Dr Ramaswamy Manimekalai

Scientist Profile

Research interests and current focus

Gene editing in sugarcane, Genomic selection, Sugarcane genomics and Bioinformatics

Membership in professional societies

Life member Society for Sugar Research and Promotion (SSRP)
Fellow of Confederation of Horticultural Association of India (CHAI)
Fellow of Society of Applied Biotechnology (SAB)
Fellow of Society for sugarcane Research and Promotion, New Delhi
Life member Indian Phytopathological Society (IPS)
Life member of Indian Society of Plantation Crops (ISPC)
Life member of Indian Horticultural Society (HIS)
Life member of Society of biochemistry and biotechnology (ISBB), India
Life member of Indian society of Plant breeding and genetics (ISPBG)
Life Member of Indian Society of Virology
Life member Soceity of Applied Biotechnology (SAB), India
Life Member Indian Society of Horticulture Research and Development

List of current external funded project

Title: CRISPR-Cas9 Crop Network – Development of Haploid inducing lines in sugarcane through CRISPR-Cas9 editing in collaboration with IARI and IISER, Trivandrum

Agency: National Agricultural Science Fund (NASF)

Amount: 94 lakhs

Title: Transgene free genome editing in sugarcane in collaboration with Punjab Agricultural University and ICAR-NRCB

Agency: Department of Biotechnology, New Delhi

Amount: 2.3 Cr

Title: Genome editing in sugarcane for flowering trait

Agency: Indian Council of Agricultural Research, New Delhi.

Amount: 1.1 Cr

Awards and honours

DBT Overseas Fellowship for Young scientists for post doctoral research, Department of Biotechnology (DBT), Ministry of Science and Technology, Govt. Of India – 2005
INSA medal for Young Scientists, Indian National Science Academy (INSA), India – 2007
External Grants Received for Research and Development : Rs 15.5 Cr (DBT, DST, NASF, ICAR, Department of Information Technology, Coconut Development Board, INSA)
FAO Technical consultant to Sri Lanka during 2009-2013
FAO expert for the Collaborative workshop at Sri Lanka, Food and Agricultural Organization, 2009
C. S. Venkat Ram Memorial Award for Plantation Crops Symposium ISPC (Indian Society for Plantation Crops), India
International Travel Grant by IAPSIT to Vietnam to Present invited talk in the International Conference “Sugarcane Gene Editing, 2025
International Travel Grant by Vietnam Academy of Science and Technology, (VAST), Vietnam, 2024 for invited talk on Genome Editing
International Travel Grant by Association of Academies and Societies for South Asia (AASSA) to Bangladesh, 2023
Society for Sugarcane Research and Promotion (SSRP) – Fellowship in Sugarcane Biotechnology, 2022
Society for Sugarcane Research and Development (SSRD) Best Paper award- International Conference – Sugarcon -2019 held at ICAR- Indian Institute of Sugarcane Research, on Novel miRNAs: Prediction and annotation in sugarcane and wild species, 2019
Best research paper – published in Journal sugarcane Research (Journal of Sugarcane Research) – 2019
Invited Presentations in national and international Conferences – 37
Member In Doctoral Committee, Tamil Nadu Agricultural University, Coimbatore
Member In Doctoral Committee, Kerala Agricultural University, Trivandrum
Number of students guided D: 4, M.Sc: 38
Award from Springer for Contribution in editing of Sugar Tech journal articles, NAAS score 7.1 – 2019
Best research paper presented at International Conference on “Plant, Pathogens and People” with mission “Challenges in Plant Pathology to benefit human kind ”, 2016
Best presentation award – National conference on Application of Bioinformatics in Agriculture 11/ 2013. ICAR-CPCRI, India
Best presentation award National Consultative meeting on Horti -informatics at ICAR- Institute of Spices Research (IISR) – 2010
Best presentation award at National symposium on Accelerating Biology held at Cdac, Pune India, 2010
Rewati Singh memorial award for women Scientist by Society for Recent Development in Agriculture, India, 2016
International Travel award by United Arab Emirates University, UAE International Symposium on biological sciences Nov 2016 on “Transcriptomics”
Group leader: International coconut genomics 2012-2014 (Bioversity International).
International sponsorship for organizing coconut genomics by Bioversity International – 2011
International Travel Grant by Dept of Science and Technology GOI for attending the Plant and Animal Genome Conference, San Diego, USA – 2011
Indian Council of Agricultural Research (ICAR), Govt of India, International fellowship in Bioinformatics to John Innes Center, UK – 2010
Mehta Young scientist Medal, Mehta Foundation, India, 2010
Fellowship of the Society Confederation of Horticultural Association of India (CHAI) – 2012
Fellow – Society for Applied Biotechnology, (SAB), India, 2011
Recognized as PhD guide for
Kannur University, Kerala, iii. Bharathiar University
University of Calicut, Kerala iv. Bharathidasan University, v. Mangalore University. In the discipline of biotechnology.
International fellowship by Post Graduate Institute of Agriculture, Sri Lanka, University of Peradenyia, Sri Lanka and Asia Pacific Coconut Community (APCC), Indonesia International travel grant to present a paper in the XVII Annual congress Post Graduate Institute Agriculture, Sri Lanka – 2005
All India 7th rank in agricultural Biotechnology Studentship, Jawaharlal Nehru University (JNU), India – 1996-1998
K.S. Krishnan Fellowship, BRNS – Department of Atomic Energy Bhabha Atomic Research Center (BARC) – 1996-1998
Junior Research Fellowship and national Eligibility Test, Council of Scientific and Industrial Research (CSIR) – 1999
Junior Research Fellowship – Centre for Cellular and Molecular Biology (CCMB) – 1999
Agricultural Research Service (ARS) in Biotechnology and NET – 1999
Agricultural Scientist Recruitment Board (ASRB) of Indian Council for Agricultural Research (ICAR) – 1999
First rank holder in B. Sc (Agri), TNAU, Coimbatore – 1995
National Merit Scholarship, Tamil Nadu State Public Examination Board
Editorial Board – BMC plant Biology, Sugar Tech, Springer, Phytopathogenic Mollicutes, Springer
Reviewer – Plant disease, Molecular Genetics and Genomics , 3 Biotech , Indian Journal of Entomology, Scientia Horticulture, Australasian Plant Pathology, American Journal of Botany, BMC genomics, Frontiers in plant sciences, Indian Journal of Plantation Crops, Plant Molecular biology reporter, Gene, Journal of Plant biochemistry and biotechnology, Plant Physiology Reporter

