National Institute of Plant Genome Research
Digital India     
    डॉ. मनोज प्रसाद
    एफ एन ए एससी, एफ एन ए ए एस, स्टाफ वैज्ञानिक V
    पीएच.डी.: कलकत्ता युनिवर्सिटी,
    पोस्टडॉक्टोरल फैलो:इंस्टिट्यूट फॉर प्लांट जेनेटिक्स एंड क्रॉप प्लांट रिसर्च (एवीएच फैलो), गैटेर्सलेबेन, जर्मनी
    दूरभाष: 91-11-26741612,14,17 एक्सटेंशन. - 160
    सीधा संपर्क - 26735160, फैक्स: 91-11-26741658
 Research Area
Plant Molecular Biology, Functional Genomics of Abiotic and Biotic stress response.
 Foxtail Millet Marker Database
 Research Program
Being sessile, plants are continually challenged by an array of environmental stresses which pose devastating threat to its existence and development. The plants which can overcome these stresses are termed tolerant (or resistant), whereas the others are called sensitive (or susceptible). Resistant cultivars are impeccably equipped with sophisticated molecular mechanisms to persuade the assailing stresses, which may be of both biotic and abiotic origin. Our research group is motivated towards dissecting the molecular machinery of signaling cascades and subsequent stress-responses mounted by the resistant plants, thereby gaining knowledge on the key for constructively manipulating the resistance factor(s) in stress-susceptible cultivars, ultimately addressing food security, an issue of global importance. To know more about our research, please see: Trends Plant Sci. , Crit. Rev. Biotechnol. , Plant Breed Rev. , J Exp. Bot. , J Exp. Bot. , J Plant Biochem. & Biotech. , Genomics , J Plant Physiol. , Biochem Biophys Res Commun. , Mol Biotechnol. , Plant Cell Rep. , Genome , Mol Plant Pathol. , Mol Biotechnol. , Protoplasma.
Abiotic Stress Response
Of the diverse abiotic stresses, salinity and drought-stress contributes extensively to the yield reduction in agronomically valued crops. In an advent to decipher the molecular mechanism involved in resistant plants towards these abiotic stresses, we had chosen foxtail millet [Setaria italica (L.) BEAUV] as our model crop, since it is one of the oldest domesticated diploid C4 Panicoid crops having a comparatively small genome size of approximately 515 Mb, short life cycle, and inbreeding nature. Its two species Setaria italica (domesticated) and Setaria viridis (wild progenitor) have characteristics that classify them as excellent model systems to examine several aspects of architectural, evolutionary, and physiological importance in Panicoid grasses especially the biofuel crops such as switchgrass and napiergrass.

With the aim to understand the molecular mechanisms underlying dehydration and salinity stress tolerance in foxtail millet, we examined its transcript profiles at different time points of dehydration and salinity stress and identified a distinct set of gene sets in response to these stresses. Further we showed that only 10% genes coincided under both the stresses suggesting a distinct mechanism to perceive and respond to salt and dehydration- stress conditions. Recently we had characterized DREB- and NAC- transcription factors, which regulate the expression of various stress-inducible genes for conferring drought and salinity tolerance, respectively. Long term goal of our research is the molecular dissection of transcriptional machinery e.g. identification and characterization of transcription factors controlling the expression of drought and salt-induced genes for understanding the drought/salt-induced signal transduction events and eventually leading towards development of crop varieties superior in stress-tolerance by genetic manipulation.

The on-going research in this area includes:
  1. Genome-wide comparative methylome analysis of drought and salinity stress.
  2. Identifying and elucidating the role of stress-responsive microRNAs.
  3. Molecular characterization of stress-responsive proteins conferring stress tolerance.
  4. Genome-wide association mapping of important yield and drought stress related agronomic traits using microsatellite markers.
