Publications
2024
Liu D, Myers EA, Xuan S, Prichard LE, Donahue LI, Ellison EE, Starker CG, Voytas DF. Heritable, multinucleotide deletions in plants using viral delivery of a repair exonuclease and guide RNAs. Plant Physiol. 2024 Jan 18:kiae015. doi: 10.1093/plphys/kiae015. Epub ahead of print. PMID: 38243587.
Forthcoming
Forthcoming
Forthcoming
2023
Chamness JC, Kumar J, Cruz AJ, Rhuby E, Holum MJ, Cody JP, Tibebu R, Gamo ME, Starker CG, Zhang F, Voytas DF. An extensible vector toolkit and parts library for advanced engineering of plant genomes. (2023) Plant Genome. 2023 Mar 9:e20312. doi: 10.1002/tpg2.20312. PMID: 36896468.
Cody JP, Maher MF, Nasti RA, Starker CG, Chamness JC, Voytas DF. Direct delivery and fast-treated Agrobacterium co-culture (Fast-TrACC) plant transformation methods for Nicotiana benthamiana. (2023) Nat Protoc. 18(1):81-107. doi: 10.1038/s41596-022-00749-9. PMID: 36253612.
Yu, Y., Hu, H., Voytas, D.F., Doust, A.N. and Kellogg, E.A. The YABBY gene SHATTERING1 controls activation rather than patterning of the abscission zone in Setaria viridis. (2023) New Phytol, 240: 846-862.
2022
Degao Liu, Shuya Xuan, Lynn E Prichard, Lilee Donahue, Changtian Pan, Ugrappa Nagalakshmi, Evan E Ellison, Colby G Starker, Savithramma P Dinesh-Kumar, Yiping Qi, Daniel F Voytas, Heritable base-editing in Arabidopsis using RNA viral vectors, Plant Physiology, 2022.
Nagalakshmi U, Meier N, Liu JY, Voytas DF, Dinesh-Kumar SP. High-efficiency multiplex biallelic heritable editing in Arabidopsis using an RNA virus. Plant Physiol, 2022. PMID: 35389493.
Cody JP, Maher MF, Nasti RA, Starker CG, Chamness JC, Voytas DF. (2022) Direct delivery and fast-treated Agrobacterium co-culture (Fast-TrACC) plant transformation methods for Nicotiana benthamiana. Nature Protocols [Preprint].
Voytas, Dan. Potential of Genome Editing on Climate Adaptation and Mitigation. Supporters of Agricultural Research (SoAR) Foundation, 2022. https://supportagresearch.org/our-projects/potential-impacts-of-genome-editing-climate-adaptation-mitigation.
2021
Ellison, E. E., Chamness, J. C., Voytas, D. F. (2021) ‘Viruses as vectors for the delivery of gene editing reagents’ in Genome editing for precision crop breeding (ed. Dr Matthew Willmann).
Atkins PAP, Gamo MES, Voytas DF. Analyzing Plant Gene Targeting Outcomes and Conversion Tracts with Nanopore Sequencing. International Journal of Molecular Sciences. 2021; 22(18):9723.
Nasti R, Zinselmeier M, Vollbrecht M, Maher M, Voytas D. (2021) Fast-TrACC: A Rapid Method for Delivering and Testing Gene Editing Reagents in Somatic Plant Cells. Frontiers in Genome Editing. 2:32.
Nasti RA, Voytas DF. Attaining the promise of plant gene editing at scale. Proc Natl Acad Sci U S A. 2021 Jun 1;118(22):e2004846117. doi: 10.1073/pnas.2004846117. Epub 2021 Apr 30. PMID: 34050019.
Cable J, Ronald PC, Voytas D, Zhang F, Levy AA, Takatsuka A, Arimura SI, Jacobsen SE, Toki S, Toda E, Gao C, Zhu JK, Boch J, Van Eck J, Mahfouz M, Andersson M, Fridman E, Weiss T, Wang K, Qi Y, Jores T, Adams T, Bagchi R. Plant genome engineering from lab to field-a Keystone Symposia report. Ann N Y Acad Sci. 2021 Aug 25. doi: 10.1111/nyas.14675. Epub ahead of print. PMID: 34435370.
