Browsing by Author "Singh, Amit Kumar"

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Assessment of diversity in anti-nutrient profile, resistant starch, minerals and carbohydrate components in different ricebean (Vigna umbellata) accessions
(Elsevier B.V., 2023) Sharma, Paras; Goudar, Giridhar; Chandragiri, Anil Kumar; Ananthan, R; Subhash, K; Chauhan, Anitha; Longvah, T; Singh, Mohar; Bhardwaj, Rakesh; Parida, Swarup K.; Singh, Amit Kumar; Gayacharan; Chattopadhyay, Debasis
Ricebean accessions (n = 38) cultivated in India were evaluated for their comprehensive nutrient, anti-nutrients and mineral composition. Protein and total dietary fibre ranged between 23.23 and 27.33 and 12.27 to 16.69 g/100 g, respectively. Among the oligosaccharides, verbascose was not detected, however, raffinose and stachyose ranged between 47 and 186 and 117 to 5765 mg/100 g, respectively. Among the free sugars, sucrose was found dominating (up to 370 mg/100 g). Resistant starch (4.13 to 8.62 %), iron (3.49 to 7.46 mg/100 g), zinc (1.90 to 3.72 mg/100 g) and selenium (0.28 to 4.48 µg/100 g) varied significantly (p < 0.05) among ricebean samples. Phytic acid, saponin, trypsin inhibitor and oxalate analysed in ricebean accessions ranged between 303 and 760 mg/100 g, 19 to 46 mg/g, 309 to 1076 mg/100 g and 219 to 431 mg/100 g, respectively. Multivariate analysis using hierarchical clustering analysis (HCA), and principal component analysis (PCA) was employed to decipher the diversity of nutrients and anti-nutrients across the ricebean accessions. Based on HCA, dendrogram-1 (nutrients) and dendrogram-2 (minerals, anti-nutrients) were produced, having four clusters in each. In the dendrogram-1 and 2, the largest cluster had (n = 21) and (n = 15) accessions, respectively. The PCA analyse the uncorrelated set of variables (principal components) and it condenses a large set of data variables. Based on the eigenvalue >1, a total of eight PCs were formed contributing total variance of 78.8 %. The factor loading contribution in the PC1 and PC2 were from iron, fructose, glucose, raffinose and total dietary fibre, selenium (Se) and protein, respectively.
Dual localization of JA receptor, CaCOI2, explains JA perception dynamics in chickpea
(John Wiley & Sons, 2025) Singh, Ajit Pal; Bhatia, Chitra; Singh, Ekampreet; Singh, Amit Kumar; Fatima, Urooj; Senthil-Kumar, Muthappa; Giri, Jitender
Jasmonates (JAs) are a group of oxylipin-derived phytohormones involved in various biotic and abiotic stress responses and regulate plant development. JAs are perceived by receptor proteins called coronatine insensitive (COI). These JA receptors encode F-box proteins that form the SCFCOI ubiquitin ligase complex (comprising Skp, Cullin, and F-box) and activate JA signaling by promoting the degradation of the transcriptional repressor JAZ (JA associated ZIM domain containing) proteins via the 26S proteasomal pathway. However, JA signaling is not well understood in chickpea, a vital legume. In this study, we identified two potential chickpea JA receptors, named CaCOI1 and CaCOI2, and characterized CaCOI2 as a functional JA receptor. Subcellular localization experiments revealed that CaCOI2 is localized outside the nucleus but moves into the nucleus upon JA perception to activate signaling. Using domain-swapping experiments between CaCOI1 and CaCOI2, we demonstrated that the leucine-rich repeat region of the receptors, which interacts with bioactive JA such as JA-Isoleucine, also plays a crucial role in controlling the subcellular localization of CaCOI proteins. Our findings identify a functional JA receptor in chickpea and reveal new aspects of JA signaling and perception, which may also be relevant to other plants.
