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Narayan JA, Manoj VM, Nerkar G, Chakravarthi M, Dharshini S, Subramonian N, Premachandran MN, Valarmathi R, Kumar RA, Gomathi R, Surendar KK, Hemaprabha G, Appunu C. Transgenic sugarcane with higher levels of BRK1 showed improved drought tolerance. Plant Cell Rep 2023; 42:1611-1628. [PMID: 37578541 DOI: 10.1007/s00299-023-03056-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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: 04/03/2023] [Accepted: 07/25/2023] [Indexed: 08/15/2023]
Abstract
KEY MESSAGE Transgenic sugarcane overexpressing BRK1 showed improved tolerance to drought stress through modulation of actin polymerization and formation of interlocking marginal lobes in epidermal leaf cells, a typical feature associated with BRK1 expression under drought stress. BRICK1 (BRK1) genes promote leaf epidermal cell morphogenesis and division in plants that involves local actin polymerization. Although the changes in actin filament organization during drought have been reported, the role of BRK in stress tolerance remains unknown. In our previous work, the drought-tolerant Erianthus arundinaceus exhibited high levels of the BRK gene expression under drought stress. Therefore, in the present study, the drought-responsive gene, BRK1 from Saccharum spontaneum, was transformed into sugarcane to test if it conferred drought tolerance in the commercial sugarcane cultivar Co 86032. The transgenic lines were subjected to drought stress, and analyzed using physiological parameters for drought stress. The drought-induced BRK1-overexpressing lines of sugarcane exhibited significantly higher transgene expression compared with the wild-type control and also showed improved physiological parameters. In addition, the formation of interlocking marginal lobes in the epidermal leaf cells, a typical feature associated with BRK1 expression, was observed in all transgenic BRK1 lines during drought stress. This is the first report to suggest that BRK1 plays a role in sugarcane acclimation to drought stress and may prove to be a potential candidate in genetic engineering of plants for enhanced biomass production under drought stress conditions.
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Affiliation(s)
- J Ashwin Narayan
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute (SBI), Tamil Nadu, Coimbatore, 641007, India
| | - V M Manoj
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute (SBI), Tamil Nadu, Coimbatore, 641007, India
| | - Gauri Nerkar
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute (SBI), Tamil Nadu, Coimbatore, 641007, India
| | - M Chakravarthi
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute (SBI), Tamil Nadu, Coimbatore, 641007, India
- Department of Genetics and Evolution, Federal University of Sao Carlos, Sao Carlos, SP, CEP 13565-905, Brazil
| | - S Dharshini
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute (SBI), Tamil Nadu, Coimbatore, 641007, India
| | - N Subramonian
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute (SBI), Tamil Nadu, Coimbatore, 641007, India
| | - M N Premachandran
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute (SBI), Tamil Nadu, Coimbatore, 641007, India
| | - R Valarmathi
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute (SBI), Tamil Nadu, Coimbatore, 641007, India
| | - R Arun Kumar
- Division of Crop Production, ICAR-Sugarcane Breeding Institute (SBI), Tamil Nadu, Coimbatore, 641007, India
| | - R Gomathi
- Division of Crop Production, ICAR-Sugarcane Breeding Institute (SBI), Tamil Nadu, Coimbatore, 641007, India
| | - K Krisha Surendar
- Deprtament of Plant Physiology, Paddy Breeding Station, Tamil Nadu Agricultural University (TNAU), Tamil Nadu, Coimbatore, 641003, India
| | - G Hemaprabha
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute (SBI), Tamil Nadu, Coimbatore, 641007, India
| | - C Appunu
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute (SBI), Tamil Nadu, Coimbatore, 641007, India.
