CRISPR/Cas9-Mediated Editing in FAD2 Gene to Enhance Oil Quality in Soybean [Glycine max (L.) Merrill] Balaji U. Rathod, Riddhi Rajyaguru, Ramesh N. Dhawale, Rukam S. Tomar, Shasikant Sharma, Manohar G. Chaskar, Omar Awad Alsaidan, Sunil Tulshiram Hajare Plos One, 2026 Conventional soybean oil contains high levels of linoleic acid, which reduces oxidative stability and necessitates hydrogenation, leading to trans-fat formation. In this study, 40 Indian soybean genotypes were screened for fatty acid composition, and Gujarat Junagadh Soybean-3 (GJS-3) was selected for CRISPR/Cas9-mediated editing of the fatty acid desaturase-2 (FAD2) gene. Agrobacterium-mediated transformation produced 22 regenerated plants, of which 57.1% were PCR-positive for Cas9/sgRNA. Targeted single-nucleotide substitutions were confirmed by Sanger sequencing in three edited lines (T3, T7, and T15), corresponding to an editing efficiency of 13.63%. These lines exhibited a marked increase in oleic acid content (42–45%) compared with the wild type (22%) and a concomitant reduction in linoleic acid (30–32% vs. 54%), resulting in nearly a two-fold improvement in the oleic/linoleic acid ratio. PCR analysis confirmed the absence of Cas9 and U3 sequences, indicating transgene-free edited plants. This study provides the first evidence of CRISPR/Cas9-mediated FAD2 editing in an Indian soybean cultivar and demonstrates its effectiveness in improving oil quality, oxidative stability, and processing efficiency.
Development of EST-SSR Markers Based on Transcriptome Sequencing in Kodo millet (Paspalum scrobiculatum l.) Humbal Nehali Bhagavanjibhair, Dhawale Ramesh Narayanrao, M. V. Dhuppe, Rukam. S. Tomar, Mukesh Soni, Vijay Upadhye, Anubhav Dubey, Sunil Tulshiram Hajare Cytology and Genetics, 2025 Abstract Kodo millet (Paspalum scrobiculatum L.) (2n = 4x = 40) mostly found in dry and semi-arid parts of Africa and Asia, also known as miraculous millets, is a staple food and a nutrient-security crop. It’s commonly known that kodo millet has the strongest tolerance to drought. Little study was done on high throughout genomic studies in relation to the creation of millets improved by genomics. In the present investigation, 21 080 571 total reads of sequence data were included in the 6.55 gigabytes of raw sequence that was produced following the genome sequencing run. After utilizing FastQC to verify the raw data quality, a total sequence of 1 087 611 and 578 123 572 bp was obtained. Three RNA samples from mature, blooming, and vegetative specimens were gathered, and the high-throughput Ion torrent sequencing method was applied to the sequencing process. In the vegetative stage, there were 1, 34, 40, and 824 raw readings; in the reproductive and mature stages, there were 1, 66, 35, 843 reads and 97, 43, 629 bp reads, respectively. At three distinct stages, the average read length was 131.6, 137.6, and 148.8 bp, in that order. The interface modules BatchPrimer3 (version 1.0) were used to construct the SSR and EST-SSR primers. Four FASTA files including contigs from the transcriptome and genome were utilized to identify SSRs. A total of thirty SSRs were found, with GC% and Tm ranges of 40–70 and 58–62°C, respectively. Of the 30 SSR and EST-SSR primers that were used for validation, only 17 were able to amplify the DNA from 27 distinct types of Kodo millet. 24 bands were obtained from the PCR amplification of 27 distinct types. We think that these findings may be applied in the future as possible candidates to enhance this significant staple crop.
