Publications

Pre-prints

Wong, K.M., Griffiths, M., Moran A, Johnston, A., Liu, A.E., Sellers, M.A., & Topp, C.N. (2023). Surveying cover crop root traits and their potential impacts on carbon and nitrogen cycling. Research Square. https://doi.org/10.21203/rs.3.rs-2649846/v1

In-press

Griffiths, M., Liu, E.A., Gunn, S.L., Mutan, N.M., Morales, E.Y. & Topp, C.N. (2023). A temporal analysis and response to nitrate availability of 3D root system architecture in diverse pennycress (Thlaspi arvense L.) accessions. Frontiers in Plant Science. https://doi.org/10.3389/fpls.2023.1145389

Peer-reviewed

Czymmek, K., Duncan, K.E., & Berg, H. (2023). Realizing the Full Potential of Advanced Microscopy Approaches for Interrogating Plant-Microbe Interactions. MPMI . https://doi.org/10.1094/MPMI-10-22-0208-FI

Yu, Y., Beyene, G., Villmer, J., Duncan, K.E., Hu, Hao., Johnson, T., Doust, A.N., Taylor, N.J., & Kellogg, E.A. (2023). Grain shattering by cell death and fracture in Eragrostis tef. Plant Physiology, kiad079. https://doi.org/10.1093/plphys/kiad079

Duncan, K.E., & Topp, C.N. (2022). Phenotyping Complex Plant Structures with a Large Format Industrial Scale High-Resolution X-Ray Tomography Instrument. In: Lorence, A., Medina Jimenez, K. (eds) High-Throughput Plant Phenotyping. Methods in Molecular Biology, vol 2539. Humana, New York, NY.. https://doi.org/10.1007/978-1-0716-2537-8_12

Dowd, T. G., Li, M., Bagnall, G. C., Johnston, A., & Topp, C. N. (2022). Root system architecture and environmental flux analysis in mature crops using 3D root mesocosms. Frontiers in Plant Science. https://doi.org/10.3389/fpls.2022.1041404

Griffiths, M., Delory, B. M., Jawahir, V., Wong, K. M., Bagnall, G. C., Dowd, T. G., Nusinow, D. A., Miller, A. J., & Topp, C. N. (2022). Optimisation of root traits to provide enhanced ecosystem services in agricultural systems: A focus on cover crops. Plant, Cell & Environment. https://doi.org/10.1111/pce.14247

Cox Jr, K. L., Gurazada, S. G. R., Duncan, K. E., Czymmek, K. J., Topp, C. N., & Meyers, B. C. (2022). Organizing your space: The potential for integrating spatial transcriptomics and 3D imaging data in plants. Plant Physiology. https://doi.org/10.1093/plphys/kiab508

Bélanger, S., Berensmann, H., Baena, V., Duncan, K.E., Meyers, B.C., Narayan, K., & Czymmek, K.J. (2022). A versatile enhanced freeze-substitution protocol for volume electron microscopy. Frontiers in Cell and Developmental Biology. https://doi.org/10.3389/fcell.2022.933376

Duncan, K. E., Czymmek, K. J., Jiang, N., Thies, A. C., & Topp, C. N. (2021). X-ray microscopy enables multiscale high-resolution 3D imaging of plant cells, tissues, and organs. Plant Physiology. https://doi.org/10.1093/plphys/kiab405

Bucciarelli, B., Xu, Z., Ao, S., Cao, Y., Monteros, M. J., Topp, C. N., & Samac, D. A. (2021). Phenotyping seedlings for selection of root system architecture in alfalfa (Medicago sativa L.). Plant Methods. https://doi.org/10.1186/s13007-021-00825-3

Zeng, D., Li, M., Jiang, N., Ju, Y., Schreiber, H., Chambers, E., Letscher, D., Ju, T., & Topp, C. N. (2021). TopoRoot: a method for computing hierarchy and fine-grained traits of maize roots from 3D imaging. Plant Methods. https://doi.org/10.1186/s13007-021-00829-z

Shao, M. R., Jiang, N., Li, M., Howard, A., Lehner, K., Mullen, J. L., Gunn, S. L., McKay, J. K., & Topp, C. N. (2021). Complementary Phenotyping of Maize Root System Architecture by Root Pulling Force and X-Ray Imaging. Plant Phenomics. https://doi.org/10.34133/2021/9859254

Topp, C. N. & Jez, J. M. (2021). Introduction to emerging technologies in plant science. Emerg Top Life Sci . https://doi.org/10.1042/ETLS20200269

Dowd, T., McInturf, S., Li, M., & Topp, C. N. (2021). Rated-M for mesocosm: allowing the multimodal analysis of mature root systems in 3D. Emerg Top Life Sci . https://doi.org/10.1042/ETLS20200278

Prunet, N., & Duncan, K.E. (2020). Imaging flowers: a guide to current microscopy and tomography techniques to study flower development. Journal of Experimental Botany. https://doi.org/10.1093/jxb/eraa094

