Plant Molecular Genetics and Genomics

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, transcripts, high throughput SNPs and SSR 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 SNPs based genetic linkage maps using intra and inter-specific 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 (NGS) technologies, the group is involved in the sequencing of the genome and transcriptome of chickpea and lentil, as well as the high throughput SNP discovery and genotyping and its use in the construction of high resolution genetic maps and mapping of QTLs controlling yield related traits.

Understanding the mechanisms involved in seed and nodule development

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 NGS technologies with the aim to understand the regulatory networks underlying seed development and nodule formation in chickpea. The information obtained is being applied for the characterization of Transcription Factors, transporters and members of two component system. Moreover, since the role of miRNAs in developmental processes has been recently established, conserved and novel miRNAs are being identified through NGS analysis and will be characterized for establishing their regulatory role in development of seeds and nodules. Further, standardization of chickpea transformation is currently in progress for functional characterization of putative genes involved in seed and nodule development in chickpea.

• Fellow,The National Academy of Sciences (NASI), India (2014).

1.Deep transcriptome of developing seeds of chickpea.

3.Deep transcriptome of lentil.

• Garg R, Shankar R, Thakkar B, Kudapa H, Krishnamurthy L, Mantri N, Varshney R, Bhatia S & Jain M (2016) Transcriptome analyses reveal genotype- and developmental stage-specific molecular responses to drought and salinity stresses in chickpea.  Scientific Reports | 6:19228 | DOI: 10.1038/srep19228
• Verma S, Gupta S, Bandhiwal N, Kumar T, Bharadwaj C & Bhatia S (2015) High-density linkage map construction and mapping of seed trait QTLs in chickpea (Cicer arietinum L.) using Genotyping-by-Sequencing (GBS). Scientific Reports 5, 17512; doi: 10.1038/srep17512.
• Gupta S, Kumar T, Verma S, Bharadwaj C & Bhatia S. (2015) Development of gene-based markers for use in construction of the chickpea (Cicer arietinum L.) genetic linkage map and identification of QTLs associated with seed weight and plant height. Mol Biol Rep, 1-10, doi: 10.1007/s11033-015-3925-3.
• Verma P, Goyal R, Chahota RK, Sharma TR, Abdin MZ & Bhatia S (2015) Construction of a genetic linkage map and identification of QTLs for seed weight and seed size traits in lentil (Lens culinaris Medik.) PlosOne, DOI:10.1371/journal.pone.0139666 October 5, 2015
• Gaur R, Jeena G, Shah N, Gupta S, Pradhan S, Tyagi AK, Jain M, Chattopadhyay D & Bhatia S (2015): High density linkage mapping of genomic and transcriptomic SNPs for synteny analysis and anchoring the genome sequence of chickpea. Scientific Reports 5, 13387; doi: 10.1038/srep 13387.
• Parween S, Nawaz K, Roy R, Pole AK, Suresh BV, Misra G, Jain M, Yadav G, Parida SK, Tyagi AK, Bhatia S & Chattopadhyay D (2015) An advanced draft genome assembly of a desi type chickpea (Cicer arietinum L.). Scientific Reports 5, 12806; doi: 10.1038/srep12806.
• Kumar S, Bhatia S (2015) Isolation of Catharanthus roseus (L.) G. Don nuclei and measurement of rate of Tryptophan decarboxylase gene transcription using nuclear run-on transcription assay. PlosOne, DOI:10.1371/journal.pone.0127892 May 29, 2015.
• Kumar T, Bharadwaj C, Alam A, Singh P, Singhal T, Chauhan SK, Bhatia S, Sarker A (2015) Development and characterization of Recombinant Inbred Lines for seed related traits in chickpea. IJTA, 33(2): 639 – 642.
• Khajuria ,Y.P., Saxena , M.S., Gaur, R., Chattopadhyay, D., Jain, M., Parida, S.K., Bhatia S. (2015) Development and integration of genome-wide polymorphic microsatellite markers onto a reference linkage map for constructing a high-density genetic map of chickpea. PlosOne, DOI: 10.1371/journal.pone.0125583.
• Gupta S, Garg V, Bhatia S (2015): A new set of ESTs from chickpea (Cicer arietinum L.) embryo reveals two novel F-box genes, CarF-box_PP2 and CarF-box_LysM, with potential roles in seed development. Plos One (DOI: 10.1371/journal.pone.0121100)
• Gupta S, Garg V, Kant C, Bhatia S (2015): Genome-wide survey and expression analysis of F-box genes in chickpea. BMC Genomics (DOI: 10.1186/s12864-015-1293-y).
• Verma P, Chandra A, Roy AK, Malaviya D R, Kaushal P, Pandey D, Bhatia S (2015): Development, characterization and cross-species transferability of genomic SSR markers in berseem (Trifolium alexandrinum L.), an important multi-cut annual forage legume. Molecular Breeding (DOI 10.1007/s11032-015-0223-7).
• 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 Vol 5, Article 698 (doi: 10.3389/fpls.2014.00698) .
• 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 (DOI: 10.1186/s12870-014-0315-2).
