Dr. Soni Gupta
@csjmu.ac.in
Assistant Professor, Department of Plant Sciences
Chhatrapati Shahuji Maharaj University Kanpur-208024
RESEARCH INTERESTS
Plant Biotechnology, reverse genetics, functional genomics, medicinal plants
Scopus Publications
Scholar Citations
Scholar h-index
Scholar i10-index
Scopus Publications
Ashish Kumar, Anil Kumar Gupta, Saba Siddiqui, Soni Gupta, R.K. Lal, Abhilasha Srivastava, and Mohammed Haris Siddiqui
Elsevier BV
Soni Gupta, A. Kumar, A.K. Gupta, A.C. Jnanesha, M. Talha, A. Srivastava, and R.K. Lal
Elsevier BV
Kapil Sharma, Soni Gupta, Supriya Sarma, Meenakshi Rai, Yellamaraju Sreelakshmi, and Rameshwar Sharma
Wiley
The role of ethylene in plant development is mostly inferred from its exogenous application. The usage of the mutants affecting ethylene biosynthesis proffers a better alternative to decipher its role. In tomato, 1-aminocyclopropane carboxylic acid synthase2 (ACS2) is a key enzyme regulating ripening-specific ethylene biosynthesis. We characterized two contrasting acs2 mutants; acs2-1 overproduces ethylene, has higher ACS activity, and increased protein levels, while acs2-2 is an ethylene under-producer, displays lower ACS activity and protein levels than wild type. Consistent with high/low ethylene emission, the mutants show opposite phenotypes, physiological responses, and metabolomic profiles than the wild type. The acs2-1 showed early seed germination, faster leaf senescence, and accelerated fruit ripening. Conversely, acs2-2 had delayed seed germination, slower leaf senescence, and prolonged fruit ripening. The phytohormone profiles of mutants were mostly opposite in the leaves and fruits. The faster/slower senescence of acs2-1/acs2-2 leaves correlated with the endogenous ethylene/zeatin ratio. The genetic analysis showed that the metabolite profiles of respective mutants co-segregated with the homozygous mutant progeny. Our results uncover that besides ripening, ACS2 participates in the vegetative and reproductive development of tomato. The distinct influence of ethylene on phytohormone profiles indicates the intertwining of ethylene action with other phytohormones in regulating plant development.
Abhilasha Srivastava, Soni Gupta, Karuna Shanker, Namita Gupta, Anil Kumar Gupta, and R.K. Lal
Elsevier BV
Sharad K. Singh, Soni Gupta, Noor Ahmad, Ashutosh K. Shukla, Ajit K. Shasany, Raj K. Lal, Madan M. Gupta, and Om P. Dhawan
Elsevier BV
S. Gupta, A. Khan, and O. P. Dhawan
Scientific Societies
Vijee Mohan, Soni Gupta, Sherinmol Thomas, Hanjabam Mickey, Chaitanya Charakana, Vineeta Singh Chauhan, Kapil Sharma, Rakesh Kumar, Kamal Tyagi, Supriya Sarma,et al.
Public Library of Science (PLoS)
Domestication of tomato has resulted in large diversity in fruit phenotypes. An intensive phenotyping of 127 tomato accessions from 20 countries revealed extensive morphological diversity in fruit traits. The diversity in fruit traits clustered the accessions into nine classes and identified certain promising lines having desirable traits pertaining to total soluble salts (TSS), carotenoids, ripening index, weight and shape. Factor analysis of the morphometric data from Tomato Analyzer showed that the fruit shape is a complex trait shared by several factors. The 100% variance between round and flat fruit shapes was explained by one discriminant function having a canonical correlation of 0.874 by stepwise discriminant analysis. A set of 10 genes (ACS2, COP1, CYC-B, RIN, MSH2, NAC-NOR, PHOT1, PHYA, PHYB and PSY1) involved in various plant developmental processes were screened for SNP polymorphism by EcoTILLING. The genetic diversity in these genes revealed a total of 36 non-synonymous and 18 synonymous changes leading to the identification of 28 haplotypes. The average frequency of polymorphism across the genes was 0.038/Kb. Significant negative Tajima’D statistic in two of the genes, ACS2 and PHOT1 indicated the presence of rare alleles in low frequency. Our study indicates that while there is low polymorphic diversity in the genes regulating plant development, the population shows wider phenotype diversity. Nonetheless, morphological and genetic diversity of the present collection can be further exploited as potential resources in future.
