Browsing by Author "Singh, Roshan Kumar"

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5M approach to decipher starch-lipid interaction in minor millets
(Springer Nature Publishing AG, 2023) Ramesh, Palakurthi; Singh, Roshan Kumar; Panchal, Anurag; Prasad, Manoj
The 5M approach can be applied to understand genetic complexity underlying nutritional traits of minor millets. It will help to systematically identify genomic regions/candidate genes imprinting metabolite profiles. Author’s work in this area is supported by research grants from Ministry of Science and Technology, Gov. of India [GrantCRG/2020/000488 and BT/Ag/Network/Wheat/2019–20].
Advances in Agrobacterium tumefaciens-mediated genetic transformation of graminaceous crops
(Springer, 2016) Singh, Roshan Kumar; Prasad, Manoj
Steady increase in global population poses several challenges to plant science research, including demand for increased crop productivity, grain yield, nutritional quality and improved tolerance to different environmental factors. Transgene-based approaches are promising to address these challenges by transferring potential candidate genes to host organisms through different strategies. Agrobacterium-mediated gene transfer is one such strategy which is well known for enabling efficient gene transfer in both monocot and dicots. Due to its versatility, this technique underwent several advancements including development of improved in vitro plant regeneration system, co-cultivation and selection methods, and use of hyper-virulent strains of Agrobacterium tumefaciens harbouring super-binary vectors. The efficiency of this method has also been enhanced by the use of acetosyringone to induce the activity of vir genes, silver nitrate to reduce the Agrobacterium-induced necrosis and cysteine to avoid callus browning during co-cultivation. In the last two decades, extensive efforts have been invested towards achieving efficient Agrobacterium-mediated transformation in cereals. Though high-efficiency transformation systems have been developed for rice and maize, comparatively lesser progress has been reported in other graminaceous crops. In this context, the present review discusses the progress made in Agrobacterium-mediated transformation system in rice, maize, wheat, barley, sorghum, sugarcane, Brachypodium, millets, bioenergy and forage and turf grasses. In addition, it also provides an overview of the genes that have been recently transferred to these graminaceous crops using Agrobacterium, bottlenecks in this technique and future possibilities for crop improvement.
Advances in omics technology for improving crop yield and stress resilience
(John Wiley & Sons, 2021) Singh, Roshan Kumar; Sood, Priyanka; Prasad, Ashish; Prasad, Manoj
Global climate change has emerged as the utmost environmental threat for agriculture. To maintain a sustainable food supply, climate-resilient high-yielding crop plants need to be developed. Over the last decade, understanding the complexity of genotype underlying agronomic traits has prompted the integrated application of various omics tools to address specific biological questions. A multi-parallel qualitative and quantitative differential analysis of gene transcripts, proteins and metabolites provides a comprehensive picture of the interconnected gene networks and cellular signalling cascade of regulatory and effector proteins. Genetic determinants of adaptation to environmental stress and yield enhancement traits are being determined and introgressed into elite accessions through either molecular breeding or genetic engineering approaches to obtain future crops with improved traits.
Big genomic data analysis leads to more accurate trait prediction in hybrid breeding for yield enhancement in crop plants
(Springer Nature Publishing AG, 2021) Singh, Roshan Kumar; Prasad, Manoj
In the high-throughput next-generation sequencing (NGS) era, it is feasible to generate huge amount of genotypic data from a large population of a given species. Population size, amount of data generated, and efficient computational analysis are the determining factors for the genomic predictions during crop improvement. Big data would generate more meaningful information from them and predict the trait behaviour more accurately in subsequent breeding cycles. The pace crop improvements and elite variety development through genomic-assisted breeding (GAB) is directly proportional to the advancements in NGS technologies occurred during the last 2 decades. Efficient evaluation of amount of crop genetic stocks is perquisite to exploit their genetic diversity to attain global food security. Making the sense from available genotypic data, genomic prediction has become a promising strategy to accurately explore the potential of large number of accessions deposited in various gene banks across the globe.
Biotechnological approaches to dissect climate-resilient traits in millets and their application in crop improvement
(Elsevier B.V., 2021) Singh, Roshan Kumar; Muthamilarasan, Mehanathan; Prasad, Manoj
'Small millets' is a generic term that includes all the millets except pearl millet and sorghum. These small or minor millets constitute eleven species that are marginally cultivated and consumed worldwide. These small millets possess excellent agronomic-, climate-resilient, and nutritional traits, although they lack popularity. Small millets withstand a broad spectrum of environmental stresses and possess better water-use and nitrogen-use efficiencies. Of note, small millets are five- to seven-fold nutritionally rich in terms of protein, bioactive compounds, micro- and macro-nutrients as compared to major cereals. Irrespective of these merits, small millets have received little research attention compared to major millets and cereals. However, the knowledge generated from such studies is significant for the improvement of millets per se and for translating the information to improve major cereals through breeding and transgene-based approaches. Given this, the review enumerates the efforts invested in dissecting the climate-resilient traits in small millets and provides a roadmap for deploying the information in crop improvement of millets as well as cereals in the scenario of climate change.
