Career Status:
Postdoctoral Scholar

Research Areas:
Genetics, Genomics, Computational Biology

Publications

1. Obala, J., Saxena, R. K., Singh, V. K., Kale, S. M., Garg, V., Kumar, C. S., Saxena, K. B., Tongoona, P., Sibiya, J., Varshney, R. K. (2020): Seed protein content and its relationships with agronomic traits in pigeonpea is controlled by both main and epistatic effects QTLs. Scientific Reports, 10, 1-17.

2. Sinha, P., Singh, V. K., Saxena, R. K., Kale, S. M., Li, Y., Garg, V., Tang, M., Khan, A. W., Kim, K. D., Chitikineni, A., Saxena, K. B., Kumar, C. V. S., Liu, X., Xu, X., Jackson, S., Powell, W., Nevo, E., Searle, I. R., Lodha, M., Varshney, R. K. (2020): Genome-wide analysis of epigenetic and transcriptional changes associated with heterosis in pigeonpea. Plant Biotechnology Journal, doi: https://doi.org/10.1111/pbi.13333.

3. Khan, A. W., Garg, V., Roorkiwal, M., Golicz, A. A., Edwards, D., Varshney, R. K. (2019): Super-Pangenome by integrating the wild side of a species for accelerated crop improvement. Trends in Plant Science, 25, 148-158.

4. Garg, V., Khan, A. W., Kudapa, H., Kale, S. M., Chitikineni, A., Qiwei, S., Sharma, M., Li, C., Zhang, B., Liu, X., Kishor, P. B. K., Varshney, R. K. (2019): Integrated transcriptome, small RNA and degradome sequencing approaches provide insights into Ascochyta blight resistance in chickpea. Plant Biotechnology Journal, 17, 914-931.

5. Zhuang, W., Chen, H., Yang, M., Wang, J., Pandey, M. K., Zhang, C., Chang, W. C., Zhang, L., Zhang, X., Tang, R., Garg, V., Wang, X., Tang, H., Chow, C., Wang, J., Deng, Y., Wang, D., Khan, A. W., Yang, Q., Cai, T., Bajaj, P., Wu, K., Guo, B., Zhang, X., Li, J., Liang, F., Hu, J., Liao, B., Liu, S., Chitikineni, A., Yan, H., Zheng, Y., Shan, S., Liu, Q., Xie, D., Wang, Z., Khan, S. A., Ali, N., Zhao, C., Li, X., Luo, C., Zhang, S., Zhuang, R., Peng, Z., Wang, S., Mamadou, G., Zhuang, Y., Zhao, Z., Yu, W., Xiong, F., Quan, W., Yuan, M., Li, Y., Zou, H., Xia, H., Zha, L., Fan, J., Yu, J., Xie, W., Yuan, J., Chen, K., Zhao, S., Chu, W., Chen, Y., Sun, P., Meng, F., Zhuo, T., Zhao, Y., Li, C., He, G., Zhao, Y., Wang, C., Kishor, P. B. K., Pan, R., Paterson, A. H., Wang, X., Ming, R., Varshney, R. K. (2019): The genome of cultivated peanut provides insight into legume karyotypes, polyploid evolution and crop domestication. Nature Genetics, 51, 865-876.

6. Varshney, R. K., Thudi, M., Roorkiwal, M., He, W., Upadhyaya, H. D., Yang, W., Bajaj, P., Cubry, P., Rathore, A., Jian, J., Doddamani, D., Khan, A. W., Garg, V., Chitikineni, A., Xu, D., Gaur, P. M., Singh, N. P., Chaturvedi, S. K., Nadigatla, G. P. V. R., Krishnamurthy, L., Dixit, G. P., Fikre, A., Kimurto, P. K., Sreeman, S. M., Kishor, P. B. K., Penmetsa, R. V., Crossa, J., Nguyen, H. T., Siddique, K. H. M., Colmer, T. D., Sutton, T., Wettberg, E. V., Vigouroux, Y., Xu, X., Liu, X. (2019): Resequencing of 429 chickpea accessions from 45 countries provides insights into genome diversity, domestication and agronomic traits. Nature Genetics, 51, 857-864.

7. Jain, A., Roorkiwal, M., Kale, S., Garg, V., Yadala, R., Varshney, R. K. (2019): InDel markers: An extended marker resource for molecular breeding in chickpea. PLoS One, 14, e0213999.

8. Kudapa, H.#, Garg, V.#, Chitikineni, A., Varshney, R. K. (2018): The RNA-Seq-based high resolution gene expression atlas of chickpea (Cicer arietinum L.) reveals dynamic spatio-temporal changes associated with growth and development. Plant, Cell & Environment, 41, 2209-2225. (# Joint first authors)

9. Mashaki, K. M., Garg, V., Ghomi, A. A. N., Kudapa, H., Chitikineni, A., Nezhad, K. Z., Yamchi, A., Soltanloo, H., Varshney, R. K., Thudi, M. (2018): RNA-Seq analysis revealed genes associated with drought stress response in kabuli chickpea (Cicer arietinum L.). PLoS One, 13, e0199774.

