Genome‐wide transcriptome dissection of the rice root system: implications for developmental and physiological functions

Abstract

SUMMARYThe 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 (http://ricexpro.dna.affrc.go.jp), thereby providing useful information for understanding the molecular mechanisms involved in root system development of crop plants.

Nuclear Transcriptomes at High Resolution Using Retooled INTACT

“…Moreover, use of the same promoters to drive INTACT and TRAP constructs might be used to target the same regions and cell types to obtain a comparative readout of nuclear pre-mRNA and translated mRNAs. The laser capture microdissection of tissue performed on rice (Jiao et al, 2009;Takehisa et al, 2012) and other species is not limited by genotype, whereas INTACT, fluorescentactivated cell sorting, and TRAP require transgenic plants (reviewed by Bailey-Serres, 2013). This disadvantage may be outweighed by the advantage of INTACT and TRAP over other methods of isolation of nuclei and transcripts from defined cells, as tissues may be cryopreserved prior to biochemical purifications.…”

Phosphate deficiency signaling pathway is a target of arsenate and phosphate transporterOsPT1is involved in As accumulation in shoots of rice

“…Per.Stel. ), according to the Rice ExPro database (Takehisa et al 2012). Taken together with the plasma membrane localization of OsPT1 (Fig.…”

Exploration of Native Mycorrhiza on Rhizosphere of Gleichenia linearis in Nickel Post-Mining Rehabilitation Area of Sorowako, Indonesia

“…The rhizosphere is an excellent habitat for microbial growth because the plant roots provide various organic matters that generally stimulate the growth of microbes. Organic matter released by the roots can be in the form of root exudate (Fajarwati, 2007;Wihardjaka, 2010), root secretion and lysates (Sari, 2015), mucigel (Takehisa et al, 2012). Several factors affecting the rhizosphere effect are soil type, soil moisture, soil pH, soil temperature, plant age, and crop conditions (Budiyanto, 2015).…”