National Institute of Plant Genome Research
Digital India     
    Dr. Sabhyata Bhatia
    Staff Scientist VI
    Tel: 91-11-26741612,14,17 Ext. - 159
    Direct - 26735159
 Research Interest
Generating genomic resources for gene discovery and crop enhancement
The group has major interest in the area of Structural and Functional Genomics in plants where the aim has been to understand and analyse genomes in order to provide new tools to enhance plant capacity. To achieve this, approaches combining molecular biology and genomics have been utilized for the development of genomic resources (cDNAs, ESTs, high throughput molecular markers, high resolution genetic linkage maps in legumes such as chickpea and lentil), evaluation of bioresources and biodiversity, molecular fingerprinting, phylogenetic analysis and DNA Barcoding. The focus in our laboratory has been on molecular mapping using DNA based molecular markers, hence novel STMS (Sequence Tagged Microsatellite Sites) markers and the EST based SSRs (Simple Sequence Repeats), SNPs (Single Nucleotide Polymorphisms), PIPs (Potential Intron Polymorphisms) markers etc. were developed through construction of conventional, enriched and cDNA libraries in chickpea and lentil. The potential of these markers for genetic diversity studies at intra and inter specific levels are studied. At the molecular level, the pattern of microsatellite evolution is unraveled and novel phylogenetic relationships elucidated. Synteny studies among the related genera are performed in order to establish the usefulness of the above markers for comparative genomics. Construction of the microsatellite based genetic linkage maps using intra and interspecific mapping populations are under progress for saturation of linkage maps and tagging of agronomically important traits related to seed yield. More recently, with the advent of the next generation sequencing technologies, the group is involved in the de novo sequencing of the chickpea genome and transcriptome, as well as the high throughput SNP and SSR genotyping and mapping projects and are amongst the very few to have established the high throughput genotyping of SNPs and its use in the construction of high resolution genetic maps.
Simultaneously, functional genomics of seed development and nodule development, the two major hallmark functions of leguminous plants, in chickpea is being done through next generation sequencing and characterization of the transcriptomes of these organs. The group is involved in the deep sequencing of the transcriptome of chickpea seeds and nodules at various stages of development, using high throughput next generation sequencing technologies with aim to understand the regulatory networks underlying seed development and nodule formation in chickpea. The information obtained will be applied in the characterization of Transcription Factors. Also, since the role miRNAs in developmental processes has been recently established, we are identifying miRNAs through NGS analysis and characterizing those that may have a regulatory role in development of seeds and nodules.
 Selected Publications
Pradhan S, Bandhiwal N, Shah N, Kant C, Gaur R, Bhatia S (2014) Global transcriptome analysis of developing chickpea (Cicer arietinum L.) seeds. Frontiers in Plant Science. (Accepted).
Verma P, Chandra A, Roy AK, Malaviya D R, Kaushal P, Pandey D, Bhatia S (2014) Development, characterization and cross-species transferability of genomic SSR markers in berseem (Trifolium alexandrinum L.), an important multi-cut annual forage legume. Molecular Breeding. (Accepted).
Misra G, Priya P, Bandhiwal N, Bareja N, Jain M, Bhatia S, Chattopadhyay D, Tyagi AK, Yadav G (2014) The Chickpea Genomic Web Resource: Visualization and Analysis of the Desi-type Cicer arietinum Nuclear Genome for Comparative Exploration of Legumes. BMC Plant Biology. (Accepted).
Verma P, Sharma TR, Srivastava PS, Abdin MZ, Bhatia S (2014) Exploring genetic variability within lentil (Lens culinaris Medik.) and across related legumes using a newly developed set of microsatellite markers. Mol Biol Rep. 41(9): 5607-25. (DOI 10.1007/s11033-014-3431-z)
Shrivastava D, Verma P, Bhatia S (2014) Expanding the repertoire of microsatellite markers for polymorphism studies in Indian accessions of mung bean (Vigna radiata L. Wilczek). Mol Biol Rep. 41(9): 5669-80.   (DOI 10.1007/s11033-014-3436-7)
Varshney RK, Mir RR, Bhatia S, Thudi M, Hu Y, Azam S, Zhang Y, Jaganathan D, You FM, Gao J, Riera-Lizarazu O, Luo M-C (2014) Integrated physical, genetic and genome map of chickpea (Cicer arietinum L.) Funct Integr Genomics 14(1): 59-73. (DOI 10.1007/s10142-014-0363-6).