Mutation spectrum and enzyme profiling of G6PD deficiency in neonates of north India: a prospective study Upasana Bhattacharyya, Preeti Deswal, Sunil Kumar Polipalli, Diksha Sharma, Manpreet Kaur, Madhulika Kabra, Neerja Gupta, Ramesh Agarwal, A. K. Deorari, V. K. Paul, Shevendru Roy, R. K. Sanjeev, R. S. Tomar, J. S. Bhasin, Amit Tyagi, V. K. Sharma, Anil Gulati, Rajesh Yadav, M. M. A. Faridi, Prerna Batra, Pooja Dewan, Veena Devgan, Alka Mathur, Aseem Bhatnagar, Sunita Bhatia, Ajay Kumar, Sushma Nangia, Arvind Saili, Anju Seth, Deepak Singla, S. K. Arora, S. Mehndiratta, Ashish Jain, Gaurav Pradhan, Sangeeta Gupta, Siddarth Ramji, Mukesh Darshan, S. K. Polipalli, Somesh Kumar, Biju Varughese, Avinash Lomash, Poonam Sidana, Sonia Mitta, Amarjeet Chitkara, Arti Maria, Harish Chellani, K. C. Aggarwa, Shobhna Gupta, Arya Sugandha, Ajay Gambhir, Surinder Bisht, Anand Aggarwal, P. M. Kohli, Indermeet Singh, Seema Kapoor, B. K. Thelma, and Journal of Genetics, 2023
Genetic Diversity Analysis of Groundnut Germplasm Lines in Respect to Early and Late Leaf Spot Diseases and Biochemical Traits Madhurjit Singh Rathore, Sushma Tiwari, M.K. Tripathi, Neha Gupta, Sunil Yadav, Sangeeta Singh, R.S. Tomar Legume Research, 2023 Background: Groundnut (Arachis hypogaea L.) is one of the most nutritious crops having versatile use. Its yield is mostly exaggerated by two foliar fungal diseases i.e., early and late leaf spot. In present investigation 96 germplasm lines were screened for early and late leaf spot diseases along with diverse biochemical parameters including protein, oil, fatty acids, proline and sugar contents. Methods: Early and late leaf spot diseases have been screened under field condition as well as employing SSR molecular markers. Nutritional profiling has also been done for protein, oil, fatty acids viz., oleic acid, linoleic acid, stearic acid and palmitic acid, proline and sugar contents. Result: In correlation analysis, oleic acid is negatively correlated with linoleic acid (r= -0.911) and palmitic acid (r= -0.688) at 1% level of significance, whereas stearic acid is positively and highly significantly correlated with oil percentage (r=0.381) at 1% significance level. The gene diversity value varied between 0.1866 to 0.4837 for markers ipahm103 and GM1536 with an average of 0.4014 and polymorphic information content (PIC) values ranged between 0.1692 to 0.3855 for the markers pahm103 to GM1536 respectively with a mean value of 0.3183.
Bionanotechnological methods in crop production and pest management Nanotechnology for Sustainable Agriculture an Innovative and Eco Friendly Approach, 2023
Genome-Wide Identification, Quantification, and Validation of Differentially Expressed miRNAs in Eggplant (Solanum melongena L.) Based on Their Response to Ralstonia solanacearum Infection Chintan Kapadia, Rahul Datta, Saiyed Mufti Mahammad, Rukam Singh Tomar, Jasmin Kumar Kheni, Sezai Ercisli ACS Omega, 2023 MicroRNAs (miRNAs), a type of short noncoding RNA molecule (21–23 nucleotides), mediate repressive gene regulation through RNA silencing at the posttranscriptional level and play an important role in the defense response to abiotic and biotic stresses. miRNAs of the plant system have been studied in model crops for their diverse regulatory role while less is known about their significance in other plants whose genome and transcriptome data are scarce in the database, including eggplant (Solanum melongena L.). In the present study, a next-generation sequencing platform was used for the sequencing of miRNA, and real-time quantitative PCR for miRNAs was used to validate the gene expression patterns of miRNAs in Solanum melongena plantlets infected with the bacterial wilt-causing pathogen Ralstonia solanacearum (R. solanacearum). Sequence analyses showed the presence of 375 miRNAs belonging to 29 conserved families. The miR414 is highly conserved miRNA across the plant system while miR5658 and miR5021 were found exclusively in Arabidopsis thaliana surprisingly, these miRNAs were found in eggplants too. The most abundant families were miR5658 and miR414. Ppt-miR414, hvu-miR444b, stu-miR8020, and sly miR5303 were upregulated in Pusa purple long (PPL) (susceptible) at 48 h postinfection, followed by a decline after 96 h postinfection. A similar trend was obtained in ath-miR414, stu-mir5303h, alymiR847-5p, far-miR1134, ath-miR5021, ath-miR5658, osa-miR2873c, lja-miR7530, stu-miR7997c, and gra-miR8741 but at very low levels after infection in the susceptible variety, indicating their negative role in the suppression of host immunity. On the other hand, osa-miR2873c was found to be slightly increased after 96 hpi from 48 hpi. Most of the miRNAs under study showed relatively lower expression in the resistant variety Arka Nidhi after infection than in the susceptible variety. These results shed light on a deeper regulatory role of miRNAs and their targets in regulation of the plant response to bacterial infection. The present experiment and their results suggested that the higher expression of miRNA leads to a decline in host mRNA and thus shows susceptibility.
