Indian Institute of Pulses Research

Division of Plant Biotechnology, ICAR-IIPR

(Plant Biotechnology and Molecular biology)

Thrust Areas

QTL Mapping and marker assisted introgression for stress tolerance
Gene identification and characterization for stress tolerance
Establishment of Rapid generation advancement systems for pulses

Significant Acheivements

Developed a marker assisted backcross (MABC) Chickpea line IPC (L4-14) for enhanced drought tolerance having QTL-hotspot region in DCP92-3 genetic background with 14.2% yield advantage under drought condition.
Generated high-density linkage map in Chickpea using Axiom®CicerSNPArray (1856 SNPs) spanning a distance of 1106.3 cM and identified QTL clusters on CaLG03 and CaLG06 harboring major QTLs for yield and yield component traits under salinity stress which harbours candidate genes for salinity tolerance in Chickpea
Developed gram pod tolerant transgenic chickpea and pigeonpea lines tested for bio efficacy under Confined Field Trials (CFTs). Best selected lines (though found to be hemizygous) are being characterized for site of transgene integration.
Developed single and Bi-directional Duplex pod specific (mod-msg) promoter (BDDP) vectors having cry genes;
Developed two vector system using pRI 201AN fornptII and tma 12 gene of interest.
Developed embryonic axis explant based highly reproducible in-vitro regeneration protocol amenable to Agrobacterium mediated transformation in two Grasspea varieties viz., Pusa-24 and Mahateora and three Mungbean varieties viz. ML267, Samrat and Virat.
In-vitroregeneration system based on direct shoot organogenesis in Fieldpea, Chickpea and Pigeonpea.
Cloned and characterized insect resistance gene Vip3Aafor insect resistance (IR) trait in chickpea
Developed rapid and efficient method for reverse genetic studies in chickpea based on Agrobacterium rhizogenes
Developed generation of CRISPR/Cas9 construct using InFusion Technology
Cloned and characterised Chickpea multi-stress responsive WRKY transcription factor and herbivory-inducible chitinase (Car_Chit-15) genes, Pigeonpea Bowman-Birk protease inhibitor and novel small secreted cysteine rich protein (SSCP-1) genes, and Lathyrus sativusoxalyl-CoA synthetase (LsAAE3) and ODAP biosysnthes genes.
Draft genome sequencing and protein profiling of potent Bacillus isolates: AK2.IIPR, F1.IIPR, F5.IIPR, F6.IIPR and F8.IIPR has been deciphered, revealing the presence of 28, 19, 26, 26 and 29 insecticidal genes, respectively.
Genome wide identification of MADS-box, Wound-induced protein (WIP) and chitinase gene families in Chickpea.
Identified major-effect QTLs for 100-seed weight and plant height in Chickpea explaining up to 59.70% phenotypic variation in a recombinant inbred line (RIL) population developed from ICC 4958 and DCP 92-3.
Identified the role of cytochrome P450, xyloglucan endotransglucosylase/hydrolase, glutamate dehydrogenase, methyl crotonoyl carboxylase and thaumatin-like genes in herbicide resistance in Chickpea through RNA-seq analysis.
Established marker trait associations (22 MTAs) in Pigeonpea for 5 ideotypic traits viz., days to initial flowering, days to 50% flowering, days to maturity, plant height, and number of primary branches which explains upto 30.76% phenotypic variation and identified 6 SSRs linked with Fusariumwilt resistance in Pigeonpea.
Generated refined genome assembly of Fusarium udumwith a genome size of 62.23 Mb, spanning 1488 contigs with largest contig size of 452.8 kb

Facilities

Instrumentation
Thermal cyclers, Real time thermal cyclers, vertical and Horizontal Gel Electrophoresis Units, , Blotting and Hybridization Systems, 2D electrophoresis, Iso-Electric Focusing (IEF), , ELISA Reader, Centrifuges, Micro-projectile Gene Gun System (PDS 1000), Gel documentation system, Hybridization oven, sonicator, .
Plant tissue culture and transformation facility
Transgenic plant containment facility and establishment unit
State–of-art insect bioassay facility
Hydroponics facility

