Browsing by Author "Prasad, Manoj"

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A 1000-loci transcript map of the barley genome: new anchoring points for integrative grass genomics
(Springer, 2007) Stein, Nils; Prasad, Manoj; Scholz, Uwe; Thiel, Thomas; Zhang, Hangning; Wolf, Markus; Kota, Raja; Varshney, Rajeev K.; Perovic, Dragan; Grosse, Ivo; Graner, Andreas
An integrated barley transcript map (consensus map) comprising 1,032 expressed sequence tag (EST)-based markers (total 1,055 loci: 607 RFLP, 190 SSR, and 258 SNP), and 200 anchor markers from previously published data, has been generated by mapping in three doubled haploid (DH) populations. Between 107 and 179 EST-based markers were allocated to the seven individual barley linkage groups. The map covers 1118.3 cM with individual linkage groups ranging from 130 cM (chromosome 4H) to 199 cM (chromosome 3H), yielding an average marker interval distance of 0.9 cM. 475 EST-based markers showed a syntenic organisation to known colinear linkage groups of the rice genome, providing an extended insight into the status of barley/rice genome colinearity as well as ancient genome duplications predating the divergence of rice and barley. The presented barley transcript map is a valuable resource for targeted marker saturation and identiWcation of candidate genes at agronomically important loci. It provides new anchor points for detailed studies in comparative grass genomics and will support future attempts towards the integration of genetic and physical mapping information.
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].
9th Solanaceae Conference 2012
(National Academy of Sciences, India/ Springer, 2013) Prasad, Manoj
Solanaceae genome community holds annual meeting every year to discuss the updates on current research in field of genetics, genomics and evolutionary biology of Solanaceous crops. The 9th Solanaceae genome conference held at University of Neuchatel, Switzerland on 26th–30th August, 2012, on the theme “SOL2012 Conference from Bench to Innovative Applications”. The salient features of the conference are presented in short in this report.
Abiotic stress-responsive expression of wali1 and wali5 genes from wheat
(Landes Bioscience, 2012) Garg, Bharti; Puranik, Swati; Tuteja, Narendra; Prasad, Manoj
Two cDNA clones, encoding Aluminum-responsive wali1 and wali5, were identified in dehydration stress-specific cDNA library from wheat. Their sequence variations and structural dissimilarities indicated them to be non-homologous genes. Expression of both genes was induced by various abiotic stresses as well as in response to plant hormones and oxidative molecules. Further, they were expressed differentially in shoot and root tissues of wheat seedlings, their transcripts being specifically abundant in roots. Previously characterized as being only Aluminum treatment induced, this report proposes them as novel candidates for stress-responsive studies.
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.
Advances in plant sciences for nutritional security
(Astral International Pvt. Ltd., 2015) Muthamilarasan, Mehanathan; Prasad, Manoj
Malnutrition and hunger among the world population at alarming rates pose serious threat to global food security. Further, the FAO Hunger Report (2012) depicts that, about 12.5 per cent of the global population (one in eight people) is starving, excluding 100 million children under the age of five. Irrespective of the adults, about 2.5 million children die every year due to starvation and malnutrition which ultimately hinder human potential (FAO Hunger Report 2012). Since, plants are the primary producers in the food chain, they serve as versatile biochemical factories capable of producing almost complete complement of essential dietary micronutrients. However, the dietary micronutrients are unevenly disseminated among different plant parts. For instance, iron content in a rice leaf is as high as 100–200 ppm (parts per million), but very low in the polished rice grain (~3 ppm) (Mayer et al., 2008). Similarly, provitamin A carotenoids are present only in rice leaves but not in its edible part. Unfortunately, economically backward people rely predominantly on starchy staples such as rice, wheat, maize, or cassava, but these crops do not supplement the biochemical diversity needed for a healthy life which leads to micronutrient malnutrition (MNM). Plant science has a central role in addressing these issues of both hunger and malnutrition. Since, MNM affects more than half of the world population, biofortification offers an economical and sustainable approach of delivering micronutrients via micronutrient-dense crops to the human population. Hence, this book chapter summarizes the strategies of generating biofortified-crop plants along with the significant achievements reported in biofortification of major crop plants such as orange sweet potato, maize, cassava, rice, wheat and other crops like lentils, banana, cowpea, sorghum and potato.
