Publications
A Doorway to Pigeonpea (Cajanus cajan (L.) Millsp.) omics research
1.Muniswamy, S., Kumar, P., Saxena, R. K., & Varshney, R. K. (2022). Stability of Advanced Medium Duration Genotypes Across Seasons for Yield in Pigeonpea [Cajanus cajan (L.) Millsp.]. Indian Journal of Agricultural Research, 56(2).
2.Singh, A., & Singh, N. (2022). Recent Advances and Applicability of GBS, GWAS, and GS in Pigeon Pea. Genotyping by Sequencing for Crop Improvement, 295-305
3.Kinhoégbè, G., Djèdatin, G., Saxena, R. K., Chitikineni, A., Bajaj, P., Molla, J. & Varshney, R. K. (2022). Genetic diversity and population structure of pigeonpea (Cajanus cajan [L.] Millspaugh) landraces grown in Benin revealed by Genotyping-By-Sequencing. PloS one, 17(7), e0271565.
4.Liu, C., Tai, Y., Luo, J., Wu, Y., Zhao, X., Dong, R. & Liu, G. (2022). Integrated multi-omics analysis provides insights into the genome evolution and phosphorus deficiency adaptation in pigeonpea (Cajanus cajan). Horticulture Research.
https://doi.org/10.1093/hr/uhac107
1.Jain, N., Farhat, S., Kumar, R. et al. Alteration of proteome in germinating seedlings of piegonpea (Cajanus cajan) after salt stress. Physiol Mol Biol Plants 27, 2833–2848 (2021).
2.Singh, N., Narula, B., Ujinwal, M., & Langyan, S. (2021). Pigeonpea sterility mosaic virus a green plague-Current status of available drug and new potential targets. DOI:
3.Prabha, A., Avinashe, H., & Dubey, N. (2021). Collection of genomic tools for pigeon pea crop improvement.
1.Singh, N., Rai, V., & Singh, N. K. (2020). Multi-omics strategies and prospects to enhance seed quality and nutritional traits in pigeonpea. The Nucleus, 63(3), 249-256. DOI:
2.Obala J, Saxena RK, Singh VK, Kale SM, Garg V, et al. Seed protein content and its relationships with agronomic traits in pigeonpea is controlled by both main and epistatic efects QTLs. Sci Rep.2020;10:214.
3.Singh S, Mahato AK, Jayaswal PK, Singh N, Dheer M, et al. A 62 K genic-SNP chip array for genetic studies and breeding applications in pigeonpea (Cajanus cajan L. Millsp.). Sci Rep.2020;10:4960.
4.Wang H, Cimen E, Singh N, Buckler E. Deep learning for plant genomics and crop improvement. Curr Opin Plant Biol. 2020;54:34–41.
5.Sinha, P., Singh, V. K., Saxena, R. K., Khan, A. W., Abbai, R., Chitikineni, A.& Varshney, R. K. (2020). Superior haplotypes for haplotype‐based breeding for drought tolerance in pigeonpea (Cajanus cajan L.). Plant biotechnology journal, 18(12), 2482-2490.
6.Saxena, R. K., Hake, A., Hingane, A. J., Kumar, C. S., Bohra, A., Sonnappa, M., … & Varshney, R. K. (2020). Translational Pigeonpea Genomics Consortium for accelerating genetic gains in pigeonpea (Cajanus cajan L.). Agronomy, 10(9), 1289.
7.Sinha, P., Singh, V. K., Saxena, R. K., Kale, S. M., Li, Y., Garg, V., … & Varshney, R. K. (2020). Genome‐wide analysis of epigenetic and transcriptional changes associated with heterosis in pigeonpea. Plant biotechnology journal, 18(8), 1697-1710.
8.Bohra, A., Saxena, K.B., Varshney, R.K. et al. Genomics-assisted breeding for pigeonpea improvement. Theor Appl Genet 133, 1721–1737 (2020).
9.Saxena, R.K., Kale, S., Mir, R.R. et al. Genotyping-by-sequencing and multilocation evaluation of two interspecific backcross populations identify QTLs for yield-related traits in pigeonpea. Theor Appl Genet 133, 737–749 (2020).
https://doi.org/10.1007/s00122-019-03504-z
10.Marla SS, Mishra P, Maurya R, Singh M, Wankhede DP, Kumar A, Yadav MC, Subbarao N, Singh SK and Kumar R (2020). Refinement of Draft Genome Assemblies of Pigeonpea (Cajanus cajan). Front. Genet. 11:607432.
http://doi: 10.3389/fgene.2020.607432
1. Fuller DQ, Murphy C, Kingwell-Banham E, Castillo CC, Naik S. (2019). Cajanus cajan (L.) Millsp. origins and domestication: the South and Southeast Asian archaeobotanical evidence. Genet Resour Crop Evol.;66:1175–88.
