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# Corrosponding Author; * Equal Contribution; ^Student/postdoc author

2024

  • Devkar V^*, Dagostino L^*, Kshetry AO^, Yong L, Nadaf AB, Thirumlaikumar VP, Skirycz A, Ma J, Stupar R, Herrera Estrella L, Deshmukh R, Patil GB#. Identification of cell-type-specific response to silicon treatment in soybean leaves through single nucleus RNA-sequencing. bioRxiv. 2024:2024-04.
  • Dhingra A^, Dagostino L^, Devkar V^, Shinde H, Rajurkar A, Sonah H, Vuong T, Siebecker M, Jiao Y, Hancock N, Nguyen H, Deshmukh R, Patil GB# (2024) Identification of Novel Germplasm and Genetic Loci for Enhancing Mineral Element Uptake in Soybean. Environmental and Experimental Botany. https://doi.org/10.1016/j.envexpbot.2023.105643  

2023

  • Vats S, Kumar V, Mandlik R, Patil G, Sonah H, Roy J, Sharma TR, Deshmukh R (2023) Reference Guided De Novo Genome Assembly of Transformation Pliable S. lycopersicum cv. Pusa Ruby. Genes. 14(3) :570. https://doi.org/10.3390/genes14030570  
  • Vats S, Shivaraj SM, Sonah H, Patil G, Roy J, Sharma TR, Deshmukh R (2023). Efficient Regeneration and Agrobacterium-Mediated Transformation Method for Cultivated and Wild Tomato. Plant Molecular Biology Reporter. 7:1-2. https://doi.org/10.1007/s11105-023-01374-w  
  • D’Agostino LW ^, Yong-Villalobos L ^, Herrera-Estrella L, Patil GB# (2023) Development of High-Quality Nuclei Isolation to Study Plant Root–Microbe Interaction for Single-Nuclei Transcriptomic Sequencing in Soybean. Plants. 2023 12(13):2466. https://doi.org/10.3390/plants12132466  
  • Thakral V, Sharma Y, Mandlik R, Patil G, Sonah H, Isenring P, Bélanger R, Sharma R, Deshmukh R (2023) Identification of VrNIP2-1 aquaporin with novel selective filter regulating the transport of beneficial as well as hazardous metalloids in mungbean. Plant Physiology and Biochemistry https://doi.org/10.1016/j.plaphy.2023.108057  
  • Saini DK, Impa SM, McCallister D, Patil GB, Abidi N, Ritchie G, Jaconis SY, Jagadish KS (2023) High day and night temperatures impact on cotton yield and quality – current status and future research direction. J Cotton Res. 6(1):1-7. 
  • Nwoko L^, Ojha AK^, Devkar V ^, Patil GB# (2023) An Improved Method for Protoplast Isolation and Gene-Editing from Soybean Root, Callus and Transgenic Hairy-Roots. J Plant Biol Crop Res.; 6(2): 1088. 

2022

  • Patil GB#, Stupar RM, Zhang F (2022) Protoplast isolation, transfection and gene editing for soybean (Glycine max) In Protoplast Technology: Methods in Molecular Biology, vol 2464. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2164-6_13.
  • Rana N, Kumawat S, Kumar V, Bansal R; Mandlik R; Dhiman P; Patil GB; Deshmukh R, Sharma T, Sonah H (2022) Deciphering haplotypic variation and gene expression dynamics associated with nutritional and cooking quality in rice. Cells (ISSN 2073-4409)

