Biology subjects

Uga, Y.

Publications and source records attributed to Uga, Y..

7 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

Multi-omics profiling with indoor-unmanned phenotyping reveals drought adaptation through constitutive ABF1 expression in wild rice

Improving drought resistance is crucial for stable crop production under climate change. Identifying the mechanisms of drought resistance using diverse genetic resources, including crop wild relatives, would be beneficial for molecular breeding. Here, we developed an indoor, unmanned phenotyping platform that can noninvasively and automatically collect temporal data on plant responses to drought stress. Using this system, we analyzed the phenotypic, transcriptomic, and environmental data of four cultivated rice varieties and five wild relatives. Multi-omics analysis revealed that one wild rice species exhibited drought adaptation through the constitutive expression of ABSCISIC ACID RESPONSIVE ELEMENT-BINDING FACTOR 1 (ABF1), which encodes a transcription factor that regulates drought resistance, before drought stress. Drought testing of introgression lines of cultivated rice with constitutive ABF1 expression revealed higher drought tolerance than in cultivars without a growth penalty. Our findings suggest that constitutive ABF1 expression contributes to drought adaptation in both cultivated and wild rice.

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↗

bioRxiv2023

Non-destructive real-time monitoring of underground root development with distributed fiber optic sensing

Crop genetic engineering for better root systems can offer practical solutions for food security and carbon sequestration; however, soil layers prevent direct visualization. Here, we demonstrate an original device with a distributed fiber-optic sensor for fully automated, real-time monitoring of underground root development. We demonstrate that spatially encoding an optical fiber with a flexible and durable polymer film in a spiral pattern can significantly enhance sensor detection. After signal processing, the resulting device can detect the penetration of a submillimeter-diameter object in the soil, indicating more than a magnitude higher spatiotemporal resolution than previously reported with underground monitoring techniques. We also developed computational models to visualize the roots of root crops and monocotyledons, and then applied them to radish and rice to compare the results with those of X-ray computed tomography. The devices groundbreaking sensitivity and spatiotemporal resolution enable seamless and laborless phenotyping of root systems that are otherwise invisible underground.

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

Synergy between a shallow root system with a DRO1 homologue and localized P application improves rice P uptake

The development of genotypes and fertilizer management practices that facilitate high phosphorus (P) use efficiency is needed given the depleting phosphorus ore deposits and increasing ecological concerns about its excessive use. Root system architecture (RSA) is important in efficiently capturing immobile P in soils, while agronomically, localized P application near the roots is a potential approach to address this issue. However, the interaction between genetic traits of RSA and localized P application has not been examined. Near-isogenic lines (NILs) and their parent of rice (qsor1-NIL, Dro1-NIL, and IR64, with shallow, deep, and intermediate root growth angles (RGA), respectively) were grown in flooded pots in a uniform and P-sufficient condition (Pinco), and with localized P application by dipping seedling roots into P-enriched slurry at transplanting (P-dipping). The P-dipping created an available P hotspot at the soil surface and substantially improved applied P-use efficiency (equivalent biomass at one fifth of application rate of the Pinco). Further, the qsor1-NIL had significantly greater biomass and P uptake than the other genotypes in the P-dipping. The qsor1-NIL consistently had a greater root biomass and surface area in the 0-3 cm soil layer, despite that there were no genotype differences in total values and that the other genotypes also reduced their RGAs responding to the P hotspot in the P-dipping. The shallow root system of qsor1-NIL facilitated P uptake from the P hotspot. P-use efficiency in crop production can be further increased by combining genetic traits of RSA and localized P application.

physiology↗