Indian wheat genomics initiative for harnessing the potential of wheat germplasm resources for breeding disease-resistant, nutrient-dense, and climate-resilient cultivars
(Frontiers Media S.A., 2022) Kumar, Sundeep; Jacob, Sherry R.; Mir, Reyazul Rouf; Vikas, V. K.; Kulwal, Pawan; Chandra, Tilak; Kaur, Satinder; Kumar, Uttam; Kumar, Suneel; Sharma, Shailendra; Singh, Ravinder; Prasad, Sai; Singh, Anju Mahendru; Singh, Amit Kumar; Kumari, Jyoti; Saharan, M. S.; Bhardwaj, Subhash Chander; Prasad, Manoj; Kalia, Sanjay; Singh, Kuldeep
Wheat is one of the major staple cereal food crops in India. However, most of the wheat-growing areas experience several biotic and abiotic stresses, resulting in poor quality grains and reduced yield. To ensure food security for the growing population in India, there is a compelling need to explore the untapped genetic diversity available in gene banks for the development of stress-resistant/tolerant cultivars. The improvement of any crop lies in exploring and harnessing the genetic diversity available in its genetic resources in the form of cultivated varieties, landraces, wild relatives, and related genera. A huge collection of wheat genetic resources is conserved in various gene banks across the globe. Molecular and phenotypic characterization followed by documentation of conserved genetic resources is a prerequisite for germplasm utilization in crop improvement. The National Genebank of India has an extensive and diverse collection of wheat germplasm, comprising Indian wheat landraces, primitive cultivars, breeding lines, and collection from other countries. The conserved germplasm can contribute immensely to the development of wheat cultivars with high levels of biotic and abiotic stress tolerance. Breeding wheat varieties that can give high yields under different stress environments has not made much headway due to high genotypes and environmental interaction, non-availability of truly resistant/tolerant germplasm, and non-availability of reliable markers linked with the QTL having a significant impact on resistance/tolerance. The development of new breeding technologies like genomic selection (GS), which takes into account the G × E interaction, will facilitate crop improvement through enhanced climate resilience, by combining biotic and abiotic stress resistance/tolerance and maximizing yield potential. In this review article, we have summarized different constraints being faced by Indian wheat-breeding programs, challenges in addressing biotic and abiotic stresses, and improving quality and nutrition. Efforts have been made to highlight the wealth of Indian wheat genetic resources available in our National Genebank and their evaluation for the identification of trait-specific germplasm. Promising genotypes to develop varieties of important targeted traits and the development of different genomics resources have also been highlighted.
Multi-environment phenotyping of ricebean (Vigna umbellata (Thunb.) Ohwi & Ohashi) germplasm and identification of core set for accelerating the crop improvement programs
(Frontiers Media S.A., 2026) Gayacharan; Joshi, Dinesh C; Aravind, J; Wankhede, D P; Singh, Badal; Kumar, Prakash; Rajkumar, S; Parida, Swarup K; Semwal, D P; Sharma, Paras; Singh, Mohar; Chattopadhyay, Debasis; Singh, Kuldeep; Singh, G. P.; Singh, Amit Kumar
Ricebean (Vigna umbellata) is a nutrient-rich rich underutilised legume crop. It is primarily grown in the uplands of India, Nepal and China. Despite its adaptation to a wide range of agroclimatic zones and resistance to various biotic and abiotic stresses, ricebean crop improvement efforts have been slow mainly because of the low levels of genetic diversity utilised in ricebean breeding. This study presents the first multi-environment phenotyping and core collection building in ricebean with 1,589 accessions maintained at the Indian National Gene Bank. The accessions were assessed in two diverse agro-ecological regions (New Delhi and Almora), indicating significant phenotypic variations for important economic traits such as days to flowering, pod length, number of seeds per pod, and seed weight. The core subsets were sampled using MStrat, PowerCore and PCSS, and CoreHunter algorithms. The sampled coresets were evaluated using diversity indices such as genetic distance, mean difference percentage (MD%), variance difference percentage (VD%), coincidence rate (CR) and variable rate of coefficient of variation. The E-EN100 approach of CoreHunter yielded the most effective representation, resulting in a final core set with 251 accessions (14.3% from the entire collection). Diversity indices, clustering methods, QQ-plots, and distributional comparisons confirmed the representativeness of the core set. Multi-environment GGE biplot analysis identified stable and high-performing accessions for early flowering, synchronous maturity, pod and seed traits, including promising genotypes such as IC351508 and IC352944 with determinate growth habit and high yield potential. The study provides a manageable subset of the entire collection, which may play a significant role in trait discovery and ricebean cultivar development.