2021

  • Nitnaware KM, Raskar KB, Agarwal G, Chávez Montes R, Chopra R, Arredondo DL, Nikam TD, Patil GB# (2021) Whole-genome characterization and comparative genomics of a novel freshwater cyanobacteria species: Pseudanabaena punensis. Molecular Phylogenetics and Evolution. 107272doi.org/10.1016/j.ympev.2021.107272.
  • Deshmukh R, Rana N, Liu Y, Zeng S, Agarwal G, Sonah H, Varshney R, Joshi T, Nguyen HT, Patil GB# (2021) Soybean transporter database: A comprehensive database for identification and exploration of natural variants in soybean transporter genes. Physiologia Plantarum. 171(4):756-70.
  • Vuong TD, Sonah H, Patil G, Meinhardt C, Usovsky M, Kim KS, Belzile F, Li Z, Robbins R, Shannon JG, Nguyen HT (2021) Identification of genomic loci conferring broad-spectrum resistance to multiple nematode species in exotic soybean accession PI 567,305. Theoretical and Applied Genetics 23:1-7.
  • Thakral V, Bhat JA, Kumar N, Myaka B, Sudhakaran S, Patil G, Sonah H, Shivaraj SM, Deshmukh R (2021) Role of silicon under contrasting biotic and abiotic stress conditions provides benefits for climate smart cropping. Environmental and Experimental Botany. 9:104545 doi.org/10.1016/j.envexpbot.2021.104545
  • Bayer PE, Valliyodan B, Hu H, Marsh JI, Yuan Y, Vuong TD, Patil G, Song Q, Batley J, Varshney RK, Lam HM, Nguyen HT (2021) Sequencing the USDA core soybean collection reveals gene loss during domestication and breeding. The Plant Genome. e20109. doi.org/10.1002/tpg2.20109
  • Usovsky M, Lakhssassi N, Patil GB, Vuong TD, Piya S, Hewezi T, Robbins RT, Stupar RM, Meksem K, Nguyen HT (2021) Dissecting nematode resistance regions in soybean revealed pleiotropic effect of soybean cyst and reniform nematode resistance genes. The Plant Genome. 16:e20083.
  • Zhang F, Stupar RM, Voytas DF, Patil G (2021) Inventors; University of Minnesota, assignee. Methods for genetic transformation and genome modification in legumes. United States Patent Application US 16/913,478. 2021 Feb 18.
  • Valliyodan B, Brown AV, Wang J, Patil GB*, Liu Y, Otyama PI, Nelson RT, Vuong T, Song Q, Musket TA, Wagner R (2021) Genetic variation among 481 diverse soybean accessions, inferred from genomic re-sequencing. Scientific Data. 8;8(1):1-9. [Equal Contributing Author]
  • Usovsky M, Ye H, Vuong TD, Patil GB, Wan J, Zhou L, Nguyen HT (2021) Fine-mapping and characterization of qSCN18, a novel QTL controlling soybean cyst nematode resistance in PI 567516C. Theoretical and Applied Genetics 134(2):621-31.

2020

  • Graham N, Patil GB, Bubeck D, Dobert R, Glenn K, Gutsche A, Kumar S, Lindbo J, Maas L, May G, Vega-Sanchez M, Stupar R, Morrell P (2019)Genome editing in dynamic genetic background: the relevance of “Off-Target” edits in plants Plant Physiology. doi.org/10.1104/pp.19.01194
  • Lakhssassi N, Zhou Z, Liu S, Piya S, Cullen MA, El Baze A, Knizia D, Patil GB, Badad O, Embaby MG, Meksem J (2020) Soybean TILLING-by-sequencing+ reveals the role of novel GmSACPD members in the unsaturated fatty acid biosynthesis while maintaining healthy nodule. Journal of Experimental Botany doi.org/10.1093/jxb/eraa402
  • Usovsky M, Ye H, Vuong TD, Patil GB, Wan J, Zhou L, Nguyen HT (2020). Fine-mapping and characterization of qSCN18, a novel QTL controlling soybean cyst nematode resistance in PI 567516C. Theoretical and Applied Genetics.
  • Kumar N, Kumawat S, Khatri P, Singla P, Tandon G, Bhatt V, Shinde S, Patil GB, Sonah H, Deshmukh R (2020) Understanding aquaporin transport system in highly stress-tolerant and medicinal plant species Jujube (Ziziphus jujuba Mill.). Journal of Biotechnology. 20;324:103-11.
  • Agarwal G, Kudapa H, Ramalingam A, Choudhary D, Sinha P, Garg V, Singh VK, Patil GB, Pandey MK, Nguyen HT, Guo B (2020) Epigenetics and epigenomics: underlying mechanisms, relevance, and implications in crop improvement. Functional & Integrative Genomics. 20, 739–761.

