Browsing by Author "Singh, Kuldeep"

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Do diverse wheat genotypes unleash their biochemical arsenal differentially to conquer cold stress? A comprehensive study in the Western Himalayas
(John Wiley & Sons, 2023) Jan, Sofora; Kumar, Sandeep; Yousuf, Munaza; Shafi, Safoora; Majid, Ronak; Khan, M. Anwar; Jeelani, Fehim; Shikari, Asif Bashir; Kaur, Satinder; Kumar, Sundeep; Kalia, Sanjay; Singh, Kuldeep; Prasad, Manoj; Varshney, Rajeev K.; Mir, Reyazul Rouf
Wheat is one of the most important cereal crops in the world. Cold stress is a major constraint in production of wheat grown in cold climate regions. In this study, we conducted a comprehensive assessment of cold stress tolerance in wheat genotypes through field screening, cell membrane stability through electrolyte leakage assay and biochemical profiling. A core set comprising 4560 genotypes was evaluated for two years (2021–2022), revealing substantial genetic variation for cold stress tolerance. Most genotypes exhibited moderate tolerance, while a smaller proportion showed susceptibility to cold stress. Based on the cold screening data in the field, a mini-core set of 350 genotypes was selected for membrane stability analysis using electrical conductivity assays. Significant differences were observed in membrane stability among the genotypes, indicating the presence of genetic variation for this trait. Furthermore, a mini-core set was narrowed down to 50 diverse candidate genotypes that were subsequently profiled for various biochemicals, including reactive oxygen species (ROS) like lipid peroxidation (MDA) and hydrogen peroxide (H202), osmoprotectant (proline) and enzymatic antioxidants including ascorbate peroxidase (APX), superoxide dismutase (SOD), guaiacol peroxidase (GPX), and catalase (CAT). Correlation analysis of the biochemicals revealed negative associations between antioxidants and reactive oxygen species (ROS), highlighting their role in mitigating oxidative damage under cold stress. This study enhances our understanding of the physiological and biochemical mechanisms underlying cold stress tolerance in wheat. The identified genotypes with superior cold stress tolerance can serve as valuable genetic resources for wheat breeding.
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.
Isolation, characterization, and expression analysis of NAC transcription factor from Andrographis paniculata (Burm. f.) nees and their role in andrographolide production
(MDPI AG, 2024) Kumar, Ramesh; Kumar, Chavlesh; Choudhury, Debjani Roy; Ranjan, Aashish; Raipuria, Ritesh Kumar; Dubey, Kaushik Kumar Dhar; Mishra, Ayushi; Kumar, Chetan; Manzoor, Malik Muzafar; Kumar, Ashok; Kumari, Abha; Singh, Kuldeep; Singh, Gyanendra Pratap; Singh, Rakesh
Andrographis paniculata (Burm. f.) Nees is an important medicinal plant known for its bioactive compound andrographolide. NAC transcription factors (NAM, ATAF1/2, and CUC2) play a crucial role in secondary metabolite production, stress responses, and plant development through hormonal signaling. In this study, a putative partial transcript of three NAC family genes (ApNAC83, ApNAC21 22 and ApNAC02) was used to isolate full length genes using RACE. Bioinformatics analyses such as protein structure prediction, cis-acting regulatory elements, and gene ontology analysis were performed. Based on in silico predictions, the diterpenoid profiling of the plant’s leaves (five-week-old) and the real-time PCR-based expression analysis of isolated NAC genes under abscisic acid (ABA) treatment were performed. Additionally, the expression analysis of isolated NAC genes under MeJA treatment and transient expression in Nicotiana tabacum was performed. Full-length sequences of three members of the NAC transcription factor family, ApNAC83 (1102 bp), ApNAC21 22 (996 bp), and ApNAC02 (1011 bp), were isolated and subjected to the promoter and gene ontology analysis, which indicated their role in transcriptional regulation, DNA binding, ABA-activated signaling, and stress management. It was observed that ABA treatment leads to a higher accumulation of andrographolide and 14-deoxyandrographolide content, along with the upregulation of ApNAC02 (9.6-fold) and the downregulation of ApNAC83 and ApNAC21 22 in the leaves. With methyl jasmonate treatment, ApNAC21 22 expression decreased, while ApNAC02 increased (1.9-fold), with no significant change being observed in ApNAC83. The transient expression of the isolated NAC genes in a heterologous system (Nicotiana benthamiana) demonstrated their functional transcriptional activity, leading to the upregulation of the NtHMGR gene, which is related to the terpene pathway in tobacco. The expression analysis and heterologous expression of ApNAC21 22 and ApNAC02 indicated their role in andrographolide biosynthesis.
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.
Production and cytological characterization of a synthetic amphiploid derived from a cross between Oryza sativa and Oryza punctata
(NRC Research Press, 2019) Kumar, Kishor; Neelam, Kumari; Singh, Gurpreet; Mathan, Jyotirmaya; Ranjan, Aashish; Brar, Darshan Singh; Singh, Kuldeep
Oryza punctata Kotschy ex Steud. (BB, 2n = 24) is a wild species of rice that has many useful agronomic traits. An interspecific hybrid (AB, 2n = 24) was produced by crossing O. punctata and Oryza sativa variety Punjab Rice 122 (PR122, AA, 2n = 24) to broaden the narrow genetic base of cultivated rice. Cytological analysis of the pollen mother cells (PMCs) of the interspecific hybrids confirmed that they have 24 chromosomes. The F1 hybrids showed the presence of 19–20 univalents and 1–3 bivalents. The interspecific hybrid was treated with colchicine to produce a synthetic amphiploid (AABB, 2n = 48). Pollen fertility of the synthetic amphiploid was found to be greater than 50% and partial seed set was observed. Chromosome numbers in the PMCs of the synthetic amphiploid were 24II, showing normal pairing. Flow cytometric analysis also confirmed doubled genomic content in the synthetic amphiploid. Leaf morphological and anatomical studies of the synthetic amphiploid showed higher chlorophyll content and enlarged bundle sheath cells as compared with both of its parents. The synthetic amphiploid was backcrossed with PR122 to develop a series of addition and substitution lines for the transfer of useful genes from O. punctata with least linkage drag.
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.