaria, 2016Co-Authors: Xianmin DiaoAbstract:In China, the systematic collection of Foxtail Millet germplasm from the 1950s to the 1980s resulted in the compilation of 27,059 accessions in the Chinese Gene Bank. There are approximately 15,000 additional Foxtail Millet accessions maintained in other gene banks in India, Japan, Korea, the United States of America, Russia, and in other countries. Evaluations of the Chinese and Indian accessions indicate that Foxtail Millet is morphologically and genetically highly diverse, especially in China. There are currently only two Foxtail Millet core collections, in China and India. Large-scale screenings of trait-specific lines have been conducted mainly in China, and have identified some special landraces, including those that are resistant to drought. There are many publications describing the inheritance of Foxtail Millet morphological characteristics in China, with the important ones being reviewed in this chapter. Dominant qualitative traits, including seedling, leaf sheath, and anther color, have been used as markers to identify hybrids. The estimated heritabilities of quantitative characteristics, such as plant height, panicle length, and heading date, have been useful for Foxtail Millet breeding programs. Additionally, the recent detection of significant quantitative trait loci has helped to characterize the underlying genetic mechanisms regulating specific traits. Cytological studies of Foxtail Millet are summarized in this chapter, especially those involving the trisomic Yugu 1 cultivar.
Jingjuan Yu - One of the best experts on this subject based on the ideXlab platform.
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SiLEA14, a novel atypical LEA protein, confers abiotic stress resistance in Foxtail Millet
BMC Plant Biology, 2014Co-Authors: Meizhen Wang, Yanlin Pan, Xiyuan Jiang, Dengyun Zhu, Ping Li, Qian Zhao, Cong Li, Jingjuan YuAbstract:BackgroundLate embryogenesis abundant (LEA) proteins are involved in protecting higher plants from damage caused by environmental stresses. Foxtail Millet ( Setaria italica ) is an important cereal crop for food and feed in semi-arid areas. However, the molecular mechanisms underlying tolerance to these conditions are not well defined.ResultsHere, we characterized a novel atypical LEA gene named SiLEA14 from Foxtail Millet. It contains two exons separated by one intron. SiLEA14 was expressed in roots, stems, leaves, inflorescences and seeds at different levels under normal growth conditions. In addition, SiLEA14 was dramatically induced by osmotic stress, NaCl and exogenous abscisic acid. The SiLEA14 protein was localized in the nucleus and the cytoplasm. Overexpression of SiLEA14 improved Escherichia coli growth performance compared with the control under salt stress. To further assess the function of SiLEA14 in plants, transgenic Arabidopsis and Foxtail Millet plants that overexpressed SiLEA14 were obtained. The transgenic Arabidopsis seedlings showed higher tolerance to salt and osmotic stress than the wild type (WT). Similarly, the transgenic Foxtail Millet showed improved growth under salt and drought stresses compared with the WT. Taken together, our results indicated that SiLEA14 is a novel atypical LEA protein and plays important roles in resistance to abiotic stresses in plants.ConclusionWe characterized a novel atypical LEA gene SiLEA14 from Foxtail Millet, which plays important roles in plant abiotic stress resistance. Modification of SiLEA14 expression may improve abiotic stress resistance in agricultural crops.
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silea14 a novel atypical lea protein confers abiotic stress resistance in Foxtail Millet
BMC Plant Biology, 2014Co-Authors: Xiyuan Jiang, Meizhen Wang, Ping Li, Qian Zhao, Cong Li, Jingjuan YuAbstract:Late embryogenesis abundant (LEA) proteins are involved in protecting higher plants from damage caused by environmental stresses. Foxtail Millet (Setaria italica) is an important cereal crop for food and feed in semi-arid areas. However, the molecular mechanisms underlying tolerance to these conditions are not well defined. Here, we characterized a novel atypical LEA gene named SiLEA14 from Foxtail Millet. It contains two exons separated by one intron. SiLEA14 was expressed in roots, stems, leaves, inflorescences and seeds at different levels under normal growth conditions. In addition, SiLEA14 was dramatically induced by osmotic stress, NaCl and exogenous abscisic acid. The SiLEA14 protein was localized in the nucleus and the cytoplasm. Overexpression of SiLEA14 improved Escherichia coli growth performance compared with the control under salt stress. To further assess the function of SiLEA14 in plants, transgenic Arabidopsis and Foxtail Millet plants that overexpressed SiLEA14 were obtained. The transgenic Arabidopsis seedlings showed higher tolerance to salt and osmotic stress than the wild type (WT). Similarly, the transgenic Foxtail Millet showed improved growth under salt and drought stresses compared with the WT. Taken together, our results indicated that SiLEA14 is a novel atypical LEA protein and plays important roles in resistance to abiotic stresses in plants. We characterized a novel atypical LEA gene SiLEA14 from Foxtail Millet, which plays important roles in plant abiotic stress resistance. Modification of SiLEA14 expression may improve abiotic stress resistance in agricultural crops.
