Dissecting the nutrient partitioning mechanism in rice grain using spatially resolved gene expression profiling. (17th November 2020)

• Record Type: Journal Article
• Authors: Ram, Hasthi; Singh, Anmol; Katoch, Megha; Kaur, Ravneet; Sardar, Shaswati; Palia, Shubham; Satyam, Rohit; Sonah, Humira; Deshmukh, Rupesh; Pandey, Ajay Kumar; Gupta, Ishaan; Sharma, Tilak Raj
• Editors: Küpper, Hendrik
• Is Part Of: Journal of experimental botany. Volume 72:Number 6(2021)
• Page Start: 2212
• Page End: 2230
• Publication Date: 2020-11-17
• Subjects: Grain -- nutrient partitioning -- rice -- spatial regulation -- transcriptomics; Botany -- Periodicals; Botany, Experimental -- Periodicals; Plant physiology -- Periodicals; 580
• DOI: 10.1093/jxb/eraa536
• Languages: English
• ISSNs: 0022-0957

Abstract

Abstract : A spatial gene expression network regulates the partitioning of different nutrients in multiple compartments of rice grain. Abstract: Rice, a staple food worldwide, contains varying amounts 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 grains 10 days after fertilization. Subsequent RNA-Seq analysis in these tissues identified 7760 differentially expressed genes. Analysis of promoter sequences of tissue-specific genes identified many known and novel cis -elements important for grain filling and seed development. Using the identified differentially expressed genes, comprehensive spatial gene expression pathways were built for accumulation of starch, proteins, lipids, and iron. The extensive transcriptomic analysis provided novel insights about nutrient partitioning mechanisms; for example, it revealed a gradient in seed storage protein accumulation across the four tissue types analysed. The analysis also revealed that the partitioning of various minerals, such as iron, is most likely regulated through transcriptional control of their transporters. We present the extensive analysis from this study as an interactive online tool that provides a much-needed resource for future functional genomics studies aimed to improve grain quality and seed development.