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Valarmathi R, Mahadeva Swamy HK, Appunu C, Suresha GS, Mohanraj K, Hemaprabha G, Mahadevaiah C, Ulaganathan V. Comparative transcriptome profiling to unravel the key molecular signalling pathways and drought adaptive plasticity in shoot borne root system of sugarcane. Sci Rep 2023; 13:12853. [PMID: 37553413 PMCID: PMC10409851 DOI: 10.1038/s41598-023-39970-1] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 08/02/2023] [Indexed: 08/10/2023] Open
Abstract
Sugarcane root system comprises of superficial sett roots as well as deeply-penetrating shoot borne roots (SBR) with latter being the permanent root system. In sugarcane, the healthy SBR contributes to a better crop yield and it also helps to produce multiple ratoon crops after the harvest. There is a dearth of in-depth knowledge on SBR system architecture and its functional role in modern day commercial hybrids. A comprehensive phenotypic, anatomical and whole transcriptome profiling, conducted between the commercial sugarcane hybrids and a wild germplasm Erianthus, found a developmental delay in both initiation and establishment of the SBR in commercial hybrid compared to Erianthus. The SBR system in Erianthus proved to be an extensive drought-adaptive root system architecture that significantly contributes to drought tolerance. On the other hand, SBRs in the commercial hybrids showed an irreversible collapse and damage of the root cells under drought stress. The outcomes from the comparative analysis of the transcriptome data showed a significant upregulation of the genes that regulate important stress signalling pathways viz., sugar, calcium, hormone signalling and phenylpropanoid biosynthesis in the SBRs of Erianthus. It was found that through these key signalling pathways, Erianthus SBRs triggered the downstream signalling cascade to impart physiological responses like osmoprotection, modification of the cell walls, detoxification of reactive oxygen species, expression of drought responsive transcription factors, maintenance of cell stability and lateral root development. The current study forms a basis for further exploration of the Shoot Borne Root system as a valuable breeding target to develop drought tolerant sugarcane genotypes.
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Affiliation(s)
- R Valarmathi
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, 641007, India.
| | - H K Mahadeva Swamy
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, 641007, India
| | - C Appunu
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, 641007, India
| | - G S Suresha
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, 641007, India
| | - K Mohanraj
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, 641007, India
| | - G Hemaprabha
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, 641007, India
| | - C Mahadevaiah
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, 641007, India
| | - V Ulaganathan
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, 641007, India
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Nerkar G, Devarumath S, Purankar M, Kumar A, Valarmathi R, Devarumath R, Appunu C. Advances in Crop Breeding Through Precision Genome Editing. Front Genet 2022; 13:880195. [PMID: 35910205 PMCID: PMC9329802 DOI: 10.3389/fgene.2022.880195] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 05/02/2022] [Indexed: 11/13/2022] Open
Abstract
The global climate change and unfavourable abiotic and biotic factors are limiting agricultural productivity and therefore intensifying the challenges for crop scientists to meet the rising demand for global food supply. The introduction of applied genetics to agriculture through plant breeding facilitated the development of hybrid varieties with improved crop productivity. However, the development of new varieties with the existing gene pools poses a challenge for crop breeders. Genetic engineering holds the potential to broaden genetic diversity by the introduction of new genes into crops. But the random insertion of foreign DNA into the plant's nuclear genome often leads to transgene silencing. Recent advances in the field of plant breeding include the development of a new breeding technique called genome editing. Genome editing technologies have emerged as powerful tools to precisely modify the crop genomes at specific sites in the genome, which has been the longstanding goal of plant breeders. The precise modification of the target genome, the absence of foreign DNA in the genome-edited plants, and the faster and cheaper method of genome modification are the remarkable features of the genome-editing technology that have resulted in its widespread application in crop breeding in less than a decade. This review focuses on the advances in crop breeding through precision genome editing. This review includes: an overview of the different breeding approaches for crop improvement; genome editing tools and their mechanism of action and application of the most widely used genome editing technology, CRISPR/Cas9, for crop improvement especially for agronomic traits such as disease resistance, abiotic stress tolerance, herbicide tolerance, yield and quality improvement, reduction of anti-nutrients, and improved shelf life; and an update on the regulatory approval of the genome-edited crops. This review also throws a light on development of high-yielding climate-resilient crops through precision genome editing.
