Nobuhiro Tsutsumi - Academia.edu (original) (raw)

Papers by Nobuhiro Tsutsumi

Plant and Cell Physiology, May 30, 2022

The awn, a needle-like structure extending from the tip of the lemma in grass species, plays a ro... more The awn, a needle-like structure extending from the tip of the lemma in grass species, plays a role in environmental adaptation and fitness. In some crops, awns appear to have been eliminated during domestication. Although numerous genes involved in awn development have been identified, several dominant genes that eliminate awns are also known to exist. For example, in sorghum (Sorghum bicolor), the dominant awn inhibiting gene has been known since 1921; however, its molecular features remain uncharacterized. In this study, we conducted quantitative trait locus analysis and a genome-wide association study of awn-related traits in sorghum and identified DOMINANT AWN INHIBITOR (DAI), which encodes the ALOG family protein on chromosome 3. DAI appeared to be present in most awnless sorghum cultivars, likely because of its effectiveness. Detailed analysis of the ALOG protein family in cereals revealed that DAI originated from duplication of its twin paralog (DAI ori) on chromosome 10. Observations of immature awns in near-isogenic lines revealed that DAI inhibits awn elongation by suppressing both cell proliferation and elongation. We also found that only DAI gained a novel function to inhibit awn elongation through an awn-specific expression pattern distinct from that of DAI ori. Interestingly, heterologous expression of DAI with its own promoter in rice inhibited awn elongation in the awned cultivar Kasalath. We found that DAI originated from gene duplication, providing an interesting example of gain-of-function that occurs only in sorghum but shares its functionality with rice and sorghum.

Frontiers in Plant Science, Mar 29, 2019

Plant Physiology, Jun 16, 2020

Plant and Cell Physiology, Apr 30, 2020

Sorghum [Sorghum bicolor (L.) Moench] grown locally by Japanese farmers is generically termed Tak... more Sorghum [Sorghum bicolor (L.) Moench] grown locally by Japanese farmers is generically termed Takakibi, although its genetic diversity compared with geographically distant varieties or even within Takakibi lines remains unclear. To explore the genomic diversity and genetic traits controlling biomass and other physiological traits in Takakibi, we focused on a landrace, NOG, in this study. Admixture analysis of 460 sorghum accessions revealed that NOG belonged to the subgroup that represented Asian sorghums, and it was only distantly related to American/African accessions including BTx623. In an attempt to dissect major traits related to biomass, we generated a recombinant inbred line (RIL) from a cross between BTx623 and NOG, and we constructed a highdensity linkage map based on 3,710 single-nucleotide polymorphisms obtained by restriction-site-associated DNA sequencing of 213 RIL individuals. Consequently, 13 fine quantitative trait loci (QTLs) were detected on chromosomes 2, 3, 6, 7, 8 and 9, which included five QTLs for days to heading, three for plant height (PH) and total shoot fresh weight and two for Brix. Furthermore, we identified two dominant loci for PH as being identical to the previously reported dw1 and dw3. Together, these results corroborate the diversified genome of Japanese Takakibi, while the RIL population and high-density linkage map generated in this study will be useful for dissecting other important traits in sorghum.

New Phytologist, Dec 20, 2020

Drought and flooding are contrasting abiotic stressors for plants. Evidence is accumulating for r... more Drought and flooding are contrasting abiotic stressors for plants. Evidence is accumulating for root anatomical traits being essential for the adaptation to drought or flooding. However, an integrated approach to comprehensively understand root anatomical traits has not yet been established. Here we analysed the root anatomical traits of 18 wild Poaceae species differing in adaptation to a range of soil water content. Regression model analyses revealed the optimal anatomical traits that were required by the plants to adapt to low or high soil water content. While the area and number of each root tissue (e.g. stele, cortex, xylem or aerenchyma) were not strongly correlated to the soil water content, the ratio of the root tissue areas (cortex to stele ratio (CSR), xylem to stele ratio (XSR) and aerenchyma to cortex ratio (ACR)) could fully explain the adaptations of the wild Poaceae species to the soil water gradients. Our results demonstrate that the optimal anatomical traits for the adaptations to soil water content can be determined by three indices (i.e. CSR, XSR and ACR), and thus we propose that these root anatomical indices can be used to improve the tolerance of crops to drought and flooding stresses.

