Rukam Singh Tomar
@jau.in
Associate Professor, Department of Biotechnology
Junagadh Agricultural University
RESEARCH INTERESTS
Genome Editing, Genome sequencing, Transcriptome sequencing, QTL mapping, Genome-Wide Association Studies, Marker Assisted Selection, Genome Assisted Breeding, Marker Assisted Backcrossing
Scopus Publications
Scholar Citations
Scholar h-index
Scholar i10-index
Scopus Publications
Srutiben A. Gundaraniya, Padma S. Ambalam, Roli Budhwar, Shital M. Padhiyar, and Rukam S. Tomar
Springer Science and Business Media LLC
Ashish Kumar G. Vala, Nasreen Bano, Yogita Deshmukh, Rukam Singh Tomar, C.G. Joshi, and N. Subhash
Springer Science and Business Media LLC
Nikita S. Patel, Jagdish B. Patel, and Rukam S. Tomar
Springer Science and Business Media LLC
Zahra Ghorbanzadeh, Rasmieh Hamid, Feba Jacob, and Rukam Singh Tomar
CRC Press
Likhindra Reang, Shraddha Bhatt, Rukam Singh Tomar, Kavita Joshi, Shital Padhiyar, U. M. Vyas, and Jasmin Kumar Kheni
Springer Science and Business Media LLC
AbstractHalophiles 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.
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,et al.
Springer Science and Business Media LLC
AbstractPearl 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.
Baibhav Kumar, Animesh Kumar, Sarika Jaiswal, Mir Asif Iquebal, Ulavappa B. Angadi, Rukam S. Tomar, Anil Rai, and Dinesh Kumar
MDPI AG
Pearl millet (Pennisetum glaucum L.) is affected by drought stress, affecting crop productivity and survival. Long non-coding RNAs (lncRNAs) are reported to play a vital role in the response to drought stress. LncRNAs represent a major part of non-protein coding RNAs and are present prevalently. These are involved in various biological processes, which may functionally act as RNA rather than getting transcribed as protein. We targeted genome-wide identification of lncRNAs in pearl millet from root and leaf tissues subjected to drought stress. A total of 879 lncRNAs were identified, out of which 209 (leaf control, root control), 198 (leaf treated, root treated), 115 (leaf control, leaf treated) and 194 (root control, root treated) were differentially expressed. Two lncRNAs were found as potential target mimics of three miRNAs from the miRBase database. Gene ontology study revealed that drought-responsive lncRNAs are involved in biological processes like ‘metabolic process’ and ‘cellular process’, molecular functions like ‘binding’ and ‘catalytic activities’ and cellular components like ‘cell’, ‘cell part’ and ‘membrane part’. LncRNA-miRNA-mRNA network shows that it plays a vital role in the stress-responsive mechanism through their activities in hormone signal transduction, response to stress, response to auxin and transcription factor activity. Only four lncRNAs were found to get a match with the lncRNAs present in the plant lncRNA database CANTATAdb, which shows its poorly conserved nature among species. This information has been cataloged in the pearl millet drought-responsive long non-coding RNA database (PMDlncRDB). The discovered lncRNAs can be used in the improvement of important traits, as well as CISPR-Cas technology, in the editing of ncRNAs in plants for trait improvement. Such a study will increase our understanding of the expression behavior of lncRNAs, as well as its underlying mechanisms under drought stress in pearl millet.
Pavan Kumar, Manmohan Dobriyal, Amey Kale, A. K. Pandey, R. S. Tomar, and Elizabeth Thounaojam
Public Library of Science (PLoS)
Tropical forest serves as an important pivotal role in terrestrial biological diversity. The present study makes an attempt to identify the concentration of species among tree diversity in Mahavir Swami Wildlife Sanctuary, Bundelkhand, India. Four important ecological indicator indices namely Shannon-Weiner index (H’), Simpson’s diversity (D), Margalef index (SR) and Pielou’s (J) indices were make the most for species diversity measurement. The research outcomes revealed that Shannon-Weiner diversity index (H/) was found to be the best index for assessing species richness while Simpson’s diversity (D) index was more suited for determining species diversity. The Shannon-Weiner index value calculated for different transects not only represent the species richness but also the species evenness in each transect. The potential application of forest diversity can be used a mechanism for forest management. The methodology will retrofit better policy implementation for maintaining the health of forest species in Mahavir Swami Wildlife Sanctuary and can be applied on other reserve forest of socio-ecological significance.
Anushree Pramanik, Sushma Tiwari, M.K. Tripathi, Sushmita Mandloi, and R.S. Tomar
Agricultural Research Communication Center
Background: Resistance to foliar fungal diseases along with oleic acid trait, are important objectives of groundnut breeding. Among foliar fungal diseases, rust and Late Leaf Spot (LLS) cause significant economic loss and high oleic trait is preferred in industry that enhances economic values of crop. Methods: Morphological characterization of the 186-groundnut germplasm lines/genotypes for ten yield attributing traits and their significance of correlation was analyzed using SPSS ver. 19 software at 1% and 5% probability level of significance. Screening for LLS and rust diseases was done employing 10X SNP assay at ICRISAT, Hyderabad, India. Selected superior groundnut germplasm line(s) were screened for presence of FAD2B allele responsible for high oleic acid traits using allele specific marker. Result: Significant and positive correlation was found between dry weight and hundred pod weight (r=0.0.801) and harvest index (r=0.0.830). Molecular characterization along with morphological characterization identified highly diversified lines of groundnut. This study reports 78 foliar fungal disease resistant groundnut germplasm lines. Selected 11 groundnut germplasm lines represented resistance against LLS and rust diseases along with FAD2B allele for oleic acid trait.
