Progress 06/15/21 to 06/14/24
Outputs
Target Audience:The target audiences for the project were other plant biology researchers working in plant development and abiotic stress biology andundergradute trainees at UC Riverside. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?This project provided training and professional development for the PD, who participated in weekly lab meetings, and met regularly with the project mentor to get feedback and guidance on scientific progress. The PD also mentored four undergraduates over the course of the project, providing him experience in mentorship and the undergraduates development in scientific methods, and communcation in oral and poster presentations.The PD also presented work at multiple conferences, with feedback from the mentor and other members of the lab on presentation and communication. Finally, the PD secured a postdoctoral researrch position to contiune to pursue a career in academic research. How have the results been disseminated to communities of interest?The results of this project have been disseminated to the scientific community through journal articles and conference presentations. The PD is a co-first author on a publication in Developmental Cell which includes much of the effort of this project. Additionally the PD is the first author of a review in press at Nature Genetics, and will prepare a first-author manucript to disseminate the results of genetic manipulation of suberin. Some of this work in progress has already been disseminated through presentations, including at an international conference. What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
Multiple accomplishments were achieved for these goals. Goal 1. A publication of analysis of using -omics data to model gene regulatory networks governing rice abiotic stress response was published in Developmental Cell. This analysis was used to prioritize candidates which were pursued in subsequent aims and by other members of the Bailey-Serres lab in new projects. Additionally, a new time-course transcriptomics dataset was generated to understand how the responses identified in this previous work develop over time in different zones of the root system. Goal 2. CRISPR-cas9 loss of function mutants of targeted genes showed reduced levels of suberin in root barrier cells. Ongoing work in the lab is continuing to characterize their responses to abiotic stress which will be reported in a manuscript. Rather than develop reporter lines for suberin gene activity, we developed a new imaging modality to visualize and quantify suberin in whole rice root systems using staining and a laser scanning fluorescent biomolecular imager. This method has been used to study temporal dynamics and mutant lines. Goal 3. Preliminary experiments attempting promoter design were not successful, so endogenous promoters were selected instead to rewire the suberin gene regulatory network. This strategy produced transgenic rice lines which have accelerated and increased suberin deposition in the root barrier cell layers. Thesetransgenic lines are being studied in parallel with the CRISPR mutants for their responses to abiotic stress.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2024
Citation:
Cant�-Pastor, A, Kajala, K, Shaar-Moshe, L, Manzano, C, Timilsena, P, De Bellis, D. Gray, S, Holbein, J, Yang, H, Mohammad, S, Nirmal, N, Suresh, K, Ursache, R, Mason, GA, Gouran, M, West, DA, Borowsky, AT, Shackel, KA, Sinha, N, Bailey-Serres, J, Geldner, N, Li, S, Franke, RB, Brady, SM. A suberized exodermis is required for tomato drought tolerance. Nature Plants, 2024
- Type:
Journal Articles
Status:
Published
Year Published:
2024
Citation:
Zhang, J, Gongol, B, Zhang, L, Borowsky, AT, Bailey-Serres, J, Girke, T. spatialHeatmap: Visualizing Spatial Bulk and Single Cell Assays in Anatomical Images. NAR Bioinformatics, 2024
- Type:
Journal Articles
Status:
Published
Year Published:
2024
Citation:
Borowsky, AT., Bailey-Serres, J. Rewiring Gene Circuitry for Plant Improvement. Nature Genetics, 2024
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2023
Citation:
10th International Symposium on Root Development, Ghent, Belgium May 16th, 2023
Borowsky, A. T., Gene network discovery and engineering to enhance rice root resilience
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2024
Citation:
ASPB Western Section Meeting, Long Beach, California, March 23rd, 2024
Borowsky, A. T., Gene network discovery and engineering to enhance rice root resilience
- Type:
Theses/Dissertations
Status:
Awaiting Publication
Year Published:
2024
Citation:
PhD Dissertation in Plant Biology, UC Riverside. Borowsky, A. T., Gene Regulatory Circuitry of Rice Root Responses to Water Availability. 2024.
