National Institute of Plant Genome Research
Digital India     
 
    डॉ. स्वरुप के. परिदा 
    स्टाफ वैज्ञानिक II
    पीएच.डी. - बायोटेक्नोलोजी, जामिया हमदर्द यूनीवर्सिटी,न्यू दिल्ली 
    पोस्ट डोक्टोरल फेलो, नेशनल रिसर्च सेंटर औन प्लांट बायोटेक्नोलोजी (NRCPB),न्यू दिल्ली 
    दूरभाष: 91-11-26741612, 14, 17 (एक्सटेंशन -228)
    सीधा संपर्क: 91-11-26735228
    फैक्स: 91-11-26741658
    ई मेल: swarup@nipgr.ac.in, swarupdbt@gmail.com
 Career
Staff Scientist II, National Institute of Plant Genome Research (NIPGR), New Delhi (2011 onwards)
Post Doctoral Fellow, National Research Centre on Plant Biotechnology (NRCPB), New Delhi (2010-11)
Ph.D. (Biotechnology), Jamia Hamdard University, New Delhi (2006-10)
Senior Research Fellow, National Research Centre on Plant Biotechnology (NRCPB), New Delhi (2004-09)
M.Sc. (Agricultural Biotechnology), Indira Gandhi Agricultural University (IGAU), Raipur, Chhattisgarh (2001-03)
B.Sc. (Agriculture), Orissa University of Agriculture and Technology (OUAT), Bhubaneswar, Orissa (1997-2001)
 Awards and Fellowships
Indian Council of Agricultural Research (ICAR) Jawaharlal Nehru Award in Plant Biotechnology-2011
National Academy of Sciences India (NASI) Young Scientist Platinum Jubilee Award-2011
Indian National Science Academy (INSA) Young Scientist Award - (2010)
Junior and Senior Research Fellowship from CSIR - (2003-04)
CEEB-JNU Fellowship from DBT during M.Sc. (Agricultural Biotechnology) - (2001-03)
OUAT Merit Scholarship from Govt. of Orissa during B.Sc. (Agriculture) - (1997-2001)
NRTS Merit Scholarship from Govt. of India - (1992-96)
 Research Area
Plant Molecular Genetics and Genomics
 Research Interest
Genomics of Seed and Pod Traits in Chickpea
The pod (fruit) and seed are the defining characteristics of chickpea and most importantly have high economic value as human diet. The seed and pod characters are also major yield contributing traits of chickpea and vary widely among cultivated desi and kabuli types, landraces and wild species accessions. Narrow genetic base and lack of requisite genetic variation in the cultivated chickpea species is the major limiting factor for the identification and fine mapping of genes for the traits contributing to higher pod and seed yield in chickpea. Molecular analysis and characterization of available diverse genetic resources of chickpea with considerable trait variation for seed and pod characteristics using new generation genomics tools and modern bioinformatics approaches could accelerate the discovery of sufficient numbers of informative genetic markers like single nucleotide polymorphisms (SNPs) and useful novel alleles in target genes and their regulatory sequences. Further, association of these candidate gene based genotypic information with the phenotypic information of specific seed and pod traits of the contrasting types would be an attractive solution for identification of genes and alleles for traits contributing to higher seed and pod yield in chickpea. Besides, validation of such genes and alleles identified by genetic association analysis in bi-parental mapping population and in different developmental stages of pod and seed of contrasting chickpea germplasm lines through expression profiling and functional analysis would enable identification of novel functionally relevant genes and alleles for major pod and seed traits and understanding their transcriptional regulation during developmental process of seed and pod formation in chickpea and other multi-seeded/podded legume species like Vigna. Keeping the above in view, the research work will be undertaken for (1) identification of genes and novel alleles for traits contributing to higher seed and pod yield in chickpea through candidate gene based association analysis and gene expression profiling, (2) functional validation of the identified genes/alleles in transgenic systems, and (3) combination and use of the identified genes/alleles in genetic enhancement of target species.
 Significant Research Contributions
Developed two new concepts "UGMS" (UniGene derived MicroSatellite) and "GNMS" (Genic Non-coding MicroSatellite) and designed novel sequence-based robust 25,318 genic and 19,281 genomic microsatellite markers in five cereal species (rice, wheat, maize, sorghum and barley) as well as in sugarcane and Brassica having large and complex genomes (NCBI Probe Database Pr009692824 to Pr009709837 and Pr010260597 to Pr010261911) for which very little sequence information is available.
 
Utilized these microsatellite markers for high-throughput genotyping, DNA fingerprinting for germplasm characterization and variety identification, developing molecular Bar Codes of commercially important Indian Basmati rice varieties, marker-based testing of seed purity of male-sterile line in rice hybrid seed production, studying genetic diversity pattern and phylogenetic relationships, construction of genic microsatellite marker-based framework physical map of rice genome and bin-map of wheat genome and genomic microsatellite marker-based Indian mustard genome map for the first-time, comparative genome mapping for understanding genome structure and evolution, development of genic functional markers for fertility restoration and mapping a major locus for male fertility restoration in rice.
 