2019

  • Patil, G., Lakhssassi, N., Wan, J., Song, L., Zhou, Z., Klepadlo, M., Vuong, T.D., Stec, A.O., Kahil, S.S., Colantonio, V. and Valliyodan, B., (2019) Whole‐genome re‐sequencing reveals the impact of the interaction of copy number variants of the rhg1 and Rhg4 genes on broad‐based resistance to soybean cyst nematode. Plant Biotechnology Journal, 17(8), pp.1595-1611.
  • Vats, S., Kumawat, S., Kumar, V., Patil, G.B., Joshi, T., Sonah, H., Sharma, T.R. and Deshmukh, R., (2019) Genome Editing in Plants: Exploration of Technological Advancements and Challenges. Cells, 8(11), p.1386.
  • Valliyodan, B., Cannon, [..]  Patil G., et al. (2019) Construction and comparison of three reference‐quality genome assemblies for soybean. The Plant Journal, 100(5), pp.1066-1082.
  • Lakhssassi, N., Patil, G*., Piya, S., Zhou, Z., Baharlouei, A., Kassem, M.A., Lightfoot, D.A., Hewezi, T., Barakat, A., Nguyen, H.T. and Meksem, K., (2019) Genome reorganization of the GmSHMT gene family in soybean showed a lack of functional redundancy in resistance to soybean cyst nematode. Scientific Reports, 9(1), pp.1-16.
  • Anderson, E.J., Ali, M.L., [..] Patil, G., et al. (2019) Soybean [Glycine max (L.) Merr.] Breeding: History, Improvement, Production and Future Opportunities. In Advances in Plant Breeding Strategies: Legumes (pp. 431-516) Springer, Cham.
  • Vishwakarma, K., Mishra, M., Patil, G., Mulkey, S., Ramawat, N., Pratap Singh, V., Deshmukh, R., Kumar Tripathi, D., Nguyen, H.T. and Sharma, S., (2019) Avenues of the membrane transport system in adaptation of plants to abiotic stresses. Critical Reviews in Biotechnology, 39(7), pp.861-883.
  • Chaudhary, J., Shivaraj, S.M., Khatri, P., Ye, H., Zhou, L., Klepadlo, M., Dhakate, P., Kumawat, G., Patil, G., Sonah, H. and Ratnaparkhe, M., (2019) Approaches, Applicability, and Challenges for Development of Climate-Smart Soybean. In Genomic Designing of Climate-Smart Oilseed Crops (pp. 1-74) Springer, Cham.
  • Do, T.D., Vuong, T.D., Dunn, D., Clubb, M., Valliyodan, B., Patil, G., Chen, P., Xu, D., Nguyen, H.T. and Shannon, J.G., (2019) Identification of new loci for salt tolerance in soybean by high-resolution genome-wide association mapping. BMC Genomics, 20(1), p.318.