Biotechnological strategies to generate climate-smart crops: Recent advances and way forward
(John Wiley & Sons, 2023) Maurya, Jyoti; Singh, Roshan Kumar; Prasad, Manoj
Industrialization and other man-made actions caused accumulation of greenhouse gases in the atmospheric troposphere layer, leading to enhanced greenhouse effect and hike in average global temperature in response. This led to unpredicted and frequent occurrences of rainfall, droughts, floods, and other climatic events. Changing climate has imposed direct abiotic stresses leading severe threat to global crop production either directly (morpho-physio-chemical effects) or indirectly (socioeconomic effects) and caused food insecurity worldwide. Moreover, these climate change effects are predicted to become more severe in the future. So, to ensure the global food security, development of climate-smart crops is an urgent need. Biotechnology-based approaches have paved the way to understand the role of different genes and their applications to achieve climate change induced stress tolerance and developed crops for sustainable agriculture in the present scenario. Keeping this in mind, the present book chapter briefs about the effect of climate change on crop growth, development, and yield, as well as plant responses and adaptations during changing environments. This chapter also discusses different strategies implied to combat the climate change and highlights the integrative-omics based approach and biotechnological strategies, as well as their advancements toward generating the climate-smart crops.
Breeding and biotechnological interventions for trait improvement: status and prospects
(Springer Nature Publishing AG, 2020) Singh, Roshan Kumar; Prasad, Ashish; Muthamilarasan, Mehanathan; Parida, Swarup K.; Prasad, Manoj
Crop improvement relies on modulating the genes and genomic regions underlying key traits, either directly or indirectly. Direct approaches include overexpression, RNA interference, genome editing, etc., while breeding majorly constitutes the indirect approach. With the advent of latest tools and technologies, these strategies could hasten the improvement of crop species. Next-generation sequencing, high-throughput genotyping, precision editing, use of space technology for accelerated growth, etc. had provided a new dimension to crop improvement programmes that work towards delivering better varieties to cope up with the challenges. Also, studies have widened from understanding the response of plants to single stress to combined stress, which provides insights into the molecular mechanisms regulating tolerance to more than one stress at a given point of time. Altogether, next-generation genetics and genomics had made tremendous progress in delivering improved varieties; however, the scope still exists to expand its horizon to other species that remain underutilized. In this context, the present review systematically analyses the diferent genomics approaches that are deployed for trait discovery and improvement in major species that could serve as a roadmap for executing similar strategies in other crop species. The application, pros, and cons, and scope for improvement of each approach have been discussed with examples, and altogether, the review provides comprehensive coverage on the advances in genomics to meet the ever-growing demands for agricultural produce.
Comparative transcriptome profiling of two contrasting foxtail millet cultivars provides insights into molecular mechanisms underlying dehydration stress response
(Springer Nature Publishing AG, 2023) Muthamilarasan, Mehanathan; Suresh, Bonthala Venkata; Singh, Roshan Kumar; Choudhary, Pooja; Aggarwal, Pooja Rani; Prasad, Manoj
Foxtail millet (Setaria italica L.) has emerged as a model system to understand its adaptation to environmental stresses in the past decade. However, studies on understanding the molecular mechanism underlying the adaptation to dehydration stress and the regulatory network involved in the process remain elusive. In the present study, RNA-seq was performed during dehydration stress in the tolerant (IC4) and sensitive (IC41) cultivars at different time points (0, 6, and 12 h). A total of 2467 and 3318 differentially expressed genes (DEGs) were identified in IC4, and 2535 and 5572 in IC41 at 6 h and 12 h compared to control (0 h), respectively. Gene ontology (GO) analysis revealed that the DEGs were enriched in water transport, response to water deprivation, oxidative stress, amino acid and sugar transport, lipid biosynthesis, and regulation of stomatal opening. Pathway analysis suggested a significant modulation of genes involved in the metabolism of glutathione and tryptophan and biosynthesis of flavonoid, ascorbate, arginine, and proline in IC4 compared to IC41. Genes encoding for DIVARICATA, SBP family protein (teosinte glume architecture 1), and SRS family proteins (LATERAL ROOT PRIMORDIUM 1 and SHI-RELATED SEQUENCE 1) were found to be exclusively upregulated in IC4 during dehydration stress. Gene co-expression networks constructed based on the expression data showed the key modules and hubs that play critical roles during dehydration stress. Altogether, the present study has identified key genes, pathways, and regulatory modules that would serve as a base for further studies to gain insights into the dehydration-responsive molecular circuitry in foxtail millet.
