Publications of NIPGR Scientists

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    Editorial: Genetics and genomics to enhance crop production, towards food security
    (Frontiers Media S.A., 2021) Kumar, Ajay; Mir, Reyazul Rouf; Sehgal, Deepmala; Agarwal, Pinky; Carter, Arron
    Twenty first century agriculture faces many challenges including new emerging abiotic and biotic stresses and decreasing arable land. These challenges pose serious threats to food security of an ever-increasing world population. One of the solutions to meet the food demands is to develop high-yielding crop varieties with greater genetic potential and resistance/tolerance to both biotic and abiotic stresses. Just like in mid-nineteenth century, when new genes and methods resulted in the first green revolution, there is a need to combine traditional plant breeding tools with new technologies to bring another green revolution for future food security.
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    Structural aspects of DNA repair and recombination in crop improvement
    (Frontiers Media S.A., 2020) Verma, Prabha; Tandon, Reetika; Yadav, Gitanjali; Gaur, Vineet
    The adverse effects of global climate change combined with an exponentially increasing human population have put substantial constraints on agriculture, accelerating efforts towards ensuring food security for a sustainable future. Conventional plant breeding and modern technologies have led to the creation of plants with better traits and higher productivity. Most crop improvement approaches (conventional breeding, genome modification, and gene editing) primarily rely on DNA repair and recombination (DRR). Studying plant DRR can provide insights into designing new strategies or improvising the present techniques for crop improvement. Even though plants have evolved specialized DRR mechanisms compared to other eukaryotes, most of our insights about plant-DRRs remain rooted in studies conducted in animals. DRR mechanisms in plants include direct repair, nucleotide excision repair (NER), base excision repair (BER), mismatch repair (MMR), non-homologous end joining (NHEJ) and homologous recombination (HR). Although each DRR pathway acts on specific DNA damage, there is crosstalk between these. Considering the importance of DRR pathways as a tool in crop improvement, this review focuses on a general description of each DRR pathway, emphasizing on the structural aspects of key DRR proteins. The review highlights the gaps in our understanding and the importance of studying plant DRR in the context of crop improvement.
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    Tweaking microRNA-mediated gene regulation for crop improvement
    (Elsevier B.V., 2020) Yadav, Sandeep; Das, Shabari Sarkar; Kumar, Pramod; Mishra, Vishnu; Sarkar, Ananda K.
    Many beneficial agronomic traits of crops have been lost in the course of domestication and selective introgression processes. One of the best strategies to prevent the exclusion of beneficial traits during the introgression of novel traits is to selectively fine-tune the expression of some candidate genes or microRNAs (miRNAs). Noncoding regulatory miRNAs of 20–24 nucleotide (nt) length have evolved as specific posttranscriptional regulators that negatively regulate the transcript abundance of their target genes via either cleavage of mRNAs or translational inhibition. In this chapter, we summarize the current knowledge on the role of miRNAs and elaborate their use in miRNA-mediated gene regulation for the improvement of agronomic traits in crop plants. Recent CRISPR-Cas9-based genome engineering technology can be applied to selectively tweak the specific miRNA-target regulation, and thus, the function of the candidate genes to improve crop plants by conferring better productivity or resistance to abiotic or biotic stresses.
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    Millets for next generation climate-smart agriculture
    (Frontiers Media S.A., 2017) Bandyopadhyay, Tirthankar; Muthamilarasan, Mehanathan; Prasad, Manoj
    Panicoids (subfamily: panicoideae) are a group of C4 grasses, which include agronomically important crops such as sorghum and maize, bioenergy feedstocks including sugarcane and miscanthus, nutri-cereals such as millets, and biofuel crops including switchgrass, napier grass and guinea grass. Among these, millets are known for their climate-resilient features including adaptation to a wide range of ecological conditions, less irrigational requirements, better growth and productivity in low nutrient input conditions, less reliance on synthetic fertilizers, and minimum vulnerability to environmental stresses (Kole et al., 2015). Also, millets are nutritionally superior to other major cereals as they are rich in dietary fibers, resistant starches, vitamins, essential amino acids, storage proteins and other bioactive compounds (Amadou et al., 2013). These attributes have made millets a crop of choice for cultivation in arid and semi-arid regions of the world; however, the less attempt has been made to study the climate-resilient features of millets compared to other major cereals. Among millets, foxtail millet (Setaria italica) and its wild progenitor, green foxtail (S. viridis) are extensively studied since they are considered as models for studying the traits related to C4 photosynthesis, stress biology, and bioenergy characteristics (Muthamilarasan and Prasad, 2015). The availability of genome sequence information of these two species (Bennetzen et al., 2012; Zhang et al., 2012) has unlocked the wealth of information pertaining to stress tolerance and biofuel characteristics. It has also expedited the development of large-scale genomic resources for crop improvement. On the other hand, studies on other millets are still in their infancy. The challenge to feed the ever-growing population with a healthy balanced diet and the threats faced by agricultural crops due to changing climate highlight the immediate requirement to exploit the beneficial attributes of millets. This could be utilized for the improvement of millets per se as well as other related grass species. The extensive gene-level synteny shared between the grass genomes would facilitate the transfer and introgression of useful genes, alleles and quantitative trait loci (QTL) of agronomic importance identified in millets to other major cereals. In the above context, this article advocates for initiating extensive research on millets to dissect their agronomic, nutritional as well as stress tolerance traits and develop strategies to transfer the useful traits to cultivated major cereals such as rice, wheat, maize, and sorghum.
