Daniel Woods


HHMI Research Associate


University of Wisconsin-Madison (2009-2015)                                          

            PhD. Genetics

California State University, Long Beach (2005-2008)                        

            B.S.  Biology: Cell & Molecular Biology (with Honors in the major).

            Minor: Chemistry & Anthropology


I am a plant developmental geneticist interested like most biologists in the diversity of life. My current work focuses on how plants sense and respond to the ever changing environment. This is essential in allowing plants to adapt to new niches. I am particularly interested in exploring what facilitated the niche transition of grasses, which originated in the tropics to the temperate zone.

I am currently a Howard Hughes Medical Institute Postdoctoral Fellow of the Life Sciences Research Foundation, 2018-2021.


University of California-Davis

Plant Sciences Department

One Shields Ave.

104 Robbins Hall

Davis, CA 95616


Research Interests

            A fundamental question in biology is to understand how the information encoded within a genome interfaces with the environment to create a range of possible phenotypes, and our understanding of this is in its infancy. The long-term goal of my research is to understand the molecular mechanism by which environmental cues are perceived and translated into various phenotypes. Given the sessile lifestyle of plants, evolutionary adaptation has favored plasticity in growth and development so that plants can thrive in changing environments. Therefore, plants are an excellent group of organisms in which to study the molecular basis of how environment influences phenotype, which will be vital to understand as global climate changes.

The transition from vegetative to reproductive development is a key decision for which the timing is often directly influenced by the environment. This critical life history trait has been shaped over evolutionary time to maximize the ability to flower at a time that optimizes reproductive success, and it has a profound influence on the appearance of plants. In global crops, such as wheat, the timing of this transition has been modified multiple times as wheat expanded through multiple environments across the globe. Furthermore, timing of flowering is one of many traits that have been manipulated by humans for increased crop productivity. Thus, the study of flowering-time is not only a fascinating topic from a basic research standpoint, but also has relevance for crop improvement particularly in a changing global climate and a growing human population. I aim to focus my flowering-time studies in Poaceae (grasses), a group of plants that dominate many ecologically important habitats throughout the world, provide for most of our species caloric intake with crops such as rice, wheat, corn, oats, barley, sorghum, and rye and, in the future, may provide a major part of a sustainable biomass energy portfolio.

            During my graduate work, I focused on establishing the temperate grass Brachypodium distachyon as a flowering-time model and I plan to continue to use this model grass to accelerate gene discovery. B. distachyon is a useful model grass because of its small, completely sequenced diploid genome, simple growth requirements, large collection of accessions, inbreeding nature, ease of transformation, and high rate of recombination. The focus of my post-doctoral studies will be to expand my work into crops with a focus in wheat.

            Broadly, I aim to understand how day-length and temperature influences time to flower; i.e., how these environmental signals are sensed and how this information is integrated to direct development. The long-term goal of this project is to provide a better understanding of the regulatory gene networks responsible for the integration of both photoperiod and temperature signals in the temperate cereals by doing comparative work between B. distachyon and wheat.



(*equal, @corresponding, ^ undergraduate/graduate/scientist trained)

21) Woods D.P.@, Li W., Sibout R., Laudencia-Chingcuanco D., Vogel J., Dubcovksy, J. and Amasino R. (2023). PHYTOCHROMEC regulation of PHOTOPERIOD1 is mediated by EARLY FLOWERING 3 in Brachypodium distachyon.  PLoS Genetics 19(5): e1010706.

20) Alvarez A., Li C., Lin H., Joe, A., Padilla M., Woods D.P. and Dubcovsky J. (2023). EARLY FLOWERING 3 interactions with PHYTOCHROME B and PHOTOPERIOD1 are critical for the photoperiodic regulation of wheat heading time. PLoS Genetics 19(5): e1010655.

19) Debernardi J., Woods D.P., Li K., Li C., and Dubcovsky J. (2022). MiR172-APETALA2-like genes integrate vernalization and plant age to control flowering time in wheat. PLoS Genetics 18(4):e1010157.

18) Kuzay S.^, Lin H., Li C., Chen S., Woods D.P., Zhang, J., Lan, T., von Korff, M., and Dubcovsky J. (2022). WAPO-A1 is the causal gene of the 7AL QTL for spikelet number per spike in wheat. PLoS Genetics (18)1: e1009747. Initially submitted as a preprint at bioRxiv (2021). https://doi.org/10.1101/2021.07.29.454276

17) Bouché F., Woods D.P., Li W., Linden J., Mayer K.^, Amasino R., and Perilleux C. (2022). ELF3 and photoperiod sensing in Brachypodium distachyon. Front. Plant Sci. 12:769194.

