• Molecular Cell Biology, Functional Genomics and CRISPR/Cas based Genome Engineering for Stress Tolerance and Genetic Improvement of Quality Traits in Plants.

• Research Expertise and Interest: :

• Cell and molecular level understanding of biotic and abiotic stress tolerance in plants
• CRISPR/Cas-based genome editing and functional genomics for crop improvement and climate resilience
• Nutritional enhancement and quality trait improvement in crops.
• Plant biotechnology and metabolic engineering of aromatic and medicinal plants.

   

  PS: Ambitious researchers (preferably with their own Fellowship or seeking Fellowship) willing to join our research group as Postdocs/Research Fellows are encouraged to contact (channakeshav@neist.res.in) with their CV and summary of research interest.

• Research and Review Articles

  • Muttappagol M, Sharma M, Adhikari DN, Remya S, Borgohain T, Saikia B, Keithellakpam A, Duua A, Laskar A, Hiremath SS, Chikkaputtaiah C*. Towards climate-resilient crops: Integrative strategies for reproductive stage abiotic stress tolerance. Physiologia Plantarum, 2025.177:e70635. DOI: 10.1111/ppl.70635.IF: 3.60
  • Saikia B*, Remya S, Debbarma J, Maharana J, Velmurugan N, Sastry GN, Chikkaputtaiah C*.CRISPR/Cas9-based genome editing and functional analysis of SlHyPRP1 and SlDEA1 genes of Solanum lycopersicumL. in imparting genetic tolerance to multiple stress factors. Frontiers in Plant Science. 15, 2024. https://doi.org/10.3389/fpls.2024.1304381. IF: 4.80
  • Saikia B, Debbarma J, Maharana J, Singha DL, Velmuruagan N, Dekaboruah H, Arunkumar KP, Chikkaputtaiah C*. SlHyPRP1 and DEA1, the multiple stress responsive eight-cysteine motif family genes of tomato (Solanum lycopersicum L.) are expressed tissue specifically, localize and interact at cytoplasm and plasma membrane in vivo. Physiol Mol Biol Plants. 2020 Dec;26(12):2553-2568. DOI: 10.1007/s12298-020-00913-z. Epub 2020 Dec 7. PMID: 33424164; PMCID: PMC7772121. IF: 3.30
  • Singh S#, Sarki YN#, Marwein R#, Singha DL, Singha, Velmurugan N, Chikkaputtaiah C*. Unraveling the role of effector proteins in Bipolaris oryzae infecting North East Indian rice cultivars through time-course transcriptomics analysis. Fungal Biology. British Mycological Society. 127, 2023, 1098e1110. DOI: 10.1016/j.funbio.2023.05.003. IF: 3.00
  • Sarki YN, Singh HB, Keot A, Marwein R, Singha DL, Dehury B, Chikkaputtaiah C*. Investigating the Role of OsHDT701 and Other Blast-associated Negative Regulatory Genes in Indica Rice Cultivar Ranjit Using Combined Wet Lab and Computational Approaches. Mol Biotechnol. 2024. DOI: 10.1007/s12033-024-01310-7. IF: 2.50
  • Debbarma J, Sarki YN, Saikia B, Boruah HPD, Singha DL, Chikkaputtaiah C*. Ethylene Response Factor (ERF) Family Proteins in Abiotic Stresses and CRISPR-Cas9 Genome Editing of ERFs for Multiple Abiotic Stress Tolerance in Crop Plants: A Review. Molecular Biotechnology, 2019 Feb;61(2):153-172. DOI: 10.1007/s12033-018-0144-x. PMID: 30600447. IF: 2.50
  • Marwein R#, Singh S#, Maharana J, Kumar S, Arunkumar KP, Velmurugan N, Chikkaputtaiah C*.Transcriptome-wide analysis of North-East Indian rice cultivars in response to Bipolaris oryzae infection revealed the importance of early response to the pathogen in suppressing the disease progression. Gene. 2022 Jan 30;809:146049. DOI: 10.1016/j.gene.2021.146049. Epub 2021 Oct 29. PMID: 34743920. IF: 3.91
