BRIC-National Institute of Plant Genome Research

Dr. Ashutosh Pandey

Staff Scientist IV,
National Institute of Plant Genome Research (NIPGR), New Delhi
Tel: 91-11-26735176
Fax: 91-11-26741658
Email: hasthi.ram@nipgr.ac.in

Book chapters

Shekhawat PK, Ram H and Soni P (2024) Genome editing for nutritional improvement of crops. In: Upadhyay SK (eds), Applications of Genome Engineering in Plants, Chapter 7. John Wiley & Sons Ltd., pp 122-152.

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. https://doi.org/10.1002/9781119672425.ch18

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. https://doi.org/10.1002/9781119487210.ch8

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. https://doi.org/10.1002/9781119487210.ch10

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. https://doi.org/10.1201/9781003055358

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. https://doi.org/10.1201/9781003055358

Profile

Research Area

Crop genetics and genomics

Research Interest

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.

Awards and 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).

Books

Gayacharan, Parida SK, Singh AK, Chattopadhyay D, Joshi DC, Katna G (2024) Rice Bean (Vigna umbellata (Thunb.) Ohwi & Ohashi) Potential Pulses: Genetic and Genomic Resources. CABI Publisher, pp. 100-115. DOI:10.1079/9781800624658.0006.

Basu U, Parida SK (2023) CLAVATA signaling pathway receptors modulate developmental traits and stress responses in crops. In: Upadhyay SK, Shumayla (eds), Plant Receptor-Like Kinases. Elsevier B.V., pp 371-392.https://doi.org/10.1016/B978-0-323-90594-7.00004-1.

Jha UC, Nayyar H, Parida SK, Siddique KHM (2022) Horse gram, an underutilized climate-resilientlegume: Breeding and genomic approach for improving future genetic gain. Developing Climate Resilient Grain and Forage Legumes. 167-178.

Daware A, Parida SK, Tyagi AK (2020) Integrated genomic strategies for cereal genetic enhancement: combining QTL and association mapping. Cereal Genomics 2072:15-25.

Tripathi S, Singh RK, Parida SK, Chaturvedi SK, Gaur PM, Kumar S, Dikshit HK, Mishra GP, Singh A (2022) Biofortification of Chickpea. Biofortification of Staple Crops, Springer Singapore, pp 335-344 doi.org/10.1007/978-981-16-3280-8_13.

Mohanty JK, Parida SK (2022) Small RNA-omics: Decoding the regulatory networks associated with horticultural traits. Omics in Horticultural Crops doi.org/10.1016/B978-0-323-89905-5.00001-X.

Jha UC, Bohra A, Nayyar H, Rani A, Devi P, Saabale PR, Parida SK (2019) Breeding and Genomics Approaches for Improving Productivity Gains in Chickpea Under Changing Climate. In: Kole C. (eds) Genomic Designing of Climate-Smart Pulse Crops. Springer, Cham, pp-135-164.

Jha UC, Barh D, Parida SK, Jha R, Singh NP (2016) Whole-genome resequencing: current status and future prospects in genomics-assisted crop improvement. Applied Molecular Biotechnology: The Next Generation of Genetic Engineering, CRC Press, Taylor & Francis Group, Inc, 209-234.

Das S, Parida SK (2015) Synergistic plant genomics and molecular breeding approaches for ensuring food security. In Genomics, Proteomics and Metabolomics in Nutraceuticals and Functional Foods, Second Edition (eds Bagchi D, Swaroop A, Bagchi M), John Wiley & Sons, Ltd, Chichester, UK. DOI: 10.1002/9781118930458.ch14.

Parida SK, Mohapatra T (2010) Whole genome sequencing. In: Kole C, Abbott AG (Eds) Principles and Practices of Plant Genomics, Vol 3, Advanced Genomics, Science Publishers, Inc, New Hampshire and Edenbridge Ltd, British Isles, pp 120-174.

Publications

Bishnoi, A., Ram, H*., & Soni, P*. (2024). Genome-wide identification, in-silico characterisation and expression analysis of multiprotein bridging factor 1 gene family members in rice. Plant Physiology Reports, 1-21. https://link.springer.com/article/10.1007/s40502-024-00813-4 (*Corresponding authors)

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. https://doi.org/10.1038/s41598-023-49093-2(*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. https://doi.org/10.1007/s10142-023-01265-z

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. https://doi.org/10.1007/s10142-023-01244-4

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. https://doi.org/10.1007/s12298-023-01343-3