Sultan, S., Snider, J., Conn, A., Li, M., Topp, C. N., & Navlakha, S. (2020). A statistical growth property of plant root architectures. Plant Phenomics. https://doi.org/10.34133/2020/2073723

Li, M., Shao, M., Zeng, D., Ju, T., Kellogg, E. A. & Topp, C. N. (2020). Comprehensive 3D phenotyping reveals continuous morphological variation across genetically diverse sorghum inflorescences. New Phytologist. https://doi.org/10.1111/nph.16533

Li, M., Klein, L. L., Duncan, K. E., Jiang, N., Chitwood, D. H., Londo, J. P., Miller, A. J. & Topp, C. N. (2020). Characterizing 3D inflorescence architecture in grapevine using X-ray imaging and advanced morphometrics: implications for understanding cluster density. Journal of Experimental Botany. https://doi.org/10.1093/jxb/erz394

Michniewicz, M., Ho, C., Enders, T. A., Floro, E., Damodaran, S., Gunther, L. K., Powers, S. K., Frick, E. M., Topp, C. N., Frommer, W. B., & Strader, L. C. (2019). TRANSPORTER OF IBA1 links auxin and cytokinin to influence root architecture. Developmental Cell. https://doi.org/10.1016/j.devcel.2019.06.010

Jiang, N., Floro, E., Bray, A. L., Laws, B., Duncan, K. E., & Topp, C. N. (2019). Three-Dimensional Time-Lapse Analysis Reveals Multiscale Relationships in Maize Root Systems with Contrasting Architectures. The Plant Cell. https://doi.org/10.1105/tpc.19.00015

Wedger, M. J., Topp, C. N. & Olsen, K. M. (2019). Convergent evolution of root system architecture in two independently evolved lineages of weedy rice. New Phytologist. https://doi.org/10.1111/nph.15791

Gleason, S. M., Cooper, M., Wiggans, D. R., Bliss, C. A., Romay, M. C., Gore, M. A., Mickelbart, M. V., Topp, C. N., Zhang, H., DeJonge, K. C., & Comas, L. H. (2019). Stomatal conductance, xylem water transport, and root traits underpin improved performance under drought and well-watered conditions across a diverse panel of maize inbred lines. Field Crops Research. https://doi.org/10.1016/j.fcr.2019.02.001

Bray, A. L. & Topp, C. N. (2018). The Quantitative Genetic Control of Root Architecture in Maize. Plant and Cell Physiology. https://doi.org/10.1093/pcp/pcy141

Li, M., Frank, M. H., Coneva, V., Mio, W., Chitwood, D. H. & Topp, C. N. (2018). The persistent homology mathematical framework provides enhanced genotype-to-phenotype associations for plant morphology. Plant Physiology. https://doi.org/10.1104/pp.18.00104

Li, M., An, H., ... Topp, C. N., Deynze, A. V., Zhang, K., Zhu, L., Zink, B. M. & Chitwood D. H. (2018). Topological data analysis as a morphometric method: using persistent homology to demarcate a leaf morphospace. Frontiers In Plant Science. https://doi.org/10.3389/fpls.2018.00553

Delory, B. M., Li, M., Topp, C. N. & Lobet, G.(2018). A new data analysis pipeline allowing the topological analysis of plant root systems. F1000Res. https://doi.org/10.12688/f1000research.13541.1

Bucksch, A., Atta-Boateng, A., Azihou, A. F., ... Sparks, E. E, Topp, C. N., Williams, J. H., & Chitwood, D. H. (2017). Morphological Plant Modeling: Unleashing Geometric and Topological Potential within the Plant Sciencess. Frontiers in plant science. https://doi.org/10.3389/fpls.2017.00900

Li, M., Duncan, K., Topp, C. N. & Chitwood, D. H. (2017). Persistent homology and the branching topologies of plants. American Journal of Botany. https://doi.org/10.3732/ajb.1700046

Agnew, E., Bray, A., Floro, E., Ellis, N., Gierer, J., Lizárraga, C., O'Brien, D., Wiechert, M., Mockler, T. C., Shakoor, N., & Topp, C. N. (2017). Whole‐Plant Manual and Image‐Based Phenotyping in Controlled Environments. Current Protocols in Plant Biology. https://doi.org/10.1002/cppb.20044

Pauli, D., Chapman, S. C., Bart, R., Topp, C. N., Lawrence-Dill, C. J., Poland, J., & Gore, M. A. (2017). The quest for understanding phenotypic variation via integrated approaches in the field environment. Plant Physiology. https://doi.org/10.1104/pp.16.00592

Delory, B. M., Baudson, C., Brostaux, Y., Lobet, G., du Jardin, P., Pagès, L. & Delaplace, P. (2016). archiDART: an R package for the automated computation of plant root architectural traits. Plant and Soil. https://doi.org/10.3389/fpls.2018.00553

Topp, C. N. (2016). Hope in change: the role of root plasticity in crop yield stability. Plant Physiology. https://doi.org/10.1104/pp.16.01257