Plant growth promoting characteristics of halophilic and halotolerant bacteria isolated from coastal regions of Saurashtra Gujarat Likhindra Reang, Shraddha Bhatt, Rukam Singh Tomar, Kavita Joshi, Shital Padhiyar, U. M. Vyas, Jasmin Kumar Kheni Scientific Reports, 2022 Halophiles are a class of microorganisms that thrive in environments with very high salt concentrations. The coastal regions of Saurashtra Gujarat host a diverse group of microorganisms including halophilic and halotolerant bacteria that may have plant growth promoting characteristics. Microorganisms with plant growth promoting characteristics are of immense importance in the field of agriculture and the present study was conducted to investigate the characteristics of halophilic and halotolerant bacteria isolated from agricultural soils of coastal regions of Junagadh and Porbandar districts of Saurashtra, Gujarat. A total of 15 isolated strains showed indole acetic acid production, solubilization of phosphate and potash, and nitrogen fixing capacity ranging from 18.77–33.48 μg ml−1, 50.10–106.10%, 180.42–239.92% and 0.170–0.480 g kg−1 of Jensen’s agar medium, respectively, while two isolates were also found positive for siderophore production. Besides, nine out of fifteen isolates also showed positive ACC deaminase activity ranging from 0.92-5.78 µM α-ketobutyrate mg−1 h−1. The isolates were further characterized by physiological, microscopic, and biochemical tests. The halophilic and halotolerant bacterial isolates were identified by 16S rRNA gene sequencing as belonging to Halomonas pacifica, H. stenophila, and Bacillus haynesii, B. licheniformis and Oceanobacillus aidingensis respectively. The 16S rRNA partial gene sequence of two isolates belonging to H. pacifica and H. stenophila were submitted to NCBI with accession number MK955347 and MK961217 respectively. The findings of the present investigation showed that isolated bacterial halophiles possess promising plant growth promoting characteristics. Their potential as bioinoculants to alleviate salinity stress in crops and for bioremediation deserves further investigation.
Stage specific comparative transcriptomic analysis to reveal gene networks regulating iron and zinc content in pearl millet [Pennisetum glaucum (L.) R. Br.] C. Tara Satyavathi, Rukam S. Tomar, Supriya Ambawat, Jasminkumar Kheni, Shital M. Padhiyar, Hiralben Desai, S. B. Bhatt, M. S. Shitap, Ramesh Chand Meena, Tripti Singhal, S. Mukesh Sankar, S. P. Singh, Vikas Khandelwal Scientific Reports, 2022 Pearl millet is an important staple food crop of poor people and excels all other cereals due to its unique features of resilience to adverse climatic conditions. It is rich in micronutrients like iron and zinc and amenable for focused breeding for these micronutrients along with high yield. Hence, this is a key to alleviate malnutrition and ensure nutritional security. This study was conducted to identify and validate candidate genes governing grain iron and zinc content enabling the desired modifications in the genotypes. Transcriptome sequencing using ION S5 Next Generation Sequencer generated 43.5 million sequence reads resulting in 83,721 transcripts with N50 of 597 bp and 84.35% of transcripts matched with the pearl millet genome assembly. The genotypes having high iron and zinc showed differential gene expression during different stages. Of which, 155 were up-regulated and 251 were down-regulated while during flowering stage and milking stage 349 and 378 transcripts were differentially expressed, respectively. Gene annotation and GO term showed the presence of transcripts involved in metabolic activities associated with uptake and transport of iron and zinc. Information generated will help in gaining insights into iron and zinc metabolism and develop genotypes with high yield, grain iron and zinc content.
