Todd C. Mockler, Ph.D.

Member, Geraldine and Robert Virgil Distinguished Investigator
Donald Danforth Plant Science Center
Honorary Adjunct Associate Professor
Biology

Plant and Microbial Biosciences Program
Computational and Systems Biology Program
Molecular Genetics and Genomics Program

  • (314) 587-1203

  • (314) 587-1794

  • 975 N Warson Rd, St. Louis, MO 63132

  • tmockler@danforthcenter.org

  • http://www.mocklerlab.org

  • genomics, functional genomics, phenomics, systems biology, bioinformatics, transcriptional regulation, plant biology, molecular biology, molecular genetics, genetics, computational biology, and developmental biology. sorghum, plant

  • Research areas include crop genome sequencing and analysis, gene regulatory networks, plant abiotic stress responses, and high-resolution, high-throughput plant phenotyping

Research Abstract:

The long-term research goals of my lab are to address the genotype-to-phenotype (or phenotype-to-genotype) challenge and to understand gene regulatory networks in economically important crops (e.g. cereals and bioenergy crops). My group uses a combination of approaches including automated imaging- and sensor-based plant phenotyping, genetics, genomics, and computational biology. The overall goal of these efforts is to integrate genomic knowledge, high-resolution phenotypic characterizations, and relevant plant physiology to make predictions about plant growth, development, and ultimately yield. These efforts are being pursued in the experimental model plant systems (e.g. Brachypodium and Setaria) as well as crops (e.g. sorghum and maize). Ultimately, we want to understand how genomic variation and gene network plasticity contribute to plant survival and performance during abiotic stresses - in particular drought, heat, and cold - and thus contribute to yield. We also have begun to interrogate gene networks that regulate photosynthesis (in collaboration with others). This work is complementary to the focus on drought and thermal stresses which interact strongly with photosynthesis and negatively impact photosynthetic productivity. Understanding genotype-phenotype associations and gene network dynamics related to stress responses will lead to reliable predictive models for plant performance under different environmental conditions and provide a foundation for engineering or breeding crops for improved productivity.

Sorghum, ARPA-E TERRA & BMGF SGT:Sorghum bicolor has emerged as the flagship among second-generation bioenergy crops. We have prioritized deep genome sequencing to enhance our understanding of the genetic diversity that exists within sorghum. Within the ARPA-E TERRA-REF project we have now sequenced 400 bioenergy sorghum genomes and plan to submit an initial manuscript describing the sorghum pan genome in the first quarter of 2019. Over the next year, in the JGI-CSP project we will de novo sequence and assemble an additional 30 reference-grade sorghum genomes, as well as re-sequence an additional 300 lines. Within the Illumina Greater Good Initiative project we re-sequenced ~1000 grain sorghum genomes and within the Gates Foundation Sorghum Genomics Toolbox (SGT) project we will de novo sequence and assemble ~15 grain sorghum genomes. These sequencing efforts will provide the most complete pan-genome in any grass species and will provide key insights and targets for the enhancement of this crop. Working with collaborators, we will continue phenotyping a large proportion of these sequenced lines in multiple environments, including at field sites in Arizona, Kansas, Missouri, India, Ethiopia, France, Mali, and Senegal. Coupled with the resulting high-resolution genotype data, our ongoing high-resolution field- and controlled-environment phenotyping efforts will enable genotype-phenotype associations and rapid mapping of key agronomic traits which can then be tested through genetic analysis and reverse genetic approaches, and ultimately be used in applied breeding efforts.

Photosynthesis-Associated Networks: The photosynthesis related research efforts in my group have focused on two areas: 1)characterization of a new member of the dicarboxylate transporter family, DCT4, in C4 grasses;and 2) comparative analysis of C4 photosynthesis associated gene networks in grass species. In the next year, we will submit a manuscript describing our identification and characterization of the previously unknown member of the DCT family, DCT4, in sorghum. In the second area of photosynthesis related work we are using comparative analysis of C4 photosynthesis-associated gene co-expression network topology to elucidate differences between C4 gene networks in sorghum, maize, and Setaria and using the network models to identify putative novel regulators and components of the C4 photosynthetic systems.

Brachypodium ENCODE: The goal of the Brachypodium ENCODE project is to gain deep knowledge of chromatin
dynamics and gene networks related to stress responses in Brachypodium through drought-focused physiological analyses and multiple layers of ENCODE ‘omics’ profiling. We continue to obtain fundamental information about the Brachypodium transcriptome, epigenome, chromatin dynamics, and regulatory dynamics of gene networks under conditions of drought stress. In the next year, I expect to submit at least one manuscript describing our findings.

