Publications of NIPGR Scientists
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Item Identifying the mechanistic basis to nitrogen responsiveness in two contrasting Setaria italica accessions(Oxford University Press, 2024) Bandyopadhyay, Tirthankar; Maurya, Jyoti; Bentley, Alison R; Griffiths, Howard; Swarbreck, Stéphanie M; Prasad, ManojNitrogen (N) is a macronutrient limiting crop productivity with varied requirements across species and genotypes. Understanding the mechanistic basis of N responsiveness by comparing contrasting genotypes could inform the development and selection of varieties with lower N demands, or inform agronomic practices to sustain yields with lower N inputs. Given the established role of millets in ensuring climate-resilient food and nutrition security, we investigated the physiological and genetic basis of nitrogen responsiveness in foxtail millet (Setaria italica L.). We had previously identified genotypic variants linked to N responsiveness, and here, we dissect the mechanistic basis of the trait by examining the physiological and molecular behaviour of N responsive (NRp-SI58) and non-responsive (NNRp-SI114) accessions at high and low N. Under high N, NRp-SI58 allocates significantly more biomass to nodes, internodes and roots, more N to developing grains, and is more effective at remobilising flag leaf N compared to NNRp-SI114. Post anthesis flag leaf gene expression suggests that differences in N induce much higher transcript abundance in NNRp-SI114 than NRp-SI58, a large proportion of which are potentially regulated by APETALA2 (AP2) transcription factors. Overall, the study provides novel insights into the regulation and manipulation of N responsiveness in S. italica.Item Multi-environment GWAS identifies genomic regions underlying grain nutrient traits in foxtail millet (Setaria italica)(Springer Nature Publishing AG, 2024) Jaiswal, Vandana; Bandyopadhyay, Tirthankar; Singh, Roshan Kumar; Gahlaut, Vijay; Muthamilarasan, Mehanathan; Prasad, ManojA total of 104 foxtail millet accessions were evaluated for 11 nutrients in three environments and 67 high-confidence marker-trait associations (MTAs) were identified. Six SNPs showed pleiotropic effect and associated with two or more nutrients, whereas 24 candidate genes were identified for 28 MTAs involving seven traits. Millets are known for their better nutritional profiles compared to major cereals. Foxtail millet (Setaria italica) is rich in nutrients essential to circumvent malnutrition and hidden hunger. However, the genetic determinants underlying this trait remain elusive. In this context, we evaluated 104 diverse foxtail millet accessions in three different environments (E1, E2, and E3) for 11 nutrients and genotyped with 30K SNPs. The genome-wide association study showed 67 high-confidence (Bonferroni-corrected) marker-trait associations (MTAs) for the nutrients except for phosphorus. Six pleiotropic SNPs were also identified, which were associated with two or more nutrients. Around 24 candidate genes (CGs) were identified for 28 MTAs involving seven nutrients. A total of 17 associated SNPs were present within the gene region, and five (5) were mapped in the exon of the CGs. Significant SNPs, desirable alleles and CGs identified in the present study will be useful in breeding programmes for trait improvement.Item GWAS identifies genetic loci underlying nitrogen responsiveness in the climate resilient C4 model Setaria italica (L.)(Elsevier B.V., 2022) Bandyopadhyay, Tirthankar; Swarbreck, Stéphanie M; Jaiswal, Vandana; Maurya, Jyoti; Gupta, Rajeev; Bentley, Alison R.; Griffiths, Howard; Prasad, ManojIntroduction N responsiveness is the capacity to perceive and induce morpho-physiological adaptation to external and internal Nitrogen (N). Crop productivity is propelled by N fertilizer and requires the breeding/selection of cultivars with intrinsically high N responsiveness. This trait has many advantages in being more meaningful in commercial/environmental context, facilitating in-season N management and not being inversely correlated with N availability over processes regulating NUE. Current lack of its understanding at the physio-genetic basis is an impediment to select for cultivars with a predictably high N response. Objectives To dissect physio-genetic basis of N responsiveness in 142 diverse population of foxtail millet, Setaria italica (L.) by employing contrasting N fertilizer nutrition regimes. Methods We phenotyped S. italica accessions for major yield related traits under low (N10, N25) and optimal (N100) growth conditions and genotyped them to subsequently perform a genome-wide association study to identify genetic loci associated with nitrogen responsiveness trait. Groups of accessions showing contrasting trait performance and allelic forms of specific linked genetic loci (showing haplotypes) were further accessed for N dependent transcript abundances of their proximal genes. Results Our study show that N dependent yield rise in S. italica is driven by grain number whose responsiveness to N availability