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Sellamuthu G, Tarafdar A, Jasrotia RS, Chaudhary M, Vishwakarma H, Padaria JC. Introgression of Δ 1-pyrroline-5-carboxylate synthetase (PgP5CS) confers enhanced resistance to abiotic stresses in transgenic tobacco. Transgenic Res 2024:10.1007/s11248-024-00385-x. [PMID: 38739244 DOI: 10.1007/s11248-024-00385-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 04/25/2024] [Indexed: 05/14/2024]
Abstract
Δ1-pyrroline-5-carboxylate synthetase (P5CS) is one of the key regulatory enzymes involved in the proline biosynthetic pathway. Proline acts as an osmoprotectant, molecular chaperone, antioxidant, and regulator of redox homeostasis. The accumulation of proline during stress is believed to confer tolerance in plants. In this study, we cloned the complete CDS of the P5CS from pearl millet (Pennisetum glaucum (L.) R.Br. and transformed into tobacco. Three transgenic tobacco plants with single-copy insertion were analyzed for drought and heat stress tolerance. No difference was observed between transgenic and wild-type (WT) plants when both were grown in normal conditions. However, under heat and drought, transgenic plants have been found to have higher chlorophyll, relative water, and proline content, and lower malondialdehyde (MDA) levels than WT plants. The photosynthetic parameters (stomatal conductance, intracellular CO2 concentration, and transpiration rate) were also observed to be high in transgenic plants under abiotic stress conditions. qRT-PCR analysis revealed that the expression of the transgene in drought and heat conditions was 2-10 and 2-7.5 fold higher than in normal conditions, respectively. Surprisingly, only P5CS was increased under heat stress conditions, indicating the possibility of feedback inhibition. Our results demonstrate the positive role of PgP5CS in enhancing abiotic stress tolerance in tobacco, suggesting its possible use to increase abiotic stress-tolerance in crops for sustained yield under adverse climatic conditions.
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Affiliation(s)
- Gothandapani Sellamuthu
- National Institute for Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
- Forest Molecular Entomology Laboratory, Excellent Team for Mitigation (ETM), Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Avijit Tarafdar
- National Institute for Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
- International Crops Research Institute for Semi-Arid Tropics, Patancheruvu, India
| | - Rahul Singh Jasrotia
- National Institute for Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
- Florida State University, Tallahassee, USA
| | - Minakshi Chaudhary
- National Institute for Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
| | - Harinder Vishwakarma
- National Institute for Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
| | - Jasdeep C Padaria
- National Institute for Plant Biotechnology, Pusa Campus, New Delhi, 110012, India.
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2
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Panzade KP, Tribhuvan KU, Pawar DV, Jasrotia RS, Gaikwad K, Dalal M, Kumar RR, Singh MP, Awasthi OP, Padaria JC. Discovering the regulators of heat stress tolerance in Ziziphus nummularia (Burm.f) wight and walk.-arn. Physiol Mol Biol Plants 2024; 30:497-511. [PMID: 38633271 PMCID: PMC11018567 DOI: 10.1007/s12298-024-01431-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 12/14/2023] [Accepted: 03/01/2024] [Indexed: 04/19/2024]
Abstract
Ziziphus nummularia an elite heat-stress tolerant shrub, grows in arid regions of desert. However, its molecular mechanism responsible for heat stress tolerance is unexplored. Therefore, we analysed whole transcriptome of Jaisalmer (heat tolerant) and Godhra (heat sensitive) genotypes of Z. nummularia to understand its molecular mechanism responsible for heat stress tolerance. De novo assembly of 16,22,25,052 clean reads yielded 276,029 transcripts. A total of 208,506 unigenes were identified which contains 4290 and 1043 differentially expressed genes (DEG) in TGO (treated Godhra at 42 °C) vs. CGO (control Godhra) and TJR (treated Jaisalmer at 42 °C) vs. CJR (control Jaisalmer), respectively. A total of 987 (67 highly enriched) and 754 (34 highly enriched) pathways were obsorved in CGO vs. TGO and CJR vs. TJR, respectively. Antioxidant pathways and TFs like Homeobox, HBP, ARR, PHD, GRAS, CPP, and E2FA were uniquely observed in Godhra genotype and SET domains were uniquely observed in Jaisalmer genotype. Further transposable elements were highly up-regulated in Godhra genotype but no activation in Jaisalmer genotype. A total of 43,093 and 39,278 simple sequence repeats were identified in the Godhra and Jaisalmer genotypes, respectively. A total of 10 DEGs linked to heat stress were validated in both genotypes for their expression under different heat stresses using quantitative real-time PCR. Comparing expression patterns of the selected DEGs identified ClpB1 as a potential candidate gene for heat tolerance in Z. nummularia. Here we present first characterized transcriptome of Z. nummularia in response to heat stress for the identification and characterization of heat stress-responsive genes. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-024-01431-y.
