BRIC-National Institute of Plant Genome Research

Dr. Senjuti Sinharoy

Staff Scientist V
National Institute of Plant Genome Research
Phone: 91-11-26741612/14/17 Extn. 214
Direct: 91-11-26735214
Email: ssinharoy@nipgr.ac.in, ssinhar@hotmail.com

Collaborations

Dr. Wilhelm Boland, Dr.Axel Mithöfer (Max Planck Institute for Chemical Ecology, Germany)
Dr. Ralf Oelmüller (Institute of General Botany and Plant
Physiology, FSU Jena, Germany)
Dr. Edgar Pieter (University of Halle-Wittenberg, Germany)
Dr. Arockiasamy Arulandu (ICGEB, Delhi)
Dr. J.C Sekhar (Indian Institute of Maize Research, Delhi)
Dr. Smrutisanchita Behra (IICT, Kolkata)

Resources

Stress Combinations and their Interactions in Plants (SCIP) Database - http://223.31.159.3/plant_complete/index_orangesunset.php and https://db.nipgr.ac.in/plant_complete/index_orangesunset.php

VIGS database - https://vigs-database.btiscience.org/index.php

pssRNAit: Designing Effective and Specific Plant RNAi siRNAs with Genome-wide Off-target Gene Assessment - https://www.zhaolab.org/pssRNAit/

Profile

Research Interests

Nitrogen is indispensable for any form of life. Only prokaryotes can reduce gaseous nitrogen to ammonia, which can then be utilized by other eukaryotes. Discovery of synthetic nitrogen fertilizer has revolutionized food production worldwide but at substantial economic and environmental cost. Legumes, being capable of hosting biological nitrogen-fixing bacteria, are blessed with their own supply of nitrogen. Legumes host these bacteria inside a newly developed organ-like structure called nodules. The de novo development of nodules involves de-differentiation of an already differentiated tissue and a huge change of gene expression.

My lab investigates the basic molecular mechanism of root nodule symbiosis (RNS) in legumes. We also try to understand how RNS has evolved in legumes. Presently, we are working on Cicer (Chickpea), Medicago (Alfalfa) and Arachis (Peanut) to understand their root nodule developmental program. Few specific questions we are trying to answer are: 1. How does the host plant guide the bacteria from the free-living lifestyle to an endocytic lifestyle? 2. How does the host plant represses the defense response to accommodate the symbiont? 3. What are the genetic differences that causes the difference in nitrogen- fixation efficiency between legumes?

Awards and Fellowships

SERB-Early Career Research Award from the Department of Science and Technology, India (2019)

Ramalingaswami Re-entry Fellowship (2013-2014) Department of Biotechnology, Ministry of Science and Technology, India.

Junior Research Fellowship and Lectureship in National Eligibility Test (NET) (2003) in Life Sciences, India.

Graduate Aptitude Test in Engineering (GATE), (2003) in Life Sciences, India.

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.

Review Articles

Mohanty JK, Parida SK (2024) Stripping off the rice panicle: induced genetic variation awakens the sheathed spikelet for a better yield. Journal of Experimental Botany 75:5459-5462.

Jha UC, Nayyar H, Roychowdhury R, Prasad PVV, Parida SK, Siddique KHM (2024) Non-coding RNAs (ncRNAs) in plant: Master regulators for adapting to extreme temperature conditions. Plant Physiology Biochemistry 205:108164

Basu U, Parida SK (2021) Restructuring plant types for developing tailor-made crops. Plant Biotechnology Journal 21:1106-1122.

Basu U and Parida SK (2023) The developmental dynamics in cool season legumes with focus on chickpea. Plant Molecular Biology 111:473-491.

Giri J, Parida SK, Raghuvanshi S and Tyagi AK (2021) Emerging molecular strategies for improving rice drought tolerance. Current Genomics 22:16-25.

Pandey S, Singh A, Parida SK, Prasad M (2022) Combining speed breeding approaches with conventional and genomics-assisted breeding for crop improvement. Plant Breeding 141:301-313.

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

Jha UC, Bohra A, Pandey S, Parida SK (2020) Breeding, genetics, and genomics approaches for improving Fusarium wilt resistance in major grain legumes. Frontiers in Genetics 11:1001.

Daware A, Parida SK, Tyagi AK (2019) Integrated Genomic Strategies for Cereal Genetic Enhancement: Combining QTL and Association Mapping. Methods Molecular Biology 2072:15-25.

Jha UC, Bohra A, Jha R, Parida SK (2019) Salinity stress response and 'omics' approaches for improving salinity stress tolerance in major grain legumes. Plant Cell Reports 38:255-277.

Jha UC, Sharma, KD, Nayyar H, Parida SK, Siddique KHM (2022) Breeding and Genomics Interventions for Developing Ascochyta Blight Resistant Grain Legumes. International Journal of Molecular Science 23:2217.