Arjun Khakhar, Cecily Wang, Ryan Swanson, Sydney Stokke, Furva Rizvi, Surbhi Sarup, John Hobbs, Daniel F Voytas, VipariNama: RNA viral vectors to rapidly elucidate the relationship between gene expression and phenotype. Plant Physiology, 2021; 186(4): 2222–2238.
2020
Atkins, P.A., Voytas, D.F. (2020) Overcoming bottlenecks in plant gene editing. Curr Opin Plant Biol. 54:79‐84.
Ellison EE, Nagalakshmi U, Gamo ME, Huang PJ, Dinesh-Kumar S, Voytas DF. (2020) Multiplexed heritable gene editing using RNA viruses and mobile single guide RNAs. Nat. Plants. 6:620–624 (2020).
Maher, M.F., Nasti, R.A., Vollbrecht, M., Starker, C.G., Clark, M.D., Voytas, D.F. (2020) Plant gene editing through de novo induction of meristems. Nat Biotechnol. 38, pp. 84–89
Dinesh-Kumar, S.P., Voytas, D.F. Editing through infection. Nat. Plants (2020).
Khakhar, A., Starker, C.G., Chamness, J.C., Lee, N., Stokke, S., Wang, C., Swanson, R., Rizvi, F., Imaizumi, T., Voytas, D.F. (2020) Building customizable auto-luminescent luciferase-based reporters in plants. Elife. 9:e52786.
Weiss, T., Wang, C., Kang, X., Zhao, H., Gamo, M.E., Starker, C.G., Crisp, P.A., Zhou, P., Springer, N.M., Voytas, D.F., et al. (2020). Optimization of multiplexed CRISPR/Cas9 system for highly efficient genome editing in Setaria viridis. Plant J.
2019
Mei, Y., Beernink, B., Ellison, E., Konečná, E., Neelakandan, A.K., Voytas, D.F., Whitham, S.A. (2019) Protein expression and gene editing in monocots using foxtail mosaic virus vectors. Plant Direct. 3(11): e00181.
Nadakuduti SS, Starker CG, Ko DK, Jayakody TB, Buell CR, Voytas DF, Douches DS. (2019) Evaluation of Methods to Assess in vivo Activity of Engineered Genome-Editing Nucleases in Protoplasts. Front Plant Sci. 10:110.
Nadakuduti SS, Starker CG, Voytas DF, Buell CR, Douches DS. (2019) Genome Editing in Potato with CRISPR/Cas9. Methods Mol Biol. 2019;1917:183-201.
2018
Bhowmik, P., Ellison, E., Polley, B., Bollina, V., Kulkarni, M., Ghanbarnia, K., Song, H., Gao, C. X., Voytas, D. F. and Kagale, S. (2018) Targeted mutagenesis in wheat microspores using CRISPR/Cas9. Scientific Reports, 8.
Hummel, A. W., Chauhan, R. D., Cermak, T., Mutka, A. M., Vijayaraghavan, A., Boyher, A., Starker, C. G., Bart, R., Voytas, D. F. and Taylor, N. J. (2018) Allele exchange at the EPSPS locus confers glyphosate tolerance in cassava. Plant Biotechnology Journal, 16(7), pp. 1275-1282.
Patrinostro, X., Roy, P., Lindsay, A., Chamberlain, C. M., Sundby, L. J., Starker, C. G., Voytas, D. F., Ervasti, J. M. and Perrin, B. J. (2018) Essential nucleotide- and protein-dependent functions of Actb/beta-actin. Proceedings of the National Academy of Sciences of the United States of America, 115(31), pp. 7973-7978.
Shaun, J. C., Classen, B., Gil-Humanes, J., Demorest, Z. and Voytas, D. F. (2018) Creating Healthier Food Products Through Genome Editing. In Vitro Cellular & Developmental Biology-Animal, 54, pp. S3-S4.
Cermak, T., Zsogon, A., Naves, E. R., Notini, M. M., Freschi, L., Kudla, J., Voytas, D. F. and Peres, L. E. P. (2018) Multiplex genome editing enables creation of a novel crop through de novo domestication. In Vitro Cellular & Developmental Biology-Plant, 54, pp. S97-S98.