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culturing of immature inflorescences and agrobacterium mediated transformation of Foxtail Millet setaria italica
African Journal of Biotechnology, 2011Co-Authors: Meizhen Wang, Qian Zhao, Cong Li, Guangming Ao, Jingjuan YuAbstract:In previous reports, we developed an Agrobacterium -mediated transformation system for Foxtail Millet. Here, we report optimization of the system through improvement of the regeneration system efficiency and optimization of conditions for gene delivery. Immature inflorescences explants of Foxtail Millet cv. Jigu 11 varying in length (0.5 to 1.0, 1.1 to 1.5, 1.6 to 2.0 and >2.0 cm) were cultured on modified MS medium for callus induction and regeneration. The highest embryogenic callus-formation efficiency (90.72%) was achieved with 0.5 to 1.0 cm long inflorescences and 25 days old calli induced from 0.5 to 1.0 cm long immature inflorescences gave rise to the highest differentiation frequency (90.93%). In addition, factors affecting T-DNA delivery were examined by transient β-glucuronidase (GUS) expression. Calli induced from younger explants (0.5 to 1.0 cm immature inflorescences) were optimal. Agrobacterium tumefaciens strain LBA4404 performed significantly better than EHA105. Co-cultivation at 22°C with 0.15 g/l dithiothreitol (DTT) in the infection solution and co-cultivation medium led to higher GUS transient expression efficiency than with other treatments. Using this optimized procedure, the lysine-rich protein encoding gene SBgLR from potato was transformed into Foxtail Millet cv. Jigu 11 with 5.5% transformation efficiency. The procedure described here will be useful for genetic improvement of Foxtail Millet. Key words : Foxtail Millet, regeneration, Agrobacterium-mediated transformation, temperature, dithiothreitol (DTT).
Meizhen Wang - One of the best experts on this subject based on the ideXlab platform.
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SiLEA14, a novel atypical LEA protein, confers abiotic stress resistance in Foxtail Millet
BMC Plant Biology, 2014Co-Authors: Meizhen Wang, Yanlin Pan, Xiyuan Jiang, Dengyun Zhu, Ping Li, Qian Zhao, Cong Li, Jingjuan YuAbstract:BackgroundLate embryogenesis abundant (LEA) proteins are involved in protecting higher plants from damage caused by environmental stresses. Foxtail Millet ( Setaria italica ) is an important cereal crop for food and feed in semi-arid areas. However, the molecular mechanisms underlying tolerance to these conditions are not well defined.ResultsHere, we characterized a novel atypical LEA gene named SiLEA14 from Foxtail Millet. It contains two exons separated by one intron. SiLEA14 was expressed in roots, stems, leaves, inflorescences and seeds at different levels under normal growth conditions. In addition, SiLEA14 was dramatically induced by osmotic stress, NaCl and exogenous abscisic acid. The SiLEA14 protein was localized in the nucleus and the cytoplasm. Overexpression of SiLEA14 improved Escherichia coli growth performance compared with the control under salt stress. To further assess the function of SiLEA14 in plants, transgenic Arabidopsis and Foxtail Millet plants that overexpressed SiLEA14 were obtained. The transgenic Arabidopsis seedlings showed higher tolerance to salt and osmotic stress than the wild type (WT). Similarly, the transgenic Foxtail Millet showed improved growth under salt and drought stresses compared with the WT. Taken together, our results indicated that SiLEA14 is a novel atypical LEA protein and plays important roles in resistance to abiotic stresses in plants.ConclusionWe characterized a novel atypical LEA gene SiLEA14 from Foxtail Millet, which plays important roles in plant abiotic stress resistance. Modification of SiLEA14 expression may improve abiotic stress resistance in agricultural crops.