Publications

Abhishek Bohra, Abhishek Rathore, Prasad Gandham, Rachit K Saxena, SJ Satheesh Naik, Dibendu Dutta, Indra P Singh, Farindra Singh, Meenal Rathore, Rajeev K Varshney, Narendra P Singh.2021. Genome-wide comparative transcriptome analysis of the A4-CMS line ICPA 2043 and its maintainer ICPB 2043 during the floral bud development of pigeonpea. Functional & Integrative Genomics 21 (2), 251-263
Antara Das, Deepti Nigam, Alim Junaid, Kishor U. Tribhuvan, Kuldeep Kumar, Kumar Durgesh, N. K. Singh, and Kishor Gaikwad. “Expressivity of the key genes associated with seed and pod development is highly regulated via lncRNAs and miRNAs in pigeonpea.” Scientific reports 9, no. 1 (2019): 1-14.
Antara Das, Swati Saxena, Kuldeep Kumar, Kishor U. Tribhuvan, N. K. Singh, and Kishor Gaikwad. “Non-coding RNAs having strong positive interaction with mRNAs reveal their regulatory nature during flowering in a wild relative of pigeonpea (Cajanus scarabaeoides).” Molecular biology reports 47, no. 5 (2020): 3305-3317.
Ayushi Tripathi, Neetu S Kushwah , Samir C Debnath , Susmita Shukla and Meenal Rathore.2022. Investigating the in vitro regeneration potential of mungbean cultivar Samrat. Journal of Food Legumes 35(3): 198-206, 2022
Barmukh R, Soren KR, Madugula P, Gangwar P, Shanmugavadivel PS, Bharadwaj C, Konda AK, Chaturvedi SK, Bhandari A, Rajain K, Singh NP, Roorkiwal M, Varshney RK. (2021). Construction of a high-density genetic map and QTL analysis for yield, yield components and agronomic traits in chickpea (Cicer arietinum L.). PLoS One. 16(5):e0251669. doi: 10.1371/journal.pone.0251669. PMID: 33989359;
Bharadwaj C, Tripathi S, Soren KR, Thudi M, Singh RK, Sheoran S, Roorkiwal M, Patil BS, Chitikineni A, Palakurthi R, Vemula A, Rathore A, Kumar Y, Chaturvedi SK, Mondal B, Shanmugavadivel PS, Srivastava AK, Dixit GP, Singh NP, Varshney RK. (2021). Introgression of “QTL-hotspot” region enhances drought tolerance and grain yield in three elite chickpea cultivars. Plant Genome. 14(1):e20076. doi: 10.1002/tpg2.20076.
Das A, Annapragada H, Singh S, Murugesan S, Singh NP (2020) Symbiotic nitrogen fixation and endophytic bacterial community structure in Bt-transgenic chickpea. Scientific Reports 10: 5453
Das A, Basu, P.S., Kumar, M. et al. (2021) Transgenic chickpea (Cicer arietinum L.) harbouring AtDREB1a are physiologically better adapted to water deficit. BMC Plant Biology 21, 39
Das A, Shukla A, Thakur S, Rathore M, Singh NP (2020) Estimation of neomycin phosphotransferase-II (NPT-II) protein in vegetative and reproductive tissues of transgenic chickpea (Cicer arietinum L.) and biosafety perspectives. Journal of Plant Biochemistry and Biotechnology 29: 568-570
Gaikwad, K., Ramakrishna, G., Srivastava, H., Saxena, S., Kaila, T., Tyagi, A., Sharma, P., Sharma, S., Sharma, R., Mahla, H.R., Kumar, K., Mithra A, Solanke, A. U., Kalia, P., Rao, A. R., Rai, A., Sharma, T. R., Singh, N. K., 2023. The chromosome-scale genome assembly of cluster bean provides molecular insight into edible gum (galactomannan) biosynthesis family genes. Scientific Reports, 13(1), p.9941.
Jay Prakash Awasthi, Kamlesh Singh Paraste, Meenal Rathore, Mayank Varun,Disha Jaggi, and Bhumesh Kumar.2018. Effect of elevated CO2 on Vigna radiata and two weed species:yield, physiology and crop–weed interaction. Crop & Pasture Science. doi: https://doi.org/10.1071/CP17192. (
Konda AK, Farmer R, Soren KR, PS S, Setti A. Structural modelling and molecular dynamics of a multi-stress responsive WRKY TF-DNA complex towards elucidating its role in stress signalling mechanisms in chickpea. Journal of Biomolecular Structure and Dynamics. 2018 Jul 4; 36(9):2279-91. doi.org/10.1080/07391102.2017.1349690
Konda AK, Sabale PR, Soren KR, Subramaniam SP, Singh P, Rathod S, Chaturvedi SK, Singh NP. Systems biology approaches reveal a multi-stress responsive WRKY transcription factor and stress associated gene co-expression networks in chickpea. Current Bioinformatics. 2019 Oct 1;14(7):591-601. doi.org/10.2174/1574893614666190204152500
