Biology subjects

Teramoto, S.

Publications and source records attributed to Teramoto, S..

5 recordsLinked to original sources

bioRxiv2026

Root shape phenotyping using three-dimensional root system vector data in rice

PurposeAlternation of root distribution in the soil is a method for improving root system architecture (RSA) in crops. If the root is straight, root distribution has been altered by regulating the angle of root growth in the vertical direction. However, the root shape should be curved and winding. This study aimed to define parameters reflecting the actual root shape. MethodsWe used three-dimensional vector data of rice (Oryza sativa L.) RSA derived from an X-ray computed tomography image to compile two sets of two-dimensional vector data for horizontal and vertical components. In the vertical component, we defined the dropping angle{theta} d, which is calculated assuming that the rice roots are bent upward. In the horizontal component, we defined the polar angle{theta}{rho} , which is the direction in which the roots grow when viewing the plant from above, and the winding degree log {sigma}w, which is calculated by assuming that root elongation is in a random walk. ResultsAssuming that{theta}{rho} is distributed uniformly in all varieties, there should be no varietal differences in this angle. We measured{theta} d and log {sigma}w of three rice varieties with different root distributions: shallow, deep, and intermediate. We found significant varietal difference in{theta} d and log {sigma}w. ConclusionsWe have shown that{theta} d and log {sigma}w are useful parameters for comparing RSA in rice varieties. We have named this methodology RSAparam3D, and it is freely available to researchers.

Plant Biology↗

bioRxiv2026

Characterization of Rhizosphere Oxidation Associated with Root Development in Rice Using Planar Oxygen Optodes

Rhizosphere oxidation is a key adaptive mechanism in reductive soil environments, in which oxygen released from roots alters rhizosphere redox conditions and regulates biogeochemical processes. Rice plants possess an internal oxygen transport system, and radial oxygen loss (ROL) from roots is closely associated with root development. However, the spatial patterns of ROL in soil and their relationships with root traits remain poorly characterized. In this study, we developed a multimodal imaging system that integrates planar oxygen optodes with X-ray computed tomography to simultaneously visualize rhizosphere oxidation and root development in rice. Daily time-course tracking of individual crown roots revealed dynamic changes in the spatial distribution and magnitude of rhizosphere oxygen in relation to root elongation and aging. Root thickness was positively correlated with dissolved oxygen levels near root tips. Genotypic comparisons further identified a cultivar with reduced rhizosphere oxidation despite possessing thicker roots among the tested genotypes, thereby indicating the involvement of additional physiological processes. Overall, these findings demonstrate that rhizosphere oxidation is regulated by root growth stage and thickness and dynamically modulated during root development.

plant biology↗

bioRxiv2025

Vertical rooting caused by enhanced functional allele of qSOR1 improves rice yield under drought stress

Drought considerably affects crop productivity, and its severity is being intensified by climate change. Therefore, enhancing drought resistance is a crucial priority in crop breeding for ensuring sustainable agriculture. The root system architecture (RSA) influences the efficiency of water acquisition from land; therefore, a deep RSA is advantageous for avoiding drought stress. Here, we demonstrated that deeper RSA promoted by the qSOR1-v mutant allele (an enhanced functional allele of the quantitative trait locus for SOIL SURFACE ROOTING 1) significantly improves rice yield under drought when compared to the deep RSA achieved through the functional qSOR1 allele that originated from natural variation. The qSOR1-v mutant exhibited stronger root gravitropism than the wild type. This was characterized by a more pronounced polarization of auxin on the lower side during root curvature, leading to a robust vertical rooting phenotype that was consistently expressed across different soil-water environments. Additionally, the qSOR1-v mutation site was well conserved among angiosperm orthologs, and the corresponding mutation in LZY3 of Arabidopsis (qSOR1 ortholog) resulted in a steeper root growth angle. The rice introgression line, which was substituted from the functional qSOR1 allele to qSOR1-v through marker-assisted selection, showed vertical rooting, resulting in increased grain yield in an upland field under drought stress. No yield penalty was observed for this line under well-watered upland conditions than the original variety. These findings highlight the potential of qSOR1-v and corresponding mutations in angiosperm orthologs to promote vertical rooting across plant species, which can help sustain crop yields in drought-prone areas. Significance StatementGenetic modification of the root system architecture in crops represents a viable strategy for the development of climate-resilient crops. This study identified the qSOR1-v allele that consistently demonstrates a vertical rooting phenotype in rice across diverse growth conditions, from dry to wet. The preservation of the qSOR1 and LZY3 orthologs in angiosperms provides opportunities for the development of genotypes characterized by vertical rooting. The introgression of the qSOR1-v allele enhanced drought resistance under upland conditions. These findings underscore the potential of these genetic modifications to improve crop resilience in an era characterized by water scarcity.

