Dr Shallu Thakur
About me
I am a Postdoctoral Associate in the Vegetable Breeding and Genomics Lab at TREC, University of Florida, where my research focuses on knocking out susceptibility genes in cucrbits to develop broad-spectrum disease resistance and resilient genotypes to powdery mildew. Previously, I worked as an independent fellow, developing customized genome-editing systems for pulses. During my PhD, I focused on trait discovery for rice blast resistance, identifying allelic variants in local landraces, developing novel haplotypes, and functional DNA markers for breeding programs. This work earned me the ICAR–Jawaharlal Nehru Award and the INSA Young Scientist Medal. I am passionate about adopting emerging technologies to advance crop improvement
I am a plant biotechnologist with a Ph.D. in Plant Biotechnology and over a decade of experience in molecular biology, marker-assisted breeding, trait discovery, plant–pathogen interactions, allele mining, plant tissue culture, plant transformation, and genome editing. I currently serve as a Postdoctoral Associate in the Department of Vegetable Breeding, Genetics and Genomics at the Tropical Research and Education Center, University of Florida, where I lead CRISPR/Cas9-mediated genome editing projects to develop powdery mildew–resistant cucurbits. My work focuses on establishing and optimizing genome editing platforms, functional validation of susceptibility genes, development of SNP/KASP markers, and analysis of large-scale genotypic datasets. In parallel, I manage core laboratory operations and mentor research assistants and interns.
Previously, I was an independent DST–INSPIRE Faculty Fellow at the Indian Institute of Pulses Research, where I led genome editing initiatives in chickpea to improve seed size, secured competitive funding, supervised research teams, and managed project execution and reporting. My doctoral research at ICAR–National Institute of Plant Biotechnology focused on trait discovery for rice blast resistance, resulting in the identification of novel allelic variants, haplotypes, and functional DNA markers for breeding applications. This work was recognized with the ICAR–Jawaharlal Nehru Award for Outstanding Doctoral Research and the INSA Young Scientist Medal.
My research career also includes experience in transgenic crop development and biosafety compliance through national flagship projects at ICAR and contributions to digital agricultural knowledge platforms at IIT Kanpur. Collectively, my expertise spans genome editing, molecular breeding, transgenics, grant writing, project leadership, and trainee mentoring, with a strong commitment to translating advanced biotechnological tools into resilient and sustainable crop improvement strategies.
Degrees:
2. Kaur S, Thakur S, Sabharwal P, Meru G (2025) Breeding for Disease Resistance in Cucumber: Current Status, Genetic Insights, and Genomic Resources. Horticulturae (Accepted) (IF: 3.0)
3. Thakur S, Sabharwal P, Shrestha S, Fu Y, Diaz AV, Quevedo L, Zhang S, Meru G (2025) Response of squash and tomato genotypes to salinity stress. Discover Pants (Minor Revision)
4. Sabharwal P, Thakur S, Shrestha S, Fu Y, Meru G (2024) Breeding and genetics of resistance to major diseases in Cucurbita—A review. Crop Science 64(6): 2998–3013 (IF: 2.32)
5. Thakur S, Meru G (2023) CRISPR/Cas9 mediated editing of phytoene desaturase gene in squash. Journal of Plant Biochemistry and Biotechnology: 1–8 (IF: 1.6)
6. Acharya SR, Shrestha S, Michael VN, Fu Y, Sabharwal P, Thakur S, Meru G (2023) Transcriptional changes during Phytophthora capsici infection reveal potential defense mechanisms in squash. Stresses 3(4): 827–841