Rice bean (Vigna umbellata (Thunb.) Ohwi & Ohashi)
(CABI, 2024) Gayacharan; Parida, Swarup K.; Singh, Amit Kumar; Chattopadhyay, Debashish; Joshi, D.C.; Katna, Gopal
Rice bean (Vigna umbellata (Thunb.) Ohwi & Ohashi) is a legume crop widely distributed throughout South and South-east Asia, and other parts of the world. It is a nutritionally rich legume crop and plays a crucial role in securing food and nutritional requirements in traditional farming systems. Its grains are a rich source of quality protein (18–32%) and minerals such as Ca (68–230 mg/100 g), P (209–370 mg/100 g), Mg (9–16 mg/100 g), K (8–1122 mg/100 g) and Fe (2.61–6.4 mg/100 g). Rice bean grain contains vitamins such as thiamine (0.5–1.09 mg), riboflavin (0.18–0.5 mg) and niacin (2.0–3.6 mg). The crop is grown in diverse agro-climatic conditions by diverse ethnic groups for food, fodder, cover crop, living hedges, etc. More importantly, the species is relatively free from pests and diseases. Therefore, it is being utilized as a donor species in pre-breeding programmes for trait introgression and genetic base broadening of V. radiata, V. mungo and V. angularis. Even though the crop has several beneficial traits and plays a crucial role in local nutritional and food security, rice bean improvement has been relatively inadequate. Therefore, the crop remains an orphan legume, and the area under crop production has continued to decline amid competition from more profitable similar crops such as mung bean, urd bean and cowpea. Nevertheless, a substantial amount of rice bean crop diversity has been collected and conserved to avoid any risk of losing it. National and international project-based initiatives are reviving, improving and introducing crop cultivation in its original habitats and new areas. Recently, significant genetic and genomic resources have been generated, which will help in crop improvement programmes.
The ricebean genome provides insight into Vigna genome evolution and facilitates genetic enhancement
(John Wiley & Sons, 2023) Francis, Aleena; Singh, Nagendra Pratap; Singh, Mohar; Sharma, Paras; Gayacharan; Kumar, Durgesh; Basu, Udita; Bajaj, Deepak; Varshney, Nidhi; Joshi, Dinesh Chandra; Semwal, Dinesh Prasad; Tyagi, Vandana; Wankhede, Dhammaprakash; Bharadwaj, Rakesh; Singh, Amit Kumar; Parida, Swarup K.; Chattopadhyay, Debasis
Ricebean [Vigna umbellata (Thunb.) Ohwi and Ohashi] (2n = 2x = 22) is a warm-season dietary pulse legume crop and was originated in the Indo-China region. It is known to provide food security to the small and marginal farmers of South and South-East Asia. Ricebean is well known for its high nutritional quality and resistance to bacterial leaf spot, Mungbean yellow mosaic virus and bruchid, which are devastating for the other Vigna family crops (Dhaliwal et al., 2022). We report a reference grade de novo genome assembly, which is anchored to the genetic linkage groups and covered almost the whole estimated genome length of ricebean and so far, the largest among the sequenced Vigna species.