Metabolomics of groundnut (Arachis hypogaea L.) genotypes during groundnut-sclerotium rolfsii interaction at different stages of infection Research Journal of Biotechnology, 2021
Fungal genomic resources for strain identification and diversity analysis of 1900 fungal species Mir Asif Iquebal, Sarika Jaiswal, Vineet Kumar Mishra, Rahul Singh Jasrotia, Ulavappa B. Angadi, Bhim Pratap Singh, Ajit Kumar Passari, Purbajyoti Deka, Ratna Prabha, Dhananjaya P. Singh, Vijai Kumar Gupta, Rukam Singh Tomar, Harinder Singh Oberoi, Anil Rai, Dinesh Kumar Journal of Fungi, 2021
Character associations, path analysis and molecular characterization in Cowpea (Vigna unguiculata L.) Research Journal of Biotechnology, 2021
Physiological and Biochemical characterization of Sclerotium rolfsii with respect to its infection on ground nut Research Journal of Biotechnology, 2020
Globalization of diets and risk of noncommunicable diseases Jan Fedacko, Toru Takahashi, Ram B. Singh, Dominik Pella, Sergey Chibisov, Krasimira Hristova, Daniel Pella, Galal Nagib Elkilany, Rukam S. Tomar, Lekh R. Juneja Role of Functional Food Security in Global Health, 2018
The Singh’s Concept of Functional Foods and Functional Farming (4 F) for World Health Toru Takahashi, Ram B. Singh, Sergey Chibisov, Rukam S. Tomar, Tanya Charkrabarti, Anil K. Chauhan, Ekasit Onsaard, Wiriya Phomkong, Hilton Chaves, Mukta Singh, Ratan Srivastav, Manushi Srivastav, Rana G. Singh, Poonam Jaglan Role of Functional Food Security in Global Health, 2018
Development of linkage map and identification of QTLs responsible for fusarium wilt resistance in castor (Ricinus communis L.) Research Journal of Biotechnology, 2016
Genetic diversity analysis in some marine fish species of Gujarat coast through morphological and molecular markers Research Journal of Biotechnology, 2016
Identification of resistance gene analogs (RGAS) from highly wilt resistant castor (Ricinus communis L.) genotype Research Journal of Biotechnology, 2015
You are what you eat, which depends on available food and agriculture? Circadian Cardiology with Focus on both Prevention and Intervention, 2015
A comparative analysis of ISSR and RAPD markers for studying genetic diversity in Trigonella foenum-graecum genotypes Research Journal of Biotechnology, 2014
Genetic diversity analysis in coriander (Coriandrum sativum) genotypes through morphological and molecular characterization Research Journal of Biotechnology, 2014
Characterization of castor (Ricinus communis L.) genotypes using different markers Research Journal of Biotechnology, 2014
You are what you eat, which depends on available food and agriculture? World Heart Journal, 2013
Identification of meta quantitative trait loci for agronomical traits in rice (Oryza sativa) Indian Journal of Genetics and Plant Breeding, 2012
Breeding for earliness and thermo-tolerance in wheat suited to early, late and very late sowing in northwestern India Indian Journal of Genetics and Plant Breeding, 2012
Development of mapping populations and their characterization for drought tolerance in wheat Indian Journal of Genetics and Plant Breeding, 2012
Inheritance of angled spikelet arrangement in Triticum durum Desf. Indian Journal of Genetics and Plant Breeding, 2009
Introgression of useful linked genes for resistance to stem rust, leaf rust and powdery mildew and their molecular validation in wheat (Triticum aestivum L.) Indian Journal of Genetics and Plant Breeding, 2009
Tobacco consumption in relation to causes of death in an urban population of north India International Journal of Copd, 2007