Konda AK, Singh P, Soren KR, Singh NP. A modified pod specific promoter for high level heterologous expression of genes in legumes. Legume Research-An International Journal. 2021; 44(1):51-9. DOI: 10.18805/LR-4073
Kumar, Kuldeep., Anjoy, P., Sahu, S., Durgesh, K., Das, Antara., Tribhuvan, K.U., Sevanthi, A.M., Joshi, R., Jain, P.K., Singh, N.K. and Rao, A.R., 2022. Single trait versus principal component based association analysis for flowering related traits in pigeonpea. Scientific Reports, 12(1), p.10453.
Kumar, Kuldeep, Harsha Srivastava, Antara Das, Kishor U. Tribhuvan, Kumar Durgesh, Rekha Joshi, Amitha Mithra Sevanthi, Pradeep Kumar Jain, Nagendra Kumar Singh, and Kishor Gaikwad. “Identification and characterization of MADS box gene family in pigeonpea for their role during floral transition.” 3 Biotech 11, no. 2 (2021): 1-15.
Kumar, N., Soren, K.R., Bharadwaj, C., PR, S.P., Shrivastava, A.K., Pal, M., Roorkiwal, M., Kumar, Kuldeep., Patil, B.S., Soni, A. and Nimmy, M.S., 2021. Genome-wide transcriptome analysis and physiological variation modulates gene regulatory networks acclimating salinity tolerance in chickpea. Environmental and Experimental Botany, 187, p.104478.
Meenal Rathore*, Ayushi Tripathi, Neetu S Kushwah and N P Singh. 2022. Multiple shoot regeneration from detached embryonic axis in greengram ( Vigna radiata ) cv. SML 668. Legume Research. DOI: 18805/LR-4693 (NAAS-6.67)
Mohd Akram, Naimuddin Kamaal, Aditya Pratap, Abdul Muin, Aniruddha Kumar Agnihotri, Utkarsh Singh Rathore, Meenal Rathore and Narendra Pratap Singh.2022. Species diversity, phylogeny and evidence of recombination in begomoviruses associated with yellow mosaic disease of moth bean (Vigna aconitifolia) in South India. Journal of Phytopathology. 2022;00:1–15. DOI: 10.1111/jph.13079
Paras Pandey, Meenal Rathore and N.P.Singh. Advances in In vitro studies for genetic enhancement of blackgram : a review. Legume Research. DOI: 10.18805/LR-4114
Prakash G patil, J Dubey, Abhishek Bohra, RKMishra, PRSaable, Alok Das, Meenal Rathore and NP Singh.2017. Association mapping to discover significant marker trait associations for resistance against fusarium wilt variant 2 in pigeonpea [Cajanus cajan (L.) Millspaugh] using SSR markers. Journal of Applied Genetics.doi:10.10 07/s1335 3-0170400-y
Prakash G. Patil* , Abhishek Bohra, Jyotirmay Dubey, Parasappa R. Saabale, Raj K. Mishra, Gaurav Pandey, Alok Das, Meenal Rathore, Farindra Singh, Narendra Pratap Singh. 2017. Genetic analysis and molecular resistance to race 2 of Fusarium wilt in pigeonpea [Cajanus cajan (L.) Millsp.]. Crop Protection. 100 (2017) 117e123.
Pratap A, Prajapati U, Singh CM, Gupta S, Rathore Meenal, et al. Potential, constraints and applications of in vitro methods in improving grain legumes. Plant Breed. 2018;00:1–15.
Rathinam M, Tyagi S, Konda AK, Rengarajan D, Prashat GR, Sreevathsa R. Relevance of methionine sulfoxide reductase (s)(MSR) as candidate proteins in redox homeostasis-mediated resistance response to Helicoverpa armigera (Hübner) in the pigeonpea wild relative Cajanus platycarpus (Benth.) Maesen. International Journal of Biological Macromolecules. 2022 Aug 31; 215:290-302. doi.org/10.1016/j.ijbiomac.2022.06.109
Revanasidda Aidbhavi, Aditya Pratap, Prasoon Verma, Amrit Lamichaney, Sanjay M Bandi, SD Nitesh, Mohd Akram, Meenal Rathore, Bansa Singh, Narendra P Singh. 2021.
Screening of endemic wild Vigna accessions for resistance to three bruchid species. Journal of Stored Products Research. 93: 101864. https://doi.org/10.1016/j.jspr.2021.101864
Saxena, Swati, Antara Das, Tanvi Kaila, G. Ramakrishna, Sandhya Sharma, and Kishor Gaikwad. “Genomic survey of high-throughput RNA-Seq data implicates involvement of long intergenic non-coding RNAs (lincRNAs) in cytoplasmic male-sterility and fertility restoration in pigeon pea.” Genes & Genomics (2023): 1-29.
Singh AK, Velmurugan A, Gupta DS, Kumar J, Kesari R, Konda A, Singh NP, Roy SD, Biswas U, Kumar RR, Singh S. Draft genome sequence of a less-known wild Vigna: Beach pea (V. marina cv. ANBp-14-03). The Crop Journal. 2019 Oct 1;7(5):660-6. doi.org/10.1016/j.cj.2019.05.007