2018

  1. Patil, G., Vuong, T.D., Kale, S., Valliyodan, B., Deshmukh, R., Zhu, C., Wu, X., Bai, Y., Yungbluth, D., Lu, F. and Kumpatla, S., (2018) Dissecting genomic hotspots underlying seed protein, oil, and sucrose content in an interspecific mapping population of soybean using high‐density linkage mapping. Plant Biotechnology Journal, 16(11), pp.1939-1953.
  • Kulkarni, K.P., Patil, G*., Valliyodan, B., Vuong, T.D., Shannon, J.G., Nguyen, H.T. and Lee, J.D., (2018) Comparative genome analysis to identify SNPs associated with high oleic acid and elevated protein content in soybean. Genome, 61(3), pp.217-222.
  • Klepadlo, M., Meinhardt, C.G., Vuong, T.D., Patil, G., Bachleda, N., Ye, H., Robbins, R.T., Li, Z., Shannon, J.G., Chen, P. and Meksem, K., (2018) Evaluation of soybean germplasm for resistance to multiple nematode species: Heterodera glycines, Meloidogyne incognita, and Rotylenchulus reniformis. Crop Science, 58(6), pp.2511-2522.
  • Do, T.D., Vuong, T.D., Dunn, D., Smothers, S., Patil, G., Yungbluth, D.C., Chen, P., Scaboo, A., Xu, D., Carter, T.E. and Nguyen, H.T., (2018) Mapping and confirmation of loci for salt tolerance in a novel soybean germplasm, Fiskeby III. Theoretical and applied genetics, 131(3), pp.513-524.

2017

  • Patil, G., Mian, R., Vuong, T., Pantalone, V., Song, Q., Chen, P., Shannon, G.J., Carter, T.C. and Nguyen, H.T., (2017) Molecular mapping and genomics of soybean seed protein: a review and perspective for the future. Theoretical and Applied Genetics, 130(10), pp.1975-1991.
  • Patil, G., Chaudhary, J., Vuong, T.D., Jenkins, B., Qiu, D., Kadam, S., Shannon, G.J. and Nguyen, H.T., (2017) Development of SNP genotyping assays for seed composition traits in soybean. International journal of plant genomics
  • Cheng, P., Gedling, C.R., Patil, G., Vuong, T.D., Shannon, J.G., Dorrance, A.E. and Nguyen, H.T., (2017) Genetic mapping and haplotype analysis of a locus for quantitative resistance to Fusarium graminearum in soybean accession PI 567516C. Theoretical and applied genetics, 130(5), pp.999-1010.

2016

  1. Patil, G., Do, T., Vuong, T.D., Valliyodan, B., Lee, J.D., Chaudhary, J., Shannon, J.G. and Nguyen, H.T., (2016) Genomic-assisted haplotype analysis and the development of high-throughput SNP markers for salinity tolerance in soybean. Scientific Reports, 6(1), pp.1-13.
  • Valliyodan, B., Qiu, D., Patil, G*., Zeng, P., Huang, J., Dai, L., Chen, C., Li, Y., Joshi, T., Song, L. and Vuong, T.D., 2016. Landscape of genomic diversity and trait discovery in soybean. Scientific reports, 6, p.23598.
  • Chen, W., Yao, Q., Patil, G.B*., Agarwal, G., Deshmukh, R.K., Lin, L., Wang, B., Wang, Y., Prince, S.J., Song, L. and Xu, D., (2016) Identification and comparative analysis of differential gene expression in soybean leaf tissue under drought and flooding stress revealed by RNA-Seq. Frontiers in plant science, 7, p.1044.
  • Kadam, S., Vuong, T.D., Qiu, D., Meinhardt, C.G., Song, L., Deshmukh, R., Patil, G., Wan, J., Valliyodan, B., Scaboo, A.M. and Shannon, J.G., (2016) Genomic-assisted phylogenetic analysis and marker development for next generation soybean cyst nematode resistance breeding. Plant Science, 242, pp.342-350.
  • Song, L., Nguyen, N., Deshmukh, R.K., Patil, G.B., Prince, S.J., Valliyodan, B., Mutava, R., Pike, S.M., Gassmann, W. and Nguyen, H.T., (2016) Soybean TIP gene family analysis and characterization of GmTIP1; 5 and GmTIP2; 5 water transport activity. Frontiers in plant science, 7, p.1564.
  • Asekova, S., Kulkarni, K.P., Patil, G., Kim, M., Song, J.T., Nguyen, H.T., Shannon, J.G. and Lee, J.D., (2016) Genetic analysis of shoot fresh weight in a cross of wild (G. soja) and cultivated (G. max) soybean. Molecular Breeding, 36(7), p.103.
  • Sonah, H., Chavan, S., Katara, J., Chaudhary, J., Kadam, S., Patil, G. and Deshmukh, R., (2016) Genome-wide identification and characterization of Xylanase Inhibitor Protein (XIP) genes in cereals. Indian J. Genet. Plant Breed, 76, pp.159-166.

