Biology subjects

Qasim, F.

Publications and source records attributed to Qasim, F..

3 recordsLinked to original sources

bioRxiv2025

Tagging and harvesting of developing rice spikelets to demarcate grain developmental stages

PremiseIn rice, grain is the major sink for nutrient storage and is a rich source of carbohydrates, seed storage proteins, lipids, minerals, and vitamins, making it a principal food source for over half of the worlds population. Grain development in rice generally spans over a month and has been divided into five stages, S1-S5, depending upon various morphological and physiological changes occurring in the developing seed. To completely understand the process, rice grain development needs to be examined at each stage. However, there are no detailed protocols available to demarcate grain developmental stages. Methods and ResultsThis protocol describes how to tag and harvest the developing rice spikelets. The process starts with anthesis and continues till seed maturation, demarcating the five stages of rice grain development. Seeds are collected, labelled, and stored for use in molecular experiments. Using this protocol, we were able to identify and distinguish different seed developmental stages as observed by histochemical screening. ConclusionThis is an easy, efficient, and cost-effective method. This protocol ensures the collection of the entire panel of rice seed developmental stages. The stored tissue can later be used for various molecular biology based experiments.

plant biology↗

bioRxiv2024

A novel repressor-activator-competitor module comprising C2H2 zinc finger and NAC transcription factors regulates rice grain development

Grain size and quality are crucial agronomic traits. We have characterized a seed-preferential C2H2 zinc finger transcriptional repressor, ZOS1-15. Its overexpression, knock-down and knock-out plants indicated a negative control over grain size due to altered cell expansion. ZOS1-15 homodimerized and directly interacted with co-repressor TOPLESS and histone deacetylases to form a repression complex. ZOS1-15 also interacted with Mediator subunit MED14_1 and a seed-preferential transcriptional activator, ONAC024, with three alternatively spliced isoforms. The ectopic expression of ONAC024 negatively affected plant growth and development. Seed-preferential overexpression and knock-down plants showed ONAC024 as a positive regulator of grain length due to increased cell proliferation and expansion. CRES-T generated transgenic rice plants indicated a functional divergence amongst ONAC024 isoforms. Tandem interactions were observed between ONAC024-ONAC023-ONAC026-ONAC020. ZOS1-15 and ONAC024 functioned antagonistically to regulate grain amylose and SSP accumulation while ONAC023 affected only amylose. ZOS1-15 and ONAC024 directly regulated the expression of two SSP encoding genes. Binding of ONAC024 was competed by ONAC025-MADS29 complex. The seed-preferential overexpression of SS1/ ONAC025 resulted in decreased grain size and amylose content, but higher yield. This study proposes a repressor-activator-competitor module, wherein ZOS1-15, ONAC024, ONAC023, ONAC025 along with their interactors synergistically and antagonistically regulate multiple aspects of rice grain development.

plant biology↗

bioRxiv2024

A zinc finger transcriptional repressor ZOS5-09 regulates rice grain size, starch and protein biosynthesis

HighlightA rice seed-preferential transcriptional repressor, ZOS5-09 controls grain size by affecting cell proliferation and expansion; and regulates starch and protein biosynthesis. It acts as a repressor by deacetylation. Grain size is the one of the key determinants of grain yield. Transcription factors form an important class of regulatory proteins that play crucial roles in regulating developmental responses. Our study focuses on a novel seed-preferential C2H2 zinc finger transcription factor, ZOS5-09 (LOC_Os05g38600) that plays an important role in regulating grain related traits in rice. Rice plants with ZOS5-09 promoter::GUS construct showed its high expression in rice endosperm. In planta reporter effector assays and localization studies showed that ZOS5-09 is a nuclear localized transcriptional repressor. It has a C-terminal NoRS (nucleolar retention signal). Ectopic and seed-preferential overexpression of ZOS5-09 resulted in lethality. Seed-preferential overexpression without NoRS was detrimental to grain filling. Rice plants with knock-down or CRISPR based knock-out of ZOS5-09 displayed reduced grain length and weight but increased grain width. Plant height, second leaf width, and panicle number were reduced and second leaf length were increased. The change in grain size was due to lower cell proliferation and increased cell size in the transverse direction due to down regulation of cell cycle related genes and increased expression of expansins. Decreased expression of ZOS5-09 also resulted in reduced total starch and protein content and higher endosperm chalkiness, thus, negatively affecting grain quality. ZOS5-09 directly regulated a seed storage protein encoding gene, GLU6 by binding to the zinc finger binding site in its promoter. It acted as a repressor by promoting deacetylation upon interaction with a histone deacetylase. In summary, our results indicate that optimum expression of ZOS5-09 is essential for proper rice grain development. Our study highlights the role of a transcriptional repressor in regulating rice grain traits and improves our understanding of the transcriptional regulatory networks affecting grain size.

plant biology↗