16) Raissig M.T.*@ and Woods D.P.*@ (2022). The wild grass Brachypodium distachyon as a developmental  model system. Invited review for "Emerging Model Systems" volume of Current Topics in  Developmental Biology. Edited by Bob Goldstein and Mansi Srivastava. (in press). Initially submitted as a preprint at zenodo (2021). https://zenodo.org/record/5548408#.YVyIX6BlBTY

15) Shaw L.*, Li C.*, Woods D.P.*, Alvarez M.A.*, Lin, H., Lau, M., Chen A., Dubcovsky J. Epistatic interactions between PHOTOPERIOD-1, CONSTANS1 and CONSTANS2 modulate the photoperiodic regulation of flowering in wheat. (2020). PLoS Genetics (16)7: e1008812. Initially submitted as a preprint at bioRxiv (2020). https://doi.org/10.1101/2020.04.29.067959

14) Woods D.P.@, Dong Y.^, Bouché F., Mayer, K.^, Varner L^, Ream T.S., Thrower N., Wilkerson C., Cartwright A., Sibout R., Laudencia-Chingcuanco D., Vogel J., and Amasino R.@. (2020). Mutations in the predicted DNA polymerase subunit POLD3 result in more rapid flowering of Brachypodium distachyonNew Phytologist. doi.org/10.1111/nph.16546

13) Woods D.P.@, Dong Y.^, Bouché F., Bednarek R.^, Rowe M.^,  Ream T.S., and Amasino R. (2019). A florigen paralog is required for short-day vernalization in a pooid grass. eLife. 8:e42153. Also submitted as a preprint at bioRxiv. doi: https://doi.org/10.1101/428995

12) Lomax A.^, Woods D.P.@, Dong Y.^, Bouché F., Rong Y., Mayer K., Zhong X., and Amasino R.@ (2018). An ortholog of CURLY LEAF/ENHANCER OF ZESTE like-1 is required for proper flowering in Brachypodium distachyon. The Plant Journal. doi: 10.1111/tpj.13815

11) Gordon, S., Contreras-Moreira, B., Woods, D.P., Des Marais, D., Burgess, B., Shu, S., Stritt, C., Roulin, A., Schackwitz, W., Tyler, L., Martin, J., Lipzen, A., Dochy, N., Phillips, J., Barry, K., Geuten, K., Juenger, T., Amasino, R., Caicedo, A., Goodstein, D., Davidson, P., Mur, L., Figueroa, M., Freeling, M., Catalan, P., and Vogel, J. (2017). Extensive gene content variation in the Brachypodium distachyon pan-genome correlates with population structure. Nature Communications. 8: 2184.

10) Woods, D.P., Ream, T.S., Bouché, F., Lee., J. Thrower, N., Wilkerson, C., and Amasino R. (2017).   Establishment of a vernalization requirement in Brachypodium distachyon requires REPRESSOR OF VERNALIZATION1. Proc. Natl. Acad. Sci. USA. 114(25), 6623-6628.                                                                                                                                                 • Featured: Divergence in how genetic pathways respond to environments. Donohue K. Trends in Plant Science. doi:dx.doi.org/10.1016/j.tplants.2017.08.008 (2017).

9) Bouché, F., Woods, D.P., and Amasino R. (2017). Winter memory throughout the plant kingdom:different paths to flowering. Plant Physiology. 173(1):27–35.

8) Woods, D.P., Bednarek, R.^, Bouché, F., Gordon, S., Vogel, J., Garvin, D., and Amasino R. (2017). Genetic architecture of flowering-time variation in Brachypodium distachyon. Plant Physiology.173(1):269–279.

7) Woods, D.P., McKeown, M., Dong, Y.^, Preston, J., and Amasino, R. (2016). Evolution of VRN2/GhD7-like genes in the vernalization-mediated repression of grass flowering. Plant Physiology. 170, 2124-2135.

6) Woods, D.P and Amasino, R. (2015). Dissecting the control of flowering time in grasses using Brachypodium distachyon. Genetics and Genomics of Brachypodium. J.P. Vogel. Switzerland. Springer. 18, 259-273.

5) Woods, D.P., Ream, T.S., Minevich, G., Hobert, O., and Amasino, R. (2014). PHYTOCHROME C is an essential light receptor for photoperiodic flowering in the temperate grass, Brachypodium distachyon. Genetics. 198(1): 397-408.           • Featured: Cereal crops see things differently. Trevaskis B. Journal of Experimental Botany Flowering   Highlights. doi:10.1093/jxb/erv113. (2014).

4) Woods, D.P., Ream, T.S., and Amasino, R. (2014). Memory of the vernalized state in plants including the model grass Brachypodium distachyon. Front. Plant Sci. 5:99.

3) Ream, T.S.,* Woods, D.P.,* Schwartz, C. A., Sanabria, C.^, Mahoy, J., Walters, E.^, Kaeppler, H., and Amasino, R. (2014). Interaction of photoperiod and vernalization determine flowering time of Brachypodium distachyon. Plant Physiology. 164, 694-709.

2) Ream, T.S.,* Woods, D.P.,* and Amasino, R. (2012). The Molecular basis of the vernalization response  in different plant groups. Cold Spring Harb Symp Quant Biol. 77, 105-115.

1) Woods, D.P., Hope, C.L.^ and Malcomber, S. T. (2011). Phylogenomic analyses of the BARREN STALK1/LAX PANICLE1 (BA1/LAX1) genes and evidence   for their roles during axillary meristem development. Molecular Biology and Evolution. 28(7):2147-59.

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