10. Singh, S., Gupta, S. K., Thudi, M., Das, R. R., Vemula, A., Garg, V., Varshney, R. K., Rathore, A., Pahuja, S. K., Yadav, D. V. (2018): Genetic diversity patterns and heterosis prediction based on SSRs and SNPs in hybrid parents of Pearl millet. Crop Science, 58, 2379-2390.

11. Roorkiwal, M., Jarquin, D., Singh, M. K., Gaur, P. M., Bharadwaj, C., Rathore, A., Howard, R., Srinivasan, S., Jain, A., Garg, V., Kale, S., Chitikineni, A., Tripathi, S., Jones, E., Robbins, K. R., Crossa, J., Varshney, R. K. (2018): Genomic-enabled prediction models using multi-environment trials to estimate the effect of genotype × environment interaction on prediction accuracy in chickpea. Scientific Reports, 8, 11701.

12. Khedikar, Y., Pandey, M. K., Sujay, V., Singh, S., Nayak, S. N., Klein-Gebbinck, H. W., Sarvamangala, C., Mukri, G., Garg, V., Upadhyaya, H. D., Nadaf, H. L., Gowda, M. V. C., Varshney, R. K., Bhat, R. S. (2018): Identification of main effect and epistatic quantitative trait loci for morphological and yield-related traits in peanut (Arachis hypogaea L.). Molecular Breeding, 38, 7.

13. Garg, V., Agarwal, G., Pazhamala, L. T., Nayak, S. N., Kudapa, H., Khan, A. W., Doddamani, D., Sharma, M., Kishor, P. B. K., Varshney, R. K. (2017): Genome-wide identification, characterization, and expression analysis of small RNA biogenesis purveyors reveal their role in regulation of biotic stress responses in three legume crops. Frontiers in Plant Science, 8, 488.

14. Varshney, R. K., Shi, C., Thudi, M., Mariac, C., Wallace, J., Qi, P., Zhang, H., Zhao, Y., Wang, X., Rathore, A., Srivastava, R. K., Chitikineni, A., Fan, G., Bajaj, P., Punnuri, S., Gupta, S. K., Wang, H., Jiang, Y., Couderc, M., Katta, M. A. V. S. K., Paudel, D. R., Mungra, K. D., Chen, W., Harris-Shultz, K. R., Garg, V., Desai, N., Doddamani, D., Kane, N. A., Conner, J. A., Ghatak, A., Chaturvedi, P., Subramaniam, S., Yadav, O. P., Berthouly-Salazar, C., Hamidou, F., Wang, J., Liang, X., Clotault, J., Upadhyaya, H. D., Cubry, P., Rhoné, B., Gueye, M. C., Sunkar, R., Dupuy, C., Sparvoli, F., Cheng, S., Mahala, R. S., Singh, B., Yadav, R. S., Lyons, E., Datta, S. K., Hash, C. T., Devos, K. M., Buckler, E., Bennetzen, J. L., Paterson, A. H., Ozias-Akins, P., Grando, S., Wang, J., Mohapatra, T., Weckwerth, W., Reif, J. C., Liu, X., Vigouroux, Y., Xu, X. (2017): Pearl millet genome sequence provides a resource to improve agronomic traits in arid environments. Nature Biotechnology, 35, 969-976.

15. Pazhamala, L. T., Purohit, S., Saxena, R. K., Garg, V., Krishnamurthy, L., Verdier, J., Varshney, R. K. (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, 68, 2037-2054.

16. Vishwakarma, M. K., Kale, S. M., Sriswathi, M., Naresh, T., Shasidhar, Y., Garg, V., Pandey, M. K., Varshney, R. K. (2017): Genome-wide discovery and deployment of insertions and deletions markers provided greater insights on species, genomes, and sections relationships in the genus Arachis. Frontiers in Plant Science, 8, 2064.

17. Pandey, M. K., Khan, A. W., Singh, V. K., Vishwakarma, M. K., Shasidhar, Y., Kumar, V., Garg, V., Bhat, R. S., Chitikineni, A., Janila, P., Guo, B., Varshney, R. K. (2017): QTL-seq approach identified genomic regions and diagnostic markers for rust and late leaf spot resistance in groundnut (Arachis hypogaea L.). Plant Biotechnology Journal, 15, 927-941.

18. Saxena, R. K., Singh, V. K., Kale, S. M., Tathineni, R., Parupalli, S., Kumar, V., Garg, V., Das, R. R., Sharma, M., Yamini, K. N., Muniswamy, S., Ghanta, A., Rathore, A., Kumar, C. V. S., Saxena, K. B., Kishor, P. B. K., Varshney, R. K. (2017): Construction of genotyping-by-sequencing based high-density genetic maps and QTL mapping for fusarium wilt resistance in pigeonpea. Scientific Reports, 7, 1911.