International Exposure

DBT Overseas Fellowship for Young scientists for post doctoral research to National Institute of Agrobiological Sciences, Japan sponsored by Department of Biotechnology (DBT), Ministry of Science and Technology, Govt. Of India – 2006-2007
Visiting Scientist, University of Florida, Gainesville, USA on gene editing in sugarcane , 03/2025-08/2025
International workshop- Indo – Australia Collaborative project workshop: at Sugar Research Australia, Australia 19/08/2017
Food And Agriculture Organization consultant to Sri Lanka ,03/2009 -12/2012
International work experience in Bioinformatics and Diagnostics at The John Innes Centre, Norwich Research Park, Colney Lane, Colney, Norwich, NR4 7UH, United Kingdom in Bioinformatics and Diagnostics at Nottingham University, Nottingham, UK,01/06/2010

Research Publications

Kumari S, Harshavardhini RK, Murugan N, Keerthana S, Aispriya, Vinayaka, Ramaswamy A, Prabhakaran J and Manimekalai, R. (2025) Comparative genomics and synteny analysis of PP2C phosphatases in modern and wild sugarcane cultivars for insights into abiotic stress response. Plant Sci.16:1596800. doi: 10.3389/fpls.2025.1596800

Aswini, N., Moniusha, J., Keerthana, S. Amaresh, Nandhini, M., Prathima,T., Mohanraj, K., Shweta Kumari and Manimekalai, R (2025). Genomic Exploration for the Sucrose Content in Sugarcane. Tropical Plant Biol. 18, 44. https://doi.org/10.1007/s12042-025-09413-4

R MANIMEKALAI, Arockiya Jainmary, K Mohanraj, Jini Narayanan, Ram vannish, K.P Mrudula, J. Saranya, M. Gokul, Rajeev Kumar, R Singh Gujjar, Selvi A, S. Vasantha, G. Hemaprabha. (2024). Evaluation of Genetic Variability, Phenotypic Stability and Interrelationships among the Quantitative Traits of Sugarcane under Drought Stress. Journal of Applied Biotechnology Reports 12 (2), 1652-1667

Boopathi,N., Karthikeyan, G., Raveendran, M., Johnson, I., Maruthasalam, S., Srinivasan, T., Manimekalai, R. (2025). Characterization of phytoplasma associated with wilt disease in coconut and approaches for its sensitive diagnostics. Journal of Microbiological Methods,228: 107072, ISSN 0167-7012,https://doi.org/10.1016/j.mimet.2024.107072.