Transcriptome analysis reveals key pathways and candidate genes controlling seed development and size in ricebean (Vigna umbellata)
(Frontiers Media S.A., 2022) Verma, Sachin Kumar; Mittal, Shikha; Gayacharan; Wankhede, Dhammaprakash Pandhari; Parida, Swarup K.; Chattopadhyay, Debasis; Prasad, Geeta; Mishra, Dwijesh Chandra; Joshi, Dinesh Chandra; Singh, Mohar; Singh, Kuldeep; Singh, Amit Kumar
Ricebean (Vigna umbellata) is a lesser known pulse with well-recognized potential. Recently, it has emerged as a legume with endowed nutritional potential because of high concentration of quality protein and other vital nutrients in its seeds. However, the genes and pathways involved in regulating seed development and size are not understood in this crop. In our study, we analyzed the transcriptome of two genotypes with contrasting grain size (IC426787: large seeded and IC552985: small seeded) at two different time points, namely, 5 and 10 days post-anthesis (DPA). The bold seeded genotype across the time points (B5_B10) revealed 6,928 differentially expressed genes (DEGs), whereas the small seeded genotype across the time point (S5_S10) contributed to 14,544 DEGs. We have also identified several candidate genes for seed development-related traits like seed size and 100-seed weight. On the basis of similarity search and domain analysis, some candidate genes (PHO1, cytokinin dehydrogenase, A-type cytokinin, and ARR response negative regulator) related to 100-seed weight and seed size showed downregulation in the small seeded genotype. The MapMan and KEGG analysis confirmed that auxin and cytokinin pathways varied in both the contrasting genotypes and can therefore be the regulators of the seed size and other seed development-related traits in ricebeans. A total of 51 genes encoding SCF TIR1/AFB , Aux/IAA, ARFs, E3 ubiquitin transferase enzyme, and 26S proteasome showing distinct expression dynamics in bold and small genotypes were also identified. We have also validated randomly selected SSR markers in eight accessions of the Vigna species (V. umbellata: 6; Vigna radiata: 1; and Vigna mungo: 1). Cross-species transferability pattern of ricebean-derived SSR markers was higher in V. radiata (73.08%) than V. mungo (50%). To the best of our knowledge, this is the first transcriptomic study conducted in this crop to understand the molecular basis of any trait. It would provide us a comprehensive understanding of the complex transcriptome dynamics during the seed development and gene regulatory mechanism of the seed size determination in ricebeans.
Transcriptome-wide association mapping provides insights into the genetic basis and candidate genes governing flowering, maturity and seed weight in rice bean (Vigna umbellata)
(BioMed Central Ltd, 2024) Sahu, Tanmaya Kumar; Verma, Sachin Kumar; Gayacharan; Singh, Nagendra Pratap; Joshi, Dinesh Chandra; Wankhede, D. P.; Singh, Mohar; Bhardwaj, Rakesh; Singh, Badal; Parida, Swarup K.; Chattopadhyay, Debasis; Singh, Gyanendra Pratap; Singh, Amit Kumar
Background: Rice bean (Vigna umbellata), an underrated legume, adapts to diverse climatic conditions with the potential to support food and nutritional security worldwide. It is used as a vegetable, minor food crop and a fodder crop, being a rich source of proteins, minerals, and essential fatty acids. However, little effort has been made to decipher the genetic and molecular basis of various useful traits in this crop. Therefore, we considered three economically important traits i.e., flowering, maturity and seed weight of rice bean and identified the associated candidate genes employing an associative transcriptomics approach on 100 diverse genotypes out of 1800 evaluated rice bean accessions from the Indian National Genebank. Results: The transcriptomics-based genotyping of one-hundred diverse rice bean cultivars followed by pre-processing of genotypic data resulted in 49,271 filtered markers. The STRUCTURE, PCA and Neighbor-Joining clustering of 100 genotypes revealed three putative sub-populations. The marker-trait association analysis involving various genome-wide association study (GWAS) models revealed significant association of 82 markers on 48 transcripts for flowering, 26 markers on 22 transcripts for maturity and 22 markers on 21 transcripts for seed weight. The transcript annotation provided information on the putative candidate genes for the considered traits. The candidate genes identified for flowering include HSC80, P-II PsbX, phospholipid-transporting-ATPase-9, pectin-acetylesterase-8 and E3-ubiquitin-protein-ligase-RHG1A. Further, the WRKY1 and DEAD-box-RH27 were found to be associated with seed weight. Furthermore, the associations of PIF3 and pentatricopeptide-repeat-containing-gene with maturity and seed weight, and aldo–keto-reductase with flowering and maturity were revealed. Conclusion: This study offers insights into the genetic basis of key agronomic traits in rice bean, including flowering, maturity, and seed weight. The identified markers and associated candidate genes provide valuable resources for future exploration and targeted breeding, aiming to enhance the agronomic performance of rice bean cultivars. Notably, this research represents the first transcriptome-wide association study in pulse crop, uncovering the candidate genes for agronomically useful traits.