7. Devanna BN, Jain P, Solanke AU, Das A, Thakur S et al. (2022) Understanding the dynamics of blast resistance in rice-Magnaporthe oryzae interactions. Journal of Fungi 8: 584 (IF: 5.724)
8. Singh P, Shukla A, Tiwari NN, Ansari J, Thakur S, Rathore M, Verma OP, Singh NP, Das A (2022) Routine and efficient in vitro regeneration system amenable to biolistic particle delivery in chickpea (Cicer arietinum L.). Plant Cell Tissue and Organ Culture 148: 699–711 (IF: 2.77)
9. Singh P, Sujayanand GK, Thakur S, Rathore M, Verma OP, Singh NP, Das A (2022) Evaluation of transgenic chickpea harboring codon-modified Vip3Aa against gram pod borer (Helicoverpa armigera H.). PLoS ONE 17(6): e0270011 (IF: 3.75)
10. Das A, Basu PS, Kumar M, Ansari J, Shukla A, Thakur S, Singh P, Datta S, Chaturvedi SK, Sheshshayee MS, Bansal KC, Singh NP (2021) Transgenic chickpea (Cicer arietinum L.) harbouring AtDREB1a are physiologically better adapted to water deficit. BMC Plant Biology 21: 39 (IF: 4.21)
11. Tiwari V, Das A, Thakur S, Trivedi RK (2021) Molecular characterization of blue-green algae, Anabaena constricta and comparative studies of biodiesel production from other species. Indian Journal of Chemical Technology 28: 150–162 (IF: 0.57)
12. Tiwari V, Das A, Thakur S, Trivedi RK (2021) Selection of indigenous algal species for potential biodiesel production. Journal of Pure and Applied Microbiology 15(2): 851–863 (IF: 0.48)
13. Das A, Shukla A, Thakur S, Rathore M, Singh NP (2020) Estimation of neomycin phosphotransferase-II (NPT-II) protein in vegetative and reproductive tissues of transgenic chickpea (Cicer arietinum L.) and biosafety perspectives. Journal of Plant Biochemistry and Biotechnology 29: 568–570 (IF: 1.17)
14. Singh PK, Ray S, Thakur S, Rathour R, Sharma V, Sharma TR (2018) Coevolutionary interactions between host resistance and pathogen avirulence genes in rice-Magnaporthe oryzae pathosystem. Fungal Genetics and Biology 115: 9–19 (IF: 3.49)
15. Das A, Datta S, Thakur S, Shukla A, Ansari J, Sujayanand GK, Kumar PA, Chaturvedi SK, Singh NP (2017) Expression of a chimeric gene encoding insecticidal crystal protein Cry1Aabc of Bacillus thuringiensis in chickpea (Cicer arietinum L.) confers resistance to gram pod borer (Helicoverpa armigera Hubner). Frontiers in Plant Science 8: 1423 (IF: 5.75)
16. Das A, Datta S, Sujayanand GK, Kumar M, Singh A, Kumar A, Shukla A, Ansari J, Kumar M, Thakur S et al. (2016) Expression of chimeric Bt gene, Cry1Aabc in transgenic pigeonpea (cv. Asha) confers resistance to gram pod borer (Helicoverpa armigera Hubner). Plant Cell Tissue and Organ Culture 127(3): 705–715 (IF: 2.71)
17. Sharma TR, Das A, Thakur S, Devanna BN (2016) Genome analysis of rice genetic resources for the identification of novel genes and alleles for biotic stress resistance. Indian Journal of Plant Genetic Resources 29(3): 373
18. Das A, Poornima KN, Thakur S, Singh NP (2016) The mungbean genome sequence: a blueprint for Vigna improvement. Current Science 110(7): 1144–1145 (IF: 0.79)
19. Thakur S, Singh PK, Das A, Rathour R, Variar M, Prashanthi SK, Singh AK, Singh UD, Chand D, Singh NK, Sharma TR (2015) Extensive sequence variation in rice blast resistance gene Pi54 makes it broad spectrum in nature. Frontiers in Plant Science 6: 345 (IF: 5.75)
20. Sharma TR, Das A, Thakur S, Devanna BN, Singh PK et al. (2015) Oscillating transcriptome during rice-Magnaporthe interaction. Current Issues in Molecular Biology 19: 99–120 (IF: 2.561)
21. Thakur S, Singh PK, Rathour R, Variar M, Prashanthi SK, Gopalakrishnan S, Singh AK, Singh UD, Chand D, Singh NK, Sharma TR (2014) Genotyping and development of single nucleotide polymorphism (SNP) marker associated with blast resistance genes in rice using GoldenGate Assay. Molecular Breeding 34(3): 1449–1463 (IF: 2.589)
