Tomomi Abiko

Enhanced formation of aerenchyma and induction of a barrier to radial oxygen loss in adventitious roots of Zea nicaraguensis contribute to its waterlogging tolerance as compared with maize (Zea mays ssp. mays)

Enhancement of oxygen transport from shoot to root tip by the formation of aerenchyma and also a barrier to radial oxygen loss (ROL) in roots is common in waterlogging-tolerant plants. Zea nicaraguensis (teosinte), a wild relative of maize (Zea mays ssp. mays), grows in waterlogged soils. We investigated the formation of aerenchyma and ROL barrier induction in roots of Z. nicaraguensis, in comparison with roots of maize (inbred line Mi29), in a pot soil system and in hydroponics. Furthermore, depositions of suberin in the exodermis/hypodermis and lignin in the epidermis of adventitious roots of Z. nicaraguensis and maize grown in aerated or stagnant deoxygenated nutrient solution were studied. Growth of maize was more adversely affected by low oxygen in the root zone (waterlogged soil or stagnant deoxygenated nutrient solution) compared with Z. nicaraguensis. In stagnant deoxygenated solution, Z. nicaraguensis was superior to maize in transporting oxygen from shoot base to root tip due to formation of larger aerenchyma and a stronger barrier to ROL in adventitious roots. The relationships between the ROL barrier formation and suberin and lignin depositions in roots are discussed. The ROL barrier, in addition to aerenchyma, would contribute to the waterlogging tolerance of Z. nicaraguensis.

Introduction of the ZmDof1 gene into rice enhances carbon and nitrogen assimilation under low-nitrogen conditions

The excessive application of nitrogen fertilizer to maximize crop yields causes negative environmental effects such as pollution and ecological imbalance. To overcome this problem, researchers have attempted to improve the nitrogen assimilation capacity of crops. Maize Dof1 (ZmDof1) is a plant-specific transcription factor shown to promote nitrogen assimilation in Arabidopsis thaliana (Arabidopsis) even under nitrogen-deficient conditions. The present study examines the effect of the introduction of the ZmDof1 gene on carbon and nitrogen assimilation in rice. ZmDof1 induced the expression of phosphoenolpyruvate carboxylase (PEPC) genes in transgenic rice plants and transactivated the PEPC promoters in protoplast transient assays, showing similar effects in rice as in Arabidopsis. Transgenic rice expressing ZmDof1 and grown in the presence of 360 μm (nitrogen-sufficient) or 90 μm (nitrogen-deficient) of nitrogen concentrations showed modulation of metabolite content and gene expression associated with the anaplerotic pathway for the TCA cycle, suggesting an increased carbon flow towards nitrogen assimilation. Furthermore, increases in carbon and nitrogen amounts per seedling were found in Dof1 rice grown under nitrogen-deficient conditions. Nitrogen deficiency also resulted in the predominant distribution of nitrogen to roots, accompanied by significant increases in root biomass and modification of the shoot-to-root ratio. Measurement of the CO₂ gas exchange rate showed a significant increase in the net photosynthesis rate in Dof1 rice under nitrogen-deficient conditions. Taken these together, the present study displayed that ZmDof1 expression in rice could induce gene expressions such as PEPC genes, modulate carbon and nitrogen metabolites, increase nitrogen assimilation and enhance growth under low-nitrogen conditions.

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

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

Changes in nitrogen assimilation, metabolism, and growth in transgenic rice plants expressing a fungal NADP(H)-dependent glutamate dehydrogenase (gdhA)

In plants, glutamine synthetase (GS) is the enzyme that is mainly responsible for the assimilation of ammonium. Conversely, in microorganisms such as bacteria and Ascomycota, NADP(H)-dependent glutamate dehydrogenase (GDH) and GS both have important roles in ammonium assimilation. Here, we report the changes in nitrogen assimilation, metabolism, growth, and grain yield of rice plants caused by an ectopic expression of NADP(H)-GDH (gdhA) from the fungus Aspergillus niger in the cytoplasm. An investigation of the kinetic properties of purified recombinant protein showed that the fungal gdhA had 5.4–10.2 times higher Vmax value and 15.9–43.1 times higher Km value for NH4+, compared with corresponding values for rice cytosolic GS as reported in the literature. These results suggested that the introduction of fungal GDH into rice could modify its ammonium assimilation pathway. We therefore expressed gdhA in the cytoplasm of rice plants. NADP(H)-GDH activities in the gdhA-transgenic lines were markedly higher than those in a control line. Tracer experiments by feeding with 15NH4+ showed that the introduced gdhA, together with the endogenous GS, directly assimilated NH4+ absorbed from the roots. Furthermore, in comparison with the control line, the transgenic lines showed an increase in dry weight and nitrogen content when sufficient nitrogen was present, but did not do so under low-nitrogen conditions. Under field condition, the transgenic line examined showed a significant increase in grain yield in comparison with the control line. These results suggest that the introduction of fungal gdhA into rice plants could lead to better growth and higher grain yield by enhancing the assimilation of ammonium.

