Surbhi Kumawat
@nabi.res.in
National Agri-Food Biotechnology Institute (NABI), Mohali Punjab
Scopus Publications
Scholar Citations
Scholar h-index
Scholar i10-index
Scopus Publications
Surbhi Kumawat and Jae Young Choi
Wiley
One of the most fascinating phenomena in evolutionary biology is the rapid evolution of genes with conserved functions across the tree of life. Because the cellular and organismal development processes are highly conserved across eukaryotes, a naive evolutionary expectation is that the genes involved in those processes would also be under high selective constraint and evolve extremely slowly. However, we now know that evolutionarily young genes can rapidly acquire crucial viability functions and even evolutionarily old genes can have unexpected levels of rapid evolution within specific lineages (Talbert et al. 2004). These studies have led to novel insights of function and evolution in molecular systems that are universally important for almost all organisms. This article is protected by copyright. All rights reserved.
Vandana Thakral, Yogesh Sharma, Rushil Mandlik, Surbhi Kumawat, Gunvant Patil, Humira Sonah, Paul Isenring, Richard Bélanger, Tilak Raj Sharma, and Rupesh Deshmukh
Elsevier BV
Gaurav Raturi, Surbhi Kumawat, Rushil Mandlik, Deepak Duhan, Vandana Thakral, Sreeja Sudhakaran, Chet Ram, Humira Sonah, and Rupesh Deshmukh
Springer Science and Business Media LLC
Gunashri Padalkar, Rushil Mandlik, Sreeja Sudhakaran, Sanskriti Vats, Surbhi Kumawat, Virender Kumar, Vineet Kumar, Anita Rani, Milind B. Ratnaparkhe, Pravin Jadhav,et al.
Elsevier BV
Nitika Rajora, Vandana Thakral, Geetika, Sanskriti Vats, Gunashri Padalkar, Sreeja Sudhakaran, Surbhi Kumawat, Humira Sonah, and Rupesh Deshmukh
Springer Science and Business Media LLC
Virender Kumar, Vinod Goyal, Rushil Mandlik, Surbhi Kumawat, Sreeja Sudhakaran, Gunashri Padalkar, Nitika Rana, Rupesh Deshmukh, Joy Roy, Tilak Raj Sharma,et al.
MDPI AG
Soybean with enriched nutrients has emerged as a prominent source of edible oil and protein. In the present study, a meta-analysis was performed by integrating quantitative trait loci (QTLs) information, region-specific association and transcriptomic analysis. Analysis of about a thousand QTLs previously identified in soybean helped to pinpoint 14 meta-QTLs for oil and 16 meta-QTLs for protein content. Similarly, region-specific association analysis using whole genome re-sequenced data was performed for the most promising meta-QTL on chromosomes 6 and 20. Only 94 out of 468 genes related to fatty acid and protein metabolic pathways identified within the meta-QTL region were found to be expressed in seeds. Allele mining and haplotyping of these selected genes were performed using whole genome resequencing data. Interestingly, a significant haplotypic association of some genes with oil and protein content was observed, for instance, in the case of FAD2-1B gene, an average seed oil content of 20.22% for haplotype 1 compared to 15.52% for haplotype 5 was observed. In addition, the mutation S86F in the FAD2-1B gene produces a destabilizing effect of (ΔΔG Stability) −0.31 kcal/mol. Transcriptomic analysis revealed the tissue-specific expression of candidate genes. Based on their higher expression in seed developmental stages, genes such as sugar transporter, fatty acid desaturase (FAD), lipid transporter, major facilitator protein and amino acid transporter can be targeted for functional validation. The approach and information generated in the present study will be helpful in the map-based cloning of regulatory genes, as well as for marker-assisted breeding in soybean.
Ruchi Bansal, Surbhi Kumawat, Pallavi Dhiman, Sreeja Sudhakaran, Nitika Rana, Rajdeep Jaswal, Akshay Singh, Humira Sonah, Tilak Raj Sharma, and Rupesh Deshmukh
Springer Science and Business Media LLC
Gaurav Raturi, Yogesh Sharma, Rushil Mandlik, Surbhi Kumawat, Nitika Rana, Hena Dhar, Durgesh Kumar Tripathi, Humira Sonah, Tilak Raj Sharma, and Rupesh Deshmukh
MDPI AG
Silicon (Si) is gaining widespread attention due to its prophylactic activity to protect plants under stress conditions. Despite Si’s abundance in the earth’s crust, most soils do not have enough soluble Si for plants to absorb. In the present study, a silicate-solubilizing bacterium, Enterobacter sp. LR6, was isolated from the rhizospheric soil of rice and subsequently characterized through whole-genome sequencing. The size of the LR6 genome is 5.2 Mb with a GC content of 54.9% and 5182 protein-coding genes. In taxogenomic terms, it is similar to E. hormaechei subsp. xiangfangensis based on average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH). LR6 genomic data provided insight into potential genes involved in stress response, secondary metabolite production, and growth promotion. The LR6 genome contains two aquaporins, of which the aquaglyceroporin (GlpF) is responsible for the uptake of metalloids including arsenic (As) and antimony (Sb). The yeast survivability assay confirmed the metalloid transport activity of GlpF. As a biofertilizer, LR6 isolate has a great deal of tolerance to high temperatures (45 °C), salinity (7%), and acidic environments (pH 9). Most importantly, the present study provides an understanding of plant-growth-promoting activity of the silicate-solubilizing bacterium, its adaptation to various stresses, and its uptake of different metalloids including As, Ge, and Si.