The Plant Cell, Mar 28, 2017

Reactive oxygen species (ROS) produced by the NADPH oxidase, respiratory burst oxidase homolog (R... more Reactive oxygen species (ROS) produced by the NADPH oxidase, respiratory burst oxidase homolog (RBOH), trigger signal transduction in diverse biological processes in plants. However, the functions of RBOH homologs in rice (Oryza sativa) and other gramineous plants are poorly understood. Ethylene induces the formation of lysigenous aerenchyma, which consists of internal gas spaces created by programmed cell death of cortical cells, in roots of gramineous plants under oxygen-deficient conditions. Here, we report that, in rice, one RBOH isoform (RBOHH) has a role in ethylene-induced aerenchyma formation in roots. Induction of RBOHH expression under oxygen-deficient conditions was greater in cortical cells than in cells of other root tissues. In addition, genes encoding group I calcium-dependent protein kinases (CDPK5 and CDPK13) were strongly expressed in root cortical cells. Coexpression of RBOHH with CDPK5 or CDPK13 induced ROS production in Nicotiana benthamiana leaves. Inhibitors of RBOH activity or cytosolic calcium influx suppressed ethylene-induced aerenchyma formation. Moreover, knockout of RBOHH by CRISPR/Cas9 reduced ROS accumulation and inducible aerenchyma formation in rice roots. These results suggest that RBOHH-mediated ROS production, which is stimulated by CDPK5 and/or CDPK13, is essential for ethylene-induced aerenchyma formation in rice roots under oxygen-deficient conditions.

Plant and Cell Physiology, 2001

The Molecular Biology Society of Japan, Nov 8, 2016

Japanese journal of breeding, 1986

Plant Science, Dec 1, 1996

ABSTRACT A cDNA library was constructed with poly(A)+ RNA prepared from 10-day-old rice seedlings... more ABSTRACT A cDNA library was constructed with poly(A)+ RNA prepared from 10-day-old rice seedlings. We have isolated three nuclear genes, rpl13, rpl24 and rpl28, that encode chloroplast ribosomal proteins L13, L24 and L28, respectively. Comparison with the amino acid sequences of L13, L24 and L28 from other dicotyledonous plants reveals that the deduced amino acid sequences of the mature peptide parts of these cDNAs are more conserved than those of the transit peptide parts. The amino acid compositions of the transit sequences of these proteins are similar to those of the other chloroplast transit sequences which are rich in serine and/or threonine and have a net positive charge. The chloroplast ribosomal proteins L13 and L24 of rice are considerably larger than their eubacterial homologues due to the presence of NH2- and COOH-terminal extensions, respectively. Such extensions are absent in L28 of rice, as is the case with the tobacco chloroplast ribosomal protein L28.

