National Institute of Plant Genome Research
Digital India   Azadi Ka Amrit Mahotsav     
    Dr. Hasthi Ram
    Staff Scientist IV,
    National Institute of Plant Genome Research (NIPGR), New Delhi
    Tel:  91-11-26735176
    Fax:  91-11-26741658
 Research Area
Crop genetics and genomics
Staff Scientist (2020- Present): National Institute of Plant Genome Research (NIPGR), New Delhi, India
DST-INSPIRE Faculty (2017-2020): National Agri-Food Biotechnology Institute (NABI), Mohali
Postdoctoral Fellow (2012-2016): European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
Ph.D. (2007-2012): National Institute of Plant Genome Research (NIPGR), New Delhi
 Awards & Honors:
Start-Up Research Grant from SERB, Govt. of India (2022).
Young Scientist Platinum Jubilee Award from the National Academy of Sciences, India (NASI) (2019).
DST-INSPIRE Faculty award by DST, Govt. of India (2017).
NET- JRF by CSIR, Govt. of India (2007).
GATE (Graduate Aptitude Test in Engineering) by MHRD, Govt. of India (2007).
 Research Interests

CRISPR Screens in Rice

High-throughput mutagenesis approaches such as EMS and T-DNA insertion have played vital role in functional genomics studies in plants. However, these approaches introduces mutations at random location. Invention of CRISPR-Cas9 system has enabled modification of DNA at precise and desired location, however the genome editing experiments in plants are typically conducted at very low scale compared to animal cell cultures. To fill this gap we are developing novel techniques and methods in rice for doing genome editing at large scale for functional screening purpose.

Nutritional improvement of rice grain

During post-harvest processing (polishing/milling) of brown rice, bran layer consisting of aleurone layer, pericarp and embryo is removed to produce white rice. Bran is nutritionally superior as it has major reservoirs of various minerals, vitamins, essential mineral oils and other bioactive compounds, whereas white rice portion is nutritionally inferior as it mainly contains starchy endosperm. Irony is that nutritionally inferior white rice is a major staple food for almost half of the country, whereas almost 2/3rd of nutrient rich bran fraction is often get wasted as inedible due to instability of the bran. Thus both the products of the rice post-harvest process, the white rice and the bran, have their own inherent problems. We aim to overcome both these problems using biotechnological approaches. This will help to increase nutritional value of the white rice and increase the stability of bran. Towards this end, using high-resolution tissue-type specific transcriptomics approach we have prepared a gene expression atlas of developing rice grain and identified cell/tissue-type specific genes. From this very highly-resolved gene expression dataset, we have identified certain genes which might be potentially involved in micronutrient accumulation, particularly iron and vitamin A, in the grain, and we are analyzing their role in nutritional enhancement of the white rice. For increasing the stability of bran we are looking at role of various hydrolytic enzymes such as lipases, estrases, etc., which have very tissue-type specific expression in our transcriptomics dataset. We are using various molecular biology tools such as cell-type specific transcriptomics, in-situ hybridisation, confocal imaging, CRISPR-Cas9 system, expression in heterologous system and plant tissue culture approaches for our studies.

Highly motivated potential PDFs, PhDs, Fellows, Trainees, etc. who want to join the lab may contact the PI directly. There may be immediate positions available.