Decarboxylation mechanisms of the C4 cycle in foxtail millet observed under salt and selenium treatments
(Springer Nature Publishing AG, 2023) Shah, Wasifa Hafiz; Rasool, Aadil; Padder, Sajad Ahmad; Singh, Roshan Kumar; Prasad, Manoj; Tahir, Inayatullah; Rehman, Reiaz ul; Hakeem, Khalid Rehman
Foxtail millet (Setaria italica L.), a millet with a smaller genome and shorter life cycle, growing in arid and semi-arid areas, is severely affected by salt stress with reduced biomass and yield. In this study, we report that salt stress poses deleterious effects on foxtail millet and in response foxtail millet shows flexibility in terms of decarboxylation under salt stress conditions. Our results indicate a significant increase in enzymatic activities as well as the expression levels of genes encoding NADP-Malic Enzyme (NADP-ME), NAD-Malic Enzyme (NAD-ME), phosphoenolpyruvate carboxykinase (PEPCK), NADP-Malate dehydrogenase (NADP-MDH), NAD-Malate dehydrogenase (NAD-MDH), Alanine aminotransferase (AlaAT) and Aspartate aminotransferase (AspAT) under salt stress. Thereby, suggesting that foxtail millet switches to mixed mode of decarboxylation mechanisms for better adaptability under salt stress. We also report that lower doses of selenium (Se) alleviated the effects of salinity. 1 µM Se supplementation enhanced the activity and gene expression of NADP-ME, NAD-ME, NADP-MDH, NAD-MDH and AlaAT. The gene expression and the activity of ATP-dependent PEPCK and AspAT were reduced by Se, making the process more energy-efficient. Hence, suggests that Se alleviated the deleterious effects of salinity by enhancing the mixed mode of decarboxylation in energy-efficient way.
Delineating the epigenetic regulation of heat and drought response in plants
(Taylor & Francis Group, 2022) Singh, Roshan Kumar; Prasad, Manoj
Being sessile in nature, plants cannot overlook the incursion of unfavorable environmental conditions, including heat and drought. Heat and drought severely affect plant growth, development, reproduction and therefore productivity which poses a severe threat to global food security. Plants respond to these hostile environmental circumstances by rearranging their genomic and molecular architecture. One such modification commonly known as epigenetic changes involves the perishable to inheritable changes in DNA or DNA-binding histone proteins leading to modified chromatin organization. Reversible epigenetic modifications include DNA methylation, exchange of histone variants, histone methylation, histone acetylation, ATP-dependent nucleosome remodeling, and others. These modifications are employed to regulate the spatial and temporal expression of genes in response to external stimuli or specific developmental requirements. Understanding the epigenetic regulation of stress-related gene expression in response to heat and drought would commence manifold avenues for crop improvement through molecular breeding or biotechnological approaches.
DNA methylation dynamics in response to abiotic and pathogen stress in plants
(Springer Nature Publishing AG, 2022) Arora, Heena; Singh, Roshan Kumar; Sharma, Shambhavi; Sharma, Namisha; Panchal, Anurag; Das, Tuhin; Prasad, Ashish; Prasad, Manoj
DNA methylation is a dynamic epigenetic mechanism that plays a significant role in gene expression and also maintains chromatin stability. The process is conserved in both plants and animals, and crucial for development and stress responses. Differential DNA methylation during adverse environmental conditions or pathogen attack facilitates the selective expression of defense-related genes. Both stress-induced DNA hypomethylation and hypermethylation play beneficial roles in activating the defense response. These DNA marks may be carried to the next generation making the progenies ‘primed’ for abiotic and biotic stress responses. Over the recent years, rapid advancements in the area of high throughput sequencing have enabled the detection of methylation status at genome levels in several plant species. Epigenotyping offers an alternative tool to plant breeders in addition to conventional markers for the selection of the desired offspring. In this review, we briefly discuss the mechanism of DNA methylation, recent understanding of DNA methylation-mediated gene regulation during abiotic and biotic stress responses, and stress memory in plants.