Advances in Setaria genomics for genetic improvement of cereals and bioenergy grasses
(Springer, 2015) Muthamilarasan, Mehanathan; Prasad, Manoj
Recent advances in Setaria genomics appear promising for genetic improvement of cereals and biofuel crops towards providing multiple securities to the steadily increasing global population. The prominent attributes of foxtail millet (Setaria italica, cultivated) and green foxtail (S. viridis, wild) including small genome size, short life-cycle, in-breeding nature, genetic close-relatedness to several cereals, millets and bioenergy grasses, and potential abiotic stress tolerance have accentuated these two Setaria species as novel model system for studying C4 photosynthesis, stress biology and biofuel traits. Considering this, studies have been performed on structural and functional genomics of these plants to develop genetic and genomic resources, and to delineate the physiology and molecular biology of stress tolerance, for the improvement of millets, cereals and bioenergy grasses. The release of foxtail millet genome sequence has provided a new dimension to Setaria genomics, resulting in large-scale development of genetic and genomic tools, construction of informative databases, and genome-wide association and functional genomic studies. In this context, this review discusses the advancements made in Setaria genomics, which have generated a considerable knowledge that could be used for the improvement of millets, cereals and biofuel crops. Further, this review also shows the nutritional potential of foxtail millet in providing health benefits to global population and provides a preliminary information on introgressing the nutritional properties in graminaceous species through molecular breeding and transgene-based approaches.
Advances in wheat genomics and its potential in ensuring food security in the scenario of climate change
(Indian National Science Academy, 2014) Muthamilarasan, Mehanathan; Parida, Swarup K.; Prasad, Manoj
Prevalence of hunger and under-nutrition among the world population at alarming rates challenges the food security. Further, the instability in global wheat production in past two years and the projection of continuing decrease in wheat inventories predominantly due to climate change add-up to food insecurity. The global climate change imposing biotic and abiotic stress made the crop improvement more challenging. However, the timely release of wheat genome sequence holds the promise of evading these tribulations, provided the researchers and breeders pertinently utilize the genome information. In view of this, this short-review highlights the intact insights for the wheat research community on how to implement the genome sequence data in breeding and engineering transgenic wheat with enhanced biotic and abiotic stress tolerance.
Application of genomics-assisted breeding for generation of climate resilient crops: progress and prospects
(Frontiers Media S.A., 2015) Kole, Chittaranjan; Muthamilarasan, Mehanathan; Henry, Robert; Edwards, David; Sharma, Rishu; Abberton, Michael; Batley, Jacqueline; Bentley, Alison; Blakeney, Michael; Bryant, John; Cai, Hongwei; Cakir, Mehmet; Cseke, Leland J.; Cockram, James; Oliveira, Antonio Costa de; Pace, Ciro De; Dempewolf, Hannes; Ellison, Shelby; Gepts, Paul; Greenland, Andy; Hall, Anthony; Hori, Kiyosumi; Hughes, Stephen; Humphreys, Mike W.; Iorizzo, Massimo; Ismail, Abdelbagi M.; Marshall, Athole; Mayes, Sean; Nguyen, Henry T.; Ogbonnaya, Francis C.; Ortiz, Rodomiro; Paterson, Andrew H.; Simon, Philipp W.; Tohme, Joe; Tuberosa, Roberto; Valliyodan, Babu; Varshney, Rajeev K.; Wullschleger, Stan D.; Yano, Masahiro; Prasad, Manoj
Climate change affects agricultural productivity worldwide. Increased prices of food commodities are the initial indication of drastic edible yield loss, which is expected to increase further due to global warming. This situation has compelled plant scientists to develop climate change-resilient crops, which can withstand broad-spectrum stresses such as drought, heat, cold, salinity, flood, submergence and pests, thus helping to deliver increased productivity. Genomics appears to be a promising tool for deciphering the stress responsiveness of crop species with adaptation traits or in wild relatives toward identifying underlying genes, alleles or quantitative trait loci. Molecular breeding approaches have proven helpful in enhancing the stress adaptation of crop plants, and recent advances in high-throughput sequencing and phenotyping platforms have transformed molecular breeding to genomics-assisted breeding (GAB). In view of this, the present review elaborates the progress and prospects of GAB for improving climate change resilience in crops, which is likely to play an ever increasing role in the effort to ensure global food security.
Application of molecular antiviral compounds: novel approach for durable resistance against geminiviruses
(Springer, 2015) Sahu, Pranav Pankaj; Prasad, Manoj
Both transgenic as well as traditional breeding approaches have not been completely successful in inducting resistance against geminiviruses in crop plants. This demands the utilization of non-viral, non-plant compounds possessing antiviral characteristics as an alternate and effective strategy for developing durable resistance against geminiviruses. In recent years, several antiviral molecules have been developed for the treatment of plant virus infections. These molecular antiviral compounds target various geminiviral-DNA and -protein via interacting with them or by cleaving viral RNA fragments. Applications of these proteins such as GroEL, g5g and VirE2 have also provided a convincing evidence of resistance against geminiviruses. Taking advantage of this information, we can generate robust resistance against geminiviruses in diverse crop plants. In this context, the present review provides epigrammatic information on these antiviral compounds and their mode of action in modulating virus infection.