Aswini N, Amaresh , M. Nandhini , Keerthana, Rajeev Kumar , Gujjar, R.S ., R. Gomathi , A. Selvi, P. Govindaraj and R. Manimekalai. 2024. Genome-Wide Expression Profiling of Cytochrome P450 Genes in Response to the Oxidative Stress in Saccharumspp. Sugar Tech . DOI : 10.1007/s12355-024- 01509-7
Manimekalai, Saranya J, S. Keerthana, Shalini, Jini, N., A. Selvi, Rabisa, Nandhini M, Ram Vannish, P.T. Prathima and R. Gomathi. 2024. Small RNA profiling and co-networking analysis identifies stress-responsive miRNAs involved in sugarcane and its wild species. Plant Physiology Reports DOI: 10.1007/s40502-024-00841-0

Nunavath, A., Amaresh, Murugan, N. Keerthana, S., Shweta Kumari, Singaravelu, B., Ramesh Sundar, A., R Manimekalai, R. (2025) Transcription Factors in Plant Biotic and Abiotic Stress Responses: Potentials and Prospects in Sugarcane. Tropical Plant Biol.18, 28. https://doi.org/10.1007/s12042-025-09398-0
Amaresh, G., Nunavath, A., Appunu, C. Viswanathan, C. Rajeev Kumar, R. S. Gujjar and Manimekalai. 2024. Advanced Genome Editing Technologies: Potentials and Prospects in Improvement of Sugar crops. Sugar Tech (2024). https://doi.org/10.1007/s12355-024-01447-4
AK Mall, R Manimekalai, V Misra, H Pandey, S Srivastava, A Sharma. CRISPR/Cas Mediated Genome Editing for Sugarcane Improvement. Sugar Tech,1-13. https://doi.org/10.1007/ s12355-023-01352
Gomathi, S. Kohila, R. Viswanathan, V. Krishnapriya, C. Appunu, R. Arun Kumar, M. Alagupalamuthirsolai, R. Manimekalai, K. Elayaraja and K. Kaverinathan. 2024. Comparative Proteomic Analysis of High‑Temperature Response in Sugarcane (Saccharum spp.). Sugar Tech. https://doi.org/10.1007/s12355-024-01400-5
Saurabh S, Raj Morya, J Durgesh Kumar, S Keerthana, S Kim , R Manimekalai, APA Pereira, JP Verma. Innovations and advances in enzymatic deconstruction of biomass and their sustainability analysis: A review. Journal Renewable and Sustainable Energy Reviews. https://doi.org/10.1016/j.rser.2023.1139
S Krishna, C. Harish, M Ravi, V Valarmathi, K Lakshmi, PT Prathima, R Manimekalai, Viswanathan, G. Hemaprabha, C. Appunu. 2023.Transgene-Free Genome Editing for Biotic and Abiotic Stress Resistance in Sugarcane: Prospects and Challenges. Agronomy. 13. https://doi.org/10.33
Nandita Banerjee, Khan, M.S., Swapna, M., Yadav, S., Tiwari, G., Jena, S.N., Patel, J.D., Manimekalai, R., Kumar, S. Dattamajuder,S.K., Kapur, R., Koebernick, J.C., Singh. R.K. 2023. QTL mapping and identification of candidate genes linked to red rot resistance in sugarcane. 3 Biotec 10.1007/s13205-023-03481-7
Manimekalai, *, Selvi, A., Jini Narayanan, Ram Vannish, R. Shalini, Gayathri, S.Rabisha, V.P. 2023. Comparative physiological and transcriptome analysis in cultivated and wild sugarcane species in response to hydrogen peroxide-induced oxidative stress. BMC Genomics 24, 155. https://doi.org/10.1186/s12864-023-09218
O’Connell A, Deo J, Deomano E, Wei X, Jackson P, Aitken KS, Manimekalai R, Mohanraj K, Hemaprabha G, Ram B, Viswanathan R, Lakshmanan P. Combining genomic selection with genome-wide association analysis identified a large-effect QTL and improved selection for red rot resistance in sugarcane. Front Plant Sci. 2022 Oct 31;13:1021182. doi: 10.3389/fpls.2022.1021182. PMID: 36388469; PMCID: PMC9660812.
M Naveenarani, P Vignesh, C Mahadevaiah, R Valarmathi, R Manimekalai, G Hemaprabha, C Appunu. 2022. Genome-Wide In Silico Identification, Structural Analysis, Promoter Analysis, and Expression Profiling of PHT Gene Family in Sugarcane Root under Salinity Stress. Sustainability 14 (23), 15893