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    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.
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    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.
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    Small RNAs in plants: recent development and application for crop improvement
    (Frontiers Media S.A., 2015) Kamthan, Ayushi; Chaudhuri, Abira; Kamthan, Mohan; Datta, Asis
    The phenomenon of RNA interference (RNAi) which involves sequence-specific gene regulation by small non-coding RNAs, i.e., small interfering RNA (siRNA) and microRNA (miRNA) has emerged as one of most powerful approaches for crop improvement. RNAi based on siRNA is one of the widely used tools of reverse genetics which aid in revealing gene functions in many species. This technology has been extensively applied to alter the gene expression in plants with an aim to achieve desirable traits. RNAi has been used for enhancing the crop yield and productivity by manipulating the gene involved in biomass, grain yield and enhanced shelf life of fruits and vegetables. It has also been applied for developing resistance against various biotic (bacteria, fungi, viruses, nematodes, insects) and abiotic stresses (drought, salinity, cold, etc.). Nutritional improvements of crops have also been achieved by enriching the crops with essential amino acids, fatty acids, antioxidants and other nutrients beneficial for human health or by reducing allergens or anti-nutrients. microRNAs are key regulators of important plant processes like growth, development, and response to various stresses. In spite of similarity in size (20–24 nt), miRNA differ from siRNA in precursor structures, pathway of biogenesis, and modes of action. This review also highlights the miRNA based genetic modification technology where various miRNAs/artificial miRNAs and their targets can be utilized for improving several desirable plant traits. microRNA based strategies are much efficient than siRNA-based RNAi strategies due to its specificity and less undesirable off target effects. As per the FDA guidelines, small RNA (sRNA) based transgenics are much safer for consumption than those over-expressing proteins. This review thereby summarizes the emerging advances and achievement in the field of sRNAs and its application for crop improvement.
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    Phosphorus starvation response in plants and opportunities for crop improvement
    (Wiley, 2013) Pandey, Bipin K.; Mehra, Poonam; Giri, Jitender
    Phosphorus (P) is one of the most essential nutrients for the adequate growth and development of plants as well as a crucial component of all life forms. Plants absorb P only in the inorganic form of orthophosphate (Pi). The availability of soluble Pi in most of the world's soil is poor as compared to its requirement for optimum growth and crop yield. Application of P fertilizers is a common practice to grow crop plants in P-poor soils. However, highly reactive Pi easily forms insoluble complexes in soil and a large fraction of applied Pi fertilizer becomes unavailable to plants. This problem is further compounded as the source of P fertilizers (i.e., P rocks) may be exhausted in the near future. Plants have evolved physiologically, biochemically, and morphologically to cope with Pi starvation through modification of the root system architecture for better Pi uptake and remobilize the internal Pi content. Genetic regulation of these adaptations has been explored to some extent and thus provides the resource for crop improvement using transgenics or plant breeding approaches. This complex network is regulated by transcription factors, microRNAs, membrane transporters, kinases/phosphatases, ubiquitin conjugase, and various hormones. Sugars have also been shown to play important roles in Pi starvation-mediated gene expression. Here, we review the recent progress made in delineating the functions of genetic elements in terms of modulating the Pi starvation response in plants. We further explore the possible strategies for crop improvement using available resources.