Bailey-Serres Group

UC Riverside

Bailey-Serres Group, Summer 2019

The Bailey-Serres group performs translational plant biology from gene to field. We aim to harness genetic mechanisms that provide climate change resilience to crops, particularly flooding, drought and nutrient stress resilience. We work from the single cell to whole plant level. Our studies have defined mechanisms of low oxygen sensing and post-transcriptional gene regulation, from the epigenome to the "mRNPome" and translatome. This knowledge is of importance to efforts that seek to stabilize crop yields as Earth’s population grows, arable land decreases, and climate patterns change.

Julia Bailey-Serres directs UCR's Center for Plant Cell Biology and NSF-funded Plants3D-NRT (National Research Trainineeship) program for graduate studies bridging plant biology and engineering.

The group is dedicated to promoting science education and professional development as well as fostering diversity and innovation in collaborative and interdisciplinary research.


Young farmer in his Swarna Sub1 field. His rice endured a 16 day flood. The non-Sub1 Swarna crop was destroyed; that area sown early with lentils. India visit with IRRI, 2008. Photo: JBS

Farmers of Bangladesh and India risk losing all or part of their rice crops each year to Monsoon floods. Fortunately, flood-resilient rice has become a reality due to the identification of a rice gene called SUB1A that allows vegetative stage plants to survive prolonged period of time underwater. New rice varieties have been bred for submergence tolerance and provided to farmers, primarily through the initiatives of the International Rice Research Institute. Our team has elucidated the complex mechanisms of function of the SUB1A gene.

Transcription and Beyond

To define low oxygen sensing and response mechanisms that enable survival for a short period of oxygen deprivation in the model plant Arabidopsis, we have studied extensively the regulation of gene expression that occurs after a gene transcript is produced, as the modulation of mRNA translation and storage provides a means to conserve energy when cells are deprived of oxygen.

Our group developed the method "Translating Ribosome Affinity Purification" (TRAP) that enables researchers to monitor the mRNAs undergoing translation by ribosomes (the Translatome). This method can be used to monitor gene activity in specific cells and developmentally defined regions of plants. We have promoted use of TRAP and INTACT for multi-scale and cell type specific gene regulation analysis in crops.

In our recent work defines transcriptional gene regulatory networks and post-transcriptional gene regulatory mechanisms across species and in response to abiotic and biotic stress.

Recent Papers

Kajala, K., Goran, M., Shaar-Moshe L., Mason, G., Rodriguez-Medina, J., et al. Cell. 2021. Innovation, conservation, and repurposing of gene function in root cell type development. Lead by our amazing collaborator Siobhan Brady, a translatome atlas for tomato root cell types, including comparisons with rice and Arabidopsis.

Bailey-Serres, J., Parker, J.E., Ainsworth, E.A. et al. Genetic strategies for improving crop yields. Nature 575, 109–118 (2019) doi:10.1038/s41586-019-1679-0 in the 150 years of Nature reviews collection.

Reynoso, Kajala, Bajic, West, Pauluzzi et al. Science. This is the NSF PGR funded "Plasticity Project" team's deep genomic study comparing root tip gene regulatory networks responding to submergence responses in rice, medicago, tomato and a wild tomato. Resources on our Data page.

Travis Lee and Julia Bailey-Serres; The Plant Cell. A deep study of nuclear gene regulatory processes in response to hypoxia and re-aeration in Arabidopsis. See chromtin, RNAPII, ATAC-seq, and four different popultions or mRNA for your favorite gene in a browser: Data page.

Traubenik S, et al. Reprogramming of Root Cells during Nitrogen-Fixing Symbiosis Involves Dynamic Polysome Association of Coding and Noncoding RNAs Plant Cell 2020.

  • A demonstration of translated "non-coding" mRNAs during nodulation

  • More about Soledad Traubenik from Maria Eugenia Zanetti's group at La Plata National University in Argentina. Sole visited us to produce her TRAP-seq and other libraries for this project.

Chantarachot et al. DHH1/DDX6-like RNA helicases maintain ephemeral half-lives of stress-response mRNAs associated with innate immunity and growth inhibition, Nature Plants. Free Read Only Version

  • Discoverd that the most short lived mRNAs in Arabidopsis are involved in stress responses including innate immunity

  • Determined that the turnover of these short-lived mRNAs under non-stress conditions is mediated by a group of conserved RNA helicases that interact with the 5' decapping apparatus. Mutation of these genes promotes innate immunity and supresses growth.

  • See the accopanying commentary by Rémy Merret and Cécile Bousquet-Antonelli.

Alam, R., Hummel, M., Locke, A., Jia, Z., Ignaci, C.C.I., Baltazar, M.D., Ismail, A., Septiningsih, E.M. and Bailey-Serres, J. (2020) Flood resilience loci SUBMERGENCE 1 and ANAEROBIC GERMINATION 1 interact in seedlings established underwater. Plant Direct.

  • Beachel lBorlaug International Scholar and PhD student, Rejbana Alam's, collaborative work with Endang Septiningshi and Abdel Ismail at International Rice Research Institute.

  • Rejbana asked, is there genetic interaction between the submergence tolerance regulator SUB1A-1 and the anaerobic germination booster Trehalose-6 Phosphate Phosphatase (OsTPP7)?

  • She performed, growth, transcriptome and metabolite analyisis of four near-isogenic lines varying at SUB1A-1 and OsTPP7 and four time points in plants developed entirely underwater.

  • The study found that SUB1A promotes photoautotrophic development in seeds of seedlings sown underwater.

  • It also provides evidence that the boost of seedling elongation by OsTPP7 /AG1 and the submergene tolerance provided by SUB1A-1 clash if the seedlings of seeds sown underwater do not escape into air before SUB1A slows underwater elongation growth. This happens after the plants become dependent upon photosynthate for growth. These findings may be relevant to farmers.

See our Publications page for more