Soni Gupta, Chaitanya Charakana, Yellamaraju Sreelakshmi, and Rameshwar Sharma
Springer Science and Business Media LLC
BackgroundTargeting Induced Local Lesions in Genomes (TILLING) is a high throughput reverse genetics tool which detects mismatches (single point mutations or small indels) in large number of individuals of mutagenized populations. Currently, TILLING is intensively used for genomics assisted molecular breeding of several crop plants for desired traits. Most commonly used platform for mutation detection is Li-COR DNA Analyzer, where PCR amplified products treated with single strand mismatch specific nuclease are resolved on denaturing gels. The molecular size of any cut product can be easily estimated by comparing with IR dye labeled markers of known sizes. Similar fluorescent dye labeled size markers are also used for several genotyping experiments. Currently, commercially available size standards are expensive and are restricted up to only 700 bp which renders estimation of products of sizes greater than 700 bases inaccurate.FindingsA simple protocol was developed for labeling 5' end of multiple DNA size markers with fluorescent dyes. This method involves cloning a pool of different size markers of DNA in a plasmid vector. PCR amplification of plasmid using IR dye labeled universal primers generates 5' fluorescent labeled products of various sizes. The size of products constituting the ladder can be customized as per the need. The generated size markers can be used without any further purification and were found to be stable up to one year at -20°C.ConclusionsA simple method was developed for generating fluorescent dye labeled size standards. This method can be customized to generate different size standards as per experimental needs. The protocol described can also be adapted for developing labeled size standards for detection on platforms other than Li-COR i.e. other than infra red range of the spectrum.
Yellamaraju Sreelakshmi, Soni Gupta, Reddaiah Bodanapu, Vineeta Singh Chauhan, Mickey Hanjabam, Sherinmol Thomas, Vijee Mohan, Sulabha Sharma, Rajeswari Srinivasan, and Rameshwar Sharma
Springer Science and Business Media LLC
Abstract Background TILLING (Targeting Induced Local Lesions in Genomes) is a reverse genetics procedure for identifying point mutations in selected gene(s) amplified from a mutagenized population using high-throughput detection platforms such as slab gel electrophoresis, capillary electrophoresis or dHPLC. One essential pre-requisite for TILLING is genomic DNA isolation from a large population for PCR amplification of selected target genes. It also requires multiplexing of genomic DNA isolated from different individuals (pooling) in typically 8-fold pools, for mutation scanning, and to minimize the number of PCR amplifications, which is a strenuous and long-drawn-out work. We describe here a simplified procedure of multiplexing, NEATTILL (Nucleic acid Extraction from Arrayed Tissue for TILLING), which is rapid and equally efficient in assisting mutation detection. Results The NEATTILL procedure was evaluated for the tomato TILLING platform and was found to be simpler and more efficient than previously available methods. The procedure consisted of pooling tissue samples, instead of nucleic acid, from individual plants in 96-well plates, followed by DNA isolation from the arrayed samples by a novel protocol. The three variants of the NEATTILL procedure (vast, in-depth and intermediate) can be applied across various genomes depending upon the population size of the TILLING platform. The 2-D pooling ensures the precise confirmation of the coordinates of the positive mutant line while scanning complementary plates. Choice of tissue for arraying and nucleic acid isolation is discussed in detail with reference to tomato. Conclusion NEATTILL is a convenient procedure that can be applied to all organisms, the genomes of which have been mutagenized and are being scanned for multiple alleles of various genes by TILLING for understanding gene-to-phenotype relationships. It is a time-saving, less labour intensive and reasonably cost-effective method. Tissue arraying can cut costs by up to 90% and minimizes the risk of exposing the DNA to nucleases. Before arraying, different tissues should be evaluated for DNA quality, as the case study in tomato showed that cotyledons rather than leaves are better suited for DNA isolation. The protocol described here for nucleic acid isolation can be generally adapted for large-scale projects such as insertional mutagenesis, transgenic confirmation, mapping and fingerprinting which require isolation of DNA from large populations.