Biotic Stress Response
Tomato (Solanum lycopersicum L.) is the second most important and popular vegetable crop after potatoes in the world. Tomato leaf curl disease (ToLCD), caused by the Tomato Leaf Curl Virus (ToLCV) is one of the most devastating diseases of tomato, especially in tropical and subtropical climates. The disease is reported to be caused by different species of whitefly-transmitted Geminiviruses (Genus: begomovirus) which has mono-/bi-partite genome. Monopartite begomoviruses infecting tomato have been reported in different parts of Southern India, whereas bipartite begomoviruses have been reported from northern and western parts. Among these divergent begomoviruses, Tomato leaf curl New Delhi Virus (ToLCNDV) has very wide distribution and host range. We focused our study towards understanding the defense mechanism employed by all the available resistance sources and introgress them into one cultivar for raising a strong and durable resistance. To study the defense-related host gene expression, we implied the suppression subtractive hybridization technique and reported a total of 106 differentially expressed genes in a tolerant cultivar of tomato. Recently, we had also reported the existence of siRNA mediated defense in the tolerant cultivar, suggesting the fact that increased level of siRNAs may have a possible correlation with the lower level of viral replication in this cultivar. Subsequently, we mapped the target regions for post-transcriptional and DNA methylation-specific RNA silencing in the ToLCV genome and showed that targeting the viral genomic regions could be a better alternate defense strategy for generating transgenics to prevent yield loss in tomato. This is important because various host factors are involved in assisting in viral replication as well as in the counter defending of viral multiplication. This involves defensive action of the ubiquitin-proteasome system (UPS) as well as epigenetic interference and miRNA-based control. In this regard, studies on detail mechanistic insight of virus tolerance in tomato are currently being undertaken in our laboratory under the following key objectives:
  1. Deciphering the mechanism of siRNA mediated resistance.
  2. Functional characterization of UPS component gene(s) as novel virus defense components in tolerant tomato cultivar.
  3. Enhancing tolerance of susceptible tomato cultivar through over-expression of candidate gene(s).
Staff Scientist V, National Institute of Plant Genome Research (2012-present).
Staff Scientist IV, National Institute of Plant Genome Research (2008-2012).
Staff Scientist III, National Institute of Plant Genome Research (2004-2008).
Post Doctoral Fellow, Institute for Plant Genetics & Crop Plant Research, Gatersleben, Germany (2000-2003).
Research Associate, Ch. Charan Singh University, Meerut (1998-2000).
 Awards and Honours
Fellow, The National Academy of Agricultural Sciences (NAAS), India (2013).
Fellow, The National Academy of Sciences (NASI), India (2012)
Editor of Plant Signaling and Behaviour , Journal of Genetics, Journal of Plant Biochemistry & Biotechnology (2012 onwards).
Associate Editor of 'Plant Cell, Tissue and Organ Culture', Plant Cell Reports, Acta Physiologiae Plantarum (2012 onwards).
Subject Editor of 'Plant Breeding' (2012 onwards).
Prof. Hira Lal Chakravarty Memorial award, Indian Science Congress Association, India (2010-2011)
Visiting Scientist, Dept. of Plant Pathology, Univ. of Minnesota, USA (2007)
Biotechnology Overseas Associateship, Department of Biotechnology, India (2006-2007)
NAAS Associateship, The National Academy of Agricultural Sciences (NAAS), India (2006-2010)
NAAS Young Scientist, The National Academy of Agricultural Sciences (NAAS), India (2003-2004)
Research Scientist, IPK, Gatersleben, Germany (2002-2003).
Alexander von Humboldt Fellow, AvH foundation, Bonn, Germany (2000-2001)
National Merit Scholarship, Government of India (1992-1994)
Medal and Certificate of Honour, Ramkrishna Mission V. C. Collage, Calcutta University, (1992)
 Group Members
 Selected Publications (View Complete List)
Kumar K, Muthamilarasan M and Prasad M (2013) Reference genes for quantitative Real-time PCR analysis in the model plant foxtail millet (Setaria italica L.) subjected to abiotic stress conditions. Plant Cell, Tissue & Organ Culture doi:10.1007/s11240-013-0335-x
Kumari K, Muthamilarasan M, Misra G, Gupta S, Subramanian A, Parida SK, Chattopadhyay D and Prasad M (2013) Development of eSSR-markers in Setaria italica and their applicability in studying genetic diversity, cross-transferability and comparative mapping in millet and non-millet species. PLoS ONE (Accepted)
Sahu PP, Pandey G, Sharma N, Puranik S, Muthamilarasan M and Prasad M (2013) Epigenetic mechanisms of plant stress responses and adaptation. Plant Cell Reports (Accepted).