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Affiliation(s)
- Gauri Nerkar
- Molecular Biology and Genetic Engineering Laboratory, Vasantdada Sugar Institute, Pune, India
| | - Suman Devarumath
- Vidya Pratishthan's College of Agricultural Biotechnology, Baramati, India
| | - Madhavi Purankar
- Molecular Biology and Genetic Engineering Laboratory, Vasantdada Sugar Institute, Pune, India
| | - Atul Kumar
- Molecular Biology and Genetic Engineering Laboratory, Vasantdada Sugar Institute, Pune, India
| | - R Valarmathi
- ICAR-Sugarcane Breeding Institute, Coimbatore, India
| | - Rachayya Devarumath
- Molecular Biology and Genetic Engineering Laboratory, Vasantdada Sugar Institute, Pune, India
| | - C Appunu
- ICAR-Sugarcane Breeding Institute, Coimbatore, India
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Vignesh P, Mahadevaiah C, Parimalan R, Valarmathi R, Dharshini S, Nisha S, Suresha GS, Swathi S, Mahadeva Swamy HK, Sreenivasa V, Mohanraj K, Hemaprabha G, Bakshi R, Appunu C. Comparative de novo transcriptome analysis identifies salinity stress responsive genes and metabolic pathways in sugarcane and its wild relative Erianthus arundinaceus [Retzius] Jeswiet. Sci Rep 2021; 11:24514. [PMID: 34972826 PMCID: PMC8720094 DOI: 10.1038/s41598-021-03735-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 05/06/2021] [Accepted: 12/08/2021] [Indexed: 11/09/2022] Open
Abstract
Erianthus arundinaceus [Retzius] Jeswiet, a wild relative of sugarcane has a high biomass production potential and a reservoir of many genes for superior agronomic traits and tolerance to biotic and abiotic stresses. A comparative physiological, anatomical and root transcriptome analysis were carried out to identify the salt-responsive genes and metabolic pathways associated with salt-tolerant E. arundinaceus genotype IND99-907 and salinity-sensitive sugarcane genotype Co 97010. IND99-907 recorded growth of young leaves, higher proline content, higher relative water content, intact root anatomical structures and lower Na+/K+, Ca2+/K+ and Mg2+/K+ ratio as compared to the sugarcane genotype Co 97010. We have generated four de novo transcriptome assemblies between stressed and control root samples of IND99-907 and Co 97010. A total of 649 and 501 differentially expressed genes (FDR<0.01) were identified from the stressed and control libraries of IND99-907 and Co 97010 respectively. Genes and pathways related to early stress-responsive signal transduction, hormone signalling, cytoskeleton organization, cellular membrane stabilization, plasma membrane-bound calcium and proton transport, sodium extrusion, secondary metabolite biosynthesis, cellular transporters related to plasma membrane-bound trafficking, nucleobase transporter, clathrin-mediated endocytosis were highly enriched in IND99-907. Whereas in Co 97010, genes related to late stress-responsive signal transduction, electron transport system, senescence, protein degradation and programmed cell death, transport-related genes associated with cellular respiration and mitochondrial respiratory chain, vesicular trafficking, nitrate transporter and fewer secondary metabolite biosynthetic genes were highly enriched. A total of 27 pathways, 24 biological processes, three molecular functions and one cellular component were significantly enriched (FDR≤ 0.05) in IND99-907 as compared to 20 pathways, two biological processes without any significant molecular function and cellular components in Co 97010, indicates the unique and distinct expression pattern of genes and metabolic pathways in both genotypes. The genomic resources developed from this study is useful for sugarcane crop improvement through development of genic SSR markers and genetic engineering approaches.
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Affiliation(s)
- P Vignesh
- ICAR-Sugarcane Breeding Institute, Coimbatore, India
| | - C Mahadevaiah
- ICAR-Sugarcane Breeding Institute, Coimbatore, India.