2.Rathinam M, Mishra P, Vasudevan M, Budhwar R, Mahato A, Prabha AL, et al. (2019). Comparative transcriptome analysis of pigeonpea, Cajanus cajan (L.) and one of its wild relatives Cajanus platycarpus (Benth) Maesen. PLoS ONE.;14(7):e0218731.
3.Yadav P, Saxena KB, Hingane A, Kumar C, Kandalkar VS, Varshney RK, Saxena RK. (2019). An “Axiom Cajanus SNP Array” based high density genetic map and QTL mapping for high-selfng fower and seed quality traits in pigeonpea. BMC Genom.;20:235.
4.Obala, J., Saxena, R.K., Singh, V.K. et al. (2019). Development of sequence-based markers for seed protein content in pigeonpea. Mol Genet Genomics 294, 57–68.
5.Bohra, A. et al. (2019). Genomic Interventions to Improve Resilience of Pigeonpea in Changing Climate. In: Kole, C. (eds) Genomic Designing of Climate-Smart Pulse Crops. Springer, Cham.
6.Chanda Venkata, S. K., Nadigatla Veera Prabha Rama, G. R., Saxena, R. K., Saxena, K., Upadhyaya, H. D., Siambi, M., & Varshney, R. K. (2019). Pigeonpea improvement: An amalgam of breeding and genomic research. Plant Breeding, 138(4), 445-454.
DOI: 10.1111/pbr.12656
1.Saxena RK, Rathore A, Bohra A, Yadav P, Das RR, et al. (2018). Development and application of high-density Axiom®Cajanus SNP Array with 56 K SNPs to understand the genome architecture of released cultivars and founder genotypes for redefining future pigeonpea breeding programs. Plant Genome.;11:180005.
2.C Sudha Rani, C Sudhakar, Rachit K Saxena, Rajeev K Varshney and CV Sameer Kumar, P. S. (2018). Genetic variability and correlation in pigeonpea genotypes. Electronic Journal of Plant Breeding, 9(1), 343-349.
https://ejplantbreeding.org/index.php/EJPB/article/view/1790
3.Mahato, A. K., Sharma, A. K., Sharma, T. R., & Singh, N. K. (2018). An improved draft of the pigeonpea (Cajanus cajan (L.) Millsp.) genome. Data in brief, 16, 376-380.
4.Biswas, S., Biswas, A. K., & De, B. (2018). Metabolomics analysis of Cajanus cajan seedlings unravelled amelioration of stress induced responses to salinity after halopriming of seeds. Plant signaling & behavior, 13(7), e1489670.
https://doi.org/10.1080/15592324.2018.1489670
1.Arora S, Mahato AK, Singh S, Mandal P, Bhutani S, Dutta S, et al. (2017). A high-density intraspecifc SNP linkage map of pigeonpea (Cajanas cajan L Millsp). PLoS ONE.;12(6):0179747.
2.Krishnan HB, Natarajan SS, Oehrle NW, Garrett WM, Darwish O. (2017). Proteomic analysis of pigeonpea (Cajanus cajan) seeds reveals the accumulation of numerous stress-related proteins. J Agric Food Chem. 65:4572–81.
3.Saxena RK, Saxena RK, Obala J, Sinjushin A, Kumar CVS, Saxena KB, Varshney RK. (2017). Characterization and mapping of Dt1 locus which co-segregates with CcTFL1 for growth habit in pigeonpea. Theor Appl Genet.130(9):1773–84.
- https://doi.org/10.1007/ s00122-017-2924-2
4.Singh A, Sharma AK, Singh NK, Sharma TR. (2017). PpTFDB: a pigeonpea transcription factor database for exploring functional genomics in legumes. PLoS ONE.12(6):e0179736.
5.Varshney RK, Saxena RK, Upadhyaya HD, Khan AW, Yu Y, Kim C, et al.( 2017). Whole-genome resequencing of 292 pigeonpea accessions identifes genomic regions associated with domestication and agronomic traits. Nat Genet.49(7):1082–8.
- https://doi. org/10.1038/ng.3872
6.Saxena, R.K., Sameer Kumar, C.V., Bohra, A., Singh, I.P., Singh, N.P. and Varshney, R.K. (2017) Pigeonpea research for enhancing crop productivity. Pulse India, 2 (7). pp. 8-10.