Puranik S, Sahu PP, Mandal SN, Venkata Suresh B, Parida SK and Prasad M (2013) Comprehensive Genome-Wide Survey, Genomic Constitution and Expression Profiling of the NAC Transcription Factor Family in Foxtail Millet (Setaria italica L.). PLOS ONE 8(5): e64594; DOI: 10.1371/journal.pone.0064594 Read...
Gupta S, Kumari K, Muthamilarasan M, Subramanian A and Prasad M (2013) Development and utilization of novel SSRs in foxtail millet [Setaria italica (L.) P. Beauv.]. Plant Breeding DOI:10.1111/pbr.12070 .
Garg B, Puranik S, Misra S, Tripathi BN and Prasad M (2013) Transcript profiling identifies novel transcripts with unknown functions as primary response components to osmotic stress in wheat (Triticum aestivum L.). Plant Cell Tiss Organ Cult. 113: 91-101.Read...
Lata C and Prasad M (2013) Setaria genome sequencing: an overview. J. Plant Biochem. Biotechnol. DOI: 10.1007/s13562-013-0216-8 .Read...
Muthamilarasan M and Prasad M (2013) Barley genome sequence emerges as a promising candidate in genetic research and breeding. Current Science 104: 998-999.Read...
Lata C and Prasad M (2013) Association of an allele-specific marker with dehydration stress tolerance in foxtail millet suggests SiDREB2 to be an important QTL. Journal of Plant Biochemistry and Biotechnology. DOI 10.1007/s13562-013-0193-y Read ...
Muthamilarasan M and Prasad M (2013) Cutting-edge research on plant miRNAs. Current Science. 104(3): 287-289 Read ...
Pandey G, Misra G, Kumari K, Gupta S, Parida SK, Chattopadhyay D and Prasad M (2013) Genome-wide development and use of microsatellite markers for large-scale genotyping applications in foxtail millet [Setaria italica (L.)]. DNA Research doi:10.1093/dnares/dst002 Read ...
Muthamilarasan M and Prasad M (2013) Plant innate immunity: an updated insight in defense mechanism. Journal of Biosciences doi: 10.1007/s12038-013-9302-2. Read ...
Muthamilarasan M and Prasad M (2013) Wheat genome sequencing: A milestone in cereal genomics and its future potentials. Current Science 104(3): 286 Read ...
Puranik S and Prasad M (2013) Transcription Factors: Modulating plant adaption in the scenario of changing climate. In: Tuteja N & Gill SS (eds) Climate Change and Abiotic Stress Tolerance, Wiley, Germany (Accepted).
Garg B, Puranik S, Tuteja N and Prasad M (2012) Abiotic stress-responsive expression of wali1 and wali5 genes from wheat. Plant Signaling & Behavior 7 (11), 1393 – 1396. Read...
Prasad M (2012) 9th Solanaceae Conference 2012. National Academy Science Letters. 36 (1), 111-114. Read...
Garg B, Lata C and Prasad M (2012) A study of the role of gene TaMYB2 and an associated SNP in dehydration tolerance in common wheat. Molecular Biology Reports 39: 10865-10871 Read...
Sharma N, Sahu PP, Puranik S and Prasad M (2012) Recent advances in plant-virus interaction with emphasis on small interfering RNAs (siRNAs). Mol. Biotechnol. (In Press). Read...
Lata C, Gupta S and Prasad M (2012) Foxtail millet: A model crop for genetic and genomic studies in bioenergy grasses. Critical Reviews in Biotechnology. DOI:10.3109/07388551.2012.716809 Read...
Mishra AK, Puranik S, Bahadur RP and Prasad M (2012) The DNA-binding activity of an AP2 protein is involved in transcriptional regulation of a stress-responsive gene, SiWD40, in foxtail millet. Genomics. DOI: 10.1016/j.ygeno.2012.06.012Read...
Mishra AK, Puranik S, and Prasad M (2012) Structure and regulatory networks of WD40 protein in plants. Journal of Plant Biochemistry and Biotechnology DOI: 10.1007/s13562-012-0134-1 Read...
Lata C and Prasad M (2012) Validation of an allele-specific marker associated with dehydration stress tolerance in a core set of foxtail millet accessions. Plant Breeding DOI: 10.1111/j.1439-0523.2012.01983.x. Read...
