Publications of NIPGR Scientists
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Item Genomics approaches to synthesis plant-based biomolecules for therapeutic applications to combat SARS-CoV-2(Elsevier B.V., 2020) Sharma, Namisha; Muthamilarasan, Mehanathan; Prasad, Ashish; Prasad, ManojCOVID-19 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is devastative to the humankind for which neither vaccines nor precise therapeutic molecules for treatment are identified. The search for new drugs and repurposing of existing drugs are being performed; however, at the same time, research on plants to identify novel therapeutic compounds or testing the existing ones is progressing at a slower phase. In this context, genomics and biotechnology offer various tools and strategies to manipulate plants for producing those complex biopharmaceutical products. This review enumerates the scope for research on plant-based molecules for their potential application in treating SARS-CoV-2 infection. Strategies to edit gene and genome, overexpression and silencing approaches, and molecular breeding for producing target biomolecules in the plant system are discussed in detail. Altogether, the present review provides a roadmap for expediting research on using plants as a novel source of active biomolecules having therapeutic applications.Item The genome sequence of segmental allotetraploid peanut Arachis hypogaea(Springer Nature Publishing AG, 2019) Bertioli, David J.; Jenkins, Jerry; Clevenger, Josh; Dudchenko, Olga; Gao, Dongying; Seijo, Guillermo; Leal-Bertioli, Soraya C. M.; Ren, Longhui; Farmer, Andrew D.; Pandey, Manish K.; Samoluk, Sergio S.; Abernathy, Brian; Agarwal, Gaurav; Ballén-Taborda, Carolina; Cameron, Connor; Campbell , Jacqueline; Chavarro, Carolina; Chitikineni, Annapurna; Chu, Ye; Dash, Sudhansu; Baidouri, Moaine El; Guo, Baozhu; Huang, Wei; Kim, Kyung Do; Korani, Walid; Lanciano, Sophie; Lui, Christopher G.; Mirouze, Marie; Moretzsohn, Márcio C.; Pham, Melanie; Shin, Jin Hee; Shirasawa, Kenta; Sinharoy, Senjuti; Sreedasyam, Avinash; Weeks, Nathan T.; Zhang, Xinyou; Zheng, Zheng; Sun, Ziqi; Froenicke, Lutz; Aiden, Erez L.; Michelmore, Richard; Varshney, Rajeev K.; Holbrook, C. Corley; Cannon, Ethalinda K. S.; Scheffler, Brian E.; Grimwood, Jane; Ozias-Akins, Peggy; Cannon, Steven B.; Jackson, Scott A.; Schmutz , JeremyLike many other crops, the cultivated peanut (Arachis hypogaea L.) is of hybrid origin and has a polyploid genome that contains essentially complete sets of chromosomes from two ancestral species. Here we report the genome sequence of peanut and show that after its polyploid origin, the genome has evolved through mobile-element activity, deletions and by the flow of genetic information between corresponding ancestral chromosomes (that is, homeologous recombination). Uniformity of patterns of homeologous recombination at the ends of chromosomes favors a single origin for cultivated peanut and its wild counterpart A. monticola. However, through much of the genome, homeologous recombination has created diversity. Using new polyploid hybrids made from the ancestral species, we show how this can generate phenotypic changes such as spontaneous changes in the color of the flowers. We suggest that diversity generated by these genetic mechanisms helped to favor the domestication of the polyploid A. hypogaea over other diploid Arachis species cultivated by humans.Item Millets genetic engineering: the progress made and prospects for the future(Springer Nature, 2019) Sood, Priyanka; Singh, Roshan Kumar; Prasad, ManojSustaining yield gains of grain legume crops under growing salt-stressed conditions demands a thorough understanding of plant salinity response and more efficient breeding techniques that effectively integrate modern omics knowledge. Grain legume crops are important to global food security being an affordable source of dietary protein and essential mineral nutrients to human population, especially in the developing countries. The global productivity of grain legume crops is severely challenged by the salinity stress particularly in the face of changing climates coupled with injudicious use of irrigation water and improper agricultural land management. Plants adapt to sustain under salinity-challenged conditions through evoking complex molecular mechanisms. Elucidating the underlying complex mechanisms remains pivotal to our knowledge about plant salinity response. Improving salinity tolerance of plants demand enriching cultivated gene pool of grain legume crops through capitalizing on 'adaptive traits' that contribute to salinity stress tolerance. Here, we review the