National Institute of Plant Genome Research
Digital India     
 
    Dr. Ananda K. Sarkar
    Staff Scientist IV
    Phone: 91-11-26735220
    Fax: 91-11-26741658
    Email: aksarkar@nipgr.ac.in
 Research Area
Plant Stem Cells and Architecture: Genetic, Epigenetic and Small RNA Mediated Regulation.
 Academic Background
Staff Scientist & Ramalingaswami Fellow (2009 - 2014): NIPGR
Ramalingaswami Fellow (2009): ICGEB (International Centre for Genetic Engineering and Biotechnology), New Delhi.
Post Doc. Fellow (2006-2009): Cold Spring Harbor Laboratory (USA).
Ph. D. (2001-2006): Albert-Ludwigs-Universitaet Freiburg (Germany).
Res. Associate (2001): NRCPB (National Research Centre on Plant Biotechnology), IARI, New Delhi.
M. Tech. (1998-2000): Indian Institute of Technology - Kharagpur.
M. Sc. (1996-1998): Visva Bharati University (Shantiniketan).
 Awards, Honors and Fellowships: (Click Here to Expand)
Ramalingaswami Re-Entry Fellowship (DBT, 2009- 2014).
Prof. Archana Sharma Memorial Award (ISCA, 2010-2011).
"Suma Cum Laude" (best grade award for Ph.D., University of Freiburg, Germany).
Member of New York Academy of Science (2007-08) & AAAS, USA (2008-10).
Postdoctoral fellowship (2006- 2009; at Cold Spring Harbor Lab, USA).
Doctoral fellowship (2001- 2006) from German/European Research Foundations (DFG/SFB/REGIA).
DBT fellowship (1998-1999) for M.Tech. (through GATE; at IIT- Kharagpur).
Academic Editor: Scientific Reports (Nature Publication Group)
 Research Interests
Genetic and epigenetic regulations of plant stem cells and architectures (root & shoot)
In higher plants, the continuous post-embryonic growth and lateral organ formation or branching is ultimately controlled by the root and shoot apical meristems through the activity of their respective "STEM CELL populations". Precise spatio-temporal regulation between diverse regulatory gene networks and their dynamic balance is quintessential for normal plant development. This balance is achieved by many layers of regulation at transcriptional, post-transcriptional and translational level. Epigenetic modifications play important role in gene transcription through DNA methylation and histone modifications. We are interested to understand the role of novel genes and epigenetic factors in regulation of plant stem cells, meristems, and patterning of root (and shoot) architecture. For this, we largely use molecular genetics, functional genomics and epigenetic work related techniques.
Role of small RNAs in plant stem cell regulation and root architecture
Besides protein coding genes, small non-coding RNAs (e.g. miRNA and siRNA) have recently been implicated in plant development and stress responses. We are exploring the role of miRNAs and other small RNAs in root meristem and architecture. We use NGS and microarray analysis to identify novel and relevant miRNAs, their targets. We further study their developmental role in plant stem cells or meristems, and root architecture through molecular genetic approaches.
Regulation of root architecture in crops (rice/maize) ‐ application and evolution
The adaptability of higher plants to the changing environmental conditions as well as their productivity largely depends on their ability to modulate the patterning of root (and shoot). Therefore, we are exploring the functional conservation of regulation of root development between monocot crops and dicot model Arabidopsis. We are also studying the aforesaid regulations in rice/maize with the goal to improve root architecture and make them environmentally/economically more sustainable.

Major techniques used: Students can learn/apply - basic DNA/RNA/Protein related works (including their isolation/ purification, gene cloning Nothern/ Western analysis. qRT-PCR etc.); ChIP, Y2H/protein interaction studies; advanced microscopy (light/ fluorescence, Confocal LSM, SEM, Laser Capture Microdissection etc.); microarray/ NGS for transcriptome/ miRNAome study; in situ localization of RNAs/ proteins; histology/ microtomy; molecular genetics, development of transgenic plants, mutational analysis, phenotyping etc.
 Positions Available
Roots and shoots are growing here; we welcome strong and efficient signaling candidates to contribute. Interested candidates may contact.
 Group Members (Click Here to Expand)
Dr. Alka Singh
Research Associate (DBT)
Ph. D., CIMAP/ JNU
Dr. Ashutosh Kumar
National Postdoctoral Fellow (DST)
Ph.D., BITS, Mesra, Jharkhand
Dr. Vibhav Gautam
Research Associate, Ph. D. from NIPGR (Sarkar Lab)
M.Sc. from University of Pune
Dr. Shalini Mukherjee
National Postdoctoral Fellow (DST)
Ph.D. from University of Manitoba, Canada
Dr. Archita Singh
Research Associate, Ph. D. from NIPGR (Sarkar Lab)
M.Sc. from BHU, Varanasi
Dr. Swati Verma
National Postdoctoral Fellow (DST)
PhD from IIT-Rurkee
Ms. Sharmila Singh
Ph. D. Student
M.Sc. from MSR University, Vadodara
Mr. Sandeep Yadav
Ph. D. Student
M.Sc. CCS HAU, Hissar, Haryana
Mr. Pramod Kumar
Ph. D. Student
M.Sc. CCS University, Meerut
Mr. Vishnu Mishra
Ph. D. Student
M.Sc. from BHU
Ms. Mahima
Ph. D. Student
M.S. from IISER - Mohali
Mr. B. Rengaswamy
Junior Research Fellow (JRF)
 Selected Publications
  Journal (5 Year)
Impact Factor
Citation till 2016
Singh A, Roy S, Singh S, Sarkar Das S, Gautam V, Yadav S, Singh A, Samantha S, & Sarkar AK. Phytohormonal crosstalk modulates the expression of miR166/165s, target Class III HD-ZIPs, and KANADI genes during root growth in Arabidopsis thaliana. Sci. Rep. 2017 Jun 13;7(1):3408. doi: 10.1038/s41598-017-03632-w.