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Affiliation(s)
- Kishor Prabhakar Panzade
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012 Delhi India
- PG School, Indian Agricultural Research Institute, New Delhi, 110 012 Delhi India
| | - Kishor U. Tribhuvan
- ICAR-Indian Institute of Agricultural Biotechnology, Ranchi, Jharkhand 834 003 India
| | - Deepak V. Pawar
- ICAR- Directorate of Weed Research, Maharajpur, Jabalpur, Madhya Pradesh 482004 India
| | - Rahul Singh Jasrotia
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012 Delhi India
- University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Dr., San Antonio, TX 78229 USA
| | - Kishor Gaikwad
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012 Delhi India
- PG School, Indian Agricultural Research Institute, New Delhi, 110 012 Delhi India
| | - Monika Dalal
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012 Delhi India
- PG School, Indian Agricultural Research Institute, New Delhi, 110 012 Delhi India
| | - Ranjeet Ranjan Kumar
- Division of Biochemistry, ICAR–Indian Agricultural Research Institute, New Delhi, 110 012 Delhi India
- PG School, Indian Agricultural Research Institute, New Delhi, 110 012 Delhi India
| | - Madan Pal Singh
- Division of Plant Physiology, ICAR-Indian Agrcultural Research Institute, New Delhi, 110 012 Delhi India
- PG School, Indian Agricultural Research Institute, New Delhi, 110 012 Delhi India
| | - Om Prakash Awasthi
- Division of Horticulture, ICAR-Indian Agrcultural Research Institute, New Delhi, 110 012 Delhi India
- PG School, Indian Agricultural Research Institute, New Delhi, 110 012 Delhi India
| | - Jasdeep Chatrath Padaria
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012 Delhi India
- PG School, Indian Agricultural Research Institute, New Delhi, 110 012 Delhi India
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3
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Khan A, Singh K, Jaiswal S, Raza M, Jasrotia RS, Kumar A, Gurjar AKS, Kumari J, Nayan V, Iquebal MA, Angadi UB, Rai A, Datta TK, Kumar D. Whole-Genome-Based Web Genomic Resource for Water Buffalo (Bubalus bubalis). Front Genet 2022; 13:809741. [PMID: 35480326 PMCID: PMC9035531 DOI: 10.3389/fgene.2022.809741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 02/14/2022] [Indexed: 11/13/2022] Open
Abstract
Water buffalo (Bubalus bubalis), belonging to the Bovidae family, is an economically important animal as it is the major source of milk, meat, and drought in numerous countries. It is mainly distributed in tropical and subtropical regions with a global population of approximately 202 million. The advent of low cost and rapid sequencing technologies has opened a new vista for global buffalo researchers. In this study, we utilized the genomic data of five commercially important buffalo breeds, distributed globally, namely, Mediterranean, Egyptian, Bangladesh, Jaffrarabadi, and Murrah. Since there is no whole-genome sequence analysis of these five distinct buffalo breeds, which represent a highly diverse ecosystem, we made an attempt for the same. We report the first comprehensive, holistic, and user-friendly web genomic resource of buffalo (BuffGR) accessible at http://backlin.cabgrid.res.in/buffgr/, that catalogues 6028881 SNPs and 613403 InDels extracted from a set of 31 buffalo tissues. We found a total of 7727122 SNPs and 634124 InDels distributed in four breeds of buffalo (Murrah, Bangladesh, Jaffarabadi, and Egyptian) with reference to the Mediterranean breed. It also houses 4504691 SSR markers from all the breeds along with 1458 unique circRNAs, 37712 lncRNAs, and 938 miRNAs. This comprehensive web resource can be widely used by buffalo researchers across the globe for use of markers in marker trait association, genetic diversity among the different breeds of buffalo, use of ncRNAs as regulatory molecules, post-transcriptional regulations, and role in various diseases/stresses. These SNPs and InDelscan also be used as biomarkers to address adulteration and traceability. This resource can also be useful in buffalo improvement programs and disease/breed management.