Sanskriti Vats, Surbhi Kumawat, Jashandeep Brar, Sukhmandeep Kaur, Karmveer Yadav, Sayali G. Magar, Pravin V. Jadhav, Prafull Salvi, Humira Sonah, Sandhya Sharma,et al.
Elsevier BV
Vandana Thakral, Himanshu Yadav, Gunashri Padalkar, Surbhi Kumawat, Gaurav Raturi, Virender Kumar, Rushil Mandlik, Nitika Rajora, and Manipal Singh
Wiley
Surbhi Kumawat, Gaurav Raturi, Pallavi Dhiman, Sreeja Sudhakarn, Nitika Rajora, Vandana Thakral, Himanshu Yadav, Gunashri Padalkar, Yogesh Sharma, Vinaykumar Rachappanavar,et al.
Wiley
Sanskriti Vats, Yogesh Sharma, Virender Kumar, Rushil Mandlik, Surbhi Kumawat, Himanshu Yadav, Pallavi Dhiman, Vandana Thakral, Md Aminul Islam, and Sreeja Sudhakaran
Wiley
Nitika Rana, Surbhi Kumawat, Virender Kumar, Ruchi Bansal, Rushil Mandlik, Pallavi Dhiman, Gunvant B. Patil, Rupesh Deshmukh, Tilak Raj Sharma, and Humira Sonah
MDPI AG
Nutritional quality improvement of rice is the key to ensure global food security. Consequently, enormous efforts have been made to develop genomics and transcriptomics resources for rice. The available omics resources along with the molecular understanding of trait development can be utilized for efficient exploration of genetic resources for breeding programs. In the present study, 80 genes known to regulate the nutritional and cooking quality of rice were extensively studied to understand the haplotypic variability and gene expression dynamics. The haplotypic variability of selected genes were defined using whole-genome re-sequencing data of ~4700 diverse genotypes. The analytical workflow identified 133 deleterious single-nucleotide polymorphisms, which are predicted to affect the gene function. Furthermore, 788 haplotype groups were defined for 80 genes, and the distribution and evolution of these haplotype groups in rice were described. The nucleotide diversity for the selected genes was significantly reduced in cultivated rice as compared with that in wild rice. The utility of the approach was successfully demonstrated by revealing the haplotypic association of chalk5 gene with the varying degree of grain chalkiness. The gene expression atlas was developed for these genes by analyzing RNA-Seq transcriptome profiling data from 102 independent sequence libraries. Subsequently, weighted gene co-expression meta-analyses of 11,726 publicly available RNAseq libraries identified 19 genes as the hub of interactions. The comprehensive analyses of genetic polymorphisms, allelic distribution, and gene expression profiling of key quality traits will help in exploring the most desired haplotype for grain quality improvement. Similarly, the information provided here will be helpful to understand the molecular mechanism involved in the development of nutritional and cooking quality traits in rice.
Surbhi Kumawat, Yogesh Sharma, Sanskriti Vats, Sreeja Sudhakaran, Shivani Sharma, Rushil Mandlik, Gaurav Raturi, Virender Kumar, Nitika Rana, Amit Kumar,et al.
Springer Science and Business Media LLC
Rushil Mandlik, Pankaj Singla, Surbhi Kumawat, Praveen Khatri, Waquar Ansari, Anuradha Singh, Yogesh Sharma, Archana Singh, Amol Solanke, Altafhusain Nadaf,et al.
Elsevier BV
Sanskriti Vats, Ruchi Bansal, Nitika Rana, Surbhi Kumawat, Vacha Bhatt, Pravin Jadhav, Vijay Kale, Atul Sathe, Humira Sonah, Ravin Jugdaohsingh,et al.
Informa UK Limited
Surbhi Kumawat, Bharti Aggarwal, Nitika Rana, Rushil Mandlik, Akrity Mehra, S. M. Shivaraj, Humira Sonah, and Rupesh Deshmukh
Springer Science and Business Media LLC
Surbhi Kumawat, Praveen Khatri, Ashique Ahmed, Sanskriti Vats, Virender Kumar, Rajdeep Jaswal, Ying Wang, Pei Xu, Rushil Mandlik, S.M. Shivaraj,et al.