22. Singh PK, Thakur S, Rathour R, Variar M, Prashanthi SK, Singh AK, Singh UD, Sharma V, Singh NK, Sharma TR (2014) Transposon-based high sequence diversity in Avr-Pita alleles increases the potential for pathogenicity of Magnaporthe oryzae populations. Functional and Integrative Genomics 14(2): 419–429 (IF: 3.410)
23. Sharma TR, Das A, Thakur S, Jalali BL (2014) Recent understanding on structure, function and evolution of plant disease resistance genes. Proceedings of the Indian National Science Academy 80(1): 83–93 (IF: 0.573)
24. Thakur S, Gupta YK, Singh PK, Rathour R, Variar M, Prashanthi SK, Singh AK, Singh UD, Chand D, Rana JC, Singh NK, Sharma TR (2013) Molecular diversity in rice blast resistance gene Pi-ta makes it highly effective against dynamic population of Magnaporthe oryzae. Functional and Integrative Genomics 13(3): 309–322 (IF: 3.410)
25. Thakur S, Singh PK, Rathour R, Variar M, Prashanthi SK, Singh AK, Singh UD, Chand D, Singh NK, Sharma TR (2013) Positive selection pressure on rice blast resistance allele Piz-t makes it divergent in Indian land races. Journal of Plant Interactions 8(1): 34–44 (IF: 4.208)
26. Kumari A, Das A, Devanna BN, Thakur S, Singh PK, Upreti HC, Singh NK, Sharma TR (2013) Mining of rice blast resistance gene Pi54 shows effect of single nucleotide polymorphism on phenotypic expression of alleles. European Journal of Plant Pathology 137(1): 55–65 (IF: 1.907)
27. Das A, Soubam D, Thakur S, Singh PK, Singh NK, Sharma TR (2012) A novel blast resistance gene, Pi54rh cloned from wild species of rice, Oryza rhizomatis, confers broad spectrum resistance to Magnaporthe oryzae. Functional and Integrative Genomics 12: 215–228 (IF: 3.410)
28. Sharma TR, Rai AK, Gupta SK, Thakur S, GuptaYK, Singh. PK and Singh NK (2011) Highquality genome sequence of rice accelerated the discovery of genes for blast resistance (EA Siddiq & K. Muralidharan Eds) Proc of International Symp on Genomics and Crop Improvement: Relevance and Reservation pp 202-219
• Das A, Mondal B, Singh P, Thakur S (2023) Genetic Improvement of Nutraceutical Traits in Chickpea (Cicer arietinum L.). In: Kole C (ed) Compendium of Crop Genome Designing for Nutraceuticals. Springer Nature Singapore, pp 1–21
• Singh P, Thakur S, Kumar S, Mondal B, Rathore M, Das A (2023) Genetic Engineering for Enhancing Abiotic Stress Tolerance in Pulses. In: Muthu Arjuna Samy P, Ramasamy A, Chinnusamy V, Sunil Kumar B (eds) Legumes: Physiology and Molecular Biology of Abiotic Stress Tolerance. Springer Nature Singapore, pp 345–357
• Thakur S, Kushwah N, Kumar S, Singh P, Rathore M, Singh NP, Das A (2021) Genome Editing using CRISPR Cas systems in Legumes. In: Gupta OP, Karkute SG (eds) Genome Editing in Plants: Principles and Applications. CRC Press, pp 89–107
• Das A, Thakur S, Shukla A, Singh P, Ansari J, Singh NP (2020) Genetic Transformation. In: Mohar Singh (ed) Chickpea: Crop Wild Relatives for Enhancing Genetic Gains. Academic Press, London, pp 205–225
• Das A, Singh P, Kushwah NS, Thakur S, Rathore M, Pratap A, Singh NP (2018) Genetic and Genomic Approaches for Improvement in Mungbean (Vigna radiata L.). In: Wani S, Jain MK (eds) Pulses Improvement. Springer Nature Switzerland AG, pp 175–189
• Das A, Thakur S, Basu P, Singh NP (2015) Novel Approaches for Enhanced Drought Tolerance in Crops. In: Dixit GP, Singh J, Singh NP (eds) Pulses: Challenges & Opportunities under Changing Climate Scenario. Indian Society of Pulses Research and Development, Kanpur-208024, Uttar Pradesh, India, pp 77–85
• Das A, Thakur S, Soren KR, Datta S, Singh NP (2016) Transgenic Strategies Towards Nutritional Enrichment of Crops. In: Singh U, Praharaj CS, Singh SS, Singh NP (eds) Biofortification of Food Crops. Springer India, Print ISBN 978-81-322-2714-4, pp 105–113