G3: Genes, Genomes, Genetics, Nov 1, 2019

Gamma-rays are the most widely used mutagenic radiation in plant mutation breeding, but detailed ... more Gamma-rays are the most widely used mutagenic radiation in plant mutation breeding, but detailed characteristics of mutated DNA sequences have not been clarified sufficiently. In contrast, newly introduced physical mutagens, e.g., heavy-ion beams, have attracted geneticists' and breeders' interest and many studies on their mutation efficiency and mutated DNA characteristics have been conducted. In this study, we characterized mutations induced by gamma rays and carbon(C)-ion beams in rice (Oryza sativa L.) mutant lines at M 5 generation using whole-genome resequencing. On average, 57.0 single base substitutions (SBS), 17.7 deletions, and 5.9 insertions were detected in each gamma-ray-irradiated mutant, whereas 43.7 single SBS, 13.6 deletions, and 5.3 insertions were detected in each C-ion-irradiated mutant. The structural variation (SV) analysis detected 2.0 SVs (including large deletions or insertions, inversions, duplications, and reciprocal translocations) on average in each C-ion-irradiated mutant, while 0.6 SVs were detected on average in each gamma-ray-irradiated mutant. Furthermore, complex SVs presumably having at least two double-strand breaks (DSBs) were detected only in C-ion-irradiated mutants. In summary, gamma-ray irradiation tended to induce larger numbers of small mutations than C-ion irradiation, whereas complex SVs were considered to be the specific characteristics of the mutations induced by C-ion irradiation, which may be due to their different radiation properties. These results could contribute to the application of radiation mutagenesis to plant mutation breeding. KEYWORDS Mutation breeding Gamma rays Heavy ions Whole genome resequencing Rice Since Muller (1927) provided the proof of mutation induction by X-rays in Drosphila and Stadler (1928) published the first results of mutation induction in crop plants, mutation breeding has been developed rapidly to become a useful method for crop improvement. Since the 1960s, gamma-ray mutagenesis has been the most commonly used method in plant mutation breeding. Among the 3,281 mutant cultivars officially registered in FAO/IAEA mutant variety database (http://mvgs.iaea.org), 1,600 were obtained by gamma-ray irradiation. In Japan, 60% of the mutant varieties have been developed by gammaray irradiation (Nakagawa and Kato 2017). During the past two decades, heavy-ion irradiation has also been accepted as an efficient mutagenesis technology. Gamma rays and heavy-ion beams are both ionizing radiations which are capable of causing the release or capture of electrons (called ionizations) and directly disrupting the chemical bonds of molecules when they pass through matter (Lagoda 2012; Mba et al. 2012). The toxic effects of ionizing radiation arise through the production of reactive oxygen species (ROS) that damage all components of a cell (Lagoda 2012).

Breeding Research, 2013

前川雅彦 1) ・金澤章 2) ・堤伸浩 3) ・木下哲 4) ・土生芳樹 5) ・柴博史 6) ・江面浩 7) 1) 岡山大学資源植物科学研究所，岡山県倉敷市，〒 710-0046 ... more 前川雅彦 1) ・金澤章 2) ・堤伸浩 3) ・木下哲 4) ・土生芳樹 5) ・柴博史 6) ・江面浩 7) 1) 岡山大学資源植物科学研究所，岡山県倉敷市，〒 710-0046 2) 北海道大学大学院農学研究院，北海道札幌市，〒 060-8589 3) 東京大学大学院農学生命科学研究科，東京都文京区，〒 113-8657 4) 奈良先端科学技術大学院大学バイオサイエンス研究科，奈良県生駒市，〒 630-0192 5) 農業生物資源研究所，茨城県つくば市，〒 305-8602 6) 茨城大学理学部，茨城県水戸市，〒 310-8512 7) 筑波大学大学院生命環境科学研究科，茨城県つくば市，〒 305-8572