Agarwal P, Parida SK, Raghuvanshi S, Kapoor S, Khurana P, Khurana JP, Tyagi AK (2016) Rice improvement through genome-based functional analysis and molecular breeding in India. Rice 9:1.

Agarwal P, Parida SK, Mahto A, Das S, Mathew IE, Malik N, Tyagi AK (2014) Expanding frontiers in plant transcriptomics in aid of functional genomics and molecular breeding. Biotechnology Journal 9:1480-1492.

Kujur A, Saxena MS, Bajaj D, Laxmi, Parida SK (2013) Integrated genomics and molecular breeding approaches for dissecting the complex quantitative traits in crop plants. Journal of Biosciences 38:971-987.

Das A, Parida SK (2013) Advances in biotechnological applications in three important food legumes. Plant Biotechnology Reports 8:83-99.

Review

Yun Kang, Minguye Li, Sinharoy S and Verdier J (2016) A Snapshot of Functional Genetic Studies in Medicago truncatula. Front Plant Sci. 2016; 7: 1175.

Edited Book

'The Medicago truncatula Genome' as a part of Compendium Plant Genomes. https://link.springer.com/book/9783030907563. ISBN 978-3-030-90756-3. Expect to be online January 2022.

Book Chapters

Bhardwaj, A., Sinharoy, S.* (2022). Understanding of Root Nodule Development at Level of System Biology as Obtained by High Throughput Transcriptomic Approach. In: Sinharoy, S., Kang, Y., Benedito, V. (eds) The Medicago truncatula Genome. Compendium of Plant Genomes. Springer, pp 91-101.

Bhardwaj, A., Sinharoy, S.* (2022). Transcriptional Networks in Medicago truncatula: Genomic and Functional Overview During Root Nodule Symbiosis. In: Sinharoy, S., Kang, Y., Benedito, V. (eds) The Medicago truncatula Genome. Compendium of Plant Genomes. Springer, pp 71-90.

Sinharoy S, Catalina I. Pislariu and Michael K. Udvardi (2015) A High-Throughput RNA Interference (RNAi)-Based Approach Using Hairy Roots for the Study of Plant–Rhizobia Interactions. Methods in Molecular Biology, Volume: 1287 Plant Gene Silencing, pp. 159-178. Edited by Kirankumar S. Mysore and Muthappa Senthil-Kumar.

Sinharoy S, Igor S. Kryvoruchko, Catalina I. Pislariu, Manuel González-Guerrero, Vagner A. Benedito, and Michael K. Udvardi (2015) Functional genomics of symbiotic nitrogen fixation in legumes with a focus on transcription factors and membrane transporters. The Biological Nitrogen Fixation. Publishers: John Wiley & Sons, Inc Chapter 82, pp 823-836. Edited by Frans J. de Bruijn.

Catalina I. Pislariu, Sinharoy S, JiangQi Wen, Jeremy D. Murray2, Pascal Ratet3, and Michael K. Udvardi. (2015) Tobacco retrotransposon (Tnt1)-insertion mutagenesis in Medicago as a tool for genetic dissection of symbiosis in legumes. The Biological Nitrogen Fixation. Publishers: John Wiley & Sons, Inc Chapter 83, pp 837- 854. Edited by Frans J. de Bruijn.

Sinharoy S, Samaddar S, Dutta S, Saha S, Raichaudhuri A, Maity MK and DasGupta M (2011) Deciphering the Molecular Code that predisposed plants to Root Nodule Symbiosis. Plant Tissue Culture and Applied Plant Biotechnology. Aavishkar Publishers.

Selected Publications

Bhattacharjee O, Raul B, Ghosh A, Bhardwaj A, Bandyopadhyay K, and Sinharoy S, (2022). Nodule INception-independent epidermal events lead to bacterial entry during nodule development in peanut (Arachis hypogaea). New Phytologist, 236(6):2265-2281.

Raul B, Sinharoy S 2022. An Improvised Hairy Root Transformation Method for Efficient Gene Silencing in Roots and Nodules of Arachis hypogaea. In: Mysore KS, Senthil-Kumar M eds. Plant Gene Silencing: Methods and Protocols. New York, NY: Springer US, 303-316.

Raul B, Bhattacharjee O, Ghosh A, Upadhyay P, Tembhare K, Singh A, Shaheen T, Ghosh A, Torres-Jerez I, Krom N, Clevenger J, Udvardi M, Scheffler B, Ozias Akins P, Dutta Sharma R, Bandyopadhyay K, Gaur V, Kumar S, and Sinharoy S* (2022) Microscopic and transcriptomic analyses of Dalbergoid legume peanut reveal a divergent evolution leading to Nod Factor dependent epidermal crack-entry and terminal bacteroid differentiation. Mol Plant Microbe Interact DOI/10.1094/MPMI-05-21-0122-R

Mandal D, Sinharoy S. (2019) A Toolbox for Nodule Development Studies in Chickpea: A Hairy-Root Transformation Protocol and an Efficient Laboratory Strain of Mesorhizobium sp. Mol Plant Microbe Interact. Apr;32(4):367-378.