Narayanan, J., Manimekalai, R., Selvi, A. Gomathi, R. And Arun, R. 2023. Physiological, Biochemical and Molecular Responses to Oxidative Stress in Saccharum spontaneum. Sugar Tech (2023). https://doi.org/10.1007/s12355-022-01189-1. Sugar Tech 25 (2), 294-294
Manimekalai, R., Gayathri, S. and Singaravelu, B. (2022). Sugarcane Transcriptomics in Response to Abiotic and Biotic Stresses: A Review. Sugar Tech (2022). https://doi.org/10.1007/s12355-021-01098-9
Srikanth, J., Mahesh, P., Manimekalai, R., Suresha, G. S., Singaravelu, B., And Salin, K. P. (2022). Web mite Schizotetranychus krungthepensis on sugarcane in India: molecular evidence for occurrence and the way forward. CURRENT SCIENCE,123(8), 1038.
Mintu R. Meena, Chinnaswamy Appunu, R. Arun Kumar, R.Manimekalai, S. Vasantha, Gopal Reddy, Ravinder Kumar, S. K.Pandey and G Hemaprabha. 2022. Recent Advances in Sugarcane Genomics, Physiology, and Phenomics for Superior Agronomic Traits. Frontiers in Genetics. 10.3389/fgene.2022.854936
Smita Nair and R. (2021). Phytoplasma diseases of plants: Molecular diagnostics and way forward”, World Journal of Microbiology and Biotechnology. DOI 10.1007/s11274-021-03061-y.
Selvi, A., Devi, K., Manimekalai, R., Prathima, P. T., Valiyaparambth, R., and Lakshmi, K. (2021). High-throughput miRNA deep sequencing in response to drought stress in sugarcane. 3 Biotech,11(7), 312. https://doi.org/10.1007/s13205-021-02857-x
Manimekalai*, Gayathri, S., Hemaprabha, G., and Selvi, A. Kandalam, M. (2020). Role of NGS and SNP Genotyping methods in Sugarcane improvement programs. Critical reviews in Biotechnology. DOI: 10.1080 /07388551. 2020. 1765730
Selvi, A., Devi, K., Manimekalai, R., Prathima, P.T. (2020). Comparative analysis of drought- responsive transcriptomes of sugarcane genotypes with differential tolerance to drought. 3 Biotech. DOI: 10.1007/s13205-020-02226-0
Taloh, A., Raju, D.V.S., Banyal, N., Kumar, G., Panda, P., Manimekalai, R., Carmine Marcone, C., and Rao, G.P. (2020). Genetic diversity of phytoplasma strains infecting chrysanthemum varieties in India and their possible natural reservoirs. 3 Biotech411. https:// doi.org/ 10.1007/ s13205- 020- 02407-x
Gayathri S, Arockiyajainmary M, Shalini R, Vannish MR, Selvi A, Manimekalai R. (2019). Identification of single nucleotide polymorphisms (SNPs ) in the transcriptome of sugarcane variety Co 86032 exposed to oxidative stress. J sugarcane Res. 9:71–85
Devi, K., Prathima, P.T., Gomathi, R., R., Lakshmi, K., and Selvi, A. 2019. Gene expression profiling in sugarcane genotypes during drought stress and rehydration Sugar Tech. https://doi.org/10.1007/s12355-018-0687-y
Devi, K., Gomathi, R. Arun Kumar, R., Manimekalai, R., and Selvi, A. Field tolerance and recovery potential of sugarcane varieties subjected to drought. Indian Journal of Plant Physiology, DOI: 10.1007/s40502-018-0367-7
Manimekalai*, Jini Narayanan, R. Ranjini, M. Gokul, A. Selvi, PradheepKumar and R. Gomathi. 2018. Hydrogen Peroxide-Induced Oxidative Stress in Sugarcane and Response Expression Pattern of Stress-Responsive Gene Through Quantitative RT-PCR. (2018). Sugar Tech. https://doi.org/10.1007/s12355-018-0604-4
Manimekalai, R.*, Jini, N., Gokul, M., Selvi, A., Gomathi, R., Arun Kumar. 2018. Bio-chemical and physiological response to oxidative stress in cultivated sugarcane and wild genera. Indian Journal of Plant Physiology. 23: 261–270. DOI :10.1007/s40502-018-0368-6.