H.A. Chaudhari, V.G. Antala, N.G. Radadiya, M.K. Mahatma, and R.S. Tomar
World Researchers Associations
Understanding the mechanism of seed germination requires a sturdy selection of reference genes for expression analysis using qRT-PCR. The accurate normalization of genes becomes necessary to circumvent erroneous result, as housekeeping genes does not remain stable over the different experimental condition in various tissue or species. Reliable and stable reference gene during ethrel induced germination of groundnut seeds is not reported yet. In this study, seven candidate reference genes were selected based on previous reports in groundnut under different experimental conditions. Seeds of NRCG 14380 (dormant) and TAG 24 (non-dormant) genotypes were treated with ethrel and sampled at 0, 6, 12 and 24 hours after incubation. The stability of reference genes such as actin1 (ACT1), actin11 (ACT11), alcohol dehydrogenase (ADH3), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), glucose-6-phosphate dehydrogenase (G6PD), ubiquitin C (UBC) and α-Tubulin (TUA) was analyzed through a different statistical algorithm such as BestKeeper, NormFinder, geNorm and its consensus stability ranking was retrieved using RefFinder. Among all reference genes studied, ACT1 was found most stable reference gene in our study. Stability and reliability of ACT1 and ADH3 (most stable) reference genes were further validated through qRT- PCR with relative quantification of two germination related genes ACC oxidase1 (ACO1) and gibberellic acid regulated protein which showed consistency in their expression level. Our result revealed a stable reference gene that could be used as an internal control gene for gene expression study of ethrel treated groundnut seed germination.
Manoj K. Sharma, Shashank Singh, Neelesh Kapoor, and R. S. Tomar
Springer Nature Singapore
Sanjay Singh, Prabha Singh, R. S. Tomar, R. A. Sharma, and Shailesh K. Singh
Springer International Publishing
Sanjay Singh, Aditi Thakur, R. S. Tomar, Sushma Tiwari, and R. A. Sharma
Springer International Publishing
Chintan Kapadia, Rahul Datta, Saiyed Mufti Mahammad, Rukam Singh Tomar, Jasmin Kumar Kheni, and Sezai Ercisli
American Chemical Society (ACS)
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.
R. S. Tomar, Prabha Singh, Sushma Tiwari, Manoj Kumar Tripathi, Sanjay Singh, K. Bhojaraja Naik, Chandan Kumar Singh, and Shailesh Kumar Singh
Springer Nature Singapore
Hiral Desai, Rasmieh Hamid, Zahra Ghorbanzadeh, Nishant Bhut, Shital M. Padhiyar, Jasminkumar Kheni, and Rukam S. Tomar
Springer Science and Business Media LLC
AbstractLittle millet is a climate-resilient and high-nutrient value plant. The lack of molecular markers severely limits the adoption of modern genomic approaches in millet breeding studies. Here the transcriptome of three samples were sequenced. A total of 4443 genic-SSR motifs were identified in 30,220 unigene sequences. SSRs were found at a rate of 12.25 percent, with an average of one SSR locus per 10 kb. Among different repeat motifs, tri-nucleotide repeat (66.67) was the most abundant one, followed by di- (27.39P), and tetra- (3.83P) repeats. CDS contained fewer motifs with the majority of tri-nucleotides, while 3′ and 5′ UTR carry more motifs but have shorter repeats. Functional annotation of unigenes containing microsatellites, revealed that most of them were linked to metabolism, gene expression regulation, and response to environmental stresses. Fifty primers were randomly chosen and validated in five little millet and 20 minor millet genotypes; 48% showed polymorphism, with a high transferability (70%) rate. Identified microsatellites can be a noteworthy resource for future research into QTL-based breeding, genetic resource conservation, MAS selection, and evolutionary genetics.
Pradeep Kumar Yadav, Sushma Tiwari, Aasha Kushwah, M K Tripathi, Neha Gupta, R S Tomar, and V S Kandalkar
Springer Science and Business Media LLC
Nidhi Radadiya, Naman Mangukia, Virali Antala, Hiral Desai, Hemangini Chaudhari, T. L. Dholaria, Denish Dholaria, Rukam Singh Tomar, B. A. Golakiya, and Mahesh Kumar Mahatma
Springer Science and Business Media LLC
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,et al.
MDPI AG
Identification and diversity analysis of fungi is greatly challenging. Though internal transcribed spacer (ITS), region-based DNA fingerprinting works as a “gold standard” for most of the fungal species group, it cannot differentiate between all the groups and cryptic species. Therefore, it is of paramount importance to find an alternative approach for strain differentiation. Availability of whole genome sequence data of nearly 2000 fungal species are a promising solution to such requirement. We present whole genome sequence-based world’s largest microsatellite database, FungSatDB having >19M loci obtained from >1900 fungal species/strains using >4000 assemblies across globe. Genotyping efficacy of FungSatDB has been evaluated by both in-silico and in-vitro PCR. By in silico PCR, 66 strains of 8 countries representing four continents were successfully differentiated. Genotyping efficacy was also evaluated by in vitro PCR in four fungal species. This approach overcomes limitation of ITS in species, strain signature, and diversity analysis. It can accelerate fungal genomic research endeavors in agriculture, industrial, and environmental management.
Riddhi Rajyaguru, Nataraja Maheshala, Chandrashekar Mootapally, Neelam Nathani, Rukamsingh Tomar, Hiren Bhalani, and Priyanka Sharma
CRC Press