Maize: The Missouri Transect-Climate, Plants and Community is a statewide collaborative research effort to understand how climate variability impacts plants and communities in Missouri. Within this project phenotypic screens under limiting water conditions, conducted both in the field and in a controlled environment, have identified promising sub-populations within the maize nested association mapping (NAM) panel. In collaboration with Chris Topp (DDPSC) and Felix Fritschi (University of Missouri), we are conducting root and shoot physiological, morphological, and molecular (transcriptome profiling) phenotyping on these sub-populations. Ultimately, the goal is to associate maize genotypes with root and shoot phenotypes affected by drought and to map traits associated with tolerance or resistance to drought stress, enabling future engineering and breeding efforts for improving crop drought tolerance.

Selected Publications:

Jung, H.S., Crisp, P.A., Estavillo, G.M., Cole, B., Hong, F., Mockler, T.C., Pogson, B.J. and Chory, J. (2013) Subset of heat-shock transcription factors required for the early response of Arabidopsis to excess light. Proc Natl Acad Sci USA. (epub ahead of print).

Ming, R., VanBuren, R., Liu, Y., Yang, M., Han, Y., Li, L.-T., Zhang, Q., Kim, M.-J., Schatz, M.C., Campbell, M., Li, J. Bowers, J.E., Tang, H., Lyons, E., Ferguson, A.A., Narzisi, G., Nelson, D.R., Blaby-Haas, C.E., Gschwend, A.R., Jiao, Y., Der, J.P., Zeng, F., Han, J., Min, X.J., Hudson, K.A. Singh, R., Grennan, A.K., Karpowicz, S.J., Watling, J.R., Ito, K., Robinson, S.A., Hudson, M.E., Yu, Q., Mockler, T.C., Carroll, A., Zheng, Y., Sunkar, R., Jia, R., Chen, N., and Arro, J. (2013) Genome of the long-lived sacred lotus (Nelumbo nucifera Gaertn). Genome Biol 14:R41.

Ibarra-Laclette, E., Lyons, E., Hernandez-Guzman, G., Perez-Torres, C.A., Carretero-Paulet, L., Chang, T.-H., Lan, T., Welch, A.J., Juarez, M.J.A., Simpson, J., Fernandez-Cortes, A., Arteaga-Vazquez, M., Gongora-Castillo, E., Acevedo-Hernandez, G., Schuster, S.C., Himmelbauer, H., Minoche, A.E., Xu, S., Lynch, M., Oropeza-Aburto, A., Cervantes-Perez, S.A., Ortega-Estrada, M. de J., Cervantes-Luevano, J.I., Michael, T.P., Mockler, T., Bryant, D., Herrera-Estrella, A., Albert, V.A. and Herrera-Estrella, L. (2013) Architecture and evolution of a minute plant genome. Nature

Filichkin, S.A. and Mockler, T.C. (2012) Unproductive alternative splicing and nonsense mRNAs: A widespread phenomenon among plant circadian clock genes. Biology Direct 7:20. PMC3403997

Wang, Y., Zeng, X., Iyer, N.J., Bryant, D.W., Mockler, T.C., and Mahalingam, R. (2012) Exploring the switchgrass transcriptome using second-generation sequencing technology. PLoS One 7:e34225. PMC3315583

Atwood A, Deconde R, Wang SS, Mockler TC, Sabir JS, Ideker T, Kay SA. (2011) Cell-autonomous circadian clock of hepatocytes drives rhythms in transcription and polyamine synthesis. Proceedings of the National Academy of Science U S A 108:18560-18565. PMC3215069

Filichkin, S.A., Breton, G., Priest, H.D., Dharmawardhana, P., Jaiswal, P., Fox, S.E., Michael, T.P., Chory, J., Kay, S.A., Mockler, T.C. (2011) Global profiling of rice and poplar transcriptomes highlights key conserved circadian-controlled pathways and cis-regulatory modules. PLoS One 6: e16907. PMC3111414

Shulaev, V., Sargent, D.J., Crowhurst, R.N., Mockler, T.C., et al. (2010) The genome of woodland strawberry (Fragaria vesca). Nature Genetics 43:109-116. PMC3326587

Bryant, D.W., Shen, R., Priest, H.D., Wong, W-K., and Mockler, T.C. (2010) Supersplat-spliced RNA-seq alignment. Bioinformatics 26: 1500-1505. PMC2881391

Vogel, J.P., Garvin, D.F., Mockler, T.C., Schmutz, J., Rokhsar, D., Bevan, M.W., et al. (2010) Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature 463: 763-768.

Last Updated: 8/9/2018 10:10:47 AM

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