2015

  1. Patil, G., Valliyodan, B., Deshmukh, R., Prince, S., Nicander, B., Zhao, M., Sonah, H., Song, L., Lin, L., Chaudhary, J. and Liu, Y., (2015) Soybean (Glycine max) SWEET gene family: insights through comparative genomics, transcriptome profiling and whole genome re-sequence analysis. BMC Genomics, 16(1), p.520.
  • Syed, N.H., Prince, S.J., Mutava, R.N., Patil, G*., Li, S., Chen, W., Babu, V., Joshi, T., Khan, S. and Nguyen, H.T., (2015) Core clock, SUB1, and ABAR genes mediate flooding and drought responses via alternative splicing in soybean. Journal of Experimental Botany, 66(22), pp.7129-7149.
  • Chaudhary, J., Patil, G.B., Sonah, H., Deshmukh, R.K., Vuong, T.D., Valliyodan, B. and Nguyen, H.T., (2015) Expanding omics resources for improvement of soybean seed composition traits. Frontiers in Plant Science, 6, p.1021.
  • Prince, S.J., Song, L., Qiu, D., dos Santos, J.V.M., Chai, C., Joshi, T., Patil, G., Valliyodan, B., Vuong, T.D., Murphy, M. and Krampis, K., (2015) Genetic variants in root architecture-related genes in a Glycine soja accession, a potential resource to improve cultivated soybean. BMC genomics, 16(1), p.132.
  • Prince, S.J., Joshi, T., Mutava, R.N., Syed, N., Vitor, M.D.S.J., Patil, G., Song, L., Wang, J., Lin, L., Chen, W. and Shannon, J.G., (2015) Comparative analysis of the drought-responsive transcriptome in soybean lines contrasting for canopy wilting. Plant Science, 240, pp.65-78.
  • Chen, W., He, S., Liu, D., Patil, G.B., Zhai, H., Wang, F., Stephenson, T.J., Wang, Y., Wang, B., Valliyodan, B. and Nguyen, H.T., 2015. A sweetpotato geranylgeranyl pyrophosphate synthase gene, IbGGPS, increases carotenoid content and enhances osmotic stress tolerance in Arabidopsis thaliana. PLoS One, 10(9)

2014

  1. Deshmukh, R., Sonah, H., Patil, G., Chen, W., Prince, S., Mutava, R., Vuong, T., Valliyodan, B. and Nguyen, H.T., (2014) Integrating omic approaches for abiotic stress tolerance in soybean. Frontiers in Plant science, 5, p.244.

2013

  • Patil G, Nicander B. Identification of two additional members of the tRNA isopentenyltransferase family in Physcomitrella patens. Plant Molecular Biology. 2013 Jul 1;82(4-5):417-26.

2009

  • Patil, G., Deokar, A., Jain, P.K., Thengane, R.J. and Srinivasan, R., (2009) Development of a phosphomannose isomerase-based Agrobacterium-mediated transformation system for chickpea (Cicer arietinum L.) Plant Cell Reports, 28(11), pp.1669-1676.
  • Patil G, Patel R, Jaat R, Pattanayak A, Jain P, Srinivasan R. (2009) Glutamine improves shoot morphogenesis in chickpea (Cicer arietinum L.) Acta Physiologiae Plantarum. 1;31(5):1077-84.