Ajit K. Shasany, Soni Gupta, Mahesh K. Gupta, Ali A. Naqvi, Janak R. Bahl, and Suman P. S. Khanuja
Wiley
Eighteen accessions of Mentha arvensis var. piperascens Holmes from the CIMAP collection (CIMAP/C01 to CIMAP/C18) consisting of wild collections and released varieties, their mutants, seed progeny and hybrids from the CIMAP gene bank were assessed for diversity through a combined morphochemical and molecular approach. Morphological characters, oil yield and essential oil components were taken into account to generate a cluster that outgrouped accession CIMAP/C05 from others. A total of 60 primers were used for RAPD and the tree generated after cluster analysis revealed accession CIMAP/C05 as the most diverse genotype. All the accessions exhibited differences in narrow range except CIMAP/C05. A wide range of compositional differences were observed in the essential oil profile of the genotypes indicating varying efficiencies of conversion of one component into other and/or existing metabolic blocks in the essential oil biosynthetic pathway in them.
Raju Naik Vankadavath, Appibhai Jakir Hussain, Reddaiah Bodanapu, Eros Kharshiing, Pinjari Osman Basha, Soni Gupta, Yellamaraju Sreelakshmi, and Rameshwar Sharma
Springer Science and Business Media LLC
Abstract Background The data generated during a course of a biological experiment/study can be sometimes be massive and its management becomes quite critical for the success of the investigation undertaken. The accumulation and analysis of such large datasets often becomes tedious for biologists and lab technicians. Most of the current phenotype data acquisition management systems do not cater to the specialized needs of large-scale data analysis. The successful application of genomic tools/strategies to introduce desired traits in plants requires extensive and precise phenotyping of plant populations or gene bank material, thus necessitating an efficient data acquisition system. Results Here we describe newly developed software "PHENOME" for high-throughput phenotyping, which allows researchers to accumulate, categorize, and manage large volume of phenotypic data. In this study, a large number of individual tomato plants were phenotyped with the "PHENOME" application using a Personal Digital Assistant (PDA) with built-in barcode scanner in concert with customized database specific for handling large populations. Conclusion The phenotyping of large population of plants both in the laboratory and in the field is very efficiently managed using PDA. The data is transferred to a specialized database(s) where it can be further analyzed and catalogued. The "PHENOME" aids collection and analysis of data obtained in large-scale mutagenesis, assessing quantitative trait loci (QTLs), raising mapping population, sampling of several individuals in one or more ecological niches etc.
Ajit K. Shasany, Soni Gupta, Mahesh K. Gupta, Anil K. Singh, Ali A. Naqvi, and Suman P. S. Khanuja
Informa UK Limited
Abstract Essential oil components of 20 Indian peppermint accessions were analyzed through GC and GC/MS and compared with the reported components found in oil samples of different countries (22 locations of 19 countries) to check the commercial potential of the germplasm collection. The comparative oil component analyses revealed the close relation of P4 and P5 (Indian collections) with Chinese and P9 to Japanese peppermint. Some of the analyzed samples (P6, P8, P11 and P17) were close to American, Canadian, European and South African oils. Essential oil profiles of Indian accessions P10, P14, P19 and P20 were quite different from others as revealed by component plot analysis. In addition to the similarities, distinct chemotypes in the germplasm were detected with unique essential oil component profiles, which have been discussed in details in this investigation. Further, Amplified fragment length polymorphism (AFLP) analysis of these 20 Indian accessions differentiated them genetically with a diversity ranging between 17–95%.