  • Das D, Chowdhury N, Sharma M, Remya S, Saikia B, Velmurugan N, Chikkaputtaiah C*. Screening of brown-spot disease and drought stress response and identification of dual-stress responsive genes in rice cultivar of Northeast India. Physiol Mol Biol Plants. 30, 647-663, 2024. https://doi.org/10.1007/s12298-024-01447-4. IF: 3.30
  • Singha DL, Das D, Sarki YN, Chowdhury N, Sharma M, Maharana J, Chikkaputtaiah C*. Harnessing tissue-specific genome editing in plants through CRISPR/Cas system: current state and future prospects. Planta. 2021 Dec 28;255(1):28. DOI: 10.1007/s00425-021-03811-0. PMID: 34962611. IF: 3.80
  • Debbarma J#, Saikia B#, Singha DL, Das D, Keot AK, Maharana J, Velmurugan N, Arunkumar KP, Reddy PS, Chikkaputtaiah C*. CRISPR/Cas9-Mediated Mutation in XSP10 and SlSAMT Genes Impart Genetic Tolerance to Fusarium Wilt Disease of Tomato (Solanum lycopersicum L.). Genes. 2023 Feb 14;14(2):488. DOI: 10.3390/genes14020488. PMID: 36833415; PMCID: PMC9956927. IF: 4.14
  • Das D, Singha DL, Paswan RR, Chowdhury N, Sharma M, Reddy PS, Chikkaputtaiah C*. Recent advancements in CRISPR/Cas technology for accelerated crop improvement. Planta. 2022 Apr 23;255(5):109. DOI: 10.1007/s00425-022-03894-3. PMID: 35460444. IF: 3.80
  • Debbarma J, Saikia B, Singha DL, Maharana J, Velmuruagan N, Dekaboruah H, Arunkumar KP, Chikkaputtaiah C*. XSP10 and SlSAMT, Fusarium wilt disease responsive genes of tomato (Solanum lycopersicum L.) express tissue specifically and interact with each other at cytoplasm in vivo. Physiol Mol Biol Plants. 2021 Jul;27(7):1559-1575. DOI: 10.1007/s12298-021-01025-y. Epub 2021 Jun 28. PMID: 34366597; PMCID: PMC8295444. IF: 3.30
  • Saikia B, Singh S, Debbarma J, Velmurugan N, Dekaboruah H, Arunkumar KP, Chikkaputtaiah C*. Multigene CRISPR/Cas9 genome editing of hybrid proline rich proteins (HyPRPs) for sustainable multi-stress tolerance in crops: the review of a promising approach. Physiol Mol Biol Plants. 2020 May;26(5):857-869. DOI: 10.1007/s12298-020-00782-6. Epub 2020 Apr 20. PMID: 32377037; PMCID: PMC7196567. IF: 3.50
  • Kor SD, Chowdhury N, Keot AK, Yogendra K, Chikkaputtaiah C, Sudhakar Reddy P. RNA Pol III promoters-key players in precisely targeted plant genome editing. Front Genet. 2023 Jan 4;13:989199. DOI: 10.3389/fgene.2022.989199. PMID: 36685866; PMCID: PMC9845283. IF: 4.77
  • Saradadevi GP#, Das D#, Mangrauthia SK#, Mohapatra S#, Chikkaputtaiah C#,Roorkiwal M, Solanki M, Sundaram RM, Chirravuri NN, Sakhare AS, Kota S, Varshney RK, Mohannath G. Genetic, Epigenetic, Genomic and Microbial Approaches to Enhance Salt Tolerance of Plants: A Comprehensive Review. Biology. 2021 Dec 1;10(12):1255. DOI: 10.3390/biology10121255. PMID: 34943170; PMCID: PMC8698797. IF: 5.16
  • Baruah I, Baruah G, Sahu J, Singha DL, Deka Boruah HP, Velmurugan N, Chikkaputtaiah C* (2020).Transient sub-cellular localization and in vivo protein-protein interaction study of multiple abiotic stress responsive AteIF4A-III and AtALY4 proteins in Arabidopsis thaliana. Plant Molecular Biology Reporter. Springer Publishers. 38, 538-553. DOI: 10.1007/s11105-020-01219-w. IF: 2.10
  • Kumar S, Gowda P.H.R, Saikia B, Debbarma J, Velmurugan N, Chikkaputtaiah C* (2018). Screening of tomato genotypes for identification of resistant lines and DNA marker against bacterial wilt (Ralstonia solanacearum). Australasian Plant Pathology. Springer Publishers. 47: 365-374. DOI: 10.1007/s13313-018-0567-7. IF: 1.40

  • Monograph

    • Sastry GN*, Chikkaputtaiah C*,Keot AK, Singha DL, Das D, Sarki YN, Saikia B. Fundamental and Advancement of CRISPR/Cas-based Genome Editing System (2023). Excel India Publishers, New Delhi, India. ISBN: 978-93-91355-37-1