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silea14 a novel atypical lea protein confers abiotic stress resistance in Foxtail Millet
BMC Plant Biology, 2014Co-Authors: Xiyuan Jiang, Meizhen Wang, Ping Li, Qian Zhao, Cong Li, Jingjuan YuAbstract:Late embryogenesis abundant (LEA) proteins are involved in protecting higher plants from damage caused by environmental stresses. Foxtail Millet (Setaria italica) is an important cereal crop for food and feed in semi-arid areas. However, the molecular mechanisms underlying tolerance to these conditions are not well defined. Here, we characterized a novel atypical LEA gene named SiLEA14 from Foxtail Millet. It contains two exons separated by one intron. SiLEA14 was expressed in roots, stems, leaves, inflorescences and seeds at different levels under normal growth conditions. In addition, SiLEA14 was dramatically induced by osmotic stress, NaCl and exogenous abscisic acid. The SiLEA14 protein was localized in the nucleus and the cytoplasm. Overexpression of SiLEA14 improved Escherichia coli growth performance compared with the control under salt stress. To further assess the function of SiLEA14 in plants, transgenic Arabidopsis and Foxtail Millet plants that overexpressed SiLEA14 were obtained. The transgenic Arabidopsis seedlings showed higher tolerance to salt and osmotic stress than the wild type (WT). Similarly, the transgenic Foxtail Millet showed improved growth under salt and drought stresses compared with the WT. Taken together, our results indicated that SiLEA14 is a novel atypical LEA protein and plays important roles in resistance to abiotic stresses in plants. We characterized a novel atypical LEA gene SiLEA14 from Foxtail Millet, which plays important roles in plant abiotic stress resistance. Modification of SiLEA14 expression may improve abiotic stress resistance in agricultural crops.
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culturing of immature inflorescences and agrobacterium mediated transformation of Foxtail Millet setaria italica
African Journal of Biotechnology, 2011Co-Authors: Meizhen Wang, Qian Zhao, Cong Li, Guangming Ao, Jingjuan YuAbstract:In previous reports, we developed an Agrobacterium -mediated transformation system for Foxtail Millet. Here, we report optimization of the system through improvement of the regeneration system efficiency and optimization of conditions for gene delivery. Immature inflorescences explants of Foxtail Millet cv. Jigu 11 varying in length (0.5 to 1.0, 1.1 to 1.5, 1.6 to 2.0 and >2.0 cm) were cultured on modified MS medium for callus induction and regeneration. The highest embryogenic callus-formation efficiency (90.72%) was achieved with 0.5 to 1.0 cm long inflorescences and 25 days old calli induced from 0.5 to 1.0 cm long immature inflorescences gave rise to the highest differentiation frequency (90.93%). In addition, factors affecting T-DNA delivery were examined by transient β-glucuronidase (GUS) expression. Calli induced from younger explants (0.5 to 1.0 cm immature inflorescences) were optimal. Agrobacterium tumefaciens strain LBA4404 performed significantly better than EHA105. Co-cultivation at 22°C with 0.15 g/l dithiothreitol (DTT) in the infection solution and co-cultivation medium led to higher GUS transient expression efficiency than with other treatments. Using this optimized procedure, the lysine-rich protein encoding gene SBgLR from potato was transformed into Foxtail Millet cv. Jigu 11 with 5.5% transformation efficiency. The procedure described here will be useful for genetic improvement of Foxtail Millet. Key words : Foxtail Millet, regeneration, Agrobacterium-mediated transformation, temperature, dithiothreitol (DTT).
Mehanathan Muthamilarasan - One of the best experts on this subject based on the ideXlab platform.
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Foxtail Millet: An Introduction
Compendium of Plant Genomes, 2017Co-Authors: Roshan Kumar Singh, Mehanathan Muthamilarasan, Manoj PrasadAbstract:Foxtail Millet (Setaria italica L.) is a versatile crop known for being genetically closely related to biofuel grasses, for its C4 photosynthesis, and for its tolerance to abiotic stresses. These attributes have made this crop a model system and, in view of this, the genome of Foxtail Millet has been sequenced. Among Millets, Foxtail Millet is the only crop possessing rich genetic and genomic resources, and globally it is the second most cultivated Millet next to pearl Millet. In the context of its importance in agronomic and research terms, the present chapter summarizes the origin, domestication, phylogeny, and agroeconomic importance of Foxtail Millet.