Plant and Cell Physiology, Mar 21, 2022

Understanding uptake and redistribution of essential minerals or sequestering of toxic elements i... more Understanding uptake and redistribution of essential minerals or sequestering of toxic elements is important for optimized crop production. Although the mechanisms controlling mineral transport have been elucidated in rice and other species, little is understood in sorghum—an important C4 cereal crop. Here, we assessed the genetic factors that govern grain ionome profiles in sorghum using recombinant inbred lines (RILs) derived from a cross between BTx623 and NOG (Takakibi). Pairwise correlation and clustering analysis of 22 elements, measured in sorghum grains harvested under greenhouse conditions, indicated that the parental lines, as well as the RILs, show different ionomes. In particular, BTx623 accumulated significantly higher levels of cadmium (Cd) than NOG, because of differential root-to-shoot translocation factors between the two lines. Quantitative trait locus (QTL) analysis revealed a prominent QTL for grain Cd concentration on chromosome 2. Detailed analysis identified SbHMA3a, encoding a P1B-type ATPase heavy metal transporter, as responsible for low Cd accumulation in grains; the NOG allele encoded a functional HMA3 transporter (SbHMA3a-NOG) whose Cd-transporting activity was confirmed by heterologous expression in yeast. BTx623 possessed a truncated, loss-of-function SbHMA3a allele. The functionality of SbHMA3a in NOG was confirmed by Cd concentrations of F2 grains derived from the reciprocal cross, in which the NOG allele behaved in a dominant manner. We concluded that SbHMA3a-NOG is a Cd transporter that sequesters excess Cd in root tissues, as shown in other HMA3s. Our findings will facilitate the isolation of breeding cultivars with low Cd in grains or in exploiting high-Cd cultivars for phytoremediation.

Scientific Reports, Apr 30, 2021

Although spikelet-related traits such as size of anther, spikelet, style, and stigma are associat... more Although spikelet-related traits such as size of anther, spikelet, style, and stigma are associated with sexual reproduction in grasses, no QTLs have been reported in sorghum. Additionally, there are only a few reports on sorghum QTLs related to grain size, such as grain length, width, and thickness. In this study, we performed QTL analyses of nine spikelet-related traits (length of sessile spikelet, pedicellate spikelet, pedicel, anther, style, and stigma; width of sessile spikelet and stigma; and stigma pigmentation) and six grain-related traits (length, width, thickness, length/width ratio, length/ thickness ratio, and width/thickness ratio) using sorghum recombinant inbred lines. We identified 36 and 7 QTLs for spikelet-related traits and grain-related traits, respectively, and found that most sorghum spikelet organ length-and width-related traits were partially controlled by the dwarf genes Dw1 and Dw3. Conversely, we found that these Dw genes were not strongly involved in the regulation of grain size. The QTLs identified in this study aid in understanding the genetic basis of spikelet-and grain-related traits in sorghum.

Plants, May 11, 2020

Internal oxygen diffusion from shoot to root tips is enhanced by the formation of aerenchyma (gas... more Internal oxygen diffusion from shoot to root tips is enhanced by the formation of aerenchyma (gas space) in waterlogged soils. Lysigenous aerenchyma is created by programmed cell death and subsequent lysis of the root cortical cells. Rice (Oryza sativa) forms aerenchyma constitutively under aerobic conditions and increases its formation under oxygen-deficient conditions. Recently, we have demonstrated that constitutive aerenchyma formation is regulated by auxin signaling mediated by Auxin/indole-3-acetic acid protein (AUX/IAA; IAA). While ethylene is involved in inducible aerenchyma formation, the relationship of auxin and ethylene during aerenchyma formation remains unclear. Here, we examined the effects of oxygen deficiency and ethylene on aerenchyma formation in the roots of a rice mutant (iaa13) in which auxin signaling is suppressed by a mutation in the degradation domain of IAA13 protein. The results showed that AUX/IAA-mediated auxin signaling contributes to ethylene-dependent inducible aerenchyma formation in rice roots. An auxin transport inhibitor abolished aerenchyma formation under oxygen-deficient conditions and reduced the expression of genes encoding ethylene biosynthesis enzymes, further supporting the idea that auxin is involved in ethylene-dependent inducible aerenchyma formation. Based on these studies, we propose a mechanism that underlies the relationship between auxin and ethylene during inducible aerenchyma formation in rice roots.

Proceedings of the National Academy of Sciences of the United States of America, Sep 23, 2019

Data deposition: A complete set of microarray data has been deposited in the Gene Expression Omni... more Data deposition: A complete set of microarray data has been deposited in the Gene Expression Omnibus (GEO) database, https://www.ncbi.nlm.nih.gov/geo (accession no. GSE130131).