Biology subjects

Jathar, V.

Publications and source records attributed to Jathar, V..

3 recordsLinked to original sources

bioRxiv2025

Integrative comparative transcriptomics using cultivated and wild rice reveals key regulators of developmental and photosynthetic progression along the rice leaf developmental gradient

A comprehensive understanding of gene regulatory networks and the key regulators underlying developmental and physiological progression along the leaf developmental gradient is crucial for optimizing photosynthetic competence. Comparisons of developmental and photosynthetic features across successive leaf developmental stages revealed pronounced differences between wild rice (Oryza australiensis) and three cultivated rice accessions. Global gene expression profiling identified three major transcriptional phases across leaf stages: a predominance of developmental genes at SAM+Pi (initiating primordia) and P3; genes for photosynthetic transition at P3 and P4; and enriched core photosynthetic genes at P4 and P5. O. australiensis showed a more prominent expression of developmental and photosynthetic genes than cultivated accessions across leaf stages. Multivariate analysis further supported a distinct transcriptional landscape in O. australiensis compared with cultivated accessions. Integration of gene expression with species-specific variations in regulatory sequences, derived from synteny-anchored orthology analysis, generated stage-resolved gene regulatory networks and identified key transcription factors (TFs) mediating the developmental and physiological progression. A cross-species comparison of TF-target regulatory networks revealed extensive stage- and accession-dependent rewiring of the regulatory networks of key TFs, with strong regulatory divergence in O. australiensis. Gene silencing of two candidate TFs, OsDOF8 and OsARID2, altered the rice photosynthetic competence with accession-specific effects. Taken together, the study highlights promoter-driven regulatory divergence as a potential mechanism underlying developmental and photosynthetic differences among the rice accessions. The resource is available through an interactive public database, Rice DEV-LEAF (https://nipgr.ac.in/DEV-LEAF/), enabling exploration of gene expression dynamics and regulatory networks across the rice leaf developmental gradient.

plant biology↗

bioRxiv2021

GA-mediated spatial control of cell division expounds the leaf size variation between cultivated and wild rice

O_LICellular 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. C_LIO_LIComparative 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. C_LIO_LIThe 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. C_LIO_LISpatial 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. C_LI

plant biology↗

bioRxiv2019

Anatomical features, efficient photosystem, and Rubisco activity contribute to high leaf photosynthesis in wild rice

The importance of increasing photosynthetic efficiency for sustainable crop yield increases to feed the growing world population is well recognized. The natural genetic variation for leaf photosynthesis in crop plants is largely unexploited for increasing genetic yield potential. The genus Oryza, including cultivated rice and wild relatives, offers tremendous genetic variability to explore photosynthetic differences, and underlying biochemical, photochemical, and developmental bases. We quantified leaf photosynthesis and related physiological parameters for six cultivated and three wild rice genotypes, and identified photosynthetically efficient wild rice accessions. Fitting A/Ci curves and biochemical analyses showed that the leaf photosynthesis in cultivated rice varieties, IR64 and Nipponbare, was limited due to leaf nitrogen content, Rubisco activity, and electron transport rate compared to photosynthetically efficient accessions of wild rice Oryza australiensis and Oryza latifolia. The selected wild rice accessions with high leaf photosynthesis per unit area had striking anatomical features, such as larger mesophyll cells with more chloroplasts, fewer mesophyll cells between two consecutive veins, and higher mesophyll cell and chloroplast surface area exposed to intercellular space. Our results show the existence of desirable variations in Rubisco activity, electron transport rate, and leaf anatomical features in the rice system itself that could be targeted for increasing the photosynthetic efficiency of cultivated rice varieties. HighlightDistinct leaf biochemical, photochemical, and developmental features contribute to efficient photosynthesis in the selected wild rice accessions that could potentially be exploited to increase rice leaf photosynthesis.

plant biology↗