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Exploiting Genome Sequence Information to Develop Genomic Resources for Foxtail Millet Improvement
Compendium of Plant Genomes, 2017Co-Authors: Mehanathan Muthamilarasan, Manoj PrasadAbstract:Foxtail Millet is an excellent model crop for studying the biology of C4 photosynthesis, abiotic stress tolerance, and biofuel traits. In addition, grains of Foxtail Millet are rich in proteins, micro- and macro-nutrients, and other bioactive compounds. Being an old domesticated crop, Foxtail Millet has contributed to the development of human civilization and is still grown as a staple food, particularly in India and China. India is the largest producer of Millets. However, the breeding technology used for Foxtail Millet is far behind that of major Millets such as pearl Millet and finger Millet, and major cereals such as rice and wheat. Development of genomic resources is the first step toward improving the breeding strategies, which subsequently lead to the development of elite cultivars with higher yield and desirable agronomic traits. Much national and international effort has been invested in this regard to develop genetic and genomic resources and these have produced significant outcomes. In this context, the present chapter enumerates the genetic and genomic resources available for Foxtail Millet improvement. In particular, the chapter discusses the development of novel molecular markers, their application in genomics-assisted breeding, and the construction of integrated databases. In addition, the genes and families identified in Foxtail Millet which have relevance to growth, development, and stress response have also been summarized.
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development of novel microrna based genetic markers in Foxtail Millet for genotyping applications in related grass species
Molecular Breeding, 2014Co-Authors: Chandra Bhan Yadav, Mehanathan Muthamilarasan, Yusuf Khan, Garima Pandey, Manoj PrasadAbstract:DNA markers are important in molecular breeding, and, hence, considering its prominence, a variety of DNA-based molecular markers have been explored and developed for expediting crop improvement programs. microRNA (miRNA)-based molecular marker is a type of functional markers exploited predominantly in animal sciences, but reported in very few plants. Considering the efficacy, stability and transferability potential of the miRNA-based markers, the present study was conducted to develop these markers in the model crop Foxtail Millet. The pre-miRNA sequences of Foxtail Millet and other related grasses including rice, maize, wheat, sorghum and Brachypodium were retrieved and aligned for identifying the conserved regions. One hundred and seventy-six primer pairs were designed for these consensus sequences, and all these 176 miRNA-based markers were mapped onto Foxtail Millet genome. Of the 176 markers, 66 were chosen for further experimentations based on representing the nine chromosomes of Foxtail Millet and presence of highly conserved regions. All the 66 markers showed 100 % amplification in five cultivars of Foxtail Millet. Moreover, all the markers showed a higher level of cross-genera transferability potential with an average of ~67 % in Millets and non-Millet species. This is the first report on the development of novel miRNA-based markers in Foxtail Millet. Promisingly, these markers would serve as novel genotyping tool for various molecular breeding approaches aiming at crop improvement in Millets and non-Millet species.
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c2h2 type of zinc finger transcription factors in Foxtail Millet define response to abiotic stresses
Functional & Integrative Genomics, 2014Co-Authors: Mehanathan Muthamilarasan, Venkata Suresh Bonthala, Awdhesh Kumar Mishra, Rohit Khandelwal, Yusuf Khan, Manoj PrasadAbstract: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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development of 5123 intron length polymorphic markers for large scale genotyping applications in Foxtail Millet
DNA Research, 2014Co-Authors: Mehanathan Muthamilarasan, Garima Pandey, Venkata B Suresh, Kajal Kumari, Swarup K Parida, Manoj PrasadAbstract:Generating genomic resources in terms ofmolecularmarkers is imperative in molecularbreeding forcrop improvement.Thoughdevelopment and application ofmicrosatellite markers inlarge-scalewas reported in the model crop Foxtail Millet, no such large-scale study was conducted for intron-length polymorphic (ILP) markers. Considering this, we developed 5123 ILP markers, of which 4049 were physically mapped onto 9 chromosomesofFoxtailMillet.BLASTanalysisof5123expressedsequencetags(ESTs)suggestedthefunction for ∼71.5% ESTs and grouped them into 5 different functional categories. About 440 selected primer pairs representingtheFoxtailMilletgenomeandthedifferentfunctionalgroupsshowedhigh-levelofcross-genera amplification at an average of ∼85% in eight Millets and five non-Millet species. The efficacy of the ILP markers for distinguishing the Foxtail Millet is demonstrated by observed heterozygosity (0.20) and Nei’s averagegenediversity(0.22).InsilicocomparativemappingofphysicallymappedILPmarkersdemonstrated substantial percentage of sequence-based orthology and syntenic relationship between Foxtail Millet chromosomes and sorghum (∼50%), maize (∼46%), rice (∼21%) and Brachypodium (∼21%) chromosomes. Hence, for the first time, we developed large-scale ILP markers in Foxtail Millet and demonstrated their utility in germplasm characterization, transferability, phylogenetics and comparative mapping studies in Millets and bioenergy grass species.