current progress in understanding the genetic makeup of salinity tolerance and highlight the role of germplasm resources and omics advances in improving salt tolerance of grain legumes. In parallel, scope of next generation phenotyping platforms that efficiently bridge the phenotyping-genotyping gap and latest research advances including epigenetics is also discussed in context to salt stress tolerance. Breeding salt-tolerant cultivars of grain legumes will require an integrated "omics-assisted" approach enabling accelerated improvement of salt-tolerance traits in crop breeding programs.Item Multi-omics approaches for strategic improvement of stress tolerance in underutilized crop species: A climate change perspective(Elsevier B.V., 2019) Muthamilarasan, Mehanathan; Singh, Nagendra Kumar; Prasad, ManojFor several decades, researchers are working toward improving the “major” crops for better adaptability and tolerance to environmental stresses. However, little or no research attention is given toward neglected and underutilized crop species (NUCS) which hold the potential to ensure food and nutritional security among the ever-growing global population. NUCS are predominantly climate resilient, but their yield and quality are compromised due to selective breeding. In this context, the importance of omics technologies namely genomics, transcriptomics, proteomics, phenomics and ionomics in delineating the complex molecular machinery governing growth, development and stress responses of NUCS is underlined. However, gaining insights through individual omics approaches will not be sufficient to address the research questions, whereas integrating these technologies could be an effective strategy to decipher the gene function, genome structures, biological pathways, metabolic and regulatory networks underlying complex traits. Given this, the chapter enlists the importance of NUCS in food and nutritional security and provides an overview of deploying omics approaches to study the NUCS. Also, the chapter enumerates the status of crop improvement programs in NUCS and suggests implementing “integrating omics” for gaining a better understanding of crops' response to abiotic and biotic stresses.Item Salinity stress response and 'omics' approaches for improving salinity stress tolerance in major grain legumes(Springer Nature, 2019) Jha, Uday Chand; Bohra, Abhishek; Jha, Rintu; Parida, Swarup K.Key message Sustaining yield gains of grain legume crops under growing salt-stressed conditions demands a thorough understanding of plant salinity response and more efficient breeding techniques that effectively integrate modern omics knowledge. Abstract Grain legume crops are important to global food security being an affordable source of dietary protein and essential mineral nutrients to human population, especially in the developing countries. The global productivity of grain legume crops is severely challenged by the salinity stress particularly in the face of changing climates coupled with injudicious use of irrigation water and improper agricultural land management. Plants adapt to sustain under salinity-challenged conditions through evoking complex molecular mechanisms. Elucidating the underlying complex mechanisms remains pivotal to our knowledge about plant salinity response. Improving salinity tolerance of plants demand enriching cultivated gene pool of grain legume crops through capitalizing on ‘adaptive traits’ that contribute to salinity stress tolerance. Here, we review the current progress in understanding the genetic makeup of salinity tolerance and highlight the role of germplasm resources and omics advances in improving salt tolerance of grain legumes. In parallel, scope of next generation phenotyping platforms that efficiently bridge the phenotyping–genotyping gap and latest research advances including epigenetics is also discussed in context to salt stress tolerance. Breeding salt-tolerant cultivars of grain legumes will require an integrated “omics-assisted” approach enabling accelerated improvement of salt-tolerance traits in crop breeding programs.Item Genomic and proteomic analysis of lignin degrading and polyhydroxyalkanoate accumulating beta-proteobacterium Pandoraea sp ISTKB(BioMed Central Ltd, 2018) Kumar, Madan; Verma, Sandhya; Gazara, Rajesh Kumar; Kumar, Manish; Pandey, Ashok; Verma, Praveen K.; Thakur, Indu ShekharBackground: Lignin is a major component of plant biomass and is recalcitrant to degradation due to its complex and heterogeneous aromatic structure. The biomass-based research mainly focuses on polysaccharides component of biomass and lignin is discarded as waste with very