19. Saxena, R. K., Kale, S. M., Kumar, V., Parupalli, S., Joshi, S., Singh, V. K., Garg, V., Das, R. R., Sharma, M., Yamini, K. N., Ghanta, A., Rathore, A., Kumar, C. V. S., Saxena, K. B., 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, 1813.

20 . Agarwal, G., Garg, V., Kudapa, H., Doddamani, D., Pazhamala, L. T., Khan, A. W., Thudi, M., Lee, S., Varshney, R. K. (2016): Genome-wide dissection of AP2/ERF and HSP90 gene families in five legumes and expression profiles in chickpea and pigeonpea. Plant Biotechnology Journal, 14, 1563-1577.

21. Singh, V. K., Khan, A. W., Jaganathan, D., Thudi, M., Roorkiwal, M., Takagi, H., Garg, V., Kumar, V., Chitikineni, A., Gaur, P. M., Sutton, T., Terauchi, R., Varshney, R. K. (2016): QTL-seq for rapid identification of candidate genes for 100-seed weight and root/total plant dry weight ratio under rainfed conditions in chickpea. Plant Biotechnology Journal, 14, 2110-2119.

22. Chen, X., Li, H., Pandey, M. K., Yang, Q., Wang, X., Garg, V., Li, H., Chi, X., Doddamani, D., Hong, Y., Upadhyaya, H. D., Guo, H., Khan, A. W., Zhu, F., Zhang, X., Pan, L., Pierce, G. J., Zhou, G., Katta, M. A. V. S. K., Chen, M., Zhong, N., Agarwal, G., Li, S., Chitikineni, A., Zhang, G., Sharma, S., Chen, N., Liu, H., Janila, P., Li, S., Wang, M., Wang, T., Sun, J., Li, X., Li, C., Wang, M., Yu, L., Wen, S., Singh, S., Yang, Z., Zhao, J., Zhang, C., Yu, Y., Bi, J., Zhang, X., Liu, Z., Paterson, A. H., Wang, S., Liang, X., Varshney, R. K., Yu, S. (2016): Draft genome of the peanut A-genome progenitor (Arachis duranensis) provides insights into geocarpy, oil biosynthesis, and allergens. Proceedings of the National Academy of Sciences (PNAS), 113, 6785-6790.

23.Kumar, V., Khan, A. W., Saxena, R. K., Garg, V., Varshney, R. K. (2016): First-generation HapMap in Cajanus spp. reveals untapped variations in parental lines of mapping populations. Plant Biotechnology Journal, 14, 1673-1681.

24. Singh, V. K., Khan, A. W., Saxena, R. K., Kumar, V., Kale, S. M., Sinha, P., Chitikineni, A., Pazhamala, L. T., Garg, V., Sharma, M., Kumar, C. V. S., Parupalli, S., Vechalapu, S., Patil, S., Muniswamy, S., Ghanta, A., Yamini, K. N., Dharmaraj, P. S., Varshney, R. K. (2016): Next-generation sequencing for identification of candidate genes for Fusarium wilt and sterility mosaic disease in pigeonpea (Cajanus cajan). Plant Biotechnology Journal, 14, 1183-1194.

25. Thudi, M., Khan, A. W., Kumar, V., Gaur, P. M., Katta, M. A. V. S. K., Garg, V., Roorkiwal, M., Samineni, S., Varshney, R. K. (2016): Whole genome re-sequencing reveals genome-wide variations among parental lines of 16 mapping populations in chickpea (Cicer arietinum L.). BMC Plant Biology, 16, 10.

26. Ramalingam, A., Kudapa, H., Pazhamala, L. T., Garg, V., Varshney, R. K. (2015): Gene expression and Yeast two-hybrid studies of 1R-MYB transcription factor mediating drought stress response in chickpea (Cicer arietinum L.). Frontiers in Plant Science, 6, 1117.

27. Kale, S. M., Jaganathan, D., Ruperao, P., Chen, C., Punna, R., Kudapa, H., Thudi, M., Roorkiwal, M., Katta, M. A. V. S. K., Doddamani, D., Garg, V., Kishor, P. B. K., Gaur, P. M., Nguyen, H. T., Batley, J., Edwards, D., Sutton, T., Varshney, R. K. (2015): Prioritization of candidate genes in “QTL-hotspot” region for drought tolerance in chickpea (Cicer arietinum L.). Scientific Reports, 5, 15296.

28. Gupta, S., Garg, V., Kant, C., Bhatia, S. (2015): Genome-wide survey and expression analysis of F-box genes in chickpea. BMC Genomics, 16, 67.

29. 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, 10, e0121100.

30. 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.

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