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Progress 06/15/22 to 06/14/23
Outputs
Target Audience:Target audiences reached during this reporting period include other plant researchers by talks by PD Borowskyat two conferences, the 10th International Symposium on Root Development in Ghent, Belgium, a virtual conference, the Plant Cell Atlas Symposium. Other target audiences reached by these efforts include two undergraduate students who recieved mentorship and training in plant molecular biology. Finally, fifth grade students were reached through a UCR Botany and Plant Sciences outreach event, Plant Discovery Day, which brought over 100 students to the UCR campus to learn from hands on activities in plant science. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?The PD met regularly with the mentor in lab meetings and one-on-one to get feedback on research progress and experimental design. How have the results been disseminated to communities of interest?Results were communicated in journal articles and conference presentaitons. What do you plan to do during the next reporting period to accomplish the goals?The goals for the next reporting period are to generate transcriptomics data and complete characterization of the new genetic material.
Impacts
What was accomplished under these goals?
In the past year, much progress was accomplished towards these goals. First, towards aim 2.1, mutants were generated in rice for additional transcription factors, and higher-order mutants were generated. In total, mutants were made that cover the five MYB TFs, one NAC TF, two WRKY TFs, and one C2H2 TF that we previously implicated in rice suberin biosynthesis by coexpression. Genotype confirmation and transgene segration in the T1 generation is in progress. Second, a new imaging methodology was developed to bypass the need for reporter lines. Previously, we were limited to histological staining of suberin with fluorol yellow on microscope slides, which did not allow visualization of entire root systems. The UCR Genomics Core recently acquired a Typhoon fluorescence imager, which has a large enough scan area to visualize suberin by fluorol yellow staining in 8-12 whole rice root systems at once. This has greatly increased our imaging throughput and we have already used it to generate time course data of rice root system suberization in response to water deficit. Towards aim 3.1, the PD designed and had synthesized 10 synthetic promoters as planned. These were used to drive the RUBY reporter in transgenic rice. No RUBY expression was observed in the roots of T0 plants, so this strategy is not being prioritized. The PD will consider array synthesis and library cloning methods to improve throughput for screening designed sequences, as time and resources allow. Instead, the goal for aim 3.2here have advanced using native promoters for expresison of MYB transcription factors. T1 seed are in hand for two different promoter:MYB fusion lines, with phenotypic characterization to come. Finally, new data are being generated to improve the impact of aim 1. Specifically, a time course experiment of water deficit response was collected in the greenhouse, and the tissue for this experiment is stored in the freezer ready for processing for RNA-seq data generation.
Publications
- Type:
Journal Articles
Status:
Awaiting Publication
Year Published:
2022
Citation:
Cant�-Pastor, A., Kajala, K., Shaar-Moshe, L., Manzano, C., Timilsena, P., De Bellis, D., Gray, S., Holbein, J., Yang, H., Mohammad, S., Nirmal, N., Suresh, K., Ursache, R., Mason, G. A., Gouran, M., West, D. A., Borowsky, A. T., Shackel, K. A., Sinha, N., Bailey-Serres, J., Geldner, N., Li, S., Franke, R. B., Brady, S. M. A suberized exodermis is required for tomato drought tolerance. bioRxiv preprint, 2022. https://doi.org/10.1101/2022.10.10.511665
- Type:
Journal Articles
Status:
Awaiting Publication
Year Published:
2023
Citation:
Zhang, J, Gongol, B, Zhang, L, Borowsky, AT, Bailey-Serres, J, Girke, T. spatialHeatmap: Visualizing Spatial Bulk and Single Cell Assays in Anatomical Images. submitted, 2023
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Progress 06/15/21 to 06/14/22
Outputs
Target Audience:The target audience ofacademic and industry plant biologists and biotechnologists was reached through conference presentations, publication, and teaching. UCR undergraduates were reached though mentorship and research opportunities. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?The PD has many training andprofessional development activities during this period, both for himself and in support of others The PD had weekly meetings with advisor Julia Bailey-Serres and collaborator Mauricio Reynoso to work on writing a manuscript, providing training in writing and publishing. Additionally, the PD presented approximately twice per quarter in a lab meeting with the Bailey-Serres group and the group of Professor Dawn Nagel, both sharing research and presenting recently published papers from others. The PD had the opportunity to develop mentorship and teaching skills by mentoring three undergraduates during this reporting period. One undergraduate, who was being mentored on a bioinformatics project, graduated and was admitted to the UCR School of Medicine. Two additional undergraduates began in Spring and started