Puranik S, Sahu PP, Srivastava PS and Prasad M (2012) NAC proteins: regulation and role in stress tolerance. Trends Plant Sci. 17(6): 369-381. Read...
Garg B, Jaiswal JP, Misra S, Tripathi BN and Prasad M (2012) A comprehensive study on dehydration-induced antioxidative responses during germination of Indian bread wheat (Triticum aestivum L. em Thell) cultivars collected from different agroclimatic zones. Physiology and Molecular Biology of Plants 18(3): 217-228. Read...
Mir RR, Kumar N, Jaiswal V, Girdharwal N, Prasad M, Balyan HS, Gupta PK, (2012) Genetic Dissection of Grain Weight (GW) in Bread Wheat through QTL Interval and Association Mapping. Molecular Breeding 29(4): 963-972. Read...
Sahu PP, Rai NK, Puranik S, Roy A, Khan M, and Prasad M (2012) Dynamics of defense related components in two contrasting genotypes of tomato upon infection with Tomato Leaf Curl New Delhi Virus. Molecular Biotechnology 52(2): 140-150. Read...
Sahu PP, Gupta S, Malaviya DR, Roy AK, Kaushal P and Prasad M (2012) Transcriptome analysis of differentially expressed genes during embryosac development in apomeiotic non parthenogenetic interspecific hybrid of Pennisetum glaucum. Molecular Biotechnology 51(3): 262-271. Read...
Gupta S, Kumari K, Sahu PP, Vidapu S and Prasad M (2012)Sequence based novel genomic microsatellite markers for robust genotyping purposes in foxtail millet [Setaria italica (L.) P. Beauv.]. Plant Cell Reports 31(2): 323-337. Read...
Puranik S and Prasad M (2012) Role of NACs in regulation of abiotic stress responses in plants. In: Goyal A & Maheshwari P (ed) Frontiers on Recent Developments in Plant Science, Bentham Science Publisher, USA, ISBN: 2213-2708, pp. 137-148-296. Read...
Lata C and Prasad M (2011) Role of DREBs in regulation of abiotic stress responses in plants. Journal of Experimental Botany 62(14): 4731-4748. Read...
Lata C, Yadav A and Prasad M (2011) Role of plant transcription factors in abiotic stress tolerance. In: Shanker A (ed.) Abiotic Stress/Book2, INTECH Open Access Publishers, Rijeka, Croatia, ISBN 979-953-307-195-3; 2011 pp. 269-296. Read...
Puranik S, Kumar K, Srivastava PS and Prasad M (2011) Electrophoretic Mobility Shift Assay reveals a novel recognition sequence for Setaria italica NAC protein. Plant Signaling and Behavior 6(10): 1588-1590 Read...
Dwivedi S, Upadhyaya H, Senthilvel S, Hash C, Fukunaga K, Diao X, Santra D, Baltensperger D, Prasad M (2011) Millets: Genetic and Genomic Resources. Plant Breeding Reviews Vol. 35, John Wiley & Sons, Inc., USA pp. 247-375. Read...
Prasad M (2011) Solanaceae conferance: A report on the 7th Solanaceae Conferance (SOL)held during 5-9 September 2010 at Dundee, Scotland. Current Science 100(5): 610-612. Read...
Gupta S, Kumari K, Das J, Lata C, Puranik S and Prasad M (2011) Development and utilization of novel intron length polymorphic markers in foxtail millet [Setaria italica (L.) P. Beauv.]. Genome 54(7): 586-602 (doi/abs/10.1139/g11-020). Read...
Puranik S, Bahadur RP, Srivastava PS, and Prasad M (2011) Molecular cloning and characterization of a membrane associated NAC family gene, SiNAC from foxtail millet [Setaria italica (L.) P. Beauv.]. Molecular Biotechnology 49(2): 138-150 (DOI: 10.1007/s12033-011-9385-7).
Lata C, Bhutty S, Bahadur RP, Majee M and Prasad M (2011) Association of an SNP in a novel DREB2-like gene SiDREB2 with stress tolerance in foxtail millet [Setaria italica (L.)]. Journal of Experimental Botany 62(10): 3387-3401 (DOI: 10.1093/jxb/err016).