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Affiliation(s)
- Aamir Khan
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Kalpana Singh
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Sarika Jaiswal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Mustafa Raza
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Rahul Singh Jasrotia
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Animesh Kumar
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Anoop Kishor Singh Gurjar
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Juli Kumari
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Varij Nayan
- ICAR-Central Institute for Research on Buffaloes, Hisar, India
| | - Mir Asif Iquebal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
- *Correspondence: Mir Asif Iquebal,
| | - U. B. Angadi
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Anil Rai
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | | | - Dinesh Kumar
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
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Agnihotry S, Agrawal P, Ajjarapu SM, Avashthi H, Awasthi A, Bani Baker Q, Bhandawat A, Bishnoi R, Chandra M, Chatterjee T, Chaudhary KK, Choubey J, Choudhari J, Gautam B, Goswami K, Harbola A, Hussain I, Jaiswar A, Jasrotia RS, Junior MC, Kaur S, Kesharwani RK, Kumar I, Kumar P, Kumar S, Manchanda M, Maurya R, Mishra A, Mishra B, Mishra P, Mishra S, Mittal S, Narad P, Naresh G, Negi A, Negi D, Ojha KK, Pant S, Pathak RK, Ramteke PW, Redhu N, Roy J, Sahariah B, Sanan-Mishra N, Saxena R, Sengupta A, Sharma G, Sharma H, Sharma PK, Sharma V, Sharma V, Shivam, Shrinet J, Shukla A, Shukla R, Shukla S, Singh A, Singh A, Singh DB, Singh I, Singh P, Singh PK, Singh R, Singh S, Singh S, Singh SP, Singh TR, Singh VK, Singla D, Sote WO, Tandon G, Thakur Z, Tiwari A, Tiwari A, Tyagi R, Verma M, Verma S, Yadav AK, Yadav IS, Yadav MK, Yadav N, Yadav NS, Yadav S. List of contributors. Bioinformatics 2022. [DOI: 10.1016/b978-0-323-89775-4.00031-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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5
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Jaiswal S, Nandi S, Iquebal MA, Jasrotia RS, Patra S, Mishra G, Udit UK, Sahu DK, Angadi UB, Meher PK, Routray P, Sundaray JK, Verma DK, Das P, Jayasankar P, Rai A, Kumar D. Revelation of candidate genes and molecular mechanism of reproductive seasonality in female rohu (Labeo rohita Ham.) by RNA sequencing. BMC Genomics 2021; 22:685. [PMID: 34548034 PMCID: PMC8456608 DOI: 10.1186/s12864-021-08001-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 05/26/2021] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Carp fish, rohu (Labeo rohita Ham.) is important freshwater aquaculture species of South-East Asia having seasonal reproductive rhythm. There is no holistic study at transcriptome level revealing key candidate genes involved in such circannual rhythm regulated by biological clock genes (BCGs). Seasonality manifestation has two contrasting phases of reproduction, i.e., post-spawning resting and initiation of gonadal activity appropriate for revealing the associated candidate genes. It can be deciphered by RNA sequencing of tissues involved in BPGL (Brain-Pituitary-Gonad-Liver) axis controlling seasonality. How far such BCGs of this fish are evolutionarily conserved across different phyla is unknown. Such study can be of further use to enhance fish productivity as seasonality restricts seed production beyond monsoon season. RESULT A total of ~ 150 Gb of transcriptomic data of four tissues viz., BPGL were generated using Illumina TruSeq. De-novo assembled BPGL tissues revealed 75,554 differentially expressed transcripts, 115,534 SSRs, 65,584 SNPs, 514 pathways, 5379 transcription factors, 187 mature miRNA which regulates candidate genes represented by 1576 differentially expressed transcripts are available in the form of web-genomic resources. Findings were validated by qPCR. This is the first report in carp fish having 32 BCGs, found widely conserved in fish, amphibian, reptile, birds, prototheria, marsupials and placental mammals. This is due to universal mechanism of rhythmicity in response to environment and earth rotation having adaptive and reproductive significance. CONCLUSION This study elucidates evolutionary conserved mechanism of photo-periodism sensing, neuroendocrine secretion, metabolism and yolk synthesis in liver, gonadal maturation, muscular growth with sensory and auditory perception in this fish. Study reveals fish as a good model for research on biological clock besides its relevance in reproductive efficiency enhancement.
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Affiliation(s)
- Sarika Jaiswal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Samiran Nandi
- ICAR- Central Institute of Freshwater Aquaculture, Bhubaneswar, Odhisa India
| | - Mir Asif Iquebal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Rahul Singh Jasrotia
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Sunita Patra
- ICAR- Central Institute of Freshwater Aquaculture, Bhubaneswar, Odhisa India
| | - Gayatri Mishra
- ICAR- Central Institute of Freshwater Aquaculture, Bhubaneswar, Odhisa India
| | - Uday Kumar Udit
- ICAR- Central Institute of Freshwater Aquaculture, Bhubaneswar, Odhisa India
| | - Dinesh Kumar Sahu
- ICAR- Central Institute of Freshwater Aquaculture, Bhubaneswar, Odhisa India
| | - U. B. Angadi
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Prem Kumar Meher
- ICAR- Central Institute of Freshwater Aquaculture, Bhubaneswar, Odhisa India
| | - Padmanav Routray
- ICAR- Central Institute of Freshwater Aquaculture, Bhubaneswar, Odhisa India
| | | | | | - Paramananda Das
- ICAR- Central Institute of Freshwater Aquaculture, Bhubaneswar, Odhisa India
| | | | - Anil Rai
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Dinesh Kumar
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
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6
