Rushil Mandlik
@nabi.res.in
National Agri-Food Biotechnology Institute, Mohali, India
Scopus Publications
Scholar Citations
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Scopus Publications
Vandana Thakral, Gaurav Raturi, Sreeja Sudhakaran, Rushil Mandlik, Yogesh Sharma, S.M. Shivaraj, Durgesh Kumar Tripathi, Humira Sonah, and Rupesh Deshmukh
Elsevier BV
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
Gaurav Raturi, Anchal Chaudhary, Varnika Rana, Rushil Mandlik, Yogesh Sharma, Vitthal Barvkar, Prafull Salvi, Durgesh Kumar Tripathi, Jagdeep Kaur, Rupesh Deshmukh,et al.
Elsevier BV
Sanskriti Vats, Virender Kumar, Rushil Mandlik, Gunvant Patil, Humira Sonah, Joy Roy, Tilak Raj Sharma, and Rupesh Deshmukh
MDPI AG
Solanum lycopersicum cv. Pusa Ruby (PR) is a superior tomato cultivar routinely used as a model tomato variety. Here, we report a reference-guided genome assembly for PR, covering 97.6% of the total single-copy genes in the solanales order. The PR genome contains 34,075 genes and 423,288 variants, out of which 127,131 are intragenic and 1232 are of high impact. The assembly was packaged according to PanSol guidelines (N50 = 60,396,827) with the largest scaffold measuring 85 megabases. The similarity of the PR genome assembly to Heinz1706, M82, and Fla.8924 was measured and the results suggest PR has the lowest affinity towards the hybrid Fla.8924. We then analyzed the regeneration efficiency of PR in comparison to another variety, Pusa Early Dwarf (PED). PR was found to have a high regeneration rate (45.51%) and therefore, we performed allele mining for genes associated with regeneration and found that only AGAMOUS-LIKE15 has a null mutation. Further, allele mining for fruit quality-related genes was also executed. The PR genome has an Ovate mutation leading to round fruit shape, causing economically undesirable fruit cracking. This genomic data can be potentially used for large scale crop improvement programs as well as functional annotation studies.
Yogesh Sharma, Praveen Soni, Gaurav Raturi, Rushil Mandlik, Vinay Kumar Rachappanavar, Manish Kumar, Prafull Salvi, Durgesh Kumar Tripathi, Hasthi Ram, and Rupesh Deshmukh
Elsevier BV
Rushil Mandlik, Shivani Sharma, Priyadarshini Rout, Shweta Singh, Gaurav Raturi, Nitika Rana, Humira Sonah, Rupesh Deshmukh, SM Shivaraj, Satyabrata Nanda,et al.
Informa UK Limited
Zhou Zhang, Sunil S. Gangurde, Songbin Chen, Rushil Ramesh Mandlik, Haiyan Liu, Rupesh Deshmukh, Jialing Xu, Zhongkang Wu, Yanbin Hong, and Yin Li
Frontiers Media SA
The 14-3-3 protein is a kind of evolutionary ubiquitous protein family highly conserved in eukaryotes. Initially, 14-3-3 proteins were reported in mammalian nervous tissues, but in the last decade, their role in various metabolic pathways in plants established the importance of 14-3-3 proteins. In the present study, a total of 22 14-3-3 genes, also called general regulatory factors (GRF), were identified in the peanut (Arachis hypogaea) genome, out of which 12 belonged to the ε group, whereas 10 of them belonged to the non- ε-group. Tissue-specific expression of identified 14-3-3 genes were studied using transcriptome analysis. The peanut AhGRFi gene was cloned and transformed into Arabidopsis thaliana. The investigation of subcellular localization indicated that AhGRFi is localized in the cytoplasm. Overexpression of the AhGRFi gene in transgenic Arabidopsis showed that under exogenous 1-naphthaleneacetic acid (NAA) treatment, root growth inhibition in transgenic plants was enhanced. Further analysis indicated that the expression of auxin-responsive genes IAA3, IAA7, IAA17, and SAUR-AC1 was upregulated and GH3.2 and GH3.3 were downregulated in transgenic plants, but the expression of GH3.2, GH3.3, and SAUR-AC1 showed opposite trends of change under NAA treatment. These results suggest that AhGRFi may be involved in auxin signaling during seedling root development. An in-depth study of the molecular mechanism of this process remains to be further explored.
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.
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.