*This article shows that crosstalk among phytohormones, such as auxin, CK, GA, ABA, SA, JA etc. dynamically regulate the expression of miR165/166, their target Class III HD-ZIP (PHB, PHV etc.) and KANADI (which work antagonistically to HD-ZIPIIIs) in developing roots. We also show that hormone influenced balanced expression and activity of miR165/166 and target HD-ZIPIIIs (thorough transcriptional and post-transcriptional regulation) are important regulator of root growth and development.


Nature Publication
   
Singh S, Singh A, Yadav S, Gautam V, Singh A, Sarkar AK*. Sirtinol, a Sir2 protein inhibitor, affects stem cell maintenance and root development in Arabidopsis thaliana by modulating auxin-cytokinin signaling components. Sci. Rep. 2017 Jan. doi: 10.1038/srep42450 (2017).

*This paper illustrates that Sirtinol and Auxin show both similar and distinct affect on regulation of stem cells, meristem maintenance, root development and lateral root development, which they affect by modulating hormone (CK and Auxin) signaling and transport components.

Nature Publication
5.5  
Singh A, Kumar P, Gautam V, Rengasamy B, Adhikari A, Udayakumar M and Sarkar AK*. Root transcriptome of two contrasting indica rice cultivars uncovers regulators of root development and physiological responses. Sci. Rep. 2016 Dec 21;6:39266. doi: 10.1038/srep39266..

*This paper describes molecular and physiological differences between two indica rice cultivars with stable and contrasting root system architecture (RSA), which we used as model system and identified many potential regulators of RSA and associated physiological responses (such as draught, salinity and nutrient availability) using functional genomics approach.

Nature Publication
5.5  
Gautam V, Singh A, Singh S, Sarkar AK. An Efficient LCM-Based Method for Tissue Specific Expression Analysis of Genes and miRNAs. Sci. Rep. 2016 Feb 10;6:21577. doi: 10.1038/srep21577.

*This  is an efficient, cost effective & improved (in tissue fixation, processing, histology, tissue/slide handling, RNA isolation, stem-loop RT-PCR  etc steps) method, which can be very useful for studying expression pattern of both genes, small RNAs/miRNAs, and their targets in less accessible small tissue samples.

Nature Publication
5.5 4
Rai V, Sanagala R, Sinilal B, Yadav S, Sarkar AK, Dantu PK, Jain A. Iron Availability Affects Phosphate Deficiency-Mediated Responses, and Evidences of Cross Talk with Auxin and Zinc in Arabidopsis. Plant Cell Physiol. 2015 Jun;56(6):1107-23. doi: 10.1093/pcp/pcv035.

*It uncovers the cross-talk between neutrients (Pi and Fe) and hormone (auxin) signalling in root development.

4.8 8
Haecker A, Gross-Hardt R, Geiges B, Sarkar A, Breuninger H, Herrmann M, Laux T. Expression dynamics of WOX genes mark cell fate decisions during early embryonic patterning in Arabidopsis thaliana. Development. 2004 Feb;131(3):657-68.

*This article describes (for the FIRST time) novel WOX (WUSCHEL-RELATED HOMEOBOX) gene family, their in situ expression dynamics, and role in embryonic patterning events. WUS, the founder WOX, is the master regulator of SHOOT STEM CELLs. This work is also incorporated in "Plant Physiology" by Taiz & Zeiger, since 2010.

6.2 494
(~41 /yr)
Sarkar AK, Luijten M, Miyashima S, Lenhard M, Hashimoto T, Nakajima K, Scheres B, Heidstra R, Laux T. Conserved factors regulate signalling in Arabidopsis thaliana shoot and root stem cell organizers. Nature. 2007 Apr 12;446(7137):811-4.