| | - R Parimalan
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Australia
| | - R Valarmathi
- ICAR-Sugarcane Breeding Institute, Coimbatore, India
| | - S Dharshini
- ICAR-Sugarcane Breeding Institute, Coimbatore, India
| | - Singh Nisha
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
- Institute for Genomic Diversity, Cornell University, Ithaca, NY, 14853, USA
| | - G S Suresha
- ICAR-Sugarcane Breeding Institute, Coimbatore, India
| | - S Swathi
- ICAR-Sugarcane Breeding Institute, Coimbatore, India
| | | | - V Sreenivasa
- ICAR-Sugarcane Breeding Institute, Coimbatore, India
| | - K Mohanraj
- ICAR-Sugarcane Breeding Institute, Coimbatore, India
| | - G Hemaprabha
- ICAR-Sugarcane Breeding Institute, Coimbatore, India
| | - Ram Bakshi
- ICAR-Sugarcane Breeding Institute, Coimbatore, India
| | - C Appunu
- ICAR-Sugarcane Breeding Institute, Coimbatore, India.
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Jun H, Jian Z, Hong Y, Jayabharathy R, Gomathi V, Valarmathi R, Bagyalakshmi G, Elamaran V, Saravanan S. Digital Hearing Aids Using Automated Varying Bandwidth Finite Impulse Response Filter Banks. j med imaging hlth inform 2020. [DOI: 10.1166/jmihi.2020.3128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
A human auditory system is a highly complex sensitive system which transfers the acoustic sound into neuroelectrical signals toward the brain. Hearing difficulties or deafness are the outcomes of the problems occurred at any part of the auditory system. Assistive technologies such as
hearing aids are developed to improve the quality of life of the hearing impaired people. Current digital hearing aids have fixed bandwidth filter banks which cannot provide enough flexibility to match with audiogram of different hearing loss. Recently, variable bandwidth filter banks have
been introduced with different technologies to match more closely with the audiogram of a particular hearing loss. This research work proposes and implements a software controlled variable bandwidth FIR filter bank using Matlab GUI. In the Matlab GUI, in the filter bank, the bandwidth of every
filter is adjusted dynamically in the Matlab GUI such that it fits more closely to the audiogram of a particular hearing loss. An experiment has been conducted in the developed Matlab GUI with various hearing loss, and the results show that the proposed system matches the filter bank magnitude
response very closely to the audiogram of a particular hearing loss and reduces the matching error.
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Affiliation(s)
- Hu Jun
- School of Civil Engineering, Chongqing Jiaotong University, Chongqing 400074, China
| | - Zeng Jian
- School of Civil Engineering, Chongqing Jiaotong University, Chongqing 400074, China
| | - Yi Hong
- School of Civil Engineering, Chongqing Jiaotong University, Chongqing 400074, China
| | - R. Jayabharathy
- School of Electrical and Electronics Engineering (EEE), Shanmugha Arts Science Technology Research Academy (SASTRA) Deemed University, Thanjavur 613403, Tamilnadu, India
| | - V. Gomathi
- School of Electrical and Electronics Engineering (EEE), Shanmugha Arts Science Technology Research Academy (SASTRA) Deemed University, Thanjavur 613403, Tamilnadu, India
| | - R. Valarmathi
- School of Electrical and Electronics Engineering (EEE), Shanmugha Arts Science Technology Research Academy (SASTRA) Deemed University, Thanjavur 613403, Tamilnadu, India
| | - G. Bagyalakshmi
- School of Electrical and Electronics Engineering (EEE), Shanmugha Arts Science Technology Research Academy (SASTRA) Deemed University, Thanjavur 613403, Tamilnadu, India
| | - V. Elamaran
- School of Electrical and Electronics Engineering (EEE), Shanmugha Arts Science Technology Research Academy (SASTRA) Deemed University, Thanjavur 613403, Tamilnadu, India
| | - S. Saravanan
- Department of Information Science and Engineering, CMR Institute of Technology, Bangalore 560037, India
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Hui W, Chang G, Saravanan S, Gomathi V, Valarmathi R, Balaji VS, Elamaran V. Revisiting FPGA Implementation of Digital Filters and Exploring Approximate Computing on Biomedical Signals. j med imaging hlth inform 2020. [DOI: 10.1166/jmihi.2020.3129] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
In recent years, the approximate computing becomes popular in the era of VLSI (very large scale integration) domain to arrive better power, area, and delay outcomes at the cost of lower precision loss. Also, the human beings are not so intelligent to see/observe/listen the processed
digital data; means even if some of the data loss occurs human beings are unable to notice them. This behavior set the engineers to research on approximate computing which are very useful in the multimedia data processing, data communications, high-volume data storage, etc. In this study,
the experiments such as hum-noise removal, filters on QRS detection are implemented on an Altera FPGA EP4CEF29C7 device using Quartus II 13.1 synthesis software tool and the simulation results on device utilization reports, the speed and the power are obtained. Simulation results reveal that
the approximate computational filters offer better power, area, and speed results than the conventional ones. Also, Matlab 9.4 (R2018a) simulation was used to carry out the functional verification of the actual and approximate filters.