projects to learn wet bench molecular biology techniques including DNA extraction and PCR. Another training and professional development activity supported by the project was the PD, along with fellow NIFA Predoctoral Fellows Marcus Harland-Dunaway and Jaimie Kenney, held a workshop for UCR graduate students to guide them through the NIFA Predoctoral fellowship application process. This two-hour event included a presentation by the fellows as well as a question and answer session. This summer, the PD was a teaching assistant at the three-week-long Cold Spring Harbor Laboratory Course: Frontiers and Techniques in Plant Science. This involved assisting visiting professors in preparing hands-on lab activities and helping the students, graduate students and postdocs working in plant science, learn plant science techniques. This course offerred the PD teaching experience as well as the opportunity to network and discuss science with visiting professors. How have the results been disseminated to communities of interest?Results of the project have been disseminated to communities of interest through publications and conference presentations. During this reporting period, the PD presented posters at two conferences: a virtual conference: the Plant Cell Atlas Virtual Symposium 2021, and AGBT Agriculture, an in-person conference in Coronado, CA. Additionally, the PD is a co-first author on a mansucript published this year inDevelopmental Cell.? What do you plan to do during the next reporting period to accomplish the goals?During the next reporting period, I will continue to make progress towards the aims. First, I will generate new RNA-seq and ATAC-seq data which will be leveraged for the goals of Aim 1. This data will include a time course of rice root response to drought which is useful for regression approaches to network inference. Simultaneously, I will work to create a visualization platform for existing network data, which can be overlaid with this new data.I will finish genotyping CRISPR mutants and I will begin phenotyping the mutants for abiotic stress response and suberin (Aim 2.2). I will measure physiological traits under drought stress in the greenhouse, use histochemical stains to evaluate suberin, and collect samples to measure suberin by metabolomics which will be accomplished through collaboration. Finally, I will design a cloning strategy for the synthetic promoters of aim 3.1 and clone them into reporter constructs. These, other reporters, and native promoter : TF fusions will be transformed into rice either in house or through collaboration.
Impacts
What was accomplished under these goals?
Preliminary work for aim 1 was published as a Resource article inDevelopmental Cell,where the PD is a co-first author. Aim 1 will continue with new data which will be generated in year two of the project. Molecular cloningwas completed to generate CRISPR mutants, reporter lines, and promoter:TF fusion lines in rice (from aims 2.1 and 3.2), and transformation of the CRISPR lines was completed through collaboration. CRISPR Mutants of 8 genes which have potential roles in suberin are in the process of being genotyped, with T1 plants which have successful edits and have the cas9 transgene segregated out identified for 3target genes growing to seed in the greenhouse. An additional gene target (enzmye involved in suberin biosynthesis) which was initiated earlier has two independent, homozygous alleles with loss of function mutations. Preliminary phenotyping by fluorol yellow staining shows a signficant reduction in suberin in the roots of these plants.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2021
Citation:
Plant Cell Atlas ConsortiumSuryatapa Ghosh JhaAlexander T BorowskyBenjamin J ColeNoah FahlgrenAndrew FarmerShao-shan Carol HuangPurva KariaMarc LibaultNicholas J ProvartSelena L RiceMaite Saura-SanchezPinky AgarwalAmir H AhkamiChristopher R AndertonSteven P BriggsJennifer AN BrophyPeter DenolfLuigi F Di CostanzoMoises Exposito-AlonsoStefania GiacomelloFabio Gomez-CanoKerstin KaufmannDae Kwan KoSagar KumarAndrey V MalkovskiyNaomi NakayamaToshihiro ObataMarisa S OteguiGergo PalfalviElsa H Quezada-Rodr�guezRajveer SinghR Glen UhrigJamie WaeseKlaas Van WijkR Clay WrightDavid W EhrhardtKenneth D BirnbaumSeung Y Rhee (2021) Science Forum: Vision, challenges and opportunities for a Plant Cell Atlas eLife 10:e66877.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2022
Citation:
AGBT Agriculture, Coronado, CA, April 2022
Defining Gene Regulatory Network Dynamics of Rice Root Cell Populations
Poster Presentation
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2021
Citation:
Plant Cell Atlas Symposium, Virtual , December 2021
Borowsky, A. T., Reynoso, M., Pauluzzi, G., Bailey-Serres, J. A field grown rice translatome atlas.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2021
Citation:
Plants 3D NRT Retreat, Lake Arrowhead, CA, November 2021
Defining Gene Regulatory Network Dynamics of Rice Root Cell Populations
Poster Presentation
- Type:
Journal Articles
Status:
Published
Year Published:
2022
Citation:
Gene regulatory networks shape developmental plasticity of root cell types under water extremes in rice
Reynoso, Mauricio A. et al.
Developmental Cell, Volume 57, Issue 9, 1177 - 1192.e6
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