Lowder, L. G., Zhou, J. P., Zhang, Y. X., Malzahn, A., Zhong, Z. H., Hsieh, T. F., Voytas, D. F., Zhang, Y. and Qi, Y. P. (2018) Robust Transcriptional Activation in Plants Using Multiplexed CRISPR-Act2.0 and mTALE-Act Systems. Molecular Plant, 11(2), pp. 245-256.
Sanchez-Leon, S., Gil-Humanes, J., Ozuna, C. V., Gimenez, M. J., Sousa, C., Voytas, D. F. and Barro, F. (2018) Low-gluten, nontransgenic wheat engineered with CRISPR/Cas9. Plant Biotechnology Journal, 16(4), pp. 902-910.
Zhang, F. and Voytas, D. F. (2018) Synthetic genomes engineered by SCRaMbLEing. Science China-Life Sciences, 61(8), pp. 975-977.
Curtin, S. J., Xiong, Y., Michno, J. M., Campbell, B. W., Stec, A. O., Cermak, T., Starker, C., Voytas, D. F., Eamens, A. L. and Stupar, R. M. (2018) CRISPR/Cas9 and TALENs generate heritable mutations for genes involved in small RNA processing of Glycine max and Medicago truncatula. Plant Biotechnology Journal, 16(6), pp. 1125-1137.
Macovei, A., Sevilla, N. R., Cantos, C., Jonson, G. B., Slamet-Loedin, I., Cermak, T., Voytas, D. F., Choi, I. R. and Chadha-Mohanty, P. (2018) Novel alleles of rice eIF4G generated by CRISPR/Cas9-targeted mutagenesis confer resistance to Rice tungro spherical virus. Plant Biotechnology Journal, 16(11), pp. 1918-1927.
Shan, Q., Baltes, N. J., Atkins, P., Kirkland, E. R., Zhang, Y., Baller, J. A., Lowder, L. G., Malzahn, A. A., Haugner, J. C., 3rd, Seelig, B., Voytas, D. F. and Qi, Y. (2018) ZFN, TALEN and CRISPR-Cas9 mediated homology directed gene insertion in Arabidopsis: A disconnect between somatic and germinal cells. J Genet Genomics.
He, J., Xu, M. L., Willmann, M. R., McCormick, K., Hu, T. Q., Yang, L., Starker, C. G., Voytas, D. F., Meyers, B. C. and Poethig, R. S. (2018) Threshold-dependent repression of SPL gene expression by miR156/miR157 controls vegetative phase change in Arabidopsis thaliana. Plos Genetics, 14(4).
Nadakuduti, S. S., Buell, C. R., Voytas, D. F., Starker, C. G. and Douches, D. S. (2018) Genome Editing for Crop Improvement - Applications in Clonally Propagated Polyploids With a Focus on Potato (Solanum tuberosum L.). Frontiers in Plant Science, 9.
Shan, Q. W. and Voytas, D. F. (2018) Editing plant genes one base at a time A new class of gene-editing reagents precisely alters plant genomes without creating a DNA double strand break. Nature Plants, 4(7), pp. 412-413.
Zsogon, A., Cermak, T., Naves, E. R., Notini, M. M., Edel, K. H., Weinl, S., Freschi, L., Voytas, D. F., Kudla, J. and Peres, L. E. P. (2018) De novo domestication of wild tomato using genome editing. Nat Biotechnol.
2017
Gil-Humanes. J., Wang, Y., Liang, Z., Shan, Q., Ozuna, CV., Sánchez-León, S., Baltes, NJ., Starker, C., Barro, F., Gao, C., Voytas, DF. (2017) High-efficiency gene targeting in hexaploid wheat using DNA replicons and CRISPR/Cas9. Plant Journal. 89, 1251–1262.
Abudayyeh, OO., Gootenberg, JS., Essletzbichler, P., Han, S., Joung, J., Belanto, JJ., Verdine, V., Cox, DBT., Kellner, MJ., Regev, A., Lander, ES., Voytas, DF., Ting, AY., Zhang, F. (2017) RNA targeting with CRISPR-Cas13. Nature. 550, pp. 280–284
Buell, C.R., Voytas, D.F. (2017) Technology turbocharges functional genomics. The Plant Cell. 29(5).