    Book Chapters

    • Chowdhury N, Das D, Sarki YN, Sharma M, Singha DL, Chikkaputtaiah C* (2022). Genome editing and CRISPR/Cas technology for enhancing abiotic stress tolerance in cereals. OMICS approach to manage abiotic stress in cereals. Springer Nature. DOI: 10.1007/978-981-19-0140-9. ISBN 978-981-19-0139-3
    • Das D, Kumar S, Kar S,Chikkaputtaiah C, Singha DL (2022). Transgenic strategies to develop abiotic stress tolerance in cereals. OMICS approach to manage abiotic stress in cereals. Springer Nature. DOI: 10.1007/978-981-19-0140-9. ISBN 978-981-19-0139-3
    • Singha DL, Das D, Paswan RR, Chikkaputtaiah C*, Kumar S* (2022). Novel approaches and advanced molecular techniques for the crop improvement. Advances and Applications in Biotechnology. Taylor & Francis (CRC Press). DOI: 10.1201/9781003171416. ISBN: 9780367774424
    • Kumar S, Sarki YN, Debbarma J and Chikkaputtaiah C* (2023). CRISPR-Cas9/Cpf1 based multi-gene editing in crops. Genome Editing Technologies for Crop Improvement, Springer Nature. ISBN: 978-981-19-0599-5
    • Pal M, Das V, Dekaboruah HP, Chikkaputtaiah C (2022). Multiplexed biosensors for virus detection. Advanced Biosensors for Virus Detection, Elsevier. ISBN 978-0-12-8244944, 219-239
    • Baruah I, Sarki YN, Chikkaputtaiah C, Baruah G (2021). Role of PGPR in conferring drought stress tolerance in rice.  In: Singh H.B., Vaishnav A., Sayyed R. (eds) Antioxidants in Plant-Microbe Interaction. Springer, Singapore. https://doi.org/10.1007/978-981-16-1350-0_20. ISBN: 978-981-16-1349-4
    • Singha DL*., Baldodiya GM., Chikkaputtaiah C* (2020). Targeting metabolic pathways for abiotic stress tolerance through genetic engineering in rice. Rice Research for Quality Improvement: Genomics and Genetic Engineering. Springer Publishers, Singapore. Vol. 1 (617-648). DOI: 10.1007/978-981-15-4120-9. ISBN: 978-981-15-4119-3.
    • Sarki YN, Marwein R, Singh S, Dekaboruah HP, Singha DL and Chikkaputtaiah C* (2020). Understanding the mechanism of host-pathogen interaction in rice through genomics approaches. Rice Research for Quality Improvement: Genomics and Genetic Engineering. Springer Publishers, Singapore. Vol. 2 (1-33). DOI: 10.1007/978-981-15-5337-0. ISBN: 978-981-15-5336-3
    • Marwein R Debbarma J, Sarki N.Y, Baruah I, Saikia B, Deka Boruah H.P, Velmurugan N and Chikkaputtaiah C*(2019). Genetic engineering/Genome editing approaches to modulate signaling processes in abiotic stress tolerance. Plant Signaling Molecules. Elsevier Publishers. pp 63-82. DOI: 10.1016/B978-0-12-816451-8-00004-6. 978-012-816451-8        
    • Das V, Chikkaputtaiah C, Pal M (2019). Aptamer-conjugated functionalized nano-biomaterials for diagnostic and drug targeting application. Functional Polysaccharides for Biomedical Applications.Elsevier Publishers. DOI: 10.1016/B978-0-08-102555-0.00014-5.
    • Parasar NR, Chikkaputtaiah C, Lal M (2018). Metabolomic study of chemo-preventive phytochemicals and their therapeutic prospects. Anticancer Plants: Mechanisms and Molecular Interactions. Springer Publishers. DOI: 10.1007/978-981-10-8417-1_8.
    • Keshavaiah C, Havlickova L, Jelinkova I and Curn V (2014).Differential expression analysis of genes involved in abiotic stress in oilseed rape. Uroda. Crop Science Publishers.v. LXII, no. 12, p. 167-170. ISSN 0139-6013
    • McKeown P#, Keshavaiah C#, Port A, Tuteja R, Chatterjee M, Varshney R and Spillane C (2012). Harnessing Genomics to Improve Nutritional Content and Bioavailability of Plant-derived Foods’ In: P.S. Panesar and S.S. Marwaha (Eds). Biotechnology in Agriculture and Food Processing: Opportunities and Challenges. Taylor & Francis Group. ISBN 9781439888360