Lata C, Jha S, Dixit V, Sreenivasulu N and Prasad M (2011) Differential antioxidative responses to dehydration-induced oxidative stress in core set of foxtail millet cultivars [Setaria italica (L.)]. Protoplasma (DOI:10.1007/s00709-010-0257-y).
Puranik S, Jha S, Srivastava PS, Sreenivasulu N, Prasad M (2011) Comparative transcriptome analysis of contrasting foxtail millet cultivars in response to short-term salinity stress. Journal of Plant Physiology 168: 280-287. (doi:10.1016/j.jplph.2010.07.005)
Gupta S, Ghose TK, Jaiswal JP & Prasad M (2012) Molecular marker systems and compilation of genetic linkage maps of cultivated plants. In: Kumar A, Arora S, Ambwani S (eds), "Biotechnology in Medicine and Agriculture: Principles and Practices". IK International Publishers, New Delhi (in press)
 Publication 2010 onwords
Sahu PP, Rai NK, Chakraborty S, Singh M, Prasanna HC, Ramesh B, Chattopadhyay, D and Prasad M (2010) Tomato cultivar tolerant to Tomato leaf curl New Delhi virus infection induces virus-specific siRNA accumulation and defense associated host gene expression. Molecular Plant Pathology 11(4): 531-544 (doi:10.1111/J.1364-3703.2010.00630-x).
Chandna R*, Gupta S*, Ahmad A, Iqbal M and Prasad M (2010) Variability in Indian bread wheat (Triticum aestivum L.) varieties differing in Nitrogen efficiency as assessed by microsatellite markers. Protoplasma 242: 55-67 (doi:10.1007/s00709-010-0122-z) *Authors contributed equally.
Lata C, Sahu PP, and Prasad M (2010) Comparative transcriptome analysis of differentially expressed genes in foxtail millet (Setaria italica L.) during dehydration stress. Biochem. Biophys. Res. Comm. 393: 720-727.
Gupta S and Prasad M (2009) Development and characterization of genic SSR-markers in Medicago trancatula and its transferability in leguminous and non-leguminous species. Genome 52: 761-771.
Mohan A, Kulwal P, Singh R, Kumar V, Mir RR, Kumar J, Prasad M, Balyan HS and Gupta PK (2009) Genome-wide QTL analysis for pre-harvest sprouting tolerance in bread wheat. Euphytica 168: 319-329.
Sharma K, Agrawal V, Gupta S, Kumar R and Prasad M (2008) ISSR marker-assisted selection of male and female plants in a promising dioecious crop: jojoba (Simmondsia chinensis). Plant Biotech. Report 2: 239-243.
Jayaraman A, Puranik S, Rai NK,Vidapu S, Sahu PP, Lata C and Prasad M (2008) cDNA-AFLP analysis reveals differential gene expression in response to salt stress in foxtail millet (Setaria italica L.). Molecular Biotechnology. 40: 241-251.
Kota R, Varshney RK, Prasad M, Zhang H, Stein N and Graner A (2008) EST-derived single nucleotide polymorphism markers for assembling genetic and physical map of the barley genome. Funct & Integ Genomics 8: 223-233.
Stein N*, Prasad M*, Scholz U, Thiel T, Zhang H, Wolf M, Kota R, Varshney RK, Perovich D, Grosse I and Graner A (2007) A 1000 loci transcript map of the barley genome new anchoring points for integrative grass genomics. Theor. Appl. Genet. 114: 823-839. * Authors contributed equally.
Gupta S, Pandey-Rai S, Srivastava S, Naithani SC, Prasad M and Kumar S (2007) Construction of primary genetic linkage map of the medicinal-cum-ornamental plant Catharanthus roseus. J of Genetics 86: 259-268.
Kumar S and Prasad M (2007) Crop breeding prospects in the genomics era. J of New Seeds 8(3): 29-49.
Zhao T, Palotta M, Langridge P, Prasad M, Graner A, Schulze-Lefert P and Koprek T (2006): Mapped Ds/T-DNA launch pads for functional genomics in barley. Plant J. 47: 811-826.
Varshney RK, Grosse I, Haehnel U, Siefken R, Prasad M, Stein N, Langridge P, Altschmied L and Graner A (2006) Genetic mapping and BAC assignment of EST-derived SSR markers shows non-uniform distribution of genes in the barley genome. Theor Appl Genet. 113: 239-250.