7.Saxena, R.K., Varshney, R.K. (2017). Whole-Genome Sequencing of Pigeonpea: Requirement, Background History, Current Status and Future Prospects for Crop Improvement. In: Varshney, R., Saxena, R., Jackson, S. (eds) The Pigeonpea Genome. Compendium of Plant Genomes. Springer, Cham.
8.Pazhamala, L. T., Saxena, R. K., Purohit, S., Bajaj, P., Kumar, V., Garg, V., … & Varshney, R. K. (2017). Next generation sequencing based transcriptomic studies for crop improvement in pigeonpea.
9.Mir, R. R., Rather, I. A., Bhat, M. A., Parray, G. A., & Varshney, R. K. (2017). Molecular mapping of genes and QTLs in pigeonpea. In The Pigeonpea Genome (pp. 55-64). Springer, Cham.
DOI 10.1007/978-3-319-63797-6_6
10.Lekha T. Pazhamala, Shilp Purohit, Rachit K. Saxena, Vanika Garg, L. Krishnamurthy, Jerome Verdier, Rajeev K. Varshney (2017). Gene expression atlas of pigeonpea and its application to gain insights into genes associated with pollen fertility implicated in seed formation, Journal of Experimental Botany, Volume 68, Issue 8, Pages 2037–2054.
11.Saxena, R. K., Kale, S. M., Kumar, V., Parupali, S., Joshi, S., Singh, V.,& Varshney, R. K. (2017). Genotyping-by-sequencing of three mapping populations for identification of candidate genomic regions for resistance to sterility mosaic disease in pigeonpea. Scientific reports, 7(1), 1-10.
DOI:10.1038/s41598-017-01535-4
12.Mishra, P., Singh, S., Rathinam, M., Nandiganti, M., Ram Kumar, N., Thangaraj, A., & Sreevathsa, R. (2017). Comparative proteomic and nutritional composition analysis of independent transgenic pigeon pea seeds harboring cry1AcF and cry2Aa genes and their nontransgenic counterparts. Journal of agricultural and food chemistry, 65(7), 1395-1400.
DOI: 10.1021/acs.jafc.6b05301
1.Pazhamala LT, Agarwal G, Bajaj P, Kumar V, Kulshreshtha A, Saxena RK, et al. (2016). Deciphering transcriptional programming during pod and seed development using RNA-Seq in pigeonpea (Cajanus cajan). PLoS ONE.11(10):e0164959.
2.Kumar V, Khan AW, Saxena RK, Garg V, Varshney RK. (2016). First generation HapMap in Cajanus reveals untapped variations in parental lines of mapping populations. Plant Biotechnol J.14(8):1673–81.
1.Khoury CK, Castaneda-alvarez NP, Achicanoy HA, Sosa CC, Bernau V, Kassa MT, Norton SL, Maesen LJGVD, Upadhyaya HD, Ramirez-villegas J, et al. (2015). Crop wild relatives of pigeonpea [Cajanus cajan (L.) Millsp.]: distributions, ex situ conservation status, and potential genetic resources for abiotic stress tolerance. Biol Conserv. 184:259–70.
2.Singh N, Jain N, Kumar R, Jain A, Singh NK, Rai V. (2015). A comparative method for protein extraction and 2-D gel electrophoresis from diferent tissues of Cajanus cajan. Front Plant Sci.6:606.
3.Saxena, R. K., Saxena, K. B., Pazhamala, L. T., Patel, K., Parupalli, S., Sameerkumar, C. V., & Varshney, R. K. (2015). Genomics for greater efficiency in pigeonpea hybrid breeding. Frontiers in Plant Science, 6, 793.
doi: 10.3389/fpls.2015.00793
4.Ramalingam, A., Kudapa, H., Pazhamala, L. T., Weckwerth, W., & Varshney, R. K. (2015). Proteomics and metabolomics: two emerging areas for legume improvement. Frontiers in Plant Science, 6, 1116.
https://doi.org/10.3389/fpls.2015.01116
1.Singh, N. K., Gupta, D. K., Jayaswal, P. K., Mahato, A. K., Dutta, S., Singh, S., & Sharma, T. R. (2012). The first draft of the pigeonpea genome sequence. Journal of plant biochemistry and biotechnology, 21(1), 98-112.
2.Varshney, R., Chen, W., Li, Y. et al. (2012). Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers. Nat Biotechnol 30, 83–89.
https://doi.org/10.1038/nbt.2022