Association of an allele-specific marker with dehydration stress tolerance in foxtail millet suggests SiDREB2 to be an important QTL
(Springer, 2014) Lata, Charu; Prasad, Manoj
Dehydration-responsive element binding (DREB) genes assist in improving stress tolerance of plants by activating the expression of several stress-responsive genes. Therefore, development of functional markers for useful alleles utilizing DREB genes is crucial for crop improvement strategies. Earlier we reported a synonymous single nucleotide polymorphism (SNP) associated with dehydration tolerance at 558th bp (an A/G transition) in the SiDREB2 gene of foxtail millet (Setaria italica L.) and developed an allele-specific marker (ASM) for SiDREB2. In the present study, we validated this ASM using a set of 122 foxtail accessions, of which 45 were investigated in an earlier study. The QTL associated with SiDREB2 contributed to ~20 % of the total phenotypic variation (PV) for relative water content (RWC) and this signified the importance of this QTL for dehydration tolerance in foxtail millet.
Association of SNP in a novel DREB2-like gene SiDREB2 with stress tolerance in foxtail millet [Setaria italica (L.)]
(Oxford University Press, 2011) Lata, Charu; Bhutty, Sarita; Bahadur, Ranjit Prasad; Majee, Manoj; Prasad, Manoj
The DREB genes code for important plant transcription factors involved in the abiotic stress response and signal transduction. Characterization of DREB genes and development of functional markers for effective alleles is important for marker-assisted selection in foxtail millet. Here the characterization of a cDNA (SiDREB2) encoding a putative dehydration-responsive element-binding protein 2 from foxtail millet and the development of an allele-specific marker (ASM) for dehydration tolerance is reported. A cDNA clone (GenBank accession no. GT090998) coding for a putative DREB2 protein was isolated as a differentially expressed gene from a 6 h dehydration stress SSH library. A 5' RACE (rapid amplification of cDNA ends) was carried out to obtain the full-length cDNA, and sequence analysis showed that SiDREB2 encoded a polypeptide of 234 amino acids with a predicted mol. wt of 25.72 kDa and a theoretical pI of 5.14. A theoretical model of the tertiary structure shows that it has a highly conserved GCC-box-binding N-terminal domain, and an acidic C-terminus that acts as an activation domain for transcription. Based on its similarity to AP2 domains, SiDREB2 was classified into the A-2 subgroup of the DREB subfamily. Quantitative real-time PCR analysis showed significant up-regulation of SiDREB2 by dehydration (polyethylene glycol) and salinity (NaCl), while its expression was less affected by other stresses. A synonymous single nucleotide polymorphism (SNP) associated with dehydration tolerance was detected at the 558th base pair (an A/G transition) in the SiDREB2 gene in a core set of 45 foxtail millet accessions used. Based on the identified SNP, three primers were designed to develop an ASM for dehydration tolerance. The ASM produced a 261 bp fragment in all the tolerant accessions and produced no amplification in the sensitive accessions. The use of this ASM might be faster, cheaper, and more reproducible than other SNP genotyping methods, and thus will enable marker-aided breeding of foxtail millet for dehydration tolerance.
Barley genome sequence emerges as a promising candidate in genetic research and breeding
(Indian Academy of Sciences, 2013) Muthamilarasan, Mehanathan; Prasad, Manoj
Barley (Hordeum vulgare L.), domesticated since 8000 BC in western Asia and Northeast Africa (Fertile Cresent), is regarded as the founder crop of Old World agriculture. Cultivated barley is derived from its wild progenitor Hordeum spontaneum C. Koch, still inhabiting the Fertile Crescent from Israel and Jordan to South Turkey, Iraqi Kurdistan, and southwestern Iran. It possesses a distinct phenotype of broader leaves, shorter stem and awns, tough ear rachis, a shorter and thicker spike, and larger grains2. Barley is the fourth largest cultivated cereal worldwide, both in terms of area harvested (1.9 m ha) and production (134 million tonnes; mt). Of its total production, 75% is used as animal feed, 20% processed into alcoholic and non-alcoholic beverages and 5% is used in the making of food products which contribute about 30% of the calories consumed worldwide.
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.
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.
Catalase regulation during plant-virus-vector interaction
(John Wiley & Sons, 2024) Sharma, Rohit; Pandey, Saurabh; Prasad, Manoj; Prasad, Ashish
Plant-virus-host interaction is a complex process involving several players. A constant arms race between the hosts and viruses has led to their co-evolution. Reactive oxygen species (ROS) are important signaling molecules that regulate plant growth, development, and stress responses. Barley yellow dwarf virus (BYDV) has a wide host range and infects several plant species such as barley, rice, oats, wheat, etc. A recent study by Tian et al. (2024) has highlighted that the movement protein (MP) of BYDV is involved in manipulation of the host ROS pathway to promote viral multiplication as well as transmission. The findings display the multifaceted role of a viral protein that is otherwise involved in movement. The limited coding ability of viruses is compensated by their proteins having multiple roles in the modulation of several different host molecular pathways. This is one of the key reasons for viruses being successful pathogens despite their limited coding ability.