From the germination of a seed to the fertilization events that lead to the next generation, plant development is exquisitely orchestrated by genetically determined processes that are fine-tuned by environmental cues. This entails the precise regulation of networks of genes in individual cells over the course of the plant life cycle. This project will decipher the complex regulation of genes within specific types of cells of the plant. This will be accomplished by transfer of methods pioneered by this team in the model plant species Arabidopsis thaliana to three important crops: rice, alfalfa, and tomato. These technologies allow for the isolation of cell nuclei containing DNA and RNA and the ribosomes that translate mRNA into protein from targeted subpopulations of cells of a leaf, root or other organs, without the need for dissection. The new genetic resources developed will be used to study how development is perturbed by two major environmental threats to US agriculture: drought and flood. The outcome will be a greater understanding of the integration of plant development with environmental cues.  The project will have multiple broader impacts. Using parallel multi-tiered and computationally robust analyses, the project will address two important biological questions: How does gene regulation in the stem cells (meristem) of roots and shoots differ across species? How does environmental stress influence the development of specialized cell types in the root? The findings will provide insights that could facilitate downstream improvement of abiotic stress tolerance. It will also generate resources for the evaluation of cell-type specific expression in three important crops. The seed material and data sets will be shared with the plant genome research community through the NCBI Short Read Archive (SRA, and Gramene ( Finally, the project will engage postdoctoral researchers and graduate students in advanced interdisciplinary training in biology and computational sciences, who will benefit from the experience of mentoring undergraduate students in research. Finally, the project will engage high school students in the classroom and the laboratory, develop teaching tools, and foster greater understanding of the importance of plant research to humankind.


PI: Julia Bailey-Serres (University of California – Riverside); CoPIs: Siobhan Brady and Neelima Sinha (University of California – Davis) and Roger Deal (Emory University)

Lab Memebers:

Kaisa Kajala, Joel Rodriguez-Medina, Niba Nirmal, Alan Rodriguez, Reina Sanz


NSF Plant Genome Research Program