Dynamics of epigenetic control in plants via SET domain containing proteins: Structural and functional insights
(Elsevier B.V., 2023) Seni, Sushmita; Singh, Roshan Kumar; Prasad, Manoj
Plants control expression of their genes in a way that involves manipulating the chromatin structural dynamics in order to adapt to environmental changes and carry out developmental processes. Histone modifications like histone methylation are significant epigenetic marks which profoundly and globally modify chromatin, potentially affecting the expression of several genes. Methylation of histones is catalyzed by histone lysine methyltransferases (HKMTs), that features an evolutionary conserved domain known as SET [Su(var)3-9, E(Z), Trithorax]. This methylation is directed at particular lysine (K) residues on H3 or H4 histone. Plant SET domain group (SDG) proteins are categorized into different classes that have been conserved through evolution, and each class have specificity that influences how the chromatin structure operates. The domains discovered in plant SET domain proteins have typically been linked to protein-protein interactions, suggesting that majority of the SDGs function in complexes. Additionally, SDG-mediated histone mark deposition also affects alternative splicing events. In present review, we discussed the diversity of SDGs in plants including their structural properties. Additionally, we have provided comprehensive summary of the functions of the SDG-domain containing proteins in plant developmental processes and response to environmental stimuli have also been highlighted.
An efficient Agrobacterium-mediated genetic transformation method for foxtail millet (Setaria italica L.)
(Springer Nature Publishing AG, 2020) Sood, Priyanka; Singh, Roshan Kumar; Prasad, Manoj
Foxtail millet (Setaria italica L.) is a model crop to study C4 photosynthesis, abiotic stress tolerance, and bioenergy traits. Advances in molecular genetics and genomics had identified several potential genes in this crop that would serve as candidates for imparting climate-resilient traits in related millets, cereals, and biofuel crops. However, the lack of an efficient genetic transformation system has been impeding the functional characterization of these genes in foxtail millet per se. Given this, an easy and efficient regeneration and transformation protocol was optimized using mature seeds as a choicest explant. The suitability of secondary embryogenic calli over primary calli is underlined due to their high competence. The use of perfect combinations of plant growth regulators together with the ionic strength of organic and inorganics salts was found to influence regeneration and genetic transformation. We studied and optimized various crucial factors that affect the genetic transformation of foxtail millet calli using Agrobacterium tumefaciens-mediated approach. Secondary embryogenic calli and LBA44404 strain were found to be the best targets for transformation. The use of high sucrose and glucose, together with freshly prepared tobacco leaves extract, Silwet L-77 and acetosyringone, improved the efficiency of the genetic transformation of foxtail millet. Moreover, the use of an in vitro regeneration system with 84% callusing efficiency and 70–74% regeneration frequency led to a high recovery of transformants. Altogether, the present study reports a highly efficient (~ 27%) transformation system in foxtail millet that will expedite forward and reverse genetic studies in this important crop.
Feeding the future: role of OsAUX5 in enhancing rice nutritional value
(Springer Nature Publishing AG, 2023) Mondal, Kongkong; Tiwari, Manish; Singh, Roshan Kumar; Prasad, Manoj; Dey, Narottam
Essential amino acids (EAAs) such as valine, leucine, isole-ucine, phenylalanine, tryptophan, threonine, lysine, methio-nine, and histidine are not synthesized in the human body. They, therefore, need to be acquired from either plant or animal sources (Sá etal. 2020). Although plant proteins sup-ply the required amount of EAAs, they are often identiﬁed as nutritionally inferior compared to animal proteins.
Foxtail millet (Setaria italica L.): a model for small millets
(Elsevier B.V., 2023) Pramitha, Lydia; Choudhary, Pooja; Rana, Sumi; Singh, Roshan Kumar; Das, Pronomita; Sharma, Shriya; Ravikesavan, R; Prasad, Manoj; Muthamilarasan, Mehanathan
Foxtail millet (Setaria italica L.) is a small millet predominantly cultivated in arid and semi-arid regions of the world. India is the second-largest producer of foxtail millet, next to China, and the crop has importance in the history and civilization of the human race in these two countries. Although the foxtail millet was widely cultivated in the ancient era, it has lost its importance with time and became a marginally grown crop catering to the nutritional requirements of a limited population. Despite this, the crop has excellent yield contributing to agronomic traits along with climate-resilient characteristics. Being a C4 panicoid species with a small diploid genome, short lifecycle, in-breeding nature, and close relationship with biofuel grasses, foxtail millet has recently been considered as a C4 model crop to understand several agronomically important traits, including stress tolerance. Given the importance, the genome sequence of foxtail millet and green foxtail (S. viridis) is now available. The postgenome era has seen several crop studies, which provided extensive genetic and genomic resources for crop improvement. Studies including genetic and genomic dissection of nutritional traits, response to biotic and abiotic stresses, water-use and nitrogen-use efficiencies, biofuel traits, and deciphering the photosynthetic machinery have provided insights into the novel genes and pathways underlying the individual traits. This has also provided a roadmap for deploying similar studies in other millets using foxtail millet as a model. In this context, the chapter describes the botany, nutritional significance, global distribution, and production technologies being implemented in foxtail millet cultivation. The chapter also summarizes the outcomes of the studies being pursued to decode complex traits and provide a roadmap for executing similar work in other millet crops.