limited usage. The sustainability and success of plant polysaccharide-based biorefinery can be possible if lignin is utilized in improved ways and with minimal waste generation. Discovering new microbial strains and understanding their enzyme system for lignin degradation are necessary for its conversion into fuel and chemicals. The Pandoraea sp. ISTKB was previously characterized for lignin degradation and successfully applied for pretreatment of sugarcane bagasse and polyhydroxyalkanoate (PHA) production. In this study, genomic analysis and proteomics on aromatic polymer kraft lignin and vanillic acid are performed to find the important enzymes for polymer utilization. Results: Genomic analysis of Pandoraea sp. ISTKB revealed the presence of strong lignin degradation machinery and identified various candidate genes responsible for lignin degradation and PHA production. We also applied label-free quantitative proteomic approach to identify the expression profile on monoaromatic compound vanillic acid (VA) and polyaromatic kraft lignin (KL). Genomic and proteomic analysis simultaneously discovered Dyp-type peroxidase, peroxidases, glycolate oxidase, aldehyde oxidase, GMC oxidoreductase, laccases, quinone oxidoreductase, dioxygenases, monooxygenases, glutathione-dependent etherases, dehydrogenases, reductases, and methyltransferases and various other recently reported enzyme systems such as superoxide dismutases or catalase-peroxidase for lignin degradation. A strong stress response and detoxification mechanism was discovered. The two important gene clusters for lignin degradation and three PHA polymerase spanning gene clusters were identified and all the clusters were functionally active on KL-VA Conclusions: The unusual aerobic'-CoA'-mediated degradation pathway of phenylacetate and benzoate (reported only in 16 and 4-5% of total seguenced bacterial genomes), peroxidase-accessory enzyme system, and fenton chemistry based are the major pathways observed for lignin degradation. Both ortho and meta ring cleavage pathways for aromatic compound degradation were observed in expression profile. Genomic and proteomic approaches providedvalidation to this strain's robust machinery for the metabolism of recalcitrant compounds and PHA production and provide an opportunity to target important enzymes for lignin valorization in future.Item Production and characterization of polyhydroxyalkanoate from lignin derivatives by Pandoraea sp. ISTKB(American Chemical Society, 2017) Kumar, Madan; Singhal, Anjali; Verma, Praveen Kumar; Thakur, Indu ShekharThe present study investigates polyhydroxyalkanoate (PHA) production from lignin and its derivatives by a previously reported lignin-degrading bacterial strain Pandoraea sp. ISTKB. PHA production was screened by fluorescence microscopy and flow cytometry using a Nile red stain. PHA and biomass accumulation, while screening, was found to be maximum on 4-hydroxybenzoic acid followed by p-coumaric acid, vanillic acid, 2,6-dimethoxyphenol, and kraft lignin after 96 h. Monomer composition was analyzed by gas chromatography–mass spectrometry (GC–MS) and was followed by Fourier transform infrared and 1H NMR analysis, indicating PHA to be a copolymer of P(hydroxybutyrate-co-hydroxyvalerate). Genomic analysis of Pandoraea sp. ISTKB also complemented the results of GC–MS and NMR, and the relevant genes responsible for the synthesis of small chain length PHA were discovered in the genome. Process parameters were optimized by response surface methodology for enhanced production of PHA and biomass on 4-hydroxybenzoate. Optimization results showed 30 and 66% increase in the biomass and PHA production, respectively. The results obtained were promising and indicated that if lignin is depolymerized into low-molecular-weight intermediates, then it can easily be utilized and converted into value-added products like PHA by microbes.Item Biotechnology for drug discovery and crop improvement(Springer, 2017) Kamthan, Ayushi; Kamthan, Mohan; Datta, AsisGenomics has emerged as the single most powerful discipline for detailed analysis of organization expression, and interaction of an organism at the genome level. Pathogens like Candida albicans, Vibrio cholerae etc. are responsible for causing morbidity and mortality in human beings. Besides, phytopathogens like Magnaporthe oryzae can lead to potential loss of yield in staple crop of rice. Genes of N-Acetyl-d-glucosamine metabolic pathway has been found to be universal in the diverse pathogens like C. albicans, V. cholerae and M. oryzae, playing an important role in their virulence. Lack of optimal treatment and emergence of multi-drug