Enhancement of porosity and aerenchyma formation in nitrogen-deficient rice roots.

Root aerenchyma provides oxygen from plant shoots to roots. In upland crops, aerenchyma formation is induced mainly by oxygen or nutrient deficiency. Unlike upland crops, rice forms root aerenchyma constitutively and also inductively in response to oxygen deficiency. However, the effects of nitrogen deficiency on aerenchyma formation in rice remain unknown although nitrogen deficiency is common in most of the worlds soils. We aimed to clarify the spatiotemporal patterns of aerenchyma formation induced in rice roots by nitrogen deficiency upon establishment of reliable growth conditions. Rice was grown hydroponically to evaluate porosity and aerenchyma formation induced by nitrogen and oxygen deficiency. Reliable growth conditions for nitrogen and oxygen deficiency were successfully established, because seedling root elongation was significantly promoted by nitrogen deficiency and inhibited by oxygen deficiency. Porosity was higher in whole roots grown under nitrogen and oxygen deficiency than in the controls. Root aerenchyma production was induced extensively by nitrogen deficiency but partially by oxygen deficiency. Thus the physiological roles of aerenchyma induced by nitrogen deficiency likely differ from those under oxygen deficiency. It indicates a possibility that inducible aerenchyma formation in nitrogen deficiency might promote adaptation to this deficiency by reducing respiration and remobilizing nitrogen, or both.

Loss of sense transgene-induced post-transcriptional gene silencing by sequential introduction of the same transgene sequences in tobacco.

RNA silencing is an epigenetic inhibition of gene expression and is guided by small interfering RNAs. Sense transgene‐induced post‐transcriptional gene silencing (S‐PTGS) occurs in a portion of a transgenic plant population. When a sense transgene encoding a tobacco endoplasmic reticulum ω‐3 fatty acid desaturase (NtFAD3) was introduced into tobacco plants, an S‐PTGS line, S44, was obtained. Introduction of another copy of the NtFAD3 transgene into S44 plants caused a phenotypic change from S‐PTGS to overexpression. Because this change was associated with the methylation of the promoter sequences of the transgene, reduced transcriptional activity may abolish S‐PTGS and residual transcription of the sense transgene may account for the overexpression. To clarify whether RNA‐directed DNA methylation (RdDM) can repress the transcriptional activity of the S44 transgene locus, we introduced several RdDM constructs targeting the transgene promoter. An RdDM construct harboring a 200‐bp‐long fragment of promoter sequences efficiently abrogated the generation of NtFAD3 small interfering RNAs in S44 plants. Transcription of the transgene was partially repressed, but the resulting NtFAD3 mRNAs successfully accumulated and an overexpressed phenotype was established. Our results indicate an example in which overexpression of the transgene is established by complex epigenetic interactions among the transgenic loci.

Phenotypic variation in root development of 162 soybean accessions under hypoxia condition at the seedling stage

Abstract Soybean is often damaged by hypoxia caused by waterlogging at the seedling stage. Hypoxia severely inhibits root development and retards plant growth. We aimed to clarify phenotypic variation in root development under hypoxia condition at the seedling stage using diverse soybean accessions. Root development in 162 accessions was evaluated in hydroponic culture. Substantial changes under hypoxia were investigated by means of WinRHIZO analysis before and after the treatment. We found significant phenotypic variation in hypoxia tolerance in root among the 162 accessions. A principal components analysis indicated an association between hypoxia tolerance and the country of origin. We found three new accessions which have a high ability to develop roots under hypoxia (Kokubu 7, Maetsue zairai 90B, and Yahagi). Root development in selected accessions was also evaluated in soil culture. Root development levels in hydroponic and soil culture were significantly correlated. These results will provide important information on waterlogging damage in regions where waterlogging occurs. The three accessions with hypoxia-tolerant roots might be useful for genetic improvement of waterlogging tolerance of modern soybean varieties.