A. Samad, A. K. Shasany, Soni Gupta, P. V. Ajayakuar, M. P. Darokar, and S. P. S. Khanuja
Scientific Societies
Withania somnifera (L.) Dunal is cultivated in India as an important medicinal cash crop. The whole plant is of great importance in the Indian system of medicine and pharmaceutical industries, but the roots are the main source of active alkaloids. Some of the important alkaloids are tro-pine, pseudotropine, somniferine, colin, withaferin A, withanoides, and a few flavanoides. Typical disease symptoms include phyllody, little leaf, dense clusters of highly proliferating branches with shortened internodes, and resulting witches'-broom. The disease was first observed in and around Lucknow, Uttar Pradesh Province, India during January and February 1992. On the basis of symptoms, transmission electron microscopy (TEM), and antibiotic treatment, the causal organism was identified as a phytoplasma (4). The disease is now spreading to other parts of the country (Gujrat, Haryana, Madhya Pradesh, Punjab, and Rajasthan provinces) with a high disease incidence (70%). In this report, molecular characterization and taxonomic position of the associated phytoplasma is reported. Total genomic DNA was extracted from healthy and infected plants with a modified cetyltrimethylammoniumbromide (CTAB) buffer method. The samples were assayed for the presence of phytoplasma using polymerase chain reaction (PCR) with universal phytoplasma primers P1/P6 (2) for amplification of ribosomal 16S rDNA. PCR product was diluted by 1:200 and used directly as DNA template for nested PCR with primers R16F2n and R16R2 (1). Results showed the presence of an expected 1.5-kb rDNA fragment amplified with the direct PCR and a 1.2-kb product of the nested PCR from infected W. somnifera samples. No PCR product was observed in the healthy counterparts. The PCR assay confirmed the presence of phytoplasma as causal agent. The PCR product was cloned with TOPO TA cloning kit (Invitrogen, Carlsbad, CA) and isolated plasmids were again assessed by restriction enzyme (EcoRI) digestion before sequencing. Purified plasmids were sequenced. Partially sequenced nucleotide sequence analysis of 16SrRNA gene cloned from W. somnifera phytoplasma showed high similarity with several isolates of the 16SrVI group of phytoplasmas. The highest nucleotide matching (99 and 98%) was observed with Centaurea solstitialis virescence phytoplasma (Genbank Accession No. AY270156) and Periwinkle little leaf phytoplasma (PPL-Bd; Genbank Accession No. AF 228053) reported in Italy and Bangladesh, respectively. In restriction fragment length polymorphism (RFLP) analysis, AluI, EcoRI, HhaI, HincII, KpnI, and Sau3AI (Promega, Madison, WI; 5 U per reaction) were used for comparison of restriction pattern of present/reference phytoplasma and with that previously reported (3). The present phytoplasma produced identical restriction profile to those of periwinkle infected by PPL-Bd (periwinkle little leaf phytoplasma, Bangladesh, group 16SrVI). On the basis of PCR studies, absence of virus particles under TEM in infected samples, RFLP analysis and nucleotide sequence matching with previously characterized phytoplasma, this phyto-plasma is classified as a member of Clover proliferation group (16SrVI). To our knowledge, this is the first report of a phytoplasma belonging to 16Sr VI group from W. somnifera. References: (1) S. Deng and C. Hiruki. J. Microbiol. Methods 14:53, 1991. (2) D. E. Gundersen and I.-M. Lee. Phytopathol. Mediterr.35:144, 1996. (3) I.-M. Lee et al. Int. J. Syst. Bacteriol. 48:1153, 1998. (4) M. Zaim and A. Samad. Plant Sci. 109:225,1995.
A. K. Shasany, M. P. Darokar, S. Dhawan, A. K. Gupta, S. Gupta, A. K. Shukla, N. K. Patra, and S. P. S. Khanuja
Oxford University Press (OUP)
Three controlled crosses were carried out involving Mentha arvensis and Mentha spicata [M. spicata CIMAP/C30 x M. spicata CIMAP/C33 (cv. Neera); M. arvensis CIMAP/C18 x CIMAP/C17 (cv. Kalka); and M. arvensis CIMAP/C17 x M. spicata CIMAP/C33]. The parents were subjected to random amplified polymorphic DNA (RAPD) analysis with 80 primers, and polymorphic primers were tested for detecting coinherited RAPD profiles among the progeny of these crosses. Of 50 seedlings tested from each intraspecific cross, all demonstrated dominant profiles with the selected RAPD primers except the detected hybrid from respective crosses. Coinherited markers could be detected with the primers OPJ 01, MAP 06, OPT 08, and OPO 20 for M. arvensis; OPJ 05, OPJ 14, OPO 19, and OPT 09 for M. spicata; and OPJ 07, OPJ 10, OPJ 11, OPJ 14, and OPO 02 for the cross M. arvensis x M. spicata. In our amplified fragment length polymorphism (AFLP) analysis, 40 coinherited marker fragments were identified for the cross involving M. arvensis, 32 for the cross involving M. spicata, and 41 for the interspecific cross between M. arvensis and M. spicata. In all crosses, similarity values between the parents were less than those between the parents and the hybrids. Although RAPD markers are generally considered dominant, it is possible to identify a few codominant markers that behave like restriction fragment length polymorphism (RFLP) markers. This molecular marker system may be helpful in rapidly screening out hybrids in crops where cross-pollination is a problem.