Publications of NIPGR Scientists
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Item Genome sequencing efforts in minor millets: Current knowledge and emerging insights(Springer Nature Publishing AG, 2025) Singh, Roshan Kumar; Panchal, Anurag; Muthamilarasan, Mehanathan; Prasad, ManojSmall 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.Item Shaping the future: Unravelling regulators modulating plant architecture for next-generation crops(Elsevier B.V., 2025) Kumbhakar, Rajib; Mondal, Mayulika; Thakro, Virevol; Tripathi, Shailesh; Parida, Swarup K.Plant architecture traits in crops are modulated through intricate interactions of various genetic pathways, which helps them to adapt to diverse environmental conditions. Key developmental pathways involved in forming plant architecture include the LAZY-TAC (Tiller Angle Control) module regulating branch and tiller angle, the CLAVATA-WUSCHEL pathway controlling shoot apical meristem fate and the GID1-DELLA pathway governing plant height and tillering in major food crops. These pathways function in concert to shape the overall architecture of plants, which is essential for optimizing light capture, resource allocation, reproductive success and eventual crop yield enhancement. Presently, plant architecture of modern crops has been shaped especially by artificial selection of natural alleles that target yield traits. Recent advances in CRISPR-Cas-based genome editing and genomics-assisted breeding strategies have enabled precise genetic manipulation of natural alleles in the functionally relevant genes regulating plant architecture traits in crops. This will assist researchers to select and introgress superior natural alleles in popular cultivars strategically for restructuring their desirable plant-types suitable for mechanical harvesting as well as enhancing the crop yield potential.Item Stress combinations and their interactions in crop plants(Springer Nature Publishing AG, 2024) Ramegowda, Venkategowda; Senthil, Alagarswamy; Senthil‑Kumar, MuthappaCombined stresses are a common occurrence in agricultural felds. There is a pressing need for empirical understanding of the plant responses and fnd ways to develop stress tolerant plants and stress management strategies to tackle combined stresses in the feld conditions. Here a comprehensive overview of the current understating and recent research on combined stress interactions in plants are presented. Here we comprehend the fndings from various studies focusing on diferent aspects of combined stress, including abiotic-abiotic, abiotic-biotic, and biotic-biotic stress interactions. In general, the studies discussed here highlight the escalating impact of climate change on plants, emphasizing the need for a deeper understanding of plant responses to concurrent abiotic and biotic stresses. Key fndings from the articles published in this issue, include the adverse efects of combined drought and high-temperature stress on crop growth and yield, the exacerbation of pathogen impacts under abiotic stresses, and the potential for melatonin and salicylic acid to mitigate stress-induced damage. Additionally, use of model systems for quicker understanding of combined stress responses and development of methods and technologies which can be extrapolated to crop plants are discussed. Overall, fndings from the articles from this special issue underscore the complexity of combined stress interactions in plants and highlight the importance of interdisciplinary research eforts to address the challenges posed by climate change and ensure global food security.Item The promise of millets in the twenty-first century: emphasis on breeding, nutrition, food security and sustainability(Springer Nature Publishing AG, 2023) Bandyopadhyay, Tirthankar; Singh, Roshan Kumar; Ramesh, Palakurthi; Maurya, Jyoti; Prasad, ManojGlobal population is expected to cross 11 billion by the turn of the century, which has put immense pressure on the existing agricultural systems worldwide. This is complicated by gradually decreasing productivity and acreage as a result of climate change in addition to ever-increasing input costs of resource hungry staple crops like rice, wheat, and maize. Unfortunately, the most affected by these events are those who have the least resources at their disposal to mitigate the issue, especially in countries of Asia and Sub-Saharan Africa. It is therefore pertinent to explore and adopt alternative and/or complementary crops that are easier to cultivate, climate change tolerant, less resource hungry, nutritionally richer for human consumption, and agriculturally sustainable. Millets are perfect cereal crops which meet all of these requirements and can realistically provide much-needed solutions to current global food and nutritional security challenges. In this review, we provide a bird’s eye view of the relevance of millets in global agro-ecosystems in the context of their nutritional and agronomic attributes. Furthermore, we share perspectives on the major areas of crop improvement programs worldwide and discuss major challenges confronting the same. Finally, we discourse on the scope of millets for wider acceptability and highlight major points at the interface of genetic intervention–crop management post-harvest practices worth considering to potentially facilitate robust millet-based nutritional and food security.Item Complex molecular mechanisms determine fitness of plants to biotic and abiotic stresses(Springer Nature Publishing AG, 2021) Prasad, Ashish; Senthil-Kumar, Muthappa; Prasad, ManojThe mode of growth and development of plants does not allow them to change their habitat upon stress imposition. Through the course of evolution, plants have acquired complex molecular pathways to deal with abiotic and biotic factors to ensure their survival. The changing climatic conditions have led to unprecedented weather patterns resulting in increased crop losses. Similarly, the spread of pathogens in an era of increasing international trade has resulted in introduction and adaptation of these pathogens to new areas and cause frequent epidemics. There is an increasing need to understand the molecular