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Wei J, Cheng J, Waddell NJ, Wang ZJ, Pang X, Cao Q, Liu A, Chitaman JM, Abreu K, Jasrotia RS, Duffney LJ, Zhang J, Dietz DM, Feng J, Yan Z. DNA Methyltransferase 3A Is Involved in the Sustained Effects of Chronic Stress on Synaptic Functions and Behaviors. Cereb Cortex 2020; 31:1998-2012. [PMID: 33230530 DOI: 10.1093/cercor/bhaa337] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 09/29/2020] [Accepted: 10/18/2020] [Indexed: 12/13/2022] Open
Abstract
Emerging evidence suggests that epigenetic mechanisms regulate aberrant gene transcription in stress-associated mental disorders. However, it remains to be elucidated about the role of DNA methylation and its catalyzing enzymes, DNA methyltransferases (DNMTs), in this process. Here, we found that male rats exposed to chronic (2-week) unpredictable stress exhibited a substantial reduction of Dnmt3a after stress cessation in the prefrontal cortex (PFC), a key target region of stress. Treatment of unstressed control rats with DNMT inhibitors recapitulated the effect of chronic unpredictable stress on decreased AMPAR expression and function in PFC. In contrast, overexpression of Dnmt3a in PFC of stressed animals prevented the loss of glutamatergic responses. Moreover, the stress-induced behavioral abnormalities, including the impaired recognition memory, heightened aggression, and hyperlocomotion, were partially attenuated by Dnmt3a expression in PFC of stressed animals. Finally, we found that there were genome-wide DNA methylation changes and transcriptome alterations in PFC of stressed rats, both of which were enriched at several neural pathways, including glutamatergic synapse and microtubule-associated protein kinase signaling. These results have therefore recognized the potential role of DNA epigenetic modification in stress-induced disturbance of synaptic functions and cognitive and emotional processes.
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Affiliation(s)
- Jing Wei
- Department of Physiology and Biophysics, School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY 14203, USA
| | - Jia Cheng
- Department of Physiology and Biophysics, School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY 14203, USA
| | - Nicholas J Waddell
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Zi-Jun Wang
- Department of Physiology and Biophysics, School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY 14203, USA
| | - Xiaodong Pang
- Department of Statistics, Florida State University, Tallahassee, FL 32306, USA
| | - Qing Cao
- Department of Physiology and Biophysics, School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY 14203, USA
| | - Aiyi Liu
- Department of Physiology and Biophysics, School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY 14203, USA
| | - Javed M Chitaman
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA.,Program in Neuroscience, Florida State University, Tallahassee, FL 32306, USA
| | - Kristen Abreu
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Rahul Singh Jasrotia
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Lara J Duffney
- Department of Physiology and Biophysics, School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY 14203, USA
| | - Jinfeng Zhang
- Department of Statistics, Florida State University, Tallahassee, FL 32306, USA
| | - David M Dietz
- Department of Pharmacology and Toxicology, State University of New York at Buffalo, Buffalo, NY 14203, USA
| | - Jian Feng
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA.,Program in Neuroscience, Florida State University, Tallahassee, FL 32306, USA
| | - Zhen Yan
- Department of Physiology and Biophysics, School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY 14203, USA
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7
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Mehra R, Jasrotia RS, Mahajan A, Sharma D, Iquebal MA, Kaul S, Dhar MK. Transcriptome analysis of Snow Mountain Garlic for unraveling the organosulfur metabolic pathway. Genomics 2020; 112:99-107. [DOI: 10.1016/j.ygeno.2019.07.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 07/05/2019] [Accepted: 07/25/2019] [Indexed: 12/20/2022]
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8
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Iquebal MA, Sharma P, Jasrotia RS, Jaiswal S, Kaur A, Saroha M, Angadi UB, Sheoran S, Singh R, Singh GP, Rai A, Tiwari R, Kumar D. RNAseq analysis reveals drought-responsive molecular pathways with candidate genes and putative molecular markers in root tissue of wheat. Sci Rep 2019; 9:13917. [PMID: 31558740 PMCID: PMC6763491 DOI: 10.1038/s41598-019-49915-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 08/12/2019] [Indexed: 01/08/2023] Open
Abstract
Drought is one of the major impediments in wheat productivity. Traditional breeding and marker assisted QTL introgression had limited success. Available wheat genomic and RNA-seq data can decipher novel drought tolerance mechanisms with putative candidate gene and marker discovery. Drought is first sensed by root tissue but limited information is available about how roots respond to drought stress. In this view, two contrasting genotypes, namely, NI5439 41 (drought tolerant) and WL711 (drought susceptible) were used to generate ~78.2 GB data for the responses of wheat roots to drought. A total of 45139 DEGs, 13820 TF, 288 miRNAs, 640 pathways and 435829 putative markers were obtained. Study reveals use of such data in QTL to QTN refinement by analysis on two model drought-responsive QTLs on chromosome 3B in wheat roots possessing 18 differentially regulated genes with 190 sequence variants (173 SNPs and 17 InDels). Gene regulatory networks showed 69 hub-genes integrating ABA dependent and independent pathways controlling sensing of drought, root growth, uptake regulation, purine metabolism, thiamine metabolism and antibiotics pathways, stomatal closure and senescence. Eleven SSR markers were validated in a panel of 18 diverse wheat varieties. For effective future use of findings, web genomic resources were developed. We report RNA-Seq approach on wheat roots describing the drought response mechanisms under field drought conditions along with genomic resources, warranted in endeavour of wheat productivity.