Vandana Thakral, Himanshu Yadav, Gunashri Padalkar, Surbhi Kumawat, Gaurav Raturi, Virender Kumar, Rushil Mandlik, Nitika Rajora, and Manipal Singh
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
S M Shivaraj, Rushil Mandlik, Javaid Akhter Bhat, Gaurav Raturi, Rivka Elbaum, Lux Alexander, Durgesh Kumar Tripathi, Rupesh Deshmukh, and Humira Sonah
Oxford University Press (OUP)
Abstract Silicon (Si) is widely accepted as a beneficial element for plants. Despite the substantial progress made in understanding Si transport mechanisms and modes of action in plants, several questions remain unanswered. In this review, we discuss such outstanding questions and issues commonly encountered by biologists studying the role of Si in plants in relation to Si bioavailability. In recent years, advances in our understanding of the role of Si-solubilizing bacteria and the efficacy of Si nanoparticles have been made. However, there are many unknown aspects associated with structural and functional features of Si transporters, Si loading into the xylem, and the role of specialized cells like silica cells and compounds preventing Si polymerization in plant tissues. In addition, despite several 1,000 reports showing the positive effects of Si in high as well as low Si-accumulating plant species, the exact roles of Si at the molecular level are yet to be understood. Some evidence suggests that Si regulates hormonal pathways and nutrient uptake, thereby explaining various observed benefits of Si uptake. However, how Si modulates hormonal pathways or improves nutrient uptake remains to be explained. Finally, we summarize the knowledge gaps that will provide a roadmap for further research on plant silicon biology, leading to an exploration of the benefits of Si uptake to enhance crop production.
Surbhi Kumawat, Bharti Aggarwal, Nitika Rana, Rushil Mandlik, Akrity Mehra, S. M. Shivaraj, Humira Sonah, and Rupesh Deshmukh
Springer Science and Business Media LLC
Atul Prakash Sathe, Amit Kumar, Rushil Mandlik, Gaurav Raturi, Himanshu Yadav, Nirbhay Kumar, S.M. Shivaraj, Rajdeep Jaswal, Ritu Kapoor, Santosh Kumar Gupta,et al.
Elsevier BV
Rice blast caused by Magnaporthe oryzae and sheath blight caused by Rhizoctonia solani, are the two major diseases of rice that cause enormous losses in rice production worldwide. Identification and utilization of broad-spectrum resistance resources have been considered sustainable and effective strategies. However, the majority of the resistance genes and QTLs identified have often been found to be race-specific, and their resistance is frequently broken down due to continuous exposure to the pathogen. Therefore, integrated approaches to improve plant resistance against such devastating pathogen have great importance. Silicon (Si), a beneficial element for plant growth, has shown to provide a prophylactic effect against many pathogens. The application of Si helps the plants to combat the disease-causing pathogens, either through its deposition in different parts of the plant or through modulation/induction of specific defense genes by yet an unknown mechanism. Some reports have shown that Si imparts resistance to rice blast and sheath blight. The present review summarizes the mechanism of Si transport and deposition and its effect on rice growth and development. A special emphasis has been given to explore the existing evidence showing Si mediated blast and sheath blight resistance and the mechanism involved in resistance. This review will help to understand the prophylactic effects of Si against sheath blight and blast disease at the mechanical, physiological, and genetic levels. The information provided here will help develop a strategy to explore Si derived benefits for sustainable rice production.
B.N. Devanna, Rushil Mandlik, Gaurav Raturi, Sreeja S. Sudhakaran, Yogesh Sharma, Shivani Sharma, Nitika Rana, Ruchi Bansal, Vitthal Barvkar, Durgesh K. Tripathi,et al.
Elsevier BV
Silicon (Si) is an omnipresent and second most abundant element in the soil lithosphere after oxygen. Silicon being a beneficial element imparts several benefits to the plants and animals. In many plant species, including the cereals the uptake of Si from the soil even exceeds the uptake of essential nutrients. Cereals are the monocots which are known to accumulate a high amount of Si, and reaping maximum benefits associated with it. Cereals contribute a high amount of Si to the human diet compared to other food crops. In the present review, we have summarized distribution of the dietary Si in cereals and its role in the animal and human health. The Si derived benefits in cereals, specifically with respect to biotic and abiotic stress tolerance has been described. We have also discussed the molecular mechanism involved in the Si uptake in cereals, evolution of the Si transport mechanism and genetic variation in the Si concentration among different cultivars of the same species. Various genetic mutants deficient in the Si uptake have been developed and many QTLs governing the Si accumulation have been identified in cereals. The existing knowledge about the Si biology and available resources needs to be explored to understand and improve the Si accumulation in crop plants to achieve sustainability in agriculture.
