Research Projects

(a) Rationale: Rice has a fibrous root system, composed of an embryonic primary root, several shoot-derived crown roots (CRs) and two types (L-type and S-type) of root-borne lateral roots (LRs). Importantly, innermost ground tissues of rice stem initiate CR formation whereas pericycle and endodermal cells located adjacent to the phloem tissues of parent roots initiate LRs, suggesting divergence in the developmental origins of various root-types in rice. Recently, using laser capture microdissection coupled RNA sequencing (LCM-seq), we revealed that WUSCHEL-related, auxin-responsive transcription factor, OsWOX10 is activated at the site of CR primordia (CRP) initiation and its function is necessary and sufficient for activating CR- and LR-specific developmental program. It has a differential role L- and S-type LRs, suggesting a functional divergence of conserved factor in different root-types. Thus, identifying key genetic regulators downstream of OsWOX10 in regulating CR and LR development would allow us to dissect-out the mechanistic divergence in regulatory function of OsWOX10 during root branching. (b) Scientific Objectives: Broad aim of the proposal is “Identifying key common and root-type-specific regulatory modules, functioning downstream of OsWOX10 during rice CR and LR development”. Specific objectives are- (i) Examining tissues-specific expression pattern of OsWOX10 during CR and LR development (ii) Detailed investigation of conservation and divergence of OsWOX10 function during CR and LR development (iii) Delineating OsWOX10-regulated common and root-type-specific global gene regulatory modules in CR and LR (iv) Uncovering temporal-spatial expression pattern of OsWOX10-regulated genes during CRP and LRP morphogenesis (c) Hypothesis and Experimental plans: We hypothesize that genome-wide identification of key genes and signaling pathways regulated by OsWOX10 during CR and LR development would provide an overview of mechanistic divergence between shoot-borne and root-borne roots. This will reveal how conserved factors modulate genetic networks for tissue trans-differentiation/lineage reprograming. It would also identify tissue-, root- and species-specific developmental programs evolved in plants. Experimentally, we would generate differential gene expression maps of CR and LR development in rice using loss-of-function CRISPR-knockout and gain-of-function inducible over-expression transgenic rice lines for OsWOX10. (d) Expected outcome and its significance: We expect to generate OsWOX10-dependent root-type-specific transcriptional maps and reveal conserved and diverged gene regulatory modules during rice CR and LR development. We also expect to provide an insight on functional and regulatory innovations of OsWOX10 in regulating root branching. The study would set a stage for functional studies of some key regulators and future manipulation of these regulators to improve root system architecture in crop species.