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

Hasthi Ram, Anmol Singh, Megha Katoch, Ravneet Kaur, Shaswati Sardar, Shubham Palia, Rohit Satyam, Humira Sonah, Rupesh Deshmukh, Ajay Kumar Pandey, Ishaan Gupta, Tilak Raj Sharma

Research output: Contribution to journalArticlepeer-review

12 Scopus citations

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.

Original languageEnglish
Pages (from-to)2212-2230
Number of pages19
JournalJournal of Experimental Botany
Volume72
Issue number6
DOIs
StatePublished - 17 Mar 2021
Externally publishedYes

Keywords

  • Grain
  • nutrient partitioning
  • rice
  • spatial regulation
  • transcriptomics

Fingerprint

Dive into the research topics of 'Dissecting the nutrient partitioning mechanism in rice grain using spatially resolved gene expression profiling'. Together they form a unique fingerprint.

Cite this