is genetically underlined. We identify 22 unique SNP loci strongly associated with this trait out of which six exhibit haplotypes and consistent allelic variation between lines with contrasting N dependent grain number response and panicle architectures. Furthermore, differential transcript abundances of specific genes proximally linked to these SNPs in same lines is indicative of their N dependence in a genotype specific manner. Conclusion The study demonstrates the value/ potential of N responsiveness as a selection trait and identifies key genetic components underlying the trait in S. italica. This has major implications for improving crop N sustainability and food security.Item Transcriptional regulators of nitrate metabolism: key players in improving nitrogen use in crops(Elsevier B.V., 2020) Maurya, Jyoti; Bandyopadhyay, Tirthankar; Prasad, ManojGreen revolution has boosted crop yields by the development of varieties which rely on high fertilizer application. Since then, higher productivity has largely witnessed excessive nitrogen (N) fertilizer application resulting in many environmentally and agronomically unsustainable consequences. One possible solution to this problem is to develop varieties with efficient N use endowed with genetically superior N metabolizing machinery, thereby significantly reducing N loss in soil and facilitating gainful yield performance at lower N conditions. Nitrate (NO3-) is the major form of N acquired by plants in aerobic soils. Hence, its efficient acquisition, transport, assimilation into complex organic compounds, and overall homeostasis is crucial to ensure productivity under optimal and suboptimal N conditions. Transcription factors are prime regulators of these processes, and insights into their mechanism of action and the resultant effect on N metabolism are crucial to generating crops with efficient and durable nitrogen use efficiency. The present review, therefore, presents a comprehensive updated account of major N responsive transcription factor families, their cross-talk with other growth factors, and explores existing and potential areas of their biotechnological application to maximize crop yields.Item IRONing out stress problems in crops: a homeostatic perspective(John Wiley & Sons, 2021) Bandyopadhyay, Tirthankar; Prasad, ManojIron (Fe) is essential for plant growth and therefore plays a key role in influencing crop productivity worldwide. Apart from its central role in chlorophyll biosynthesis and oxidative phosphorylation (electron transfer), it is an important constituent of many enzymes involved in primary metabolism. Fe has different accessibilities to the roots in the rhizosphere depending upon whether it is ferrous (soluble) or ferric (insoluble) oxidation stages, which in turn, determine two kinds of Fe uptake strategies employed by the plants. The reduction strategy is exclusively found in non‐graminaceous plants wherein the ferrous Fe2+ is absorbed and translocated from the soil through specialized transporters. In contrast, the chelation strategy (widespread in graminaceous plants) relies on the formation of Fe (III)‐chelate complex as the necessary requirement of Fe uptake. Once inside the cell, Fe is translocated, compartmentalized and stored through a common set of physiological processes involving many transporters and enzymes whose functions are controlled by underlying genetic components, so that a fine balance of Fe homeostasis is maintained. Recently, molecular and mechanistic aspects of the process involving the role of transcription factors, signalling components, and cis‐acting elements have been obtained, which has enabled a much better understanding of its ecophysiology. This mini‐review summarizes recent developments in our understanding of Fe transport in higher plants with particular emphasis on crops in the context of major agronomically important abiotic stresses. It also highlights outstanding questions on the regulation of Fe homeostasis and lists potentially useful genes/regulatory pathways that may be useful for subsequent crop improvement under the stresses discussed through either conventional or transgenic approaches.Item A precise method for analyzing nitrogen use in foxtail millet(Springer Nature Publishing AG, 2020) Bandyopadhyay, Tirthankar; Prasad, ManojOptimization of biological nitrogen (N) use is instrumental in ensuring higher crop yields and preventing environmental degradation due to excessive N fertilizer application. Furthermore, understanding how genetic differences differentially influence N remobilization into seeds under contrasting nitrogen nutrition regimes is crucial to our understanding of nitrogen use efficiency (NUE) in crops in addition to enabling a deeper mechanistic understanding of the dynamics of nitrogen metabolism in plants. In this chapter, a method is proposed to precisely measure and analyze nitrogen use efficiency (NUE) in a pot-based system under different nitrogen nutrition regimes in foxtail millet (Setaria italica L.), a climate change-resilient C4 model crop with great