Dr. Manoj Prasad
    Staff Scientist IV
    Ph.D: Calcutta University
    Postdoctoral Fellow: Institute for Plant Genetics & Crop Plant Research
    (AvH fellow), Gatersleben, Germany
    Tel: 91-11-26741612,14,17 Ext. - 160
    Direct - 26735160, Fax: 91-11-26741658
 Research Interest
Transcript profiling of salt and drought stress in foxtail millet (Setaria italica (L.) BEAUV) and cloning-characterization of stress related genes.
Abiotic environmental stresses, primarily salt and drought-stress contributes most significantly to the reduction in potential yield. Improvements to salt, cold and drought tolerance in crops has been elusive, partially because they are quantitative traits and part of the multigenic responses are detectable under salt and drought stress conditions. Informations on the response of crops to salt and drought stress have been merely descriptive, with the suggested functions of only a few salt and drought induced genes.
Foxtail millet (known for its drought tolerance) is one of the world's oldest cultivated crops and still the staple food to large section of people in the semi-arid regions of India. Foxtail millet ranks 2nd in the total world production of millets and it continues to have an important place in world agriculture providing six million tons of food to millions of people, mainly on poor or marginal soils in southern Europe and in temperate, sub tropical and tropical Asia, where monsoon failure and drought are frequent and land terrain is difficult. These regions are also hot spots of poverty and frequent starvations in populous countries. Foxtail millet is a self-pollinating crop (2n = 2x = 18) with a haploid nuclear DNA content estimated to be 0.82 pg. The small genome size (similar to rice), low proportion of repetitive DNA (30%), the presence of a high melting point component (4.7-6.7% of the genome and has a functional role in genomic adaptations to specific environments) and diploid nature of foxtail millet should have made it a suitable organism for genetic and molecular studies. However, as the crop is considered a minor cereal of only regional importance, genetic and molecular level studies have lagged behind those of other staple cereals. The objectives of our laboratory are (1) Cloning and characterization of stress related transcription factors (e.g. DREB) form foxtail millet and (2) Comparison of transcript accumulation in salt and drought resistant and susceptible plants upon salt and drought stress in foxtail millet.
The other areas of study in the laboratory are as follows:
Association Mapping of Agronomic Traits and Abiotic Stress using DNA-Based Markers in Foxtail Millet (Setaria italica (L.) BEAUV).
Most phenotypic traits of interest to plant breeders are quantitatively inherited. QTL mapping offers the possibility of indirect selection of phenotypic traits using DNA-based markers but the method is rather time consuming and limited to few crops. As this method requires a biparent mapping population that is a time consuming effort to produce it. This mapping population does not provide a high resolution QTL mapping as there is only few cross over/recombination events occurred during its generation. A high resolution of QTL map requires a large number of cross over events. This can only be found in a natural population. The method that uses a natural population for QTL mapping is association mapping. This method is very successful in human genetics for identification of genes for disease resistance. This method is now being used in plant due to advances in association mapping statistics. Association mapping is a statistical approach of establishing a significant association between a gene/QTL and a phenotypic trait. There are three objectives for this study: (i) to detect any population structure if it is present in foxtail natural population; (ii) estimation of level and extend of linkage disequilibrium (LD) in foxtail millet and (iii) association mapping by using population structure, DNA-based marker and phenotypic data. The results of this effort will facilitate several long-range goals for foxtail millet breeding and genetics: (1) an understanding of the marker-trait relationships for important traits in Indian foxtail breeding programs; (2) a characterization of the genetic diversity in the Indian foxtail millet breeding programs; (3) linkage disequilibrium estimates in foxtail millet; and (4) germplasm exchange between breeding programs.
Molecular Mapping of Tomato Leaf Curl Virus (ToLCV) Resistance Gene(s) in Tomato.
Tomato leaf curl disease caused by whitefly borne tomato leaf curl virus of family geminiviridae, is a major viral disease causing more than 90% yield losses during summer in south India and autumn in north India. Different breeding groups working on this problem have identified the wild sources of resistance and transferred them to the cultivated species to develop resistant varieties with desirable horticultural traits. In the background of existence of different strains of viruses in south and north India and high potential for evolution of viruses it is important to use all the available resistance sources and introgress into one cultivar for strong and durable resistance. The use of molecular markers linked to genes for resistance is a tool, which can be used efficiently in plant breeding for indirect selection of quantitative resistance and for accelerated transfer of resistance from different sources in to a single cultivar. Hence it is imperative to map and find the breeder friendly markers linked to available resistance genes. By using the suppression subtractive hybridization (SSH) technique, we have identified 37 significantly differentially expressed genes between a resistant and susceptible cultivar. Characterizations of the genes are ongoing.
Staff Scientist IV, National Institute of Plant Genome Research (2008-present).
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).
Awarded Post Doctoral Fellowship for the year 2002-03 from GABI (BMBF), Germany.
Awarded with a Fellowship to attend the 10th IAPTC&B/SIVB Congress being held at Disney's Coronado Springs Resort; Orlando, Florida, USA from June 23-28, 2002.
Awarded Alexander von Humboldt Fellowship for the year 2000-01 from AvH foundation, Bonn, Germany.
Awarded Prof. Hira Lal Chakravarty Memorial award in Plant Sciences(2011) by the Indian Science Congress Association (ISCA).
Members of the National Academy of Sciences, India.
Awarded Biotechnology Overseas Associateship (2006-2007) of the Department of Biotechnology, Govt. of India.
Awarded "NAAS Associate" of the National Academy of Agricultural Sciences (NAAS), New Delhi, India.
Awarded Young Scientist of biennium 2003-2004 by the National Academy of Agricultural Sciences (NAAS) for outstanding contributions to Crop Sciences. The award consists of a citation, a medal and cash prize of Rs. 25,000/-
Awarded Young Scientist Fellowship in 2004 form the Department of Science & Technology, Govt. of India.
Research poster entitled "Physical mapping of microsatellite markers on wheat chromosome arms 2DL, 6BS and 7DL carrying loci for grain protein content and pre-harvest sprouting tolerance" was appreciated widely and got the best poster award at 4th ADNAT symposium on DNA Technologies in the Management of Biodiversity held at M. S. Swaminathan Research Fundation, Chennai during February 20-21, 2000.
Awarded National Merit Scholarship (1992-1994), from Government of India.
Recipient of Medal and certificate of Honour from Ramkrishna Mission Vivekananda Centenary Collage (Calcutta University) for the year 1992-1994 from Government of india.
 Selected Publications
(a) Research Paper Published
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 (Accepted).
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 (Accepted).
Lata C, Bhutty S, Bahadur RP, Majee M and Prasad M (2011) Association of SNP in a novel DREB2-like gene SiDREB2 with stress tolerance in foxtail millet [Setaria italica (L.)]. Journal of Experimental Botany (Accepted).
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)
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.
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.
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.
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, 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.
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.
(b) Scientific Reviews
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 (Accepted)
Kumar S and Prasad M (2007) Crop breeding prospects in the genomics era. J of New Seeds 8(3): 29-49.
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.
Prasad M and Chaudhuri RK (2000) Genome organization, Molecular markers and Linkage maps of rice. J Natl Bot Soc 54: 114-125.
Gupta PK, Roy JK and Prasad M (1999) DNA chips, microarrays and genomics. Current Science 77(7): 875-884.
(c) Book Chapters
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
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.