mechanisms underlying stress responses in plants and envision ways to develop new crop varieties with improved features.Item Constructing synthetic pathways in plants: Strategies and tools(Elsevier B.V., 2020) Dwivedi, Anuj; Kumar, Kamal; Verma, Praveen K.Plants, being primary producers, are the ultimate choice for the synthetic biology and metabolite engineering. For thousands of years, conventional methods allowed plants to meet various human requirements. Synthetic biology is a combination of engineering and biological science that facilitates with large number of new opportunities toward generation of reprogrammed cell with new biological behavior. The application of this technology can enhance traditional crop production and maximize the desired biomass production in required plants. Efforts in establishments of such individual plant systems will result in pioneering in various applications, such as generation of food, fuel, fiber, and biomedical therapies. The primary goal of this chapter is to discuss the advancement in strategies and tools form the core of synthetic pathway construction. However, synthetic biology in plant system is still at infancy stage and thus implications of synthetic biology strategies deployed in crops for biomass production have been discussed.Item 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.Item The Mediator subunit OsMED15a is a transcriptional co-regulator of seed size/weight-modulating genes in rice(Elsevier B.V., 2019) Dwivedi, Nidhi; Maji, Sourobh; Waseem, Mohd; Thakur, Pallabi; Kumar, Vinay; Parida, Swarup K.; Thakur, Jitendra K.Although several transcription factors (TFs) that regulate seed size/weight in plants are known, the molecular landscape regulating this important trait is unclear. Here, we report that a Mediator subunit, OsMED15a, links rice grain size/weight-regulating TFs to their target genes. Expression analysis and high-resolution quantitative trait loci (QTL) mapping suggested that OsMED15a is involved in rice seed development. OsMED15a has an N-terminal, three-helical KIX domain. Two of these helices, α1 and α3, and three amino acids, 76LRC78, within OsMED15a helix α3 were important for its interaction with several proteins, including interactions with the transactivation domains of two NAC-type TFs, OsNAC024 and OsNAC025. Moreover, OsMED15a, OsNAC024, and OsNAC025 all exhibited increased expression during seed development, and we identified several grain size/weight-associated SNPs in these genes in 509 low- and high-grain-weight rice genotypes. RNAi-mediated repression of OsMED15a expression down-regulated the expression of the grain size/weight regulating genes GW2, GW5 and DR11 and reduced grain length, weight, and yield. Of note, both OsNAC024 and OsNAC025 bound to the promoters of these three genes. We conclude that the transactivation domains of OsNAC024 and OsNAC025 target the KIX domain of OsMED15a in the regulation of grain size/weight-associated genes such as GW2, GW5, and D11. We propose that the integrated molecular-genetics approach used here could help identify networks of functional alleles of other regulator and co-regulator genes and thereby inform efforts for marker-assisted introgression of useful alleles in rice crop improvement.Item Legume proteomics: Progress, prospects and challenges(John Wiley & Sons, 2016) Rathi, Divya; Gayen, Dipak; Gayali, Saurabh; Chakraborty, Subhra; Chakraborty, NiranjanLegumes are the major sources of food and fodder with strong commercial relevance, and are essential components of agricultural ecosystems owing to their ability to carry out endosymbiotic nitrogen fixation. In recent years, legumes have become one of the major choices of plant research. The legume proteomics is currently represented by more than 100 reference maps and an equal number of stress-responsive proteomes. Among the 48 legumes in the protein databases, most proteomic studies have been accomplished in two model legumes, soybean, and barrel medic. This review highlights recent contributions in the field of legume proteomics to comprehend the defence and regulatory mechanisms during development and adaptation to climatic changes. Here, we attempted to provide a concise overview of the progress in legume proteomics and discuss future developments in three broad perspectives: (i) proteome of organs/tissues; (ii) subcellular compartments; and (iii) spatiotemporal changes in response to stress. Such data mining may aid in discovering potential biomarkers for plant growth, in general, apart from essential components involved in stress tolerance. The prospect of integrating proteome data with genome information from legumes will provide exciting opportunities for plant biologists to achieve long-term goals of crop improvement and sustainable agriculture.Item Setaria genome sequencing: an overview(Springer, 2013) Lata, Charu; Prasad, ManojThe genus Setaria includes two important C4 Panicoid grass species, namely S. italica (cultivated) and S. viridis (weed; wild ancestor), which together represent an appropriate model system for architectural, physiological, evolutionary, and genomic studies in related grasses. It is a diploid, inbreeder, self-fertile annual cereal grass having short life cycle and minimal growth requirements. There close relatedness to biofuel crops like switch grass and napier grass further signifies their importance. Further, foxtail millet is an important food and fodder grain crop grown in arid and semi-arid regions in many parts of the world. Therefore, an increasing interest in these species has led to a gradual accumulation and development of genomic data and genetic resources. Setaria genome sequencing is an outcome of such endeavors. These sequencing efforts uncovered several distinctive attributes of Setaria genome that may help in understanding its physiology, evolution and adaptation. This will not only aid in comparative genomics studies of Setaria and related crops including bioenergy grasses but also help in rapid advancements of genomics information for developing varieties with superior traits either through marker-assisted selection (MAS) or using transgenic approaches in these crops.