Mrinalini Manna, Tanika Thakur, Oceania Chirom, Rushil Mandlik, Rupesh Deshmukh, and Prafull Salvi
Wiley
Amid apprehension of global climate change, crop plants are inevitably confronted with a myriad of abiotic stress factors during their growth that inflicts a serious threat to their development and overall productivity. These abiotic stresses comprise extreme temperature, pH, high saline soil, and drought stress. Among different abiotic stresses, drought is considered the most calamitous stressor with its serious impact on the crops' yield stability. The development of climate-resilient crops that withstands reduced water availability is a major focus of the scientific fraternity to ensure the food security of the sharply increasing population. Numerous studies aim to recognize the key regulators of molecular and biochemical processes associated with drought stress tolerance response. A few potential candidates are now considered as promising targets for crop improvement. Transcription factors act as a key regulatory switch controlling the gene expression of diverse biological processes and, eventually, the metabolic processes. Understanding the role and regulation of the transcription factors will facilitate the crop improvement strategies intending to develop and deliver agronomically-superior crops. Therefore, in this review, we have emphasized the molecular avenues of the transcription factors that can be exploited to engineer drought tolerance potential in crop plants. We have discussed the molecular role of several transcription factors, such as bZIP, DREB, DOF, HSF, MYB, NAC, TCP and WRKY. We have also highlighted candidate transcription factors that can be used for the development of drought-tolerant crops. This article is protected by copyright. All rights reserved.
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.
Sanskriti Vats, Sreeja Sudhakaran, Anupriya Bhardwaj, Rushil Mandlik, Yogesh Sharma, Sudhir Kumar, Durgesh Kumar Tripathi, Humira Sonah, Tilak Raj Sharma, and Rupesh Deshmukh
Elsevier BV
Uptake of hazardous metal(loid)s adversely affects plants and imposes a threat to the entire food chain. Here, the role of aquaporins (AQPs) providing tolerance against hazardous metal(loid)s in plants is discussed to provide a perspective on the present understanding, knowledge gaps, and opportunities. Plants adopt complex molecular and physiological mechanisms for better tolerance, adaptability, and survival under metal(loid)s stress. Water conservation in plants is one such primary strategies regulated by AQPs, a family of channel-forming proteins facilitating the transport of water and many other solutes. The strategy is more evident with reports suggesting differential expression of AQPs adopted by plants to cope with the heavy metal stress. In this regard, numerous studies showing enhanced tolerance against hazardous elements in plants due to AQPs activity are discussed. Consequently, present understanding of various aspects of AQPs, such as tertiary-structure, transport activity, solute-specificity, differential expression, gating mechanism, and subcellular localization, are reviewed. Similarly, various tools and techniques are discussed in detail aiming at efficient utilization of resources and knowledge to combat metal(loid)s stress. The scope of AQP transgenesis focusing on heavy metal stresses is also highlighted. The information provided here will be helpful to design efficient strategies for the development of metal(loid)s stress-tolerant crops.
Roberto Berni, Rushil Mandlik, Jean-Francois Hausman, and Gea Guerriero
Wiley
Silicon, a quasi-essential element for plants, improves vigour and resilience under stress. Recently, studies on textile hemp (Cannabis sativa L.) showed its genetic predisposition to uptake silicic acid and accumulate it as silica in epidermal leaf cells and trichomes. Here, microscopy, silicon quantification and gene expression analysis of candidate genes involved in salt stress were performed in hemp to investigate whether the metalloid protects against salinity. The results obtained with microscopy reveal that silicon treatment ameliorated the symptoms of salinity in older fan leaves, where the xylem tissue showed vessels with a wider lumen. In younger ones, it was difficult to assess any mitigation of stress symptoms after silicon application. At the gene level, salinity with and without silicon induced the expression of a putative Si efflux transporter gene 2 (Lsi2). The addition of the metalloid did not result in any statistically significant changes in the expression of genes involved in stress response, although a trend towards a decrease was observed. In conclusion, the results showed that hemp stress symptoms can be alleviated in older leaves by silicon application, that the metalloid is accumulated in fan leaves and highlight one putative rice Lsi2 ortholog as responsive to salinity. This article is protected by copyright. All rights reserved.