 Group Members


Sinha, S., Sahadevan, S., Ohno, C. Ram H*, Heisler M* (2023) Global gene regulatory network underlying miR165a in Arabidopsis shoot apical meristem. Sci Rep 13, 22258.*Corresponding authors)
Shekhawat PK, Sardar S, Yadav B, Salvi P, Soni P, Ram, H* (2023) Meta-analysis of transcriptomics studies identifies novel attributes and set of genes involved in iron homeostasis in rice. Functional & Integrative Genomics 23, 336.
Yadav B, Majhi M, Phagna K, Meena M, Ram H* (2023) Negative regulators of grain yield and mineral contents in rice: potential targets for CRISPR-Cas9-mediated genome editing. Functional & Integrative Genomics 23, 317.
Bansal S, Sundararajan S, Shekhawat PK, Singh S, Soni P, Tripathy MK*, Ram H* (2023) Rice lipases: a conundrum in rice bran stabilization: a review on their impact and biotechnological interventions. Physiol Mol Biol Plants 29(7) 985-1003.
Sharma Y, Soni P, Raturi G, Mandlik R, Rachappanavar VK, Kumar M, Salvi P, Tripathi D, Ram H*, Deshmukh R* (2022) Regulation of metalloid uptake in plants by transporters and their solute specificity. Environmental and Experimental Botany (IF=6.0) (*Corresponding authors)
Bishnoi A, Jangir P, Shekhawat PK, Ram H*, Soni P* (2022) Silicon Supplementation as a Promising Approach to Induce Thermotolerance in Plants: Current Understanding and Future Perspectives. Journal of Soil Science and Plant Nutrition (IF=3.6) (*Corresponding author)
Shekhawat PK, Jangir P, Bishnoi A, Roy S, Ram H*, Soni P* (2021). Serendipita indica: Harnessing its versatile potential for food and nutritional security.Physiological and Molecular Plant Pathology 116, 101708 (*Corresponding authors) (IF=2.8)
Kaur R, Das S, Bansal S, Singh G, Sardar S, Dhar H, Ram H* (2021) Heavy Metal Stress in Rice: Uptake, Transport, Signaling and Tolerance Mechanisms. Physiologia Plantarum, DOI: 10.1111/ppl.13491 (*Corresponding author) (IF=4.5)
Jangir P, Shekhawat PK, Bishnoi A, Ram H, Soni P (2021) Role of Serendipita indica in enhancing drought tolerance in crops, Physiological and Molecular Plant Pathology, (IF=2.8)
Bansal, S, Sardar, S, Sinha, K, Bhunia R, Katoch M, Sonah H, Deshmukh R, Ram H* (2021) Identification and molecular characterization of rice bran-specific lipases. Plant Cell Reports 40, 1215–1228 (*Corresponding author) (IF=4.6)
P Soni, R Shivhare, A Kaur, S Bansal, H Sonah, R Deshmukh, J Giri, Lata C, Ram H* (2021) Reference gene identification for gene expression analysis in rice under different metal stress. Journal of Biotechnology 332, 83-93 (*Corresponding author) (IF=3.3)
Ram H*, Sardar S, Gandass N (2021) Vacuolar Iron Transporter-(Like) Proteins: Regulators of Cellular Iron Accumulation in Plants. Physiologia Plantarum, 171(4) 823:832 ( (*Corresponding author) (IF=4.5)
Ram H*, Singh A, Katoch M, Kaur R, Sardar S, Palia S, Satyam R, Sonah S, Deshmukh R, Pandey A, Gupta I, Sharma TR (2021) Dissecting the nutrient partitioning mechanism in rice grain using spatially resolved gene expression profiling. Journal of experimental Botany 72(6) 2212–2230, (*Corresponding author) (IF=7.0)
Shivaraj SM, Sharma Y, Chaudhary J, Rajora N, Sharma S, Thakral V, Ram H, Sonah H, Singla-Pareek SL, Sharma TR, Deshmukh R (2021) Dynamic role of aquaporin transport system under drought stress in plants. Environmental and Experimental Botany 484, 104367 (IF=5.5)
Ram H, Sahadevan S, Caggiano MP, Yu X, Ohno C, Heisler MG (2020) An integrated analysis of cell-type specific gene expression reveals targets of REVOLUTA and KANADI1 in the Arabidopsis shoot apical meristem. PLoS Genetics 16(4): e1008661 (IF=5.9)
Ram H*, Gandass N, Sharma A, Singh A, Deshmukh D, Sonah H, Pandey AK, Sharma TR (2020) Spatio-temporal distribution of micronutrients in rice grains and its regulation. Critical Reviews in Biotechnology 40(4), 490-507 (*Corresponding author) (IF=8.4)
Sharma S, Kaur G, Kumar A, Ram H, Kaur J, Pandey AK. (2020) Gene Expression Pattern of Vacuolar-Iron Transporter-Like (VTL) Genes in Hexaploid Wheat during Metal Stress. Plants 9(2), 220. (IF=3.9)
Ram H*, Kaur A, Gandass N, Singh S, Sonah H, Deshmukh R, Sharma TR* (2019) Molecular characterization and expression dynamics of MTP genes under various spatio-temporal stages and metal stress conditions in rice. PLoS One 14(5), e0217360 (*Corresponding author) (IF=3.2)