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Affiliation(s)
- Mir Asif Iquebal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, PUSA, New Delhi, 110012, India
| | - Pradeep Sharma
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, 132001, India
| | - Rahul Singh Jasrotia
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, PUSA, New Delhi, 110012, India
| | - Sarika Jaiswal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, PUSA, New Delhi, 110012, India
| | - Amandeep Kaur
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, 132001, India
| | - Monika Saroha
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, 132001, India
| | - U B Angadi
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, PUSA, New Delhi, 110012, India
| | - Sonia Sheoran
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, 132001, India
| | - Rajender Singh
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, 132001, India
| | - G P Singh
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, 132001, India
| | - Anil Rai
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, PUSA, New Delhi, 110012, India
| | - Ratan Tiwari
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, 132001, India.
| | - Dinesh Kumar
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, PUSA, New Delhi, 110012, India.
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9
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Jasrotia RS, Jaiswal S, Yadav PK, Raza M, Iquebal MA, Rai A, Kumar D. Genome-Wide Analysis of HSP70 Family Protein in Vigna radiata and Coexpression Analysis Under Abiotic and Biotic Stress. J Comput Biol 2019; 27:738-754. [PMID: 31464514 DOI: 10.1089/cmb.2019.0166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Heat shock protein 70 (Hsp70), a 70-kDa protein, also known as a molecular chaperone, is highly conserved. It plays a major role in cellular functions such as protein folding, regulation of protein degradation, translocation of proteins across membranes, receptor signaling, and protein assembly or disassembly. Vigna radiata is an important legume crop with available whole-genome sequence, but no such study on the HSP70 family is reported. A total of 32 V. radiate HSP70s (Vr-HSP70s) were identified and described. They are phylogenetically clustered into four subgroups. Vr-HSP70s show variations in intron/exon organization. This indicates that introns may play an essential role in gene regulating. The coexpression analysis of Vr-HSP70s revealed that these genes were involved in both abiotic and biotic stresses. Three cytoplasmic hub genes namely Vr-HSP70-C-14, Vr-HSP70-C-29, and Vr-HSP70-C-30 were found common in both stresses. Our findings provide directions for future studies to dissect functional analysis of Vr-HSP70s in response to abiotic and biotic stresses.
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Affiliation(s)
- Rahul Singh Jasrotia
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India.,Department of Computational Biology & Bioinformatics, Sam Higginbottom University of Agriculture, Technology & Sciences (SHUATS), Allahabad, India
| | - Sarika Jaiswal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Pramod Kumar Yadav
- Department of Computational Biology & Bioinformatics, Sam Higginbottom University of Agriculture, Technology & Sciences (SHUATS), Allahabad, India
| | - Mustafa Raza
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Mir Asif Iquebal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Anil Rai
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Dinesh Kumar
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
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10
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Jaiswal S, Jadhav PV, Jasrotia RS, Kale PB, Kad SK, Moharil MP, Dudhare MS, Kheni J, Deshmukh AG, Mane SS, Nandanwar RS, Penna S, Manjaya JG, Iquebal MA, Tomar RS, Kawar PG, Rai A, Kumar D. Transcriptomic signature reveals mechanism of flower bud distortion in witches'-broom disease of soybean (Glycine max). BMC Plant Biol 2019; 19:26. [PMID: 30646861 PMCID: PMC6332543 DOI: 10.1186/s12870-018-1601-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 12/12/2018] [Indexed: 05/10/2023]
Abstract
BACKGROUND Soybean (Glycine max L. Merril) crop is major source of edible oil and protein for human and animals besides its various industrial uses including biofuels. Phytoplasma induced floral bud distortion syndrome (FBD), also known as witches' broom syndrome (WBS) has been one of the major biotic stresses adversely affecting its productivity. Transcriptomic approach can be used for knowledge discovery of this disease manifestation by morpho-physiological key pathways. RESULTS We report transcriptomic study using Illumina HiSeq NGS data of FBD in soybean, revealing 17,454 differentially expressed genes, 5561 transcription factors, 139 pathways and 176,029 genic region putative markers single sequence repeats, single nucleotide polymorphism and Insertion Deletion. Roles of PmbA, Zn-dependent protease, SAP family and auxin responsive system are described revealing mechanism of flower bud distortion having abnormalities in pollen, stigma development. Validation of 10 randomly selected genes was done by qPCR. Our findings describe the basic mechanism of FBD disease, right from sensing of phytoplasma infection by host plant triggering molecular signalling leading to mobilization of carbohydrate and protein, phyllody, abnormal pollen development, improved colonization of insect in host plants to spread the disease. Study reveals how phytoplasma hijacks metabolic machinery of soybean manifesting FBD. CONCLUSIONS This is the first report of transcriptomic signature of FBD or WBS disease of soybean revealing morphological and metabolic changes which attracts insect for spread of disease. All the genic region putative markers may be used as genomic resource for variety improvement and new agro-chemical development for disease control to enhance soybean productivity.
