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Project properties |
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| Title | Mapping the salt-induced gene regulatory network that guides root branching |
| Group | Plant Physiology, Laboratory of |
| Project type | thesis |
| Credits | 24-36 |
| Supervisor(s) | Yiyun Li, Dr. Aalt-Jan van Dijk |
| Examiner(s) | Christa Testerink |
| Contact info | yiyun.li@wur.nl AND thesis.PPH@wur.nl |
| Begin date | 2023/03/01 |
| End date | 2023/10/01 |
| Description | As a major abiotic stress, high soil salinity severely affects plant growth and crop productivity globally. Plants are unable to move from their location, and therefore require various effective mechanisms to cope with salinity. In presence of salt, the root architecture is reshaped, which is often characterized by changes in lateral root (LR) development [1]. Though several interactions of genes involved in LR development have been identified under control condition [2], genes and pathways involved in root branching in response to salt remain unclear.
In this project, you will use bioinformatics approaches to analyze salt-related root transcriptome data to identify candidate genes contributes to the salt-induced root branching. You will implement comparative analysis among multiple in-house and publicly available salt-induced root transcriptomic datasets to highlight the similarities and differences in the tissue-specific mechanism of root branching in salt. With the identified candidate genes, you will study the regulatory interactions using gene regulatory network (GRN) inference [3] to map the salt-induced transcriptional regulatory networks that are involved in root branching. Further reading: [1] Van Zelm, E., Zhang, Y., & Testerink, C. (2020). Salt Tolerance Mechanisms of Plants. Annual Review of Plant Biology, 71, 403–433. https://doi.org/10.1146/annurev-arplant-050718-100005 [2] Lavenus, J., Goh, T., Guyomarc’H, S., Hill, K., Lucas, M., Voß, U., Kenobi, K., Wilson, M. H., Farcot, E., Hagen, G., Guilfoyle, T. J., Fukaki, H., Laplaze, L., & Bennett, M. J. (2015). Inference of the arabidopsis lateral root gene regulatory network suggests a bifurcation mechanism that defines primordia flanking and central zones. Plant Cell, 27(5), 1368–1388. https://doi.org/10.1105/tpc.114.132993 [3] Van den Broeck, L., Gordon, M., Inzé, D., Williams, C., & Sozzani, R. (2020). Gene Regulatory Network Inference: Connecting Plant Biology and Mathematical Modeling. Frontiers in Genetics, 11(May), 1–12. https://doi.org/10.3389/fgene.2020.00457 If you are interested in this project please contact the supervisor via email with a copy to thesis.PPH@wur.nl with: 1. Your motivation for choosing this project 2. For which purpose (BSc or MSc thesis, research practice, etc) 3. Your BSc/MSc program 4. When you would like to start Please be aware that if you do not provide the required information above it may cause a delay in our reply. |
| Used skills | Data analysis in R or Python
RNA-seq analysis Network inference |
| Requirements | (Advanced) Bioinformatics (e.g. BIF-30806 Advanced Bioinformatics, SSB-30306 Molecular Systems Biology or relevant course) and basic knowledge of plant physiology |