Biology subjects

Kitomi, Y.

Publications and source records attributed to Kitomi, Y..

3 recordsLinked to original sources

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↗

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↗