Dissecting the nutrient partitioning mechanism in rice grain using spatially resolved gene expression profiling

Abstract

Rice, a staple food worldwide, contains varying amount of nutrients in different grain tissues. The underlying molecular mechanism of such distinct nutrient partitioning remains poorly-investigated. Here, an optimized rapid Laser Capture Microdissection (LCM) approach was used to individually collect pericarp, aleurone, embryo and endosperm from 10 Days After Fertilization (DAF) old grains. Subsequent RNA-Seq analysis in these tissues have identified 7760 differentially expressed genes (DEGs). Analysis of promoter sequences of tissue specific genes identified many known and novel cis-elements important for grain filling and seed development. Using identified DEGs, comprehensive spatial gene expression pathways were built for spatial accumulation of starch, proteins, lipids and iron. The extensive transcriptomic analysis has provided many novel insights about nutrient partitioning mechanisms, for instance, it reveals a gradient in Seed Storage Protein accumulation across the analysed four tissue-types. It further reveals that partitioning of various minerals, such as iron, is most likely regulated through transcriptional control of their transporters. In addition, the extensive analysis of this study is presented as an interactive online tool (https://biogeek.shinyapps.io/DEGs/) that provides a much-needed resource for future functional genomics studies aimed to improve grain quality and seed development.

Vacuolar Iron Transporter (Like) proteins: Regulators of cellular iron accumulation in plants

“…The rice genome also contain five VTL genes (Sharma et al, 2020). In recent RNA‐Seq study, it was observed that OsVTL2 has strong expression in endosperm compared to the embryo and pericarp (Ram et al, 2020).…”

Integration of embryo-endosperm interaction into a holistic and dynamic picture of seed development using a rice mutant with notched-belly grains

“…These comprehensive studies provided insights into the molecular networks and pathway interactions that function during the development of individual seed compartments for Arabidopsis (Belmonte et al, 2013), maize (Chen et al, 2014;Yi et al, 2019), wheat (Triticum aestivum; Xiang et al, 2019), and barley (Hordeum vulgare; Bian et al, 2019). In rice, laser-capture microdissection (LCM) has been employed to unravel the molecular mechanisms underpinning grain development and its response to abiotic stress (Ishimaru et al, 2019;Ram et al, 2020;Wu et al, 2020). Regardless of a large number of comprehensive studies on the transcriptome atlas for the developing seed with high spatio-temporal resolutions, detailed information about the communications between embryo and endosperm is still lacking, which is partly attributed to the complexity of seed structures (Doll et al, 2020).…”

The cellulose--lignin balance affects the twisted growth of Yunnan pine trunk

“…Each sample consisted of three independent biological replicates. The quantity and quality of RNA samples were analyzed using a 2100 Bioanalyzer (Agilent Technologies, USA) (Ram et al, 2020). High-quality RNA samples were used to construct cDNA libraries, and the starting RNA material for library construction was total RNA.…”