    Patents

• Chikkaputtaiah C*, Keot A, Phukan T, Gogoi DJ, SS Hiremath, Velmurugan N. Development of a Recombinant RUBY-CRISPR/Cas9 vector for Visually Monitoring the Transformation of Gene Editing Components in Rice. Submitted to CSIR-IP Unit for Patent Filing in India and Foreign Countries (PCT countries)on 21/10/2025.
• Chikkaputtaiah C*, Singha DL, Keot A, Velmurugan N. A recombinant vector useful for endosperm-specific genome editing in rice. Submitted to CSIR-IP Unit for Filing of Patent in Foreign Countries (PCT Countries)on 19/08/2025.
• Chikkaputtaiah C, Singha DL, Keot A, Velmurugan N. A recombinant vector useful for endosperm-specific genome editing in rice. 2025. Indian Patent Filed on 23/12/2024. Application No. 202411102373.
• Velmurugan N, Saikia DK, Chikkaputtaiah C. Development of nutritionally enriched eco-friendly feed formulation and process thereof. 2023. US Patent Application No.: 18/504,260 Filed on 08-Nov-2023. Priority Application No. 202311058900. Granted on 26 March 2025.

R&D Related Activities

• PhDs as Major Advisor: Awarded: 4; On-going: 6
• PhDs as Co-Advisor: Awarded: 2, On-going: 1
• R&D Projects as Principal Investigator: Completed: 6; On-going: 3
• R&D Projects as Co-Investigator: Completed: 8; On-going: 3
• Organizing Secretary & Convenor of International Conference on CRISPR/Cas-based Plant Functional Genomics and Computational Modeling, CSIR-NEIST Jorhat (17-21, Jan 2023)
• Research Advisor Council (RAC) Member, Central Muga Eri Research & Training Institute, Central Silk Board, Jorhat, Assam (Feb 2024- present)
• Member of Technical Evaluation Committee (TEC), DBT, Govt. of India (Dec 2023-present)
• Member of Institutional Biosafety Committee, CSIR-NEIST, Jorhat (Jan 2021-present)
• Member of Society for Ethnopharmacology, Jorhat Chapter (Jan 2022- present)
• Review Editor, Frontiers Editorial Board, Frontiers in Plant Science (IF: 5.60)(April 2022-present)
• Regular Reviewer of Peer-Reviewed SCI Journals such as Trends in Genetics, The Plant Journal, Planta, Frontiers in Plant Science, Frontiers Journals, Scientific Reports, Molecular Biotech, etc.
• Regular reviewer of research grant applications received from SERB, DBT, DST, NMPB, ICAR, CSIR, CSB, etc.

Awards, Fellowships and Recognitions(selected only):

• Ramanujan Fellowship: SERB, Govt. of India as PI (2015-2020)
• Selected for Young Investigator Meet: IndiaBioSciences, Govt. of India (2019)
• Postdoctoral Research Fellowship: Science Foundation Ireland, Ireland (2009-2012)
• SFI-TIDA Entrepreneurship & Career Development Award: SFI, Dublin, Ireland (2011)
• International PhD Fellowship: International Graduate School in Genetics and Functional Genomics (IGS-GFG), University of Cologne, Germany (2004-2008)
• Joint CSIR-UGC Junior Research Fellowship: CSIR New Delhi, India (2003)
• Institute of Agricultural Technologists (IAT) Fellowship: Bangalore, India (2002)

PhDs awarded under the AcSIR Program as Major Advisor:

• Dr Vishal Das (2021)

• Dr Indrani Baruah (2022)

• Dr Johni Debbarma (2023)

• Dr Banashree Saikia (2023)

• Dr Riwandahun Marwein (2024)

• Dr Yogita N Sarki (2025)

Lab Members (Present)

• Dr Banashree Saikia: DST-Woman Scientist (WISE-PDF Life Sciences) (2025-present)
• Dr Mantesh Muttappagol: CSIR-Senior Project Associate (2024-present)
• Dr Dipen N Adhikari:CSIR-Senior Project Associate (2024-present)
• Dr Tarinee Phukan:CSIR-Senior Project Associate (2025-present)
• Dr Yogita N. Sarki:ANRF-Senior Project Associate (2025-present)
• Mr Ajay Kumar Keot: UGC-Senior Research Fellow&AcSIR PhD Student (2021-Present)
• Ms Tarali Borgohain: CSIR-Senior Research Fellow&AcSIR PhD Student (2022-present)
• Ms Monica Sharma: UGC-Senior Research Fellow &AcSIR PhD Student(2022-present)
• Mr Dhrubo J. Gogoi: UGC-Junior Research Fellow&AcSIR PhD Student(2023-present)
• Ms Remya S: DBT-Project Associate&AcSIR PhD Student (2023-present)
• Ms Aditi Dutt: CSIR-Project Associate (2024-present)
• Ms Arnika Keithellakpam: CSIR-Project Associate (2024-present)
• Ms Adity Laskar: CSIR-Project Associate (2024-present)
• Mr Debojit Saikia: CSIR-Project Assistant (2024-present)