promise for food security and nutrition in the twenty-first century.Item Genome-wide association study of major agronomic traits in foxtail millet (Setaria italica L.) using ddRAD sequencing(Springer Nature, 2019) Jaiswal, Vandana; Gupta, Sarika; Gahlaut, Vijay; Muthamilarasan, Mehanathan; Bandyopadhyay, Tirthankar; Ramchiary, Nirala; Prasad, ManojFoxtail millet (Setaria italica), the second largest cultivated millet crop after pearl millet, is utilized for food and forage globally. Further, it is also considered as a model crop for studying agronomic, nutritional and biofuel traits. In the present study, a genome-wide association study (GWAS) was performed for ten important agronomic traits in 142 foxtail millet core eco-geographically diverse genotypes using 10 K SNPs developed through GBS-ddRAD approach. Number of SNPs on individual chromosome ranged from 844 (chromosome 5) to 2153 (chromosome 8) with an average SNP frequency of 25.9 per Mb. The pairwise linkage disequilibrium (LD) estimated using the squared-allele frequency correlations was found to decay rapidly with the genetic distance of 177 Kb. However, for individual chromosome, LD decay distance ranged from 76 Kb (chromosome 6) to 357 Kb (chromosome 4). GWAS identified 81 MTAs (marker-trait associations) for ten traits across the genome. High confidence MTAs for three important agronomic traits including FLW (flag leaf width), GY (grain yield) and TGW (thousand-grain weight) were identified. Significant pyramiding effect of identified MTAs further supplemented its importance in breeding programs. Desirable alleles and superior genotypes identified in the present study may prove valuable for foxtail millet improvement through marker-assisted selection.Item Genome-wide association study (GWAS) delineates genomic loci for ten nutritional elements in foxtail millet (Setaria italica L.)(Elsevier B.V., 2019) Jaiswal, Vandana; Bandyopadhyay, Tirthankar; Gahlaut, Vijay; Gupta, Sarika; Dhaka, Annvi; Ramchiary, Nirala; Prasad, ManojNutritional deficiency is found to be a major threat to human health, especially in low-income countries. Thus it is essential to improve nutritional qualities of important food crops. Foxtail millet is second largest cultivated millet and 2–5 times nutritionally richer than major cereal crops. During the present study, we identified genetic determinants of ten nutritional elements including potassium, nickel, calcium, boron, magnesium, phosphorus, sulphur, zinc, manganese and iron for the first time in foxtail millet. For this purpose, genome-wide association studies (GWAS) were conducted using 93 diverse accessions and 10 K SNPs (distributed across all the nine foxtail millet chromosomes). Altogether, 74 marker-trait associations (MTAs) were identified to be associated with above mentioned ten elements, out of which ten (10) MTAs (associated with B, Mg, Zn and Fe) showed high confidence [-log(p) > 5.78]. Identified desirable SNP alleles and favourable haplotypes may prove useful in foxtail breeding. Also, significant pyramiding effect suggested that associated elements can be substantially enhanced through combining more than one MTA. Candidate genes residing within or near the association signal may be selected for functional characterization. Superior genotypes identified may prove as a potential donor in foxtail millet breeding assisted through the molecular marker.Item Nutrition potential of foxtail millet in comparison to other millets and major cereals(Springer, 2017) Bandyopadhyay, Tirthankar; Jaiswal, Vandana; Prasad, ManojGlobal population is burgeoning at an alarming rate and is expected to reach 9.7 billion by 2050 and 11.2 billion by the end of this century. This has led to immense pressure on global agriculture, compounded by dwindling productivity of the existing systems and acreage because of climate change, resulting in ever-increasing input costs for the cultivation of most resource-intensive cereal crops such as rice, wheat, and maize. Ironically, the most affected populations are those with least resources to mitigate the problem—those belonging to Asian and Sub-Saharan Africa. It is against this backdrop that there is an ever-increasing need for adopting cereal crops that are easy to cultivate, less resource hungry, climate resilient, and importantly, that meet the major nutritional requirement of the feeding population. Foxtail millet is a perfect cereal crop in this light and stands to help significantly global endeavors toward food security and nutrition. The present chapter provides a comparative nutritional assessment of foxtail millet with other cereal crops, summarizes the major scientific approaches currently being undertaken for its biofortification and highlights potential avenues of crop improvement using conventional breeding, genomics, and other interdisciplinary “omic” tools.Item Millets for next generation climate-smart agriculture(Frontiers Media S.A., 2017) Bandyopadhyay, Tirthankar; Muthamilarasan, Mehanathan; Prasad, ManojPanicoids (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.