Singh P, Shukla A, Tiwari NN, Ansari J, Thakur S, Rathore M, Verma OP, Singh NP, Das A* (2022) Routine and efficient in vitro regeneration system amenable to biolistic particle delivery in chickpea (Cicer arietinum L.). Plant Cell Tissue Organ Culture 148: 699–711
Singh P, Sujayanand GK, Thakur S, Rathore M, Verma OP, Singh NP, Das A* (2022) Evaluation of transgenic chickpea harboring codon-modified Vip3Aa against gram pod borer (Helicoverpa armigera H.) PLoS ONE 17(6): e0270011
Sudhir Kumar Jha, Kuldeep Kumar, Kalpana Tewari, et al.. 2022. Gene expression and biochemical profiling of contrasting Vigna mungo genotypes against Mungbean Yellow Mosaic India Virus (MYMIV). Journal of Food Legumes 35 (2). 107-116.
Sudhir Kumar Jha, Kuldeep Kumar, Rahul Kumar, Jyotishree Pandey, Pritee Sagar, Meenal Rathore and Awnindra K Singh. 2023. Screening for days to Flowering and Photo Insensitivity in Vigna mungo. Ecology, Environment and Conservation. 29: S7-11.
Sudhir Kumar Jha, Man Mohan Deo, Kuldeep Kumar, Meenal Rathore, Mohd. Akram and Aditya Pratap. 2023. Detection and Classification of Yellow Mosaic Disease in Vigna mungo using Convolutional Neural Network Deep Learning Models. Ecology, Environment and Conservation. 29: S177-181.
Sudhir Kumar Jha, Man Mohan Deo, Kuldeep Kumar, Meenal Rathore, Mohd. Akram and Aditya Pratap. 2022. Comparative evaluation of deep learning models for Yellow Mosaic Disease identification in blackgram. Journal of Food Legumes 35 (2). 140-144.
Sudhir Kumar Jha, Pritee Sagar, Jyotishree Pandey, Kuldeep Kumar, Aditya Pratap1, Narendra Pratap Singh and Meenal Rathore*. 2023. Genetic diversity and population structure analysis in popular cowpea (Vigna unguiculata (L.) Walp) cultivars. Indian J. Genet. Plant Breed., 83(1): 143-145.
Tribhuvan, Kishor U., Antara Das, Harsha Srivastava, Kuldeep Kumar, Kumar Durgesh, SV Amitha Mithra, Pradeep K. Jain, and Kishor Gaikwad. “Identification and characterization of PEBP family genes reveal CcFT8 a probable candidate for photoperiod insensitivity in C. cajan.” 3 Biotech 10, no. 5 (2020): 1-12.
Rohilla V, Yadav RK, Poonia A, Sheoran R, Kumari G, Shanmugavadivel PS, Pratap A. (2022) Association Mapping for Yield Attributing Traits and Yellow Mosaic Disease Resistance in Mung Bean [Vigna radiata(L.) Wilczek]. Front Plant Sci.12:749439. doi: 10.3389/fpls.2021.749439.
Kumari G, Roopa Lavanya G, Shanmugavadivel PS, Singh Y, Singh P, Patidar B, Madhavan L, Gupta S, Singh NP, Pratap A. (2021). Genetic diversity and population genetic structure analysis of an extensive collection of wild and cultivated Vigna accessions. Mol Genet Genomics. 296(6):1337-1353. doi: 10.1007/s00438-021-01825-7.
Kumari G, Shanmugavadivel PS, Lavanya GR, Tiwari P, Singh D, Gore PG, Tripathi K, Madhavan Nair R, Gupta S, Pratap A. (2022). Association mapping for important agronomic traits in wild and cultivated Vignaspecies using cross-species and cross-genera simple sequence repeat markers. Front Genet. 13:1000440. doi: 10.3389/fgene.2022.1000440.
Kushwah, N.S., Shanmugavadivel, P.S., Das, A., Rathore, M., Singh, A., Singh, N.P. (2022) Identification of oxalyl-CoA synthetase gene (LsAAE3) and its regulatory role in β-ODAP biosynthesis in grasspea (Lathyrus sativus L.). Journal of food legume, 35(1):27-40
Kushwah, N.S., Shanmugavadivel, P.S., Das, A., Rathore, Meenal., Singh, A., Singh, N.P. (2021)Identification of oxalyl-CoA synthetase gene (LsAAE3) and its regulatory role in β-ODAP biosynthesis in grasspea (Lathyrus sativus L.). BioRvix. DOI: 1101/2021.04.23.441068.
Soren KR, Madugula P, Kumar N, Barmukh R, Sengar MS, Bharadwaj C, Sharma PC, Singh S, Bhandari A, Singh J, Sanwal SK, Pal M, PR, SP, Mann A, Sagurthi SR, PS S, Siddique KH, Singh NP, Roorkiwal M, Varshney RK (2020) Genetic Dissection and Identification of Candidate Genes for Salinity Tolerance Using Axiom®CicerSNP Array in Chickpea. Int. J. Mol. Sci., 21, 5058.
Varshney, R. K., Roorkiwal, M., Sun, S., Bajaj, P., Chitikineni, A., Thudi, M. …Soren, K R & Liu, X. (2021). A chickpea genetic variation map based on the sequencing of 3,366 genomes. Nature, 1-6.