book chapters

R.Manimekalai, K. Mohan Raj, G. Hemaprabha, R. Viswanathan and A. Selvi. 2024. Tools for Genomic selection (GS) and Genome wide Association studies (GWAS) for sugarcane Breeding. In climate smart Agriculture for food and Energy security in India. Ed. G. Hemaprabha and C. Appunu. ISSN: 978 – 93-85267-42-0
Perera, R Manimekalai, Yang Pavani, D., Chongxi, K. Sundaravelpandian, 2024. Breeding and Genetics for Coconut Improvement. The Coconut: Botany, Production and Uses. CABI. https://doi.org/10.1079/9781789249736.00
Sumi, Govind Pratap Rao, Saman Abeysinghe, A.K. Tiwari, R. Manimekalai, Vinayak Hegde, M. Kochu Babu, 2023. – Up-to-date information of phytoplasma diseases associated with palm species in Asian countries, Editor(s): A.K. Tiwari, e al. In Phytoplasma Diseases in Asian Countries, Phytoplasma Diseases of Major Crops, Trees, and Weeds, 2 : 141-166, ISBN 9780323918978. https://doi.org/10.1016/B978-0-323-91897-8.00019-8.
R.Manimekalai, G. Hemaprabha, K. Mohan Raj, A. Selvi, S. Vasantha, R. Viswanathan, Bakshi Ram, Jini Narayanan, A. J. Mary, Ram Vannish And J.Saranya (2021). Assessment of genetic variability and inter-relationship among the quantitative traits of sugarcane under drought stress. In. Palaniswami, C., Hemaprabha, G., Viswanathan, R., Karuppaiyan, R., Mohanraj, K., Mahadeva Swamy, H.K., and Bakshi Ram (Eds). 2021. P 793. PP. 112-115. ISBN 978-93-85267-30-7
Manimekalai, G. Hemaprabha, K. Mohan Raj, Emily Dm, A. Selvi, S. Vasantha, R. Viswanathan, Bakshi Ram, Ram Vannish, Infant,R., Wei, X., Phillip, J. And Prakash Laksmanan. (2021). Genomic prediction of sucrose content in sugarcane clones with prediction models. In. Palaniswami, C., Hemaprabha, G., Viswanathan, R., Karuppaiyan, R., Mohanraj, K., Mahadeva Swamy, H.K., and Bakshi Ram (Eds). 2021. P 793. PP.199-201. ISBN 978-93-85267-30-7
Selvi., K. Devi. R. Manimekalai, .T. Prathima, V. P. Rabisha and K. Lakshmi. (2021). Micro RNA regulation in sugarcane cultivars with differential tolerance to drought. In. Palaniswami, C., Hemaprabha, G., Viswanathan, R., Karuppaiyan, R., Mohanraj, K., Mahadeva Swamy, H.K., and Bakshi Ram (Eds). 2021. PP.192-193. ISBN 978-93-85267-30-7
A.Selvi, R. Manimekalai, K.Devakumar, K. Lakshmi, P.T. Prathima and R.Gomathi. 2020. Genomic and Proteomic Approaches for Improving Abiotic Stress Tolerance in Sugarcane. In Physiological Interventions for Developing Climate Resilient Commercial crops. (Eds). R. Gomathi, A. H. Prakash, Bakshi Ram. Pp188-270. E-ISBN : 978-93-90660-54-4
Perera, L., Manimekalai, R. S. Sudarsono, S. (2019). Advances in breeding of coconut In. Achieving sustainable cultivation of tropical fruits. DOI: 10.19103/AS.2019.0054.21
P. Rao., R. Manimekalai, Manish Kumar, Hemavati Ranebennur, Shigeyuki Kakizawa, Assunta Bertaccini. (2019). Host Metabolic Interaction and Perspectives in Phytoplasma Research. In book: Phytoplasmas: Plant Pathogenic Bacteria – III. DOI: 10.1007/978-981-13-9632-8_10
Manimekelai, R., Y Yaodong, L Baudouin* 2018. Utilization of coconut genetic resources. MG Pereira. 2.5.8 Genomics and DNA markers. In. A Global Strategy for the Conservation and Use of Coconut Genetic Resources, 2018-2028. (R. Bourdeix and A Prades, compilers). Bioversity International, Montpellier, France. pp 91-93 SBN: 978-92-9043-984-4