Foxtail millet: An introduction
(Springer, 2017) Singh, Roshan Kumar; Muthamilarasan, Mehanathan; Prasad, Manoj
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.
Genetics and genomics interventions for promoting millets as functional foods
(Bentham Science, 2021) Dhaka, Annvi; Singh, Roshan Kumar; Muthamilarasan, Mehanathan; Prasad, Manoj
Several crops, including millets with immense nutritional and therapeutic values, were once a part of our regular diet. However, due to domestication and selection pressures, many of them have become marginally cultivated crops confined to a particular region, race, or locality. Millets are a perfect example of neglected species that have the potential to address both food and nutritional insecurities prevalent among the ever-growing global population. Starvation and malnutrition contribute to a large number of health-related issues, being the main reason behind the occurrence of most of the severe diseases worldwide. These constraints are repeatedly disturbing both the social and economic health of global society. Naturally, millets are rich in minerals, nutrients, and bioactive compounds, and these crops are less dependent on synthetic fertilizers, systemic irrigation, and pest/weed control. Given this, the review emphasizes the nutritional values, health benefits, processing techniques, and genomic advancements of millets. In addition, it proposes a roadmap for enhancing the utility and commercialization of millets.
Genome sequencing efforts in minor millets: Current knowledge and emerging insights
(Springer Nature Publishing AG, 2025) Singh, Roshan Kumar; Panchal, Anurag; Muthamilarasan, Mehanathan; Prasad, Manoj
Small millets (or minor millets) include finger millet (Eleusine coracana), foxtail millet (Setaria italica), proso millet (Panicum miliaceum), barnyard millet (Echinochloa crus-galli), kodo millet (Paspalum scrobiculatum), little millet (Panicum sumatrense), teff (Eragrostis tef), fonio (Digitaria exilis), job’s tears (Coix lacryma-jobi), guinea millet (Brachiaria deflexa), and browntop millet (Urochloa ramosa). These millets are highly nutritious and climate-resilient but marginally cultivated for the production and consumption of particular communities. Though called “poor men’s crops,” minor millets possess the potential to ensure food and nutritional security amid the threat of global climate change. Thus, scope exists to improve the agronomic traits of these minor millets for commercial cultivation; however, lack of genomic resources remains a bottleneck to this advancement. Genome sequencing not only provides an opportunity to decode the genes encoded by the genome, but also provides avenue for the development of genomic resources. The success of genome sequencing for resource development and further implementation of these resources have been proven in other crop plants. Among minor millets, genomes of a few species have been sequenced, including finger millet, foxtail millet, proso millet, barnyard millet, teff, fonio, and job’s tears. However, the genomes of kodo millet, little millet, guinea millet, and browntop millet remains to be sequenced. In this context, the chapter summarizes the outcomes of sequencing efforts and the application of genome sequence information in accelerating genomics studies in minor millets. The chapter also enumerates the status of transcriptome sequencing and its application in dissecting the genes underlying important traits.
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, Manoj
Heat 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.
Genome-wide association studies for improving agronomic traits in foxtail millet
(Springer, 2017) Singh, Roshan Kumar; Prasad, Manoj
With the immense advancements in sequencing and data mining approaches, identification of genome-wide genetic variants in a population has become very popular. The use of these resources in the development of a dense genetic map of genome variations and to identify associated quantitative traits has become widespread in crop genetics. In recent years, genome-wide association study (GWAS) has become a powerful tool in revealing the relationship between natural variation of complex genotype and genetic locus. A slight variation in the genetic architecture of an individual in a population results in contrasting agronomic traits compared to the other individuals. GWAS utilized high-throughput genotyping platform and extensively phenotyping data to detect the links between genetic variations that underlie variations in agronomic traits. These studies can accelerate the use of genomic selection in marker-assisted breeding for crop improvement. Here, a brief discussion of available genomic resources and their utilization, quantitative trait loci (QTL) underlying agronomic traits, GWAS in foxtail millet, and the prospects for this field in crop designing is given.