Browsing by Author "Rani, Ruchi"

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Integration of metabolite and transcriptome profiles of cultivated and wild rice to unveil gene regulatory networks and key genes determining rice source and sink strength
(Springer Nature Publishing AG, 2025) Singh, Anuradha; Mathan, Jyotirmaya; Dwivedi, Aditi; Rani, Ruchi; Ranjan, Aashish
Targeting source and sink strength for crop yield increase requires a comprehensive genetic and metabolic understanding of desirable source and sink features. We performed comprehensive metabolite and transcriptomic comparisons of the photosynthetic flag leaves and milky-stage developing grains of two cultivated rice varieties (Oryza sativa L. ssp. Indica cv. IR64 and Oryza sativa L. ssp. Japonica cv. Nipponbare) and two wild rice accessions (Oryza rufipogon and Oryza australiensis). The selected wild rice accessions had stronger source strength as evidenced by a higher photosynthesis rate and more abundance of primary metabolites in the photosynthetic leaves than the cultivated varieties. In contrast, cultivated varieties had efficient sink as grains were bigger and accumulated more sugars, amino acids, and fatty acids than the selected wild rice. Transcriptomic analyses identified 9,309 genes for efficient source in wild rice, enriched for biological pathways related to photosynthesis, carbohydrate metabolism, and sucrose transport. 7,062 genes, enriched for starch biosynthesis and lipid metabolism, were associated with the efficient sink strength in the cultivated varieties. Gene co-expression networks showed 267 hub genes for source strength in wild rice that included important genes for photosynthetic reactions and sucrose metabolism. 196 hub genes for sink strength in cultivated rice included genes involved in sucrose, amino acid, and fatty acid metabolism. Gene co-expression modules further identified the candidate transcription regulators, such as zinc finger proteins and NAC for source strength and MYB55/80 and MADS64 for sink strength. Moreover, our analyses suggested a complex interplay of phytohormones regulating rice source and sink strength.
Spatial control of cell division by GA-OsGRF7/8 module in a leaf explains the leaf length variation between cultivated and wild rice
(John Wiley & Sons, 2022) Jathar, Vikram; Saini, Kumud; Chauhan, Ashish; Rani, Ruchi; Ichihashi, Yasunori; Ranjan, Aashish
Cellular and genetic understanding of rice leaf size regulation is limited, despite rice being the staple food of more than half of the global population. We investigated the mechanism controlling the rice leaf length using cultivated and wild rice accessions that remarkably differed for leaf size. Comparative transcriptomics, Gibberellic Acid (GA) quantification, and leaf kinematics of the contrasting accessions suggested the involvement of GA, cell cycle, and Growth-Regulating Factors (GRFs) in the rice leaf size regulation. Zone-specific expression analysis and VIGS established the functions of specific GRFs in the process. The leaf length of the selected accessions was strongly correlated with GA levels. Higher GA content in wild rice accessions with longer leaves and GA-induced increase in the leaf length via an increase in cell division confirmed a GA-mediated regulation of division zone in rice. Downstream to GA, OsGRF7 and OsGRF8 function for controlling cell division to determine the rice leaf length. Spatial control of cell division to determine the division zone size mediated by GA and downstream OsGRF7 and OsGRF8 explains the leaf length differences between the cultivated and wild rice. This mechanism to control rice leaf length might have contributed to optimizing leaf size during domestication.