Potokina E, Prasad M, Malysheva L, Roeder MS and Graner A (2006) Expression genetics and haplotype analysis reveal cis regulation of serine carboxypeptidese I (Cxp 1), a candidate gene for malting quality in barley (Hordeum vulgare L.). Funct & Integ Genomics 6(1): 25-35.
Potokina E, Caspers M, Prasad M, Kota R, Zhang H, Sreenivasulu N, Wang M and Graner A (2004) Functional association between malting quality trait components and cDNA array based expression patterns in barley (Hordeum vulgare L.). Molecular Breeding 14: 153-170.
Perovich D, Steins N, Zhang H, Drescher A, Prasad M, Kota R, Kopahnke D and Graner A (2004) An integrated approach for comparative mapping in rice and barley with special reference to the Rph16 resistance locus. Funct & Integ Genomics 4(2): 74-83.
Maucher H, Stenzel I, Miersch O, Stein N, Prasad M, Zierold U, Schweizer P, Dorer C, Hause B and Wasternack C (2004): The allene oxide cyclase of barley (Hordeum vulgare L.)- Cloning and organ-specific expression. Phytochemistry 65(7): 801-811.
Varshney RK, Prasad M and Graner A (2004) Molecular Marker maps of barley: a resource for intra-and interspecific genomics. In: Lrz H. and Wenzel G. (eds), "Molecular Markers in Plant Breeding and Crop Improvement" Springer-Verlag Publishers, Germany pp 229-239
Prasad M, Kumar N, Kulwal PL, Roeder MS, Balyan HS, Dhaliwal HS and Gupta PK (2003). QTL analysis for grain protein content using SSR markers and validation studies using NILs in bread wheat. Theor Appl Genet 106: 659-667.
Roy JK, Balyan HS, Prasad M and Gupta PK (2002) Use of SAMPL for a study of DNA polymorphism, genetic diversity and possible gene tagging in bread wheat. Theor Appl Genet 104: 465-472.
Gupta PK, Varshney RK and Prasad M (2002) Molecular Markers: Principles and methodology. In: Jain SM, Ahloowalia BS and Brar DS (eds), "Molecular Techniques in Crop Improvement" Kluwer Academic Publishers, Netherlands pp 9-54.
Gupta PK, Roy JK and Prasad M (2001) Single nucleotide polymorphisms (SNPs): a new paradigm in molecular marker technology and DNA polymorphism detection with emphasis on their use in plants. Current Science 80(4): 524-535.
Harjit-Singh, Prasad M, Varshney RK, Roy JK, Balyan HS, Dhaliwal HS and Gupta PK (2001): STMS markers for grain protein content and their validation using near-isogenic lines in bread wheat. Plant Breeding 120: 273-278.
Prasad M, Varshney RK, Roy JK, Balyan HS and Gupta PK (2000) The use of microsatellites for detecting DNA polymorphism, genotype identification and genetic diversity in wheat. Theor Appl Genet 100: 584-592.
Varshney RK, Prasad M, Kumar N, Balyan HS, Roy JK and Gupta PK (2000) Identification of eight chromosomes and a microsatellite marker on 1AS associated with QTL for grain weight in bread wheat. Theor Appl Genet 100: 1290-1294.
Prasad M and Chaudhuri RK (2000) Genome organization, Molecular markers and Linkage maps of rice. J Natl Bot Soc 54: 114-125.
Roy JK, Prasad M, Varshney RK, Balyan HS, Blake TK, Dhaliwal HS, Singh H, Edwards KJ and Gupta PK (1999) Identification of a microsatellite on chromosome 6B and a STS on 7D of bread wheat showing association with pre-harvest sprouting tolerance. Theor Appl Genet 99: 336-340.
Gupta PK, Roy JK and Prasad M (1999) DNA chips, microarrays and genomics. Current Science 77(7): 875-884.
Prasad M, Varshney RK, Kumar A, Balyan HS, Sharma PC, Edwards KJ, Singh H, Dhaliwal HS, Roy JK and Gupta PK (1999) A microsatellite marker associated with a QTL for grain protein content on chromosome arm 2DL of bread wheat. Theor Appl Genet 99: 341-345.