Bertioli et al., (2019) The genome sequence of segmental allotetraploid peanut Arachis hypogaea. Nat Genet. 2019 May;51(5):877-884.

Pislariu CI, Sinharoy S, Torres-Jerez I, Nakashima J, Blancaflor EB, Udvardi MK. (2019) The nodule-specific PLAT-domain protein NPD1 is required for nitrogen-fixing symbiosis. Plant Physiol. (In Press).

Kryvoruchko IS*, Routray P*, Sinharoy S*, Torres-Jerez I, Tejada-Jiménez M, Finney LA, Nakashima J, Pislariu CI, Benedito VA, González-Guerrero M, Roberts DM, Udvardi MK. (2018) An Iron-Activated Citrate Transporter, MtMATE67, Is Required for Symbiotic Nitrogen Fixation. Mar;176(3):2315-2329. *Equally contributed.

Kryvoruchko I*, Sinharoy S*, Ivone Torres-Jerez, Davide Sosso, Catalina Pislariu, Vagner A. Benedito, Wolf Frommer, and Michael Udvardi. (2016) MtSWEET11, a sucrose transporter in the symbiosome membrane of Medicago truncatula root nodules is partially redundant for nitrogen fixation. Plant Physiology 171(1): 554-65, *Equally contributed.

Sinharoy S, Liu C., Breakspear A, Guan D, Jiangqi W, Murray J, Udvardi M, (2016). Cystathionine Beta Synthase domain-containing protein is required for infection thread propagation and nodule development in Medicago. Plant Physiology 170(4): 2204-17.

Veerappan V, Kadel K, Alexis N, Scott A, Kryvoruchko I, Sinharoy S, Taylor M, Udvardi M and Dickstein R (2014). Keel petal incision: a simple and efficient method for genetic crossing in Medicago truncatula. Plant Methods 10, 11.

Dai X*, Sinharoy S*, Udvardi M and Zhao PX (2013). PlantTFcat: an online plant transcription factor and transcriptional regulator categorization and analysis tool. BMC Bioinformatics 14, 321. * Equally contributed.

Sinharoy S, Torres-Jerez I, Bandyopadhyay K, Kereszt A, Pislariu CI, Nakashima J, Benedito VA, Kondorosi E and Udvardi MK (2013). The C2H2 transcription factor regulator of symbiosome differentiation represses transcription of the secretory pathway gene VAMP721a and promotes symbiosome development in Medicago truncatula. Plant Cell 25, 3584-601.

Samaddar S, Dutta A, Sinharoy S, Paul A, Bhattacharya A, Saha S, Chien KY, Goshe MB and DasGupta M. (2013). Autophosphorylation of gatekeeper tyrosine by symbiosis receptor kinase. FEBS Lett 587, 2972-9.

Young ND, Debellé F, Oldroyd GE, Geurts R, Cannon SB, Udvardi MK, Benedito VA, Mayer KF, Gouzy J, Schoof H, Van de Peer Y, Proost S, Cook DR, Meyers BC, Spannagl M, Cheung F, De Mita S, Krishnakumar V, Gundlach H, Zhou S, Mudge J, Bharti AK, Murray JD, Naoumkina MA, Rosen B, Silverstein KA, Tang H, Rombauts S, Zhao PX, Zhou P, Barbe V, Bardou P, Bechner M, Bellec A, Berger A, Bergès H, Bidwell S, Bisseling T, Choisne N, Couloux A, Denny R, Deshpande S, Dai X, Doyle JJ, Dudez AM, Farmer AD, Fouteau S, Franken C, Gibelin C, Gish J, Goldstein S, González AJ, Green PJ, Hallab A, Hartog M, Hua A, Humphray SJ, Jeong DH, Jing Y, Jöcker A, Kenton SM, Kim DJ, Klee K, Lai H, Lang C, Lin S, Macmil SL, Magdelenat G, Matthews L, McCorrison J, Monaghan EL, Mun JH, Najar FZ, Nicholson C, Noirot C, O'Bleness M, Paule CR, Poulain J, Prion F, Qin B, Qu C, Retzel EF, Riddle C, Sallet E, Samain S, Samson N, Sanders I, Saurat O, Scarpelli C, Schiex T, Segurens B, Severin AJ, Sherrier DJ, Shi R, Sims S, Singer SR, Sinharoy S, Sterck L, Viollet A, Wang BB, Wang K, Wang M, Wang X, Warfsmann J, Weissenbach J, White DD, White JD, Wiley GB, Wincker P, Xing Y, Yang L, Yao Z, Ying F, Zhai J, Zhou L, Zuber A, Dénarié J, Dixon RA, May GD, Schwartz DC, Rogers J, Quétier F, Town CD, Roe BA. (2011) The Medicago genome provides insight into the evolution of rhizobial symbioses. Nature. 480, 520.