Kumar S, Shah N, Garg V, Bhatia S (2014) Large scale in-silico identification and characterization of simple sequence repeats (SSRs) from de novo assembled transcriptome of Catharanthus roseus (L.) G. Don. Plant Cell Reports 33: 905–918. (DOI 10.1007/s00299-014-1569-8).
Gaur R, Bhatia S, Gupta M (2014) Generation of expressed sequence tags under cadmium stress for gene discovery and development of molecular markers in chickpea. Protoplasma 251: 955-72.  (DOI: 10.1007/s00709-013-0609-5)
Verma P, Shah N, Bhatia S (2013) Development of an expressed gene catalogue and molecular markers from the de novo assembly of short sequence reads of the lentil (Lens culinaris Medik.) transcriptome. Plant Biotechnol J. 11: 894-905
Jain M, Misra G, Patel RK, Priya P, Jhanwar S, Khan AW, Shah N, Singh VK, Garg R, Jeena G, Yadav M, Kant C, Sharma P, Yadav G, Bhatia S, Tyagi AK, Chattopadhyay D (2013) A draft genome sequence of the pulse crop chickpea (Cicer arietinum L.). Plant J. 74: 715-29
Gaur R, Azam S, Jeena G, Khan AW, Chaudhary S, Jain M, Yadav G, Tyagi AK, Chattopadhyay D, Bhatia S (2012) High-throughput SNP discovery and genotyping for constructing a saturated linkage map of chickpea (Cicer arietinum L.). DNA Research 19: 357–373.
Choudhary S, Gaur R, Gupta S, and Bhatia S (2012) EST derived genic molecular markers: Development and utilization for generating an advanced transcript map of chickpea. Theor Appl Genet. 124:1449–1462.
Gupta M, Verma B, Kumar N, Chahota RK, Rathour R, Sharma SK, Bhatia S, Sharma TR (2012) Construction of intersubspecific molecular genetic map of lentil based on ISSR, RAPD and SSR markers. J Genet 91: 279-87
Shokeen B, Choudhary S, Sethy NK, Bhatia S (2011) Development of SSR and gene-targeted markers for construction of a framework linkage map of Catharanthus roseus. Annals of Botany 108: 321-336.
Gaur R, Sethy NK, Choudhary S, Shokeen B, Gupta V, and Bhatia S (2011) Advancing the STMS genomic resources for defining new locations on the intraspecific genetic linkage map of chickpea (Cicer arietinum L.) BMC Genomics 12: 117
Chaudhary S, Sharma V, Prasad M, Bhatia S, Tripathi BN, Yadav G, Kumar S (2011) Characterization and genetic linkage mapping of the horticulturally important mutation leafless inflorescence (lli) in periwinkle Catharanthus roseus. Scientia Horticulturae 129: 142-153.
Garg R, Patel RK, Jhanwar S, Priya P, Bhattacharjee A, Yadav G, Bhatia S, Chattopadhyay D, Tyagi AK, Jain M (2011b) Gene discovery and tissue-specific transcriptome analysis in chickpea with massively parallel pyrosequencing and web resource development. Plant physiology 156(4): 1661-78.
Gujaria N, Kumar A, Dauthal P, Dubey A, Hiremath P, Bhanu Prakash A, Farmer A, Bhide M, Shah T, Gaur P, Upadhyaya HD, Bhatia S, Cook DR, May GD, Varshney RK (2011) Development and use of genic molecular markers (GMMs) for constructing a transcript map of chickpea (Cicer arietinum L.). Theor Appl Genet. 122: 1577-1589.
Choudhary S, Sethy NK, Shokeen B and Bhatia S (2009) Development of chickpea EST-SSR markers and analysis of allelic variation across related species. Theor. Appl. Genet. 118: 591-608.
Shokeen B, Sethy NK, Kumar S and Bhatia S (2007) Isolation and characterization of microsatellite markers for analysis of molecular variation in the medicinal plant Madagascar periwinkle (Catharanthus roseus (L.) G. Don.). Plant Science 172: 441-451.