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Affiliation(s)
- Wang Hui
- Network & Information Center, Chengdu Normal University, Chengdu, 610100, China
| | - Gong Chang
- Network & Information Center, Chengdu Normal University, Chengdu, 610100, China
| | - S. Saravanan
- Department of Information Science and Engineering, CMR Institute of Technology, Bangalore, India
| | - V. Gomathi
- School of Electrical Electronics Engineering, Shanmugha Arts Science Technology Research Academy Deemed University, Thanjavur 613403, Tamilnadu, India
| | - R. Valarmathi
- School of Electrical Electronics Engineering, Shanmugha Arts Science Technology Research Academy Deemed University, Thanjavur 613403, Tamilnadu, India
| | - V. S. Balaji
- School of Electrical Electronics Engineering, Shanmugha Arts Science Technology Research Academy Deemed University, Thanjavur 613403, Tamilnadu, India
| | - V. Elamaran
- School of Electrical Electronics Engineering, Shanmugha Arts Science Technology Research Academy Deemed University, Thanjavur 613403, Tamilnadu, India
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Shoba D, Raveendran M, Manonmani S, Utharasu S, Dhivyapriya D, Subhasini G, Ramchandar S, Valarmathi R, Grover N, Krishnan SG, Singh AK, Jayaswal P, Kale P, Ramkumar MK, Mithra SVA, Mohapatra T, Singh K, Singh NK, Sarla N, Sheshshayee MS, Kar MK, Robin S, Sharma RP. Development and Genetic Characterization of A Novel Herbicide (Imazethapyr) Tolerant Mutant in Rice (Oryza sativa L.). Rice (N Y) 2017; 10:10. [PMID: 28378144 PMCID: PMC5380566 DOI: 10.1186/s12284-017-0151-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Accepted: 03/28/2017] [Indexed: 05/04/2023]
Abstract
BACKGROUND Increased water and labour scarcity in major rice growing areas warrants a shift towards direct seeded rice cultivation under which management of weeds is a major issue. Use of broad spectrum non-selective herbicides is an efficient means to manage weeds. Availability of rice genotypes with complete tolerance against broad-spectrum non-selective herbicides is a pre-requisite for advocating use of such herbicides. In the present study, we developed an EMS induced rice mutant, 'HTM-N22', exhibiting tolerance to a broad spectrum herbicide, 'Imazethapyr', and identified the mutations imparting tolerance to the herbicide. RESULTS We identified a stable and true breeding rice mutant, HTM-N22 (HTM), tolerant to herbicide, Imazethapyr, from an EMS-mutagenized population of approximately 100,000 M2 plants of an upland rice variety, Nagina 22 (N22). Analysis of inheritance of herbicide tolerance in a cross between Pusa 1656-10-61/HTM showed that this trait is governed by a single dominant gene. To identify the causal gene for Imazethapyr tolerance, bulked segregant analysis (BSA) was followed using microsatellite markers flanking the three putative candidate genes viz., an Acetolactate Synthase (ALS) on chromosome 6 and two Acetohydroxy Acid Synthase (AHAS) genes, one on chromosomes 2 and another on chromosome 4. RM 6844 on chromosome 2 located 0.16 Mbp upstream of AHAS (LOC_Os02g30630) was found to co-segregate with herbicide tolerance. Cloning and sequencing of AHAS (LOC_Os02g30630) from the wild type, N22 and the mutant HTM and their comparison with reference Nipponbare sequence revealed several Single Nucleotide Polymorphisms (SNPs) in the mutant, of which eight resulted in non-synonymous mutations. Three of the eight amino acid substitutions were identical to Nipponbare and hence were not considered as causal changes. Of the five putative candidate SNPs, four were novel (at positions 30, 50, 81 and 152) while the remaining one, S627D was a previously reported mutant, known to result in Imidazolinone tolerance in rice. Of the novel ones, G152E was found to alter the hydrophobicty and abolish an N myristoylation site in the HTM compared to the WT, from reference based modeling and motif prediction studies. CONCLUSIONS A novel mutant tolerant to the herbicide "Imazethapyr" was developed and characterized for genetic, sequence and protein level variations. This is a HTM in rice without any IPR (Intellectual Property Rights) infringements and hence can be used in rice breeding as a novel genetic stock by the public funded organizations in the country and elsewhere.