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 https://www.sciencedirect.com/science/article/pii/S0098847222004026 (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 https://doi.org/10.1007/s42729-022-00914-9 (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 https://doi.org/10.1016/j.pmpp.2021.101708 (*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, https://doi.org/10.1016/j.pmpp.2021.101691 (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 https://doi.org/10.1007/s00299-021-02714-4 (*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 https://doi.org/10.1016/j.jbiotec.2021.03.019 (*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 (https://doi.org/10.1111/ppl.13363) (*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, https://doi.org/10.1093/jxb/eraa536 (*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 https://doi.org/10.1016/j.envexpbot.2020.104367 (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 https://doi.org/10.1371/journal.pgen.1008661 (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 https://doi.org/10.1080/07388551.2020.1742647 (*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. https://doi.org/10.3390/plants9020229 (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 https://doi.org/10.1371/journal.pone.0217360 (*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 https://doi.org/10.3390/plants8090310 (*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 https://doi.org/10.31742/IJGPB.79.2.15 (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 https://doi.org/10.1111/tpj.14381 (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 https://doi.org/10.1111/tpj.13608 (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
America 113 (42), 11973-11978 https://doi.org/10.1073/pnas.1516110113 (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 http://dx.doi.org/10.1093/mp/sst143 (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 http://dx.doi.org/10.1093/mp/sst140(IF=13.2)

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 https://doi.org/10.4161/psb.22703 (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)

Group Members

Current Group Members

	Ashis Majhi PhD Scholar MSc (Botany), Banaras Hindu University, Varanasi, Uttar Pradesh Email: majhiashis638@gmail.com
	Banita Yadav PhD Scholar MSc (Botany), University of Delhi, New Delhi Email: yadavbanita.by105by@gmail.com
	Sankhadeep Chowdhury PhD Scholar M.Sc.: (Botany) Banaras Hindu University, Varanasi, Uttar Pradesh Email: schowdhury98@nipgr.ac.in
	Alka Bishnoi Visiting Research Fellow University of Rajasthan, Jaipur Email: bishnoiasr112947@gmail.com
	Pooja Kanwar Shekhawat Visiting Research Fellow University of Rajasthan, Jaipur Email: shekhawat019@gmail.com
	Rohit Majhi Lab Attendant
Lab Alumni
	Suprava P Nayak Project Associate-I (March 2021-June 2022) M.Sc. Assam Agriculture University Email: Email: nayaksuprava.sn@gmail.com
	Shaswati Sardar Project Assistant/Associate-I (March 2021-October 2023) M.Sc.: Biotechnology Jaipur National University Email: shaswatisardar12345@gmail.com
	Rajashree Pattanayak Project Associate-I (May 2022-November 2022) Integrated M. Tech (Biotechnology) Kalinga Institute of Industrial Technology, Bhubaneswar Email: rajashree141997@gmail.com
	Dr. Sathish Sundararajan Research associate I (May-Nov 2022) PhD Bharathiar University, Tamil Nadu Email: sathish216@gmail.com
	Sonia Project Associate-I (Jan 2023- Aug 2023) M.Sc. (Plant Molecular Biology and Biotechnology) University of Delhi Email: soniabeniwal767@gmail.com
	Sayantan Bhattacharya Project Associate-I (August 2023 - October 2023) M.Tech (Biotechnology) Kalinga Institute of Industrial Technology, Bhubaneswar Email: sayantanbhattacharya1403@gmail.com
	Sanjay T D PhD Scholar M.Sc.(Agri): Indian Agricultural Research Institute, New Delhi Email: sanjaytd927@gmail.com
	Pallavi Project Associate-I M.sc (Life sciences), Jawaharlal Nehru University Delhi Email: pallvimukta555@gmail.com
	Aryaman Project Associate-I M.Sc. (Plant Biology & Biotechnology) University of Hyderabad Email: aryamanjangra@gmail.com
Trainees (Undergraduate and Post graduate)
	Shivangi Singh Trainee (January 2022-May 2022) MSc (Genomics ) Amity University , Noida Email: sshivangi537@gmail.com
	Annapurna Kumari Roy Trainee (Jan. 2022-June 2022) M.sc (Bioinformatics) Central University of South Bihar (Gaya) Email: annapurnakumari945@gmail.com
	Kanika Phagna MS dissertation (June 2022 - April 2023) Integrated BS-MS Indian Institute of Science Education and Research, Berhampur Email: kpdck@missouri.edu
	Pranay Upadhyay Trainee (Sep 2022-Feb 2023) M.Sc (Biotechnology) Patliputra University Email: upadhyaypranay15@gmail.com
	Sonali Sinha Trainee (January 2023 - June 2023) M.sc (Bioinformatics) Central University of South Bihar (Gaya) Email: sonalsonali.sinha@gmail.com
	Mohini Gautam Trainee ( June-July 2023) M.Sc (Biotechnology) Pondicherry University Email: mohinigautam129@gmail.com
	Rupam Sarkar Trainee (Jul-Aug 2023) M.Sc (Biotechnology) Central University of Haryana Email: upamsarkar3107@gmail.com
	ZUBIDA BANO Trainee (Jul-Aug 2023) M.Sc (Biotechnology) Central University of Haryana Email: zaidabano03@gmail.com
	Anjali Sahu Trainee (July-Aug 2023) B.Tech (Biotechnology University - Amity University Gwalior (M.P) Email: anjalisahu1508@gmail.com