Detected and validated the SNPs and InDels in important sugar pathway and disease resistance genes through cloned amplicons sequencing and DHPLC analysis and using a cost-efficient CAPS genotyping assay and developed CAPS markers which can be of immense use for various marker-assisted genetic improvement of sugar content and disease resistance in sugarcane. Identified a large number of SNPs and InDels in coding and regulatory sequence components of stress-responsive rice genes by whole genome resequencing and transcriptome sequencing of commercially important Indian rice varieties. Demonstrated large-scale validation and high-throughput genotyping of these SNPs from stress-responsive rice genes in a set of domesticated rice cultivars and wild species accessions using the Illumina GoldenGate assay and utilized large number of such validated useful SNP alleles/haplotypes for candidate-gene based association analysis of important stress-tolerance traits in rice. (Read more......)
 Group Members
Dr. Maneesha S. SaxenaNIPGR Postdoc
Ms. Alice KujurPh.D Student
Mr. Deepak Bajaj Junior Research Fellow
 Selected Publications
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 (In Press).
Dixit N, Dokku P, Amitha Mithra SV, Parida SK, Singh AK, Singh NK, Mohapatra T (2013) Haplotype structure in grain weight gene GW2 and its association with grain characteristics in rice. Euphytica DOI 10.1007/s10681-012-0852-4.
Agarwal G, Jhanwar S, Priya P, Singh VK, Saxena MS, Parida SK, Garg R, Tyagi AK, Jain M (2012) Comparative analysis of kabuli chickpea transcriptome with desi and wild chickpea provides a rich resource for development of functional markers. PLoS ONE 7: e52443
Jhanwar S, Priya P, Garg R, Parida SK, Tyagi AK and Jain M (2012) Transcriptome sequencing of wild chickpea as a rich resource for marker development. Plant Biotechnology Journal 10: 690-702.
Parida SK, Mukerji M, Singh AK, Singh NK and Mohapatra T (2012) SNPs in stress-responsive rice genes: validation, genotyping, functional relevance and population structure. BMC Genomics 13: 426.
Parida SK, Kalia SK, Kaul S, Dalal V, Pandit A, Gaikwad K, Sharma TR, Srivastava PS, Singh NK and Mohapatra T (2012) Single nucleotide polymorphism in sugar pathway and disease resistance genes in sugarcane. Theoretical and Applied Genetics (In Press).
Bharathi LK, Parida SK*, Munshi AD, Behera TK, Raman KV and Mohapatra T (2011) Molecular diversity and phylogeny of Momordica spp. of Indian occurrence. Genetic Resources and Crop Evolution 59: 937-948 (*As joint first author).
Parida SK, Pandit A, Gaikwad K, Sharma TR, Srivastava PS, Singh NK and Mohapatra T (2010). Functionally relevant microsatellites in sugarcane unigenes. BMC Plant Biology 10: 251. (Highly Accessed: More than 2,500 times during one month of being on-line).
Parida SK, Yadava DK and Mohapatra T (2010). Microsatellites in Brassica unigenes: Relative abundance, marker design and use in comparative physical mapping and genome analysis. Genome 53: 55-67. (No. of citations: 13).
Parida SK, Dalal V, Singh NK and Mohapatra T (2009) Genic non-coding microsatellites in the rice genome: characterization, marker design and use in assessing genetic and evolutionary relationships among domesticated groups. BMC Genomics 10: 140. (No. of citations: 10; Highly Accessed: More than 3,500 times during three months of being on-line).
Parida SK, Kalia SK, Kaul S, Dalal V, Hemaprabha G, Selvi A, Pandit A, Singh A, Gaikwad K, Sharma TR, Srivastava PS, Singh NK and Mohapatra T (2009) Informative genomic microsatellite markers for efficient genotyping applications in sugarcane. Theoretical and Applied Genetics 118: 327-338. (No. of citations: 10).
Parida SK, Raj Kumar KA, Dalal V, Singh NK and Mohapatra T (2006) Unigene derived microsatellite markers for the cereal genomes. Theoretical and Applied Genetics 112: 808-817. (No. of citations: 56; A Most Viewed and Highly Accessed article during three months of being on-line).
Umakanta N, Parida SK*, Dey SK, Raj Kumar KA, Singh AK, Singh NK and Mohapatra T (2010). Genic markers for WA cytoplasm based male sterility and its fertility restoration in rice. Molecular Breeding 26: 275-292. (*As joint first author) (No. of citations: 4).
Yadava DK, Parida SK, Dwivedi VK, Varshney A, Ghazi IA, Sujata V and Mohapatra T (2009). Cross-transferability and polymorphic potential of genomic STMS markers of Brassica species. Journal of Plant Biochemistry and Biotechnology 18: 29-36. (No. of citations: 8).
Koundal V, Parida SK, Yadava DK, Ali A, Koundal KR and Mohapatra T (2008). Evaluation of microsatellite markers for Genome mapping in Indian Mustard (Brassica juncea L.). Journal of Plant Biochemistry and Biotechnology 17: 69-72. (No. of citations: 6).
Verma VK, Behera TK, Munshi AD, Parida SK and Mohapatra T (2007). Genetic diversity of ash gourd [(Benincasa hispida (Thunb.) Cogn.] inbred lines based on RAPD and ISSR markers and their hybrid performance. Scientia Horticulturae 113: 231-237. (No. of citations: 22).
Naik PK, Alam MA, Singh H, Goyal V, Parida SK, Kalia S and Mohapatra T (2010) Assessment of genetic diversity through RAPD, ISSR and AFLP markers in Podophyllum hexandrum: a medicinal herb from the Northwestern Himalayan region. Physiology and Molecular Biology of Plants 16: 1-13. (No. of citations: 4).
Sonah H, Desmukh R, Parida SK and Kotasthane A (2009) Morphological and genetic variation among different isolates of Magnaporthe grisea collected from Chhattisgarh. Indian Phytopathology 62: 469-477. (No. of citation: 1).
 Book Chapters
Parida SK and 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.