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Affiliation(s)
- Sarika Jaiswal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, PUSA, New Delhi, 110012 India
| | - Pravin V. Jadhav
- Post Graduate Institute, Dr. Panjabrao Deshmukh Krishi Vidyapeeth, Akola, Maharashtra, 444104 India
| | - Rahul Singh Jasrotia
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, PUSA, New Delhi, 110012 India
| | - Prashant B. Kale
- National Research Centre on Plant Biotechnology, LBS Centre, PUSA Campus, New Delhi, 110012 India
| | - Snehal K. Kad
- Post Graduate Institute, Dr. Panjabrao Deshmukh Krishi Vidyapeeth, Akola, Maharashtra, 444104 India
| | - Mangesh P. Moharil
- Post Graduate Institute, Dr. Panjabrao Deshmukh Krishi Vidyapeeth, Akola, Maharashtra, 444104 India
| | - Mahendra S. Dudhare
- Post Graduate Institute, Dr. Panjabrao Deshmukh Krishi Vidyapeeth, Akola, Maharashtra, 444104 India
| | - Jashminkumar Kheni
- Department of Biotechnology, Junagadh Agricultural University, Junagadh, Gujarat India
| | - Amit G. Deshmukh
- Post Graduate Institute, Dr. Panjabrao Deshmukh Krishi Vidyapeeth, Akola, Maharashtra, 444104 India
| | - Shyamsundar S. Mane
- Post Graduate Institute, Dr. Panjabrao Deshmukh Krishi Vidyapeeth, Akola, Maharashtra, 444104 India
| | - Ravindra S. Nandanwar
- Post Graduate Institute, Dr. Panjabrao Deshmukh Krishi Vidyapeeth, Akola, Maharashtra, 444104 India
| | - Suprasanna Penna
- Nuclear Agriculture and Biotechnology Division, Homi Bhabha National Institute, Bhabha Atomic Research Centre (BARC), Trombay, Mumbai, 400 085 India
| | - Joy G. Manjaya
- Nuclear Agriculture and Biotechnology Division, Homi Bhabha National Institute, Bhabha Atomic Research Centre (BARC), Trombay, Mumbai, 400 085 India
| | - Mir Asif Iquebal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, PUSA, New Delhi, 110012 India
| | - Rukam Singh Tomar
- Department of Biotechnology, Junagadh Agricultural University, Junagadh, Gujarat India
| | - Prashant G. Kawar
- ICAR- Directorate of Floricultural Research, College of Agriculture, Pune, Maharashtra, 411 005, India
| | - Anil Rai
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, PUSA, New Delhi, 110012 India
| | - Dinesh Kumar
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, PUSA, New Delhi, 110012 India
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Jasrotia RS, Yadav PK, Iquebal MA, Bhatt SB, Arora V, Angadi UB, Tomar RS, Jaiswal S, Rai A, Kumar D. VigSatDB: genome-wide microsatellite DNA marker database of three species of Vigna for germplasm characterization and improvement. Database (Oxford) 2019; 2019:5506750. [PMID: 31147679 PMCID: PMC6542692 DOI: 10.1093/database/baz055] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 03/20/2019] [Accepted: 04/05/2019] [Indexed: 11/25/2022]
Abstract
Genus Vigna represented by more than 100 species is a source of nutritious edible seeds and sprouts that are rich sources of protein and dietary supplements. It is further valuable because of therapeutic attributes due to its antioxidant and anti-diabetic properties. A highly diverse and an extremely ecological niche of different species can be valuable genomic resources for productivity enhancement. It is one of the most underutilized crops for food security and animal feeds. In spite of huge species diversity, only three species of Vigna have been sequenced; thus, there is a need for molecular markers for the remaining species. Computational approach of microsatellite marker discovery along with evaluation of polymorphism utilizing available genomic data of different genotypes can be a quick and an economical approach for genomic resource development. Cross-species transferability by e-PCR over available genomes can further prioritize the potential SSR markers, which could be used for genetic diversity and population differentiation of the remaining species saving cost and time. We present VigSatDB—the world’s first comprehensive microsatellite database of genus Vigna, containing >875 K putative microsatellite markers with 772 354 simple and 103 865 compound markers mined from six genome assemblies of three Vigna species, namely, Vigna radiata (Mung bean), Vigna angularis (Adzuki bean) and Vigna unguiculata (Cowpea). It also contains 1976 validated published markers. Markers can be selected on the basis of chromosomes/location specificity, and primers can be generated using Primer3core tool integrated at backend. Efficacy of VigSatDB for microsatellite loci genotyping has been evaluated by 15 markers over a panel of 10 diverse genotype of V. radiata. Our web genomic resources can be used in diversity analysis, population and varietal differentiation, discovery of quantitative trait loci/genes, marker-assisted varietal improvement in endeavor of Vigna crop productivity and management.