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Affiliation(s)
- D. Shoba
- Tamil Nadu Agricultural University, Coimbatore, 641003 India
| | - M. Raveendran
- Tamil Nadu Agricultural University, Coimbatore, 641003 India
| | - S. Manonmani
- Tamil Nadu Agricultural University, Coimbatore, 641003 India
| | - S. Utharasu
- Tamil Nadu Agricultural University, Coimbatore, 641003 India
| | - D. Dhivyapriya
- Tamil Nadu Agricultural University, Coimbatore, 641003 India
| | - G. Subhasini
- Tamil Nadu Agricultural University, Coimbatore, 641003 India
| | - S. Ramchandar
- Tamil Nadu Agricultural University, Coimbatore, 641003 India
| | - R. Valarmathi
- Tamil Nadu Agricultural University, Coimbatore, 641003 India
| | - Nitasha Grover
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - S. Gopala Krishnan
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - A. K. Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Pawan Jayaswal
- ICAR-National Research Centre on Plant Biotechnology, Pusa, New Delhi, 110012 India
| | - Prashant Kale
- ICAR-National Research Centre on Plant Biotechnology, Pusa, New Delhi, 110012 India
| | - M. K. Ramkumar
- ICAR-National Research Centre on Plant Biotechnology, Pusa, New Delhi, 110012 India
| | - S. V. Amitha Mithra
- ICAR-National Research Centre on Plant Biotechnology, Pusa, New Delhi, 110012 India
| | - T. Mohapatra
- Indian Council of Agriculture Research, New Delhi, 110 001 India
| | - Kuldeep Singh
- Punjab Agricultural University, Ludhiana, 141004 India
- Present address: ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi, 110012 India
| | - N. K. Singh
- ICAR-National Research Centre on Plant Biotechnology, Pusa, New Delhi, 110012 India
| | - N. Sarla
- Indian Institute of Rice Research, Rajendranagar, Hyderabad, 500030 India
| | | | - M. K. Kar
- National Rice Research Institute, Cuttack, Odisha 753006 India
| | - S. Robin
- Tamil Nadu Agricultural University, Coimbatore, 641003 India
| | - R. P. Sharma
- INSA Honorary Scientist, NRCPB, IARI, Pusa, New Delhi, 110012 India
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Rahman H, Jagadeeshselvam N, Valarmathi R, Sachin B, Sasikala R, Senthil N, Sudhakar D, Robin S, Muthurajan R. Transcriptome analysis of salinity responsiveness in contrasting genotypes of finger millet (Eleusine coracana L.) through RNA-sequencing. Plant Mol Biol 2014; 85:485-503. [PMID: 24838653 DOI: 10.1007/s11103-014-0199-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Accepted: 05/10/2014] [Indexed: 05/20/2023]
Abstract
Finger millet (Eleusine coracana L.) is a hardy cereal known for its superior level of tolerance against drought, salinity, diseases and its nutritional properties. In this study, attempts were made to unravel the physiological and molecular basis of salinity tolerance in two contrasting finger millet genotypes viz., CO 12 and Trichy 1. Physiological studies revealed that the tolerant genotype Trichy 1 had lower Na(+) to K(+) ratio in leaves and shoots, higher growth rate (osmotic tolerance) and ability to accumulate higher amount of total soluble sugar in leaves under salinity stress. We sequenced the salinity responsive leaf transcriptome of contrasting finger millet genotypes using IonProton platform and generated 27.91 million reads. Mapping and annotation of finger millet transcripts against rice gene models led to the identification of salinity responsive genes and genotype specific responses. Several functional groups of genes like transporters, transcription factors, genes involved in cell signaling, osmotic homeostasis and biosynthesis of compatible solutes were found to be highly up-regulated in the tolerant Trichy 1. Salinity stress inhibited photosynthetic capacity and photosynthesis related genes in the susceptible genotype CO 12. Several genes involved in cell growth and differentiation were found to be up-regulated in both the genotypes but more specifically in tolerant genotype. Genes involved in flavonoid biosynthesis were found to be down-regulated specifically in the salinity tolerant Trichy 1. This study provides a genome-wide transcriptional analysis of two finger millet genotypes differing in their level of salinity tolerance during a gradually progressing salinity stress under greenhouse conditions.