Sethy NK, Shokeen B, Edwards KJ and Bhatia S (2006) Development of microsatellite markers and analysis of intra-specific genetic variability in chickpea (Cicer arietinum L.). Theor. Appl. Genet. 112: 1416-1428.
Sethy NK, Choudhary S, Shokeen B and Bhatia S (2006) Identification of microsatellite markers from Cicer reticulatum: Molecular variation and phylogenetic analysis. Theor. Appl. Genet. 112: 347-357
Choudhary S, Sethy NK, Shokeen B and Bhatia S (2006) Development of sequence-tagged microsatellite site markers for chickpea (Cicer arietinum L.). Molecular Ecology Notes 6(1): 93-95.
Shokeen B, Sethy NK, Choudhary S and Bhatia S (2005) Development of STMS markers from the medicinal plant Madagascar periwinkle (Catharanthus roseus (L.) G. Don.). Mol. Ecol. Notes 5: 818-820.
Sethy N. K, Shokeen B and Bhatia S (2003) Isolation and characterization of sequence-tagged microsatellite sites markers in chickpea (Cicer arietinum L.). Mol. Ecol. Notes 3: 428-430.
Rajagopal J, Bashyam L, Bhatia S, Khurana DK, Srivastava PS and Lakshmikumaran M (2000) Evaluation of genetic diversity in the Himalayan Poplar using RAPD markers. Silvae Genetica 49(2): 60-66
Singh A, Negi MS, Rajagopal J, Bhatia S, Tomar UK, Srivastava PS and Lakshmikumaran M (1999) Assessment of genetic diversity in Azadirachta indica using AFLP markers. Theor Appl Genet. 99(1/2): 272-279
Das S, Rajagopal J, Bhatia S, Srivastava PS and Lakshmikumaran M (1999). Assessment of genetic variation within Brassica campestris cultivars using AFLP and RAPD markers. J. of Biosciences 24(4): 433-440
Bhatia S, Negi MS and Lakshmikumaran M (1996) Structural Analysis of the rDNA Intergenic Spacer of Brassica nigra: Evolutionary Divergence of the Spacers of the Three Diploid Brassica Species. Journal of Molecular Evolution 43(5): 460-468.
Bhatia S, Das S, Jain A and Lakshmikumaran M (1995) DNA fingerprinting of Brassica juncea cultivars using microsatellite probes. Electrophoresis 16: 1750-1754.
Jain A, Bhatia S, Banga SS, Prakash S and Lakshmikumaran M (1994) Potential use of the random amplified polymorphic DNA (RAPD) to study the genetic diversity in Indian mustard (Brassica juncea) and its relationship to heterosis. Theoretical and Applied Genetics 88: 116-122.
Singh K, Bhatia S and Lakshmikumaran M (1994) Novel variants of the 5S rRNA genes in Eruca sativa. Genome 37: 121-128.
Bhatia S, Singh K, Jagannathan V and Lakshmikumaran M (1993) Organization and analysis of the 5S rRNA genes in B. campestris. Plant Science 92: 47-55.
 Book Chapter
Varshney RK, Hoisington DA, Upadhyaya HD, Gaur PM, Nigam SN, Saxena K, Vadez V, Sethy NK, Bhatia S, Aruna R, Gowda MVC, Singh NK (2007) Molecular genetics and breeding of grain legume crops for the semi-arid tropics. In Springer publication: Genomic Assisted Crop Improvement: Vol 2: Genomics Applications in Crops; R. Varshney and R. Tuberosa (eds.) pp. 207-241.
Lakshmikumaran M, Das S, Rajagopal J, Goswami J, Negi MS, Bhatia S (1998) Repeated DNA sequences in plants: Organization, Evolution and Applications. In Genetics and Biotechnology in Crop Improvement pp. 63-93. Rastogi Publications, Meerut, India; Editors: PK Gupta, SP Singh, HS Balyan, PC Sharma and B Ramesh
Lakshmikumaran M, and Bhatia S. 1996. DNA fingerprinting of medicinal plants : A means to preserve valuable genetic resources. RGICS Project No. 11. Rajiv Gandhi Institute for Contemporary Studies. Rajiv Gandhi Foundation, New Delhi.