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

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.