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Affiliation(s)
- Hifzur Rahman
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, 641 003, India
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Valarmathi R, Hariharan GN, Venkataraman G, Parida A. Characterization of a non-reducing polyketide synthase gene from lichen Dirinaria applanata. Phytochemistry 2009; 70:721-729. [PMID: 19427006 DOI: 10.1016/j.phytochem.2009.04.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2008] [Revised: 04/08/2009] [Accepted: 04/09/2009] [Indexed: 05/27/2023]
Abstract
Lichens are known to produce a variety of secondary metabolites including polyketides that have diverse biological role(s). The biosynthesis of fungal polyketides is governed by type I polyketide synthases (PKS), enzymes with a multidomain structure, including the beta-ketoacyl synthase (KS), acyl transferase (AT), ketoreductase (KR), dehydratase (DH), enoyl reductase (ER) and acyl carrier protein (ACP) domains. Established soredial cultures of Dirinaria applanata (Fée) producing atranorin and divaricatic acid were used to characterize a polyketide synthase gene (DnPKS). A 743bp fragment corresponding to the ketosynthase domain (KS) was isolated using degenerate primers. Complete sequence information for DnPKS (8162bp) was obtained by walking in the 5'and 3' directions of the isolated KS domain using TAIL PCR. A translation of the DnPKS sequence identified the presence of KS, AT, two ACP and TE domains with eight intervening introns. TBLASTX analysis and comparison with other PKS sequences suggest that the coding region of DnPKS sequence is complete with the identification of putative start and stop codons and a stretch of 1226 upstream of the start codon corresponding to the putative promoter. This sequence shows the presence of putative binding sites for fungal transcription factors such as AflR, AreA and PacC. Southern blot analysis suggests that additional DnPKS-like genes may be present in the D. applanata genome. Additionally, expression of a DnPKS-like transcript was examined under different culture conditions and found to be down-regulated by sucrose and up-regulated by mannitol, UV and neutral pH.
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Affiliation(s)
- R Valarmathi
- Lichen Ecology and Bioprospecting Laboratory, M.S. Swaminathan Research Foundation, Taramani, Chennai, India
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Akilandeswari S, Mainmaran S, Valarmathi R, Kumara SK, Loganathan SV. Phytochemical observation on leaf of justicia tranquebariesis. L.f. Anc Sci Life 2001; 20:60-1. [PMID: 22557013 PMCID: PMC3336403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Photochemical studies of leaf of the herbs Justicia tranquebariensis. (Acanthaceae) carried out in the presence of phytosterols, flavonoids, Glycosides and absence of triterpenoids, alkaloids, saponins tannins have been reported in this herb for the first time.
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Affiliation(s)
- S. Akilandeswari
- Periyar College of Pharmacentical sciences, Trichirapalli - 21, India
| | - S. Mainmaran
- Periyar College of Pharmacentical sciences, Trichirapalli - 21, India
| | - R. Valarmathi
- Periyar College of Pharmacentical sciences, Trichirapalli - 21, India
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