Ram H*, Soni P, Salvi P, Gandass N, Sharma A, Kaur A, Sharma TR* (2019) Insertional Mutagenesis Approaches And Their Use in Rice for Functional Genomics. Plants 8(9), 310 (*Corresponding author) (IF=3.9)
Ram H, Singh BP, Katara J, Kumar P, Jaiswal R, Geetika, Deshmukh R, Sonah H. (2019). A Genome-wide Resource of Intron Spanning Primers Compatible for Quantitative PCR and Intron Length Polymorphism in Rice. Indian Journal of Genetics and Plant Breeding 79(2), 499-502 (IF=0.5)
Chakraborty M, Gangappa S, Maurya J, Sethi V, Srivastava A, Singh A, Dutta S, Gupta N, Sengupta M, Ram H, Chattopadhyay S. (2019). Functional Interrelation of MYC2 and HY5 Plays an Important Role in Arabidopsis Seedling Development. The Plant Journal 99, 1080-1097 (IF=6.4)
Caggiano MP, Yu X, Bhatia N, Larsson A, Ram H, Ohno CK, et al. (2017). Cell type boundaries organize plant development. eLife 6, e27421  10.7554/eLife.27421 (IF=8.1)
Giri MK, Banday ZZ, Singh N, Singh V, Ram H, Singh D, Chattopadhyay S, Nandi AK. (2017). GBF1 differentially regulates CAT2 and PAD4 transcription to promote pathogen defence in Arabidopsis thaliana. The Plant Journal 91(5), 802-815 (IF=6.4)
Merelo P, Ram H, Pia Caggiano M, Ohno C, Ott F, Straub D, Graeff M, Cho SK, Yang SW, Wenkel S, et al. (2016). Regulation of MIR165/166 by Class II and Class III homeodomain leucine zipper proteins establishes leaf polarity. Proceedings of the National Academy of Sciences of the United States Of
113 (42), 11973-11978  (IF=11.2)
Ram H, Jain M, Singh A, Chattopadhyay S. (2016). Functional Relationship of GBF1 with HY5 and HYH in Genome-Wide Gene Expression in Arabidopsis. Plant Molecular Biology Reporter 34(1), 211–220 10.1007/s11105-015-0910-x (IF=1.6)
Ram H, Priya P, Jain M, Chattopadhyay S. (2014). Genome-wide DNA binding of GBF1 is modulated by its heterodimerizing protein partners, HY5 and HYH. Molecular Plant 7, 448-51 (IF=13.2)
Gangappa SN, Srivastava AK, Maurya JP, Ram H, Chattopadhyay S. (2014). Z-box binding transcription factors (ZBFs): a new class of transcription factors in Arabidopsis seedling development. Molecular Plant 6, 1758-68
Ram H, Chattopadhyay S. (2013). Molecular interaction of bZIP domains of GBF1, HY5 and HYH in Arabidopsis seedling development. Plant Signaling & Behavior 8, 1-3 (IF=2.2)
#Singh A, #Ram H, Abbas N, Chattopadhyay S. (2012). Molecular interactions of GBF1 with HY5 and HYH proteins during light-mediated seedling development in Arabidopsis thaliana. J Biol Chem. 287, 25995-26009 10.1074/jbc.M111.333906 (#Equal contribution) (IF=5.2)
Mallappa C, Singh A, Ram H, and Chattopadhyay S (2008) GBF1, a transcription factor of blue light signaling in Arabidopsis, is degraded in the dark by a proteasome-mediated pathway independent of COP1 and SPA1. J Biol Chem. 283, 35772–35782,  10.1074/jbc.M803437200 (IF=5.2)
 Book Chapters
Roy S, Kushwaha NK, Ram H, and Soni, P (2021) Genome Editing for Improving Abiotic Stress Tolerance in Rice. Genome Engineering for Crop Improvement, pp.314-332.
Ram H, Kaur A, Gandass N, Katoch M, Roy S, Kushwaha NK and Soni P (2020) Stomatal Adaptive Response in Plants Under Drought Stress. In Plant Stress Biology (pp. 167-183). Apple Academic Press. 10.1201/9781003055358-8
Chaudhary J, Bhat JA, Ram H, Rana N, Khatri P, Agarwal G, Kumar V, Sonah H and Deshmukh R (2020) Distribution of metals and metalloids in plants: Tools and techniques for efficient imaging and quantification. Metalloids in Plants: Advances and Future Prospects, pp.125-147.
Aminedi R, Ram H, Kumar G, Koramutla MK, Vasupalli N, Deshmukh R, Negi M and Bhattacharya R (2020) Mechanisms of plant resistance to metalloid ions and potential biotechnological applications. Metalloids in Plants: Advances and Future Prospects, pp.185-211.
Kushwaha NK, Roy S, Ram H, and Soni, P (2020) Molecular Approaches for Engineering Plants Resistant to Viruses. In Plant Stress Biology (pp. 123-142). Apple Academic Press.
Roy S, Kushwaha NK, Ram H, and Soni, P (2020) Understanding the Epigenetic Regulation of Plants Under Stress and Potential Application in Agriculture. In Plant Stress Biology (pp. 185-205). Apple Academic Press.