Ongoing Research Projects

Title	Funding Agency	PI
Development of early flowering chickpea genotype using CRISPR/Cas9 technology	SERB (DST)	Dr. Alok Das
CRISPR Crop Network: Targeted improvement of stress tolerance, nutritional quality and yield of crops by using genome editing	NASF (ICAR)	Dr Alok Das (Pigeonpea)
Functional characterization of the Cicer arietinum Short Vegetative Phase (SVP) genes, their promoters, and potential microRNAs regulating them towards elucidating their role in floral transition	DST-SERB	Dr. Aravind K Konda
Improving the nutritional quality of grasspea using the mutagenesis approach	DST-SERB	Dr. Neetu S Kushwah
Genomics, Genetic Engineering and New Breeding Technologies for Pulses Improvement	ICAR	Coordinator: Dr Meenal Rathore
Molecular mapping of heat stress tolerance QTLs and understanding heat stress induced transcriptome dynamics in chickpea (PI:)	ICAR	Dr.Shanmugavadivel P.S
Molecular diagnosis of Fusarium sp. infecting chickpea and pigeon pea	ICAR	Dr.Shanmugavadivel P.S
Molecular dissection of loci for Powdery Mildew Resistance and Photo-thermo insensitivity in Urdbean	ICAR	Mr.Sudhir Kumar Jha
Precision Plant Breeding and Rapid Generation Advancement in Chickpea	ICAR	Dr. Alok Das
Molecular approaches for improving the nutritional quality of grasspea (Lathyrus sativus L.)	ICAR	Dr. Neetu S Kushwah
Transforming Vigna for tolerance to whitefly (Bemisia tabaci) (PI :Dr M.Rathore)	ICAR	Dr Meenal Rathore
Gene Identification and development of triple gene technologies for pod borer resistance in transgenic chickpea.	ICAR	Dr. Aravinda K Konda
Identification of genes/QTLs for salinity tolerance in urdbean and earliness in Lentil	ICAR	Dr. Kuldeep Kumar