* QC specific transcription factor WOX5 is required for maintenance of QC and root stem cells. It provides first molecular evidence for role of conserved regulators in shoot and root stem cell maintenance. This work is also incorporated in "Plant Physiology" by Taiz & Zeiger, since 2010.

41.4 484
(~47 /yr)
Brooks L, Strable J, Elshire R, Zhang X, Ohtsu K, Sarkar AK, Hargreaves S., Eudy D., Pawlowska T, Nettleton D, Timmermans MCP, Schnable PS, Scanlon MJ. Microdissection of Shoot Meristem Functional Domains in Maize. PLoS Genet. 2009 May;5(5):e1000476.

*Using Laser Capture Microdissection (LCM)-Microarray approach, it describes maize shoot meristem domain or organ specific gene expression signature and indicates function.

9.17 53
Douglas RD, Wiley D, Sarkar AK, Springer N, Timmermans MCP and Scanlon MJ. ragged seedling2 Encodes an ARGONAUTE7-Like Protein Required for Mediolateral Expansion, but Not Dorsiventrality, of Maize Leaves. Plant Cell. 2010 May;22(5):1441-51.

*It demonstrates role of small RNA (tasi-RNA) in maize leaf development.

10.5 41
Singh A, Singh A, Panigrahi KC, Reski R and Sarkar AK. Balanced activity of microRNA166/165 and its target transcripts from the class III homeodomain leucine-zipper family regulates root growth in Arabidopsis thaliana. Plant Cell Rep. 2014 Jun;33(6):945-53.

2.8 16
 Other Publications
Barik S, Kumar A, SarkarDas S, Yadav S, Gautam V, Singh A, Singh S and Sarkar AK. Coevolution Pattern and Functional Conservation or Divergence of miR167s and their Targets across Diverse Plant Species. Sci. Rep. 2015 Oct. 5:14611. DOI: 10.1038/srep14611.
Kumar A and Sarkar AK*. Apple CALCINEURIN B-LIKE PROTEIN10 genes have evolved to be novel targets of miR167s through sequence variation. Current Sci. 2017 Jan 10, 112 (1). doi: 10.18520/cs/v112/i01/147-150.
Gupta A, Sarkar AK, Senthil-Kumar M. Global Transcriptional Analysis Reveals Unique and Shared Responses in Arabidopsis thaliana Exposed to Combined Drought and Pathogen Stress. Front Plant Sci. 2016 May 24;7:686. doi: 10.3389/fpls.2016.00686. eCollection 2016.
Gautam V, Sarkar AK. Laser Assisted Microdissection, an Efficient Technique to Understand Tissue Specific Gene Expression Patterns and Functional Genomics in Plants. Mol Biotechnol. 2014 Nov 18. doi: 10.1007/s12033-014-9824-3.
Kaur C, Mustafiz A, Sarkar AK, Ariyadasa TU, Singla-Pareek SL, Sopory SK. Expression of abiotic stress inducible ETHE1-like protein from rice is higher in roots and is regulated by calcium. Physiol Plant. 2014 Sep;152(1):1-16. doi: 10.1111/ppl.12147.
Barik S, SarkarDas S, Singh A, Gautam V, Kumar P, Majee M, Sarkar AK. Phylogenetic analysis reveals conservation and diversification of miR166 genes among diverse plant species. Genomics. 2014 Jan;103(1):114-21. doi:10.1016/j.ygeno.2013.11.004.
Singh S, Singh A, Roy S and Sarkar AK. SWP1 negatively regulates lateral root initiation and elongation in Arabidopsis. Plant Signal Behav. 2012 Dec;7(12):1522-5. doi: 10.4161/psb.22099.
Deyhle F, Sarkar AK, Tucker EJ, Laux T. WUSCHEL regulates cell differentiation during anther development. Dev Biol. 2007 Feb 1;302(1):154-9.
Nogueira FT, Sarkar AK, Chitwood DH, Timmermans MC. Organ Polarity in plants is specified through the opposing activity of two distinct small regulatory RNAs. Cold Spring Harb Symp Quant Biol. 2006;71:157-6.
Pathre UV, Sarkar AK and Nath P. Modulation of Sucrose-Phosphate-Synthase Activity by Glucose-6-phosphate and Inorganic Phosphate during Post harvest Ripening in Banana. J. Plant Biol., 2001; Dec; vol. 28 (3), pp 301-305.
 Book Chapter
Sarkar AK, Karthikeyan M, Gautam V, Barik S and SarkarDas S. Improving the Plant Root System Architecture to Combat Abiotic Stresses Incurred by Global Climate Changes. CLIMATE CHANGE AND ABIOTIC STRESS TOLERANCE. Wiley Wiley-VCH Verlag GmbH & Co. Weinheim, Germany, 2014.