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Affiliation(s)
- Rahul Singh Jasrotia
- Sam Higginbottom University of Agriculture, Technology and Sciences, Allahabad, Uttar Pradesh, India.,Centre for Agricultural Bioinformatics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Statistics Research Institute, New Delhi , India
| | - Pramod Kumar Yadav
- Sam Higginbottom University of Agriculture, Technology and Sciences, Allahabad, Uttar Pradesh, India
| | - Mir Asif Iquebal
- Centre for Agricultural Bioinformatics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Statistics Research Institute, New Delhi , India
| | - S B Bhatt
- Department of Biochemistry and Biotechnology, Junagadh Agricultural University, Junagadh, Gujarat, India
| | - Vasu Arora
- Centre for Agricultural Bioinformatics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Statistics Research Institute, New Delhi , India
| | - U B Angadi
- Centre for Agricultural Bioinformatics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Statistics Research Institute, New Delhi , India
| | - Rukam Singh Tomar
- Department of Biochemistry and Biotechnology, Junagadh Agricultural University, Junagadh, Gujarat, India
| | - Sarika Jaiswal
- Centre for Agricultural Bioinformatics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Statistics Research Institute, New Delhi , India
| | - Anil Rai
- Centre for Agricultural Bioinformatics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Statistics Research Institute, New Delhi , India
| | - Dinesh Kumar
- Centre for Agricultural Bioinformatics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Statistics Research Institute, New Delhi , India
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Jaiswal S, Antala TJ, Mandavia MK, Chopra M, Jasrotia RS, Tomar RS, Kheni J, Angadi UB, Iquebal MA, Golakia BA, Rai A, Kumar D. Transcriptomic signature of drought response in pearl millet (Pennisetum glaucum (L.) and development of web-genomic resources. Sci Rep 2018; 8:3382. [PMID: 29467369 PMCID: PMC5821703 DOI: 10.1038/s41598-018-21560-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 02/04/2018] [Indexed: 01/12/2023] Open
Abstract
Pearl millet, (Pennisetum glaucum L.), an efficient (C4) crop of arid/semi-arid regions is known for hardiness. Crop is valuable for bio-fortification combating malnutrition and diabetes, higher caloric value and wider climatic resilience. Limited studies are done in pot-based experiments for drought response at gene-expression level, but field-based experiment mimicking drought by withdrawal of irrigation is still warranted. We report de novo assembly-based transcriptomic signature of drought response induced by irrigation withdrawal in pearl millet. We found 19983 differentially expressed genes, 7595 transcription factors, gene regulatory network having 45 hub genes controlling drought response. We report 34652 putative markers (4192 simple sequence repeats, 12111 SNPs and 6249 InDels). Study reveals role of purine and tryptophan metabolism in ABA accumulation mediating abiotic response in which MAPK acts as major intracellular signal sensing drought. Results were validated by qPCR of 13 randomly selected genes. We report the first web-based genomic resource ( http://webtom.cabgrid.res.in/pmdtdb/ ) which can be used for candidate genes-based SNP discovery programs and trait-based association studies. Looking at climatic change, nutritional and pharmaceutical importance of this crop, present investigation has immense value in understanding drought response in field condition. This is important in germplasm management and improvement in endeavour of pearl millet productivity.
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Affiliation(s)
- Sarika Jaiswal
- Centre for Agricultural Bioinformatics (CABin), ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Tushar J Antala
- Department of Biochemistry and Biotechnology, Junagadh Agricultural University, Junagadh, Gujarat, India
| | - M K Mandavia
- Department of Biochemistry and Biotechnology, Junagadh Agricultural University, Junagadh, Gujarat, India
| | - Meenu Chopra
- Centre for Agricultural Bioinformatics (CABin), ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Rahul Singh Jasrotia
- Centre for Agricultural Bioinformatics (CABin), ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Rukam S Tomar
- Department of Biochemistry and Biotechnology, Junagadh Agricultural University, Junagadh, Gujarat, India
| | - Jashminkumar Kheni
- Department of Biochemistry and Biotechnology, Junagadh Agricultural University, Junagadh, Gujarat, India
| | - U B Angadi
- Centre for Agricultural Bioinformatics (CABin), ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - M A Iquebal
- Centre for Agricultural Bioinformatics (CABin), ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - B A Golakia
- Department of Biochemistry and Biotechnology, Junagadh Agricultural University, Junagadh, Gujarat, India
| | - Anil Rai
- Centre for Agricultural Bioinformatics (CABin), ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Dinesh Kumar
- Centre for Agricultural Bioinformatics (CABin), ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India.