Elsevier BV
Aquaporins (AQPs) facilitates the transport of small solutes like water, urea, carbon dioxide, boron, and silicon (Si) and plays a critical role in important physiological processes. In this study, genome-wide characterization of AQPs was performed in bottle gourd. A total of 36 AQPs were identified in the bottle gourd, which were subsequently analyzed to understand the pore-morphology, exon-intron structure, subcellular-localization. In addition, available transcriptome data was used to study the tissue-specific expression. Several AQPs showed tissue-specific expression, more notably the LsiTIP3-1 having a high level of expression in flowers and fruits. Based on the in-silico prediction of solute specificity, LsiNIP2-1 was predicted to be a Si transporter. Silicon was quantified in different tissues, including root, young leaves, mature leaves, tendrils, and fruits of bottle gourd plants. More than 1.3% Si (d.w.) was observed in bottle gourd leaves, testified the in-silico predictions. Silicon deposition evaluated with an energy-dispersive X-ray coupled with a scanning electron microscope showed a high Si accumulation in the shaft of leaf trichomes. Similarly, co-localization of Si with arsenic and antimony was observed. Expression profiling performed with real-time quantitative PCR showed differential expression of AQPs in response to Si supplementation. The information provided in the present study will be helpful to better understand the AQP transport mechanism, particularly Si and other metalloids transport and localization in plants.
Virender Kumar, Sanskriti Vats, Surbhi Kumawat, Ashita Bisht, Vacha Bhatt, S. M. Shivaraj, Gunashri Padalkar, Vinod Goyal, Sajad Zargar, Sanjay Gupta,et al.
Informa UK Limited
Nirbhay Kumar, Surbhi Kumawat, Praveen Khatri, Pankaj Singla, Gitanjali Tandon, Vacha Bhatt, Suhas Shinde, Gunvant B. Patil, Humira Sonah, and Rupesh Deshmukh
Elsevier BV
Nitika Rana, Mohammed Saba Rahim, Gazaldeep Kaur, Ruchi Bansal, Surbhi Kumawat, Joy Roy, Rupesh Deshmukh, Humira Sonah, and Tilak Raj Sharma
Informa UK Limited
Shweta Singh, Vacha Bhatt, Virender Kumar, Surbhi Kumawat, Praveen Khatri, Pankaj Singla, S.M. Shivaraj, Altaf Nadaf, Rupesh Deshmukh, Tilak Raj Sharma,et al.
MDPI AG
Aquaporins (AQPs) play a pivotal role in the cellular transport of water and many other small solutes, influencing many physiological and developmental processes in plants. In the present study, extensive bioinformatics analysis of AQPs was performed in Aquilegia coerulea L., a model species belonging to basal eudicots, with a particular focus on understanding the AQPs role in the developing petal nectar spur. A total of 29 AQPs were identified in Aquilegia, and their phylogenetic analysis performed with previously reported AQPs from rice, poplar and Arabidopsis depicted five distinct subfamilies of AQPs. Interestingly, comparative analysis revealed the loss of an uncharacterized intrinsic protein II (XIP-II) group in Aquilegia. The absence of the entire XIP subfamily has been reported in several previous studies, however, the loss of a single clade within the XIP family has not been characterized. Furthermore, protein structure analysis of AQPs was performed to understand pore diversity, which is helpful for the prediction of solute specificity. Similarly, an AQP AqcNIP2-1 was identified in Aquilegia, predicted as a silicon influx transporter based on the presence of features such as the G-S-G-R aromatic arginine selectivity filter, the spacing between asparagine-proline-alanine (NPA) motifs and pore morphology. RNA-seq analysis showed a high expression of tonoplast intrinsic proteins (TIPs) and plasma membrane intrinsic proteins (PIPs) in the developing petal spur. The results presented here will be helpful in understanding the AQP evolution in Aquilegia and their expression regulation, particularly during floral development.
Sheelavanta M. Shivaraj, Sanskriti Vats, Javaid A. Bhat, Priyanka Dhakte, Vinod Goyal, Praveen Khatri, Surbhi Kumawat, Akshay Singh, Manoj Prasad, Humira Sonah,et al.
Wiley
Juhi Chaudhary, Praveen Khatri, Pankaj Singla, Surbhi Kumawat, Anu Kumari, Vinaykumar R, Amit Vikram, Salesh Kumar Jindal, Hemant Kardile, Rahul Kumar,et al.
MDPI AG
Tomato, one of the most important crops worldwide, has a high demand in the fresh fruit market and processed food industries. Despite having considerably high productivity, continuous supply as per the market demand is hard to achieve, mostly because of periodic losses occurring due to biotic as well as abiotic stresses. Although tomato is a temperate crop, it is grown in almost all the climatic zones because of widespread demand, which makes it challenge to adapt in diverse conditions. Development of tomato cultivars with enhanced abiotic stress tolerance is one of the most sustainable approaches for its successful production. In this regard, efforts are being made to understand the stress tolerance mechanism, gene discovery, and interaction of genetic and environmental factors. Several omics approaches, tools, and resources have already been developed for tomato growing. Modern sequencing technologies have greatly accelerated genomics and transcriptomics studies in tomato. These advancements facilitate Quantitative trait loci (QTL) mapping, genome-wide association studies (GWAS), and genomic selection (GS). However, limited efforts have been made in other omics branches like proteomics, metabolomics, and ionomics. Extensive cataloging of omics resources made here has highlighted the need for integration of omics approaches for efficient utilization of resources and a better understanding of the molecular mechanism. The information provided here will be helpful to understand the plant responses and the genetic regulatory networks involved in abiotic stress tolerance and efficient utilization of omics resources for tomato crop improvement.