Topp, C. N., Bray, A. L., Ellis, N. A. & Liu, Z. (2016). How can we harness quantitative genetic variation in crop root systems for agricultural improvement?. Journal of Integrative Plant Biology. https://doi.org/10.1111/jipb.12470

Das, A., Schneider, H., Burridge, J., Ascanio, A. K. M., Wojciechowski, T., Topp, C. N., Lynch, J. P., Weitz, J. S. & Bucksch, A. (2016). Digital imaging of root traits (DIRT): a high-throughput computing and collaboration platform for field-based root phenomics. Plant Methods. https://doi.org/10.1186/s13007-015-0093-3

Symonova, O., Topp, C. N. & Edelsbrunner, H. (2015). DynamicRoots: a software platform for the reconstruction and analysis of growing plant roots. PLOS One. https://doi.org/10.1371/journal.pone.0127657

Goggin, F. L., Lorence, A. & Topp, C. N. (2015). Applying high-throughput phenotyping to plant–insect interactions: picturing more resistant crops. Current Opinion in Insect Science. https://doi.org/10.1016/j.cois.2015.03.002

Zurek, P. R., Topp, C. N. & Benfey, P. N. (2015). Quantitative trait locus mapping reveals regions of the maize genome controlling root system architecture. Plant Physiology. https://doi.org/10.1104/pp.114.251751

Chitwood, D. H. & Topp, C. N. (2015). Revealing plant cryptotypes: defining meaningful phenotypes among infinite traits. Current Opinion in Plant Biology. https://doi.org/10.1016/j.pbi.2015.01.009

Topp, C. N., Iyer-Pascuzzi, A. S., Anderson, J. T., Lee, C. R., ... & Benfey, P. N. (2013). 3D phenotyping and quantitative trait locus mapping identify core regions of the rice genome controlling root architecture. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1304354110

Galkovskyi, T., Mileyko, Y., Bucksch, A., Moore, B., Symonova, O., Price, C. A., Topp, C. N., ... Benfey, P. N. & Weitz, J. S. (2012). GiA Roots: software for the high throughput analysis of plant root system architecture. BMC Plant Biology. https://doi.org/10.1186/1471-2229-12-116

Topp, C. N. & Benfey, P. N. (2012). Growth control of root architecture. Plant Biotechnology and Agriculture. https://doi.org/10.1016/B978-0-12-381466-1.00024-9

Li, W., Topp, C. N. & Dawe, R. K. (2012). Maize antibody procedures: Immunolocalization and chromatin immunoprecipitation. Plant Cytogenetics. https://doi.org/10.1007/978-0-387-70869-0_11

Gent, J. I., Schneider, K. L., Topp, C. N., Rodriguez, C., Presting, G. G. & Dawe, R. K. (2012). Distinct influences of tandem repeats and retrotransposons on CENH3 nucleosome positioning. Epigenetics & Chromatin. https://doi.org/10.1186/1756-8935-4-3

Du, Y., Topp, C. N. & Dawe, R. K. (2010). DNA binding of centromere protein C (CENPC) is stabilized by single-stranded RNA. PLoS Genetics. https://doi.org/10.1371/journal.pgen.1000835

Topp, C. N., Okagaki, R. J., Melo, J. R., Kynast, R. G., Phillips, R. L. & Dawe, R. K. (2009). Identification of a maize neocentromere in an oat-maize addition line. Cytogenetic and Genome Research. https://doi.org/10.1159/000218128

Phan, B. H., Jin, W., Topp, C. N., Zhong, C. X., Jiang, J., Dawe, R. K., & Parrott, W. A. (2009). Transformation of rice with long DNA-segments consisting of random genomic DNA or centromere-specific DNA. Transgenic Research. https://doi.org/10.1007/s11248-006-9041-3

Deal, R. B., Topp, C. N., McKinney, E. C., & Meagher R. B. (2007). Repression of Flowering in Arabidopsis Requires Activation of FLOWERING LOCUS C Expression by the Histone Variant H2A.Z. The Plant Cell. https://doi.org/10.1105/tpc.106.048447

Topp, C. N. & Dawe R. K. (2006). Reinterpreting pericentromeric heterochromatin. Current Opinion in Plant Biology. https://doi.org/10.1016/j.pbi.2006.09.008

Topp, C. N., Zhong, C. X. & Dawe R. K. (2004). Centromere-encoded RNAs are integral components of the maize kinetochore. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.0407154101

Zhong, C. X., Marshall, J. B., Topp, C. N., Mroczek, R., Kato, A., Nagaki, K., Birchler, J. A., Jiang, J. & Dawe R. K. (2002). Centromeric retroelements and satellites interact with maize kinetochore protein CENH3. The Plant Cell. https://doi.org/10.1105/tpc.006106

Topp, C. N., Ruiz-Herrera, J., Martínez-Espinoza, A. D. & Gold, S. E. (2002). Integration of the gene for carboxin resistance does not impact the Ustilago maydis–maize interaction. Current Microbiology. https://doi.org/10.1007/s00284-001-0076-7