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Jasrotia RS, Iquebal MA, Yadav PK, Kumar N, Jaiswal S, Angadi UB, Rai A, Kumar D. Development of transcriptome based web genomic resources of yellow mosaic disease in Vigna mungo. Physiol Mol Biol Plants 2017; 23:767-777. [PMID: 29158627 PMCID: PMC5671452 DOI: 10.1007/s12298-017-0470-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 09/06/2017] [Accepted: 09/11/2017] [Indexed: 05/27/2023]
Abstract
Vigna mungo (Urdbean) is cultivated in the tropical and sub-tropical continental region of Asia. It is not only important source of dietary protein and nutritional elements, but also of immense value to human health due to medicinal properties. Yellow mosaic disease caused by Mungbean Yellow Mosaic India Virus is known to incur huge loss to crop, adversely affecting crop yield. Contrasting genotypes are ideal source for knowledge discovery of plant defence mechanism and associated candidate genes for varietal improvement. Whole genome sequence of this crop is yet to be completed. Moreover, genomic resources are also not freely accessible, thus available transcriptome data can be of immense use. V. mungo Transcriptome database, accessible at http://webtom.cabgrid.res.in/vmtdb/ has been developed using available data of two contrasting varieties viz., cv. VM84 (resistant) and cv. T9 (susceptible). De novo assembly was carried out using Trinity and CAP3. Out of total 240,945 unigenes, 165,894 (68.8%) showed similarity with known genes against NR database, and remaining 31.2% were found to be novel. We found 22,101 differentially expressed genes in all datasets, 44,335 putative genic SSR markers, 4105 SNPs and Indels, 64,964 transcriptional factor, 546 mature miRNA target prediction in 703 differentially expressed unigenes and 137 pathways. MAPK, salicylic acid-binding protein 2-like, pathogenesis-related protein and NBS-LRR domain were found which may play an important role in defence against pathogens. This is the first web genomic resource of V. mungo for future genome annotation as well as ready to use markers for future variety improvement program.
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Affiliation(s)
- Rahul Singh Jasrotia
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012 India
- Department of Computational Biology & Bioinformatics, Sam Higginbottom University of Agriculture, Technology & Sciences (SHUATS), Allahabad, 211007 India
| | - Mir Asif Iquebal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012 India
| | - Pramod Kumar Yadav
- Department of Computational Biology & Bioinformatics, Sam Higginbottom University of Agriculture, Technology & Sciences (SHUATS), Allahabad, 211007 India
| | - Neeraj Kumar
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012 India
| | - Sarika Jaiswal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012 India
| | - U. B. Angadi
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012 India
| | - Anil Rai
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012 India
| | - Dinesh Kumar
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012 India
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Shukla S, Iquebal M, Jaiswal S, Angadi U, Fatma S, Kumar N, Jasrotia RS, Fatima Y, Rai A, Kumar D. The Onion Genomic Resource: A genomics and bioinformatics driven resource for onion breeding. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.plgene.2016.09.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Padaria JC, Vishwakarma H, Biswas K, Jasrotia RS, Singh GP. Molecular cloning and in-silico characterization of high temperature stress responsive pAPX gene isolated from heat tolerant Indian wheat cv. Raj 3765. BMC Res Notes 2014; 7:713. [PMID: 25304397 PMCID: PMC4209082 DOI: 10.1186/1756-0500-7-713] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Accepted: 10/02/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Heat stress leads to accelerated production of reactive oxygen species (ROS) which causes a huge amount of oxidative damage to the cellular components of plants. A large number of heat stress related genes as HSPs, catalases, peroxidases are overexpressed at the time of stress. A potent stress responsive gene peroxisomal ascorbate peroxidase (TapAPX) obtained from heat stress (42 °C) responsive subtractive cDNA library from a thermo tolerant wheat cv. Raj3765 at anthesis stage was cloned, characterized and its role was validated under heat stress by proteomics and in-silico studies. In the present study we report the characterization at molecular and in-silico level of peroxisomal TapAPX gene isolated from heat tolerant wheat cultivar of India. RESULTS qPCR studies of TapAPX gene displayed up to 203 fold level of expression at 42 °C heat stress exposure. A full length cDNA of 876 bp obtained by RACE deduced a protein of 292 amino acid residues which gives a complete 3D structure of pAPX by homology modeling. TapAPX cDNA was cloned in expression vector pET28 (a+) and the recombinant protein over-expressed in E. coli BL21 showed highest homology with APX protein as deduced by peptide mass fingerprinting. CONCLUSIONS TapAPX gene from wheat cv Raj3765 has a distinct role in conferring thermo tolerance to the plants and thus can be used in crop improvement programmes for development of crops tolerant to high temperature.
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Affiliation(s)
- Jasdeep Chatrath Padaria
- Biotechnology and Climate Change Laboratory, National Research Centre on Plant Biotechnology, Pusa Campu, New Delhi 110012, India.
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