Sinharoy S, Saha S, Chaudhury SR and Dasgupta M. (2009). Transformed hairy roots of Arachis hypogea: a tool for studying root nodule symbiosis in a non-infection thread legume of the Aeschynomeneae tribe. Mol. Plant Microbe. Interact 22, 132-42.

Sinharoy S and DasGupta M. (2009). RNA interference highlights the role of CCaMK in dissemination of endosymbionts in the Aeschynomeneae legume Arachis. Mol. Plant Microbe. Interact 22, 1466-75.

Group Members

	Mr. Bikash Raul (5th year Ph.D student) I have done B.Sc. in botany from Ravenshaw University and M.Sc. in botany from Banaras Hindu University. In Ph.D. I am studying different aspects of root nodule symbiosis in Arachis (Peanut). Email: bikashraul1@nipgr.ac.in
	Ms. Akanksha Bhardwaj (5th Year Ph.D student) I did Masters and Bachelors in Botany from Ramjas College, University of Delhi. Our lab focuses on root nodule symbiosis development. I am working on model legume Medicago to study transcriptional network involved in nodulation. Our team is a bunch of vibrant and enthusiastic people. We as a budding lab-group work together under the guidance of a more enthusiastic PI. Email: abhardwaj@nipgr.ac.in
	Ms.Deevita Srivastava (5th Year Ph.D student) I did my B.Sc and M.Sc from Banaras Hindu University and currently perusing my Ph.D. in the lab that focuses on Root nodule symbiosis. I work on legume Cicer arietinum with the purpose to enhance nitrogen fixation efficiency under phosphate deficiency. Email: deevitasrivastava13@nipgr.ac.in
	Ms.Priya Upadhyay (3rd year P.hD student) I have done B.Sc and M.Sc (Botany) from Banaras Hindu University. Currently I am trying to explore factors behind the higher nitrogen fixation efficiency in peanut. Email: priyaupadhyay67@gmail.com
	Ms. Ahana Sengupta (1st year P.hD student) I did my bachelor's in Biotechnology from Maulana Abul Kalam Azad University of Technology, WB and my master's in Biotechnology from NIT Rourkela. I am studying diazotropic bacteria and their adaptation in Indian subcontinent. Email:
	Dr. Nandita Pasari (MK Bhan Fellow) After completing my Ph.D. in synthetic biology and biofuels from ICGEB New Delhi, I have joined Dr. Senjuti�s lab as a MK Bhan Fellow. In this project we aim to identify the crosstalk that modulates the immune response during plant root nodulation. We will be using transcriptomics approach to identify the differentially expressed genes as well as the small RNAs regulating the different stages of nodule formation. Email:
	Dr. Vinod Kumar Jangid (Research Associate) I have done B.Sc. (Agriculture) from Junagadh Agricultural University, M.Sc. (Agril. Plant Biotechnology) from University of Agricultural Sciences, Bengaluru and Ph.D. (Molecular Biology and Biotechnology) from Indian Agricultural Research Institute, New Delhi. Currently, I am trying to generate "retrotransposon-based mutant population of chickpea for functional genomic studies" Email: vinod_shikher@yahoo.co.in
	Mr. Asim Kumar Ghosh (Project Associate) I have done my Master's and Bachelor's in Computer Applications, from Techno India(Saltlake), Maulana Abul Kalam Azad University of Technology. Currently I am working as a bioinformatician in this lab.
	Mr. Vikash Bhadu (P.hD student) I have done my B.Sc. in Biology from MGSU and M.Sc. in Botany from Rajasthan University. In Ph.D., I am exploring the molecular mechanism of symbiosome development during nodulation in peanut (Arachis). Email: vikashbhadu39@gmail.com
	Ms. Farheen Saifi (Project associate) I have spent five years of my PhD studying the symbiosis process in the model legume Medicago truncatula in in Hungary through the Stipendium Hunagricum Scholarship. During my PhD I have investigated the nodule specific cysteine-rich peptides (NCRs), Regulator of Symbiosome differentiation (RSD) and sulphate transporter genes. I have completed my B.Sc. and M.Sc. in Botany with Honors from Hindu College, University of Delhi. Presently, I am working as a Project associate in the lab on "Characterization of chickpea germplasm resource to accelerate genomics-assisted crop improvement." Email: farheensaifi2004@gmail.com