description
- Root angle is an important agronomic trait, which enable plants to capture soil resources from different soil profiles. For instance, steeper roots can capture mobile water and nitrogen from deep soil, whereas shallow roots capture immobile phosphorous from topsoil. Root-types such as primary, seminal and crown emerge and grow at distinct angles, called gravitropic setpoint angles (GSA), which are determined by competing gravitropic and anti-gravitropic offset (AGO) mechanisms. GSA of root-types can be easily visualised and studied in wheat, an important UK and worldwide crop, by subjecting vertically grown roots to gravistimulus. Primary root bends faster than 1st set and much faster than the 2nd set of seminal roots until they reset to their original GSA over time. Despite our recent discovery of EGT1 controlling root angle in cereal crops (Fusi et al., 2022), we lack fundamental understanding about (i) root-type specific downstream components functioning in competing gravitropic and AGO mechanisms (ii) whether the number or the amount of expression of these components determine the GSA in each root-type and (iii) how (i and ii) are modulated during environmental conditions. To address this knowledge-gap, we are currently generating transcriptome dataset for individual root-types harvested at different timepoints after gravistimulus (addition to dataset mentioned in rotation project). DTP student will use systems biology approach to build the gene regulatory networks (GRNs), identify predictors of GSA in each root-type and validate them using existing genetic and genomic resources. Work plan: Year1-2: Building root-type specific GRNs functioning in gravitropic and AGO mechanisms Generated transcriptome datasets will be analysed to find differentially expressed genes (DEGs) in each and between root-types. Statistical and machine learning based tools (e.g., ARACNE, GENE3) will be used to build GRNs. These GRNs will be studied in combination with DEGs identified in egt1 mutant vs Wildtype (impaired in AGO) to find gravitropic and AGO specific modules. Year2-3: Predicting regulators that determine GSA in each root-type. Implement computational models at cellular and macroscopic scales and use parameters to identify best predictors (e.g., genes/TFs) of root angle in each root-type using sensitivity analysis. This will also help determine whether number of these predictors (operating in gravitropic vs AGO mechanisms) or their amplitude of expression underpins the GSA in each root-type. Year3-4: Validating GSA predictors using genetic and genomic resources in wheat. To prioritise key predictors, we will investigate how much natural variation in root-type specific GSA (being generated for >800 Watkins landraces, available through JIC) is explained by the polymorphism within predictor genes. Prioritised predictors will be validated using TILLING mutants, RNAi or CRISPR-Cas9 approaches under optimal/sub-optimal conditions. Hormones such as auxin are known to influence both gravitropic and AGO mechanisms. If any predictors are involved in hormone signaling pathways or related processes, we will validate them using existing mutants at RRes. Output and impact: The identified genetic components and fundamental knowledge will provide innovative genetic solutions to breeders (via the BBSRC Developing Future Wheat Breeder Tool kit) to help expedite improvements in wheat and other related cereal crops