plant biology↗

bioRxiv2020

The transcriptomic landscapes of diverse rice cultivars grown under mild drought conditions

Root system architecture affects plant drought tolerance and other key agronomic traits such as lodging. However, although phenotypic and genomic variation has been extensively analyzed, few field studies have integrated phenotypic and transcriptomic information, especially for below-ground traits such as root system architecture. Here, we report the phenotypic and transcriptomic landscape of 61 rice (Oryza sativa) accessions with highly diverse below-ground traits grown in an upland field under mild drought stress. We found that four principal components explained the phenotypic variation and that accessions could be classified into four admixture groups (admixed, aus, indica, and japonica) based on their tiller numbers and crown root diameters. Transcriptome analysis revealed that differentially expressed genes associated with specific admixture groups were enriched with stress response-related genes, suggesting that admixture groups have distinct stress response mechanisms. Root growth was negatively correlated with auxin-inducible genes, suggesting an association between auxin signaling and mild drought stress. A negative correlation between crown root diameter and stress response-related genes suggested that thicker crown root diameter is associated with resistance to mild drought stress. Finally, co-expression network analysis implemented with DNA affinity purification followed by sequencing (DAP-seq) analysis identified phytohormone signaling networks and key transcription factors negatively regulating crown root diameter. Our datasets provide a useful resource for understanding the genomic and transcriptomic basis of phenotypic variation under mild drought stress. ONE-SENTENCE SUMMARYCatalog of the phenomes and transcriptomes of rice cultivars grown in upland fields provides a resource for further studies toward breeding climate-resilient crops.

plant biology↗

bioRxiv2020

OsNLP4 is required for nitrate assimilation gene expressions and nitrate-dependent growth in rice

In plants, nitrate is important nutrient and signaling molecule that modulates the expression of many genes and regulates growth. In paddy grown rice, nitrogen is mostly supplied in the form of ammonium, but nitrate also shares substantial portion of available nitrogen. A number of nitrogen transporters and nitrate assimilation enzymes have been identified and functionally characterized. However, little is known about the nitrate sensor system and regulatory mechanisms of these nitrate related genes. In recent years, NIN-like proteins (NLPs) have been described as key transcription factors of nitrogen responses in Arabidopsis thaliana. But the functions of OsNLPs in rice are still elusive. Here we report the characterization of OsNLP4 to reveal its function in rice. Growths of OsNLP4 knockout mutants were reduced under the nitrate supply, but not under ammonium supply. The mRNA accumulation of genes involved in nitrate assimilation were declined significantly and nitrate uptake rate and nitrate reductase activity were also impaired in the mutants. Using rice protoplast transient expression system, OsNLP4-GFP fusion was localized to nucleus irrespective of nitrate conditions. OsNLP4 was also required for normal yield under paddy field conditions. We propose the OsNLP4 is essential for regulation of genes involved in nitrate assimilation and nitrate-dependent growth in rice. One sentence summaryThe osnlp4 mutants exhibit abnormal nitrate response and poor growth under nitrate supply and in paddy field conditions.

plant biology↗