Genome-wide transcriptome dissection of the rice root system: Implications for developmental and physiological functions

Hinako Takehisa, Yutaka Sato, Motoko Igarashi, Tomomi Abiko, Baltazar A. Antonio, Kaori Kamatsuki, Hiroshi Minami, Nobukazu Namiki, Yoshiaki Inukai, Mikio Nakazono, Yoshiaki Nagamura

Research output: Contribution to journalArticlepeer-review

94 Citations (Scopus)


The root system is a crucial determinant of plant growth potential because of its important functions, e.g. uptake of water and nutrients, structural support and interaction with symbiotic organisms. Elucidating the molecular mechanism of root development and functions is therefore necessary for improving plant productivity, particularly for crop plants, including rice (Oryza sativa). As an initial step towards developing a comprehensive understanding of the root system, we performed a large-scale transcriptome analysis of the rice root via a combined laser microdissection and microarray approach. The crown root was divided into eight developmental stages along the longitudinal axis and three radial tissue types at two different developmental stages, namely: epidermis, exodermis and sclerenchyma; cortex; and endodermis, pericycle and stele. We analyzed a total of 38 microarray data and identified 22 297 genes corresponding to 17 010 loci that showed sufficient signal intensity as well as developmental- and tissue type-specific transcriptome signatures. Moreover, we clarified gene networks associated with root cap function and lateral root formation, and further revealed antagonistic and synergistic interactions of phytohormones such as auxin, cytokinin, brassinosteroids and ethylene, based on the expression pattern of genes related to phytohormone biosynthesis and signaling. Expression profiling of transporter genes defined not only major sites for uptake and transport of water and nutrients, but also distinct signatures of the radial transport system from the rhizosphere to the xylem vessel for each nutrient. All data can be accessed from our gene expression profile database, RiceXPro (), thereby providing useful information for understanding the molecular mechanisms involved in root system development of crop plants.

Original languageEnglish
Pages (from-to)126-140
Number of pages15
JournalPlant Journal
Issue number1
Publication statusPublished - Jan 2012
Externally publishedYes

All Science Journal Classification (ASJC) codes

  • Genetics
  • Plant Science
  • Cell Biology


Dive into the research topics of 'Genome-wide transcriptome dissection of the rice root system: Implications for developmental and physiological functions'. Together they form a unique fingerprint.

Cite this