resistance necessitate the designing of better/new drugs against these pathogens. Research on these pathogens has increased the understanding of virulence and pathogenicity factors which can serve as potential drug targets that can be efficiently utilized to design a successful therapy to combat various diseases. Agricultural biotechnology has provided new tools for effectively ensuring food and nutritional security that can overcome many of the technical roadblocks that limit the application of conventional biological techniques in agricultural research. Limitations of water resources, decreased fertility of arable land skyrocketing cost of energy and galloping increases in the population make it imperative that food supplies of the 21st century will depend on a new form of agriculture in which custom-made food plants will dominate the world market. The ultimate goal is to create crops that are tailored to provide better nutrition for humans, improved fruit shelf life and enhanced tolerance to various stresses.Item Ultra-high density intra-specific genetic linkage maps accelerate identification of functionally relevant molecular tags governing important agronomic traits in chickpea(Nature Publishing Group, 2015) Kujur, Alice; Upadhyaya, Hari D.; Shree, Tanima; Bajaj, Deepak; Das, Shouvik; Saxena, Maneesha S.; Badoni, Saurabh; Kumar, Vinod; Tripathi, Shailesh; Gowda, C. L. L.; Sharma, Shivali; Singh, Sube; Tyagi, Akhilesh K.; Parida, Swarup K.We discovered 26785 and 16573 high-quality SNPs differentiating two parental genotypes of a RIL mapping population using reference desi and kabuli genome-based GBS assay. Of these, 3625 and 2177 SNPs have been integrated into eight desi and kabuli chromosomes, respectively in order to construct ultra-high density (0.20-0.37 cM) intra-specific chickpea genetic linkage maps. One of these constructed high-resolution genetic map has potential to identify 33 major genomic regions harbouring 35 robust QTLs (PVE: 17.9-39.7%) associated with three agronomic traits, which were mapped within <1 cM mean marker intervals on desi chromosomes. The extended LD (linkage disequilibrium) decay (~15 cM) in chromosomes of genetic maps have encouraged us to use a rapid integrated approach (comparative QTL mapping, QTL-region specific haplotype/LD-based trait association analysis, expression profiling and gene haplotype-based association mapping) rather than a traditional QTL map-based cloning method to narrow-down one major seed weight (SW) robust QTL region. It delineated favourable natural allelic variants and superior haplotype-containing one seed-specific candidate embryo defective gene regulating SW in chickpea. The ultra-high-resolution genetic maps, QTLs/genes and alleles/haplotypes-related genomic information generated and integrated strategy for rapid QTL/gene identification developed have potential to expedite genomics-assisted breeding applications in crop plants, including chickpea for their genetic enhancement.Item Laser assisted microdissection, an efficient technique to understand tissue specific gene expression patterns and functional genomics in plants(Springer, 2015) Gautam, Vibhav; Sarkar, Ananda K.Laser assisted microdissection (LAM) is an advanced technology used to perform tissue or cell-specific expression profiling of genes and proteins, owing to its ability to isolate the desired tissue or cell type from a heterogeneous population. Due to the specificity and high efficiency acquired during its pioneering use in medical science, the LAM technique has quickly been adopted for use in many biological researches. Today, it has become a potent tool to address a wide range of questions in diverse field of plant biology. Beginning with comparative transcriptome analysis of different tissues such as reproductive parts, meristems, lateral organs, roots etc., LAM has also been extensively used in plant-pathogen interaction studies, proteomics, and metabolomics. In combination with next generation sequencing and proteomics analysis, LAM has opened up promising opportunities in the area of large scale functional studies in plants. Ever since the advent of this technique, significant improvements have been achieved in term of its instrumentation and method, which has made LAM a more efficient tool applicable in wider research areas. Here, we discuss the advancement of LAM technique with special emphasis on its methodology and highlight its scope in modern research areas of plant biology. Although we put emphasis on use of LAM in transcriptome studies, which is mostly used, we also discuss its recent application and scope in proteome and metabolome studies.