Ongoing Research Projects 

• Genome Editing for Crop Improvement (Role: PI, Funding: CSIR-Mission Project, Govt. of India)

• CRISPR/Cpf1-based dual-gene editing of OsEBP89 and OsCRK10 genes, and molecular genetic analysis for dual-stress tolerance to brown spot disease-drought in Indica rice (North East Indian) cultivar (Role: PI; Funding: SERB-Core Research Grant, Govt. of India)

• To improve the efficiency of genome editing with CRISPR-Cas9 and- to create novel sources of epigenetic variation in plants (Role: PI; Funding: DBT, Govt. of India (Multi-institutional Project with ICAR-IIRR Hyderabad & BITS Pilani Hyderabad)

• Nutritionally Enriched Indigenous Fruit Peel Waste as Aquaculture Feed (Role: Co-PI; Funding: CSIR-FTT Project, Govt. of India)

• Evaluation of Bacterial Endophytes for Medicinal Plants & Crop Productivity (Role: Co-PI; Funding: State Horticultural Research & Development Dept., Govt. of Arunachal Pradesh)

• Biomedical Genomics Advancement Program for North Eastern Researchers (Role: Co-PI; Funding: DHR-ICMR, Govt. of India)

• Transcriptome-wide identification of early blight disease (Alternaria solani) regulatory genes and CRISPR/Cas-based genome editing system for dual-stress (early and late blight) in tomato cv Arka Vikas (Role: Mentor & Co-PI; Funding: DST-ANRF, Govt. of India)

Completed Projects (Last 5 years)

• Elucidation of the genetic mechanism of brown spot disease-drought stress and development of sustainable dual-stress tolerance in North East Indian rice cultivar through CRISPR-Cas9/Cpf1 mediated active genetics (Role: PI; Funding: CSIR-FBR, Govt. of India; 2020-2023)

• DEAD-box RNA helicases, STRS1 and STRS2 in regulating responses to multiple abiotic stresses (Role: PI; Funding: SERB-Ramanujan Fellowship, Govt. of India; 2015-2020) 

• Development of multiple abiotic and biotic stress resistance in tomato (Solanum lycopersicum L.) through dual-gene multiplex CRISPR/Cas9 genome editing (Role: PI; Funding: SERB-Early Career Research Grant, Govt. of India; 2017-2020)

• Development of sustainable brown leaf spot (Drechslera oryzae) disease resistance in rice through multiplex CRISPR-Cas9/Cpf1 genome editing system (Role: PI; Funding: CSIR-FBR Project, Govt. of India; 2018-2020)

• Biofertilizer for yield enhancement in normal to water stress conditions for entrepreneurship development (Role: Co-PI; Funding: DBT, Govt. of India; 2021-2025)

• Deciphering the mechanism(s) of host–endophyte coevolution, enhanced secondary metabolite production and crop productivity (Role: Co-PI; Funding: CSIR-FBR Project, Govt. of India; 2020-2023)

• Characterization and chemical composition of high-yielding varieties of Amada Haldi (Curcuma zedoaria Rose) and Kali Haldi (Curcuma caesiaRoxb.): endangered high-value medicinal plants (Role: Co-PI; Funding: NMPB–Ministry of Ayush, Govt. of India; 2017-2020)

• Study of potentially novel carbohydrases from cultivable bacteria and functional metagenomics library obtained from biodiversity hotspot of NE India (Role: Co-PI; Funding: DBT-Twinning Project, Govt. of India; 2017-2020)

• Regional mapping of carbon stock, sequestration and sink potential of reserve forest ecosystem of Assam for improvement of ecosystem health and services (Role: Co-PI; Funding: National Mission on Himalayan Studies, Govt. of India; 2018-2021)

• Improvement of grain filling in inferior spikelet of rice through CRISPR-Cas9/ CRISPR-Cpf1 genome editing system (Role: Mentor & Co-PI, Funding: SERB, Govt. of India; 2019-2021)