Curtin SJ, Tiffin P, Guhlin J, Trujillo DI, Burghardt LT, Atkins P, Baltes NJ, Denny R, Voytas DF, Stupar RM, Young ND. (2017) Validating Genome-Wide Association candidates through quantitative variation in nodulation. Plant Physiol. 173(2):921-931.
Hummel AW, Chauhan RD, Cermak T, Mutka AM, Vijayaraghavan A, Boyher A, Starker CG, Bart R, Voytas DF, Taylor NJ. (2017) Allele exchange at the EPSPS locus confers glyphosate tolerance in cassava. Plant Biotechnol J. 16(7):1275-1282.
Van Etten, JL., Nyquist, M., Li, Y., Yang, R., Ho, Y., Johnson, R., Ondigi, O., Voytas, DF., Henzler, C., Dehm, SM. (2017) Targeting a Single Alternative Polyadenylation Site Coordinately Blocks Expression of Androgen Receptor mRNA Splice Variants in Prostate Cancer. Cancer Res. 77(19):5228-5235.
Songstad, D,D., Petolino, J.F., Voytas, D.F., Reichert, N.A. (2017) Genome Editing of Plants. Critical Reviews in Plant Sciences. 1-23.
Tang, X., Lowder, L.G., Zhang, T., Malzahn, A.A., Zheng, X., Voytas, D.F., Zhong, Z., Chen, Y., Ren, Q., Li, Q., Kirkland, E.R., Zhang, Y., Qi, Y. (2017) A CRISPR-Cpf1 system for efficient genome editing and transcriptional repression in plants. Nature Plants. 3.
Lowder LG, Zhou J, Zhang Y, Malzahn A, Zhong Z, Hsieh TF, Voytas DF, Zhang Y, Qi Y. (2017) Robust transcriptional activation in plants using multiplexed CRISPR-Act2.0 and mTALE-Act systems. Mol Plant. pii: S1674-2052.
Holme, IB., Wendt, T., Gil-Humanes, J., Deleuran, LC., Starker, CG., Voytas, DF., Brinch-Pedersen, H. (2017) Evaluation of the mature grain phytase candidate HvPAPhy_a gene in barley (Hordeum vulgare L.) using CRISPR/Cas9 and TALENs. Plant Mol Biol. 95(1-2): 111-121.
Liska, F., Landa, V., Zidek, V., Mlejnek, P., Silhavy, J., Simakova, M., Strnad, H., Trnovska, J., Skop, V., Kazdova, L., Strarker, C.G., Voytas, D.F., Izsvak, Z., Mancini, M., Seda, O., Kren, V., Pravenec, M. (2017) Downregulation of Plzf gene ameliorates metabolic and cardiac traits in the spontaneously hypertensive rat. Hypertension. 69(6):1084-1091.
Curtin SJ, Xiong Y, Michno JM, Campbell BW, Stec AO, Čermák T, Starker C, Voytas DF, Eamens AL, Stupar RM. (2017) CRISPR/Cas9 and TALENs generate heritable mutations for genes involved in small RNA processing of Glycine max and Medicago truncatula. Plant Biotechnology Journal. 16(6):1125-1137.
Baltes, NJ., Gil-Humanes, J. Voytas, DF. (2017) Genome Engineering and Agriculture: Opportunities and Challenges. Prog Mol Biol Transl Sci. 149:1-26.
Cermak, T., Curtin, S.J., Gill-Humanes, J., Cegan, R., Kono, T.J.Y., Konecna, E., Belanto, J.J., Starker, C.G., Mathre, J.W., Greenstein, R.L., Votas, D.F. (2017) A multi-purpose toolkit to enable advance genome engineering in plants. The Plant Cell. 29(5).
Wilson, M.C., Mutka, A.M., Hummel, A.W., Berry, J., Chauhan, R.D., Vijayaraghavan, A., Taylor, N.J., Voytas, D.F., Chitwood, D.H., Bart, R.S. (2017) Gene expression atlas for the food security crop cassava. New Phytologist. 213(4):1632-1641.