• 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).
• 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).
• 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).
• Verma P, Shah N and 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 Biotech. J. 11: 894-905  (doi: 10.1111/pbi.12082).
• Jain M, Misra G, Patel RK, Priya P, Jhanwar S, Khan AW, Shah N, Singh VK, Garg R, Jeena G, Yadav M, Chandra Kant, 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: 715-729 (DOI: 10.1111/tpj.12173).
• Gaur R, Azam S, Jeena G, Khan AW, Choudhary 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 (doi: 10.1093/dnares/dss018).
• Choudhary S, Gaur R., Gupta S, 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 (DOI 10.1007/s00122-012-1800-3).
• 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. Jour. Genet. 12, 91(3):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. Ann. Bot., London, 108, 321–336.
• Garg R, Patel RK, Jhanwar S, Priya P, Bhattacharjee A, Yadav G, Bhatia S, Chattopadhyay D, Tyagi AK, Jain M (2011) Gene discovery and tissue-specific transcriptome analysis in chickpea with massively parallel pyrosequencing and web resource development, Plant Physiol., 156: 1661–1678.
• Chaudhary S, Sharma V, Prasad Manoj, Bhatia S, Tripathi BN, Yadav Gitanjali, 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, DOI : 10.1016/j.scientia.2011.02.025.
• Gaur R, Sethy NK, Choudhary S, Gupta V, Shokeen B, Bhatia S (2011) Advancing the STMS genomic resources and defining their locations on the intra-specific genetic linkage map of chickpea (Cicer arietinum L.) BMC Genomics 12: 117.
• Gujaria N, Kumar A, Dauthal P, Dubey A, Hiremath P, Bhanu Prakash A, Farmer A, Bhide M, Shah T, Gaur P, Upadhyaya H D, Bhatia S, Cook D R, May G D, Varshney R K (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 (DOI 10.1007/s00122-011-1556-1).
• Gupta V, Bhatia S, Mohanty NA, Sethy N, Tripathy BC (2010) Comparative analysis of photosynthetic and biochemical characteristics of Desi and Kabuli genepools of chickpea (Cicer arietinum L.) Int. Jour of Genetic Engineering and Biotechnology. Vol 1, Num 1, 65 – 76.
• Choudhary S, Sethy NK, Shokeen B, Bhatia S (2009) Development of chickpea EST-SSR markers and analysis of allelic variation across related species. Theor Appl Genet 118:591–608 (DOI10.1007/s00122-008-0923-z). 
• Shokeen B, Sethy NK, Kumar S, 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, ShokeenB, Edwards KJ, Bhatia S (2006) Development of microsatellite markers and analysis of intraspecific genetic variability in chickpea (Cicer arietinum L.). Theor. and Appl. Genet. 112:1426 -1428.
• Sethy NK, Choudhary S, Shokeen B, 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, Bhatia S (2006): Development of sequence-tagged microsatellite site markers for chickpea (Cicer arietinum L.). Mol Ecol. Notes 6(1): 93-95.
• Shokeen B, Sethy NK, Choudhary S, Bhatia S (2005): Development of STMS markers from the medicinal plant Madagascar periwinkle (Catharanthus roseus (L.) G. Don.) Mol Ecol. Notes 5, 818-820 (IF: Currently Mol. Ecol.Res:7.2).
• Sethy NK, Shokeen B, Bhatia S (2003): Isolation and characterization of sequence-tagged microsatellite sites (STMS) markers in chickpea (Cicer arietinum L.). Mol Ecol. Notes, 3, 428-430.
• Rajagopal J, Bashyam L, Bhatia S, Khurana DK, Srivastava PS, 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, 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, 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, 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, Lakshmikumaran M (1995) DNA fingerprinting of Brassica juncea cultivars using microsatellite probes.  Electrophoresis 16: 1750-1754.
• Jain A, Bhatia S, Banga SS, Prakash S, 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.  Theor Appl Genet 88: 116-122.
• Singh K, Bhatia S, Lakshmikumaran M (1994) Novel variants of the 5S   rRNA genes in Eruca sativa.  Genome 37: 121-128.
• Bhatia S, Singh K, Jagannathan V, Lakshmikumaran M (1993): Organization and   analysis of the 5S rRNA genes in B. campestris.  Plant Science 92: 47-55.

• Bhatia S and Shokeen B (2009) Isolation of Microsatellites from Catharanthus roseus (L.) G. Don Using Enriched Libraries. In: Mohan Jain S and Saxena PK (eds) Methods in Molecular Biology-Protocols for In Vitro Cultures and Secondary Metabolite Analysis of Aromatic and Medicinal Plants, vol. 547, Humana Press, a part of Springer Science + Business Media, pp 289-302.
• 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: Varshney R and Tuberosa R. (eds) Genomic Assisted Crop Improvement: Genomics Applications in Crops Vol 2, Springer publication, 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: Gupta PK, Singh SP, Balyan HS, Sharma PC and Ramesh B (eds) Genetics and Biotechnology in Crop Improvement, Rastogi Publications, Meerut, India, pp. 63–93.

• 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.