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Tokuyama Y, Omachi M, Kushida S, Hikichi K, Okada S, Onishi K, Ishii T, Kishima Y, Koide Y. Different contributions of PROG1 and TAC1 to the angular kinematics of the main culm and tillers of wild rice (Oryza rufipogon). PLANTA 2023; 259:19. [PMID: 38085356 DOI: 10.1007/s00425-023-04300-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Accepted: 11/18/2023] [Indexed: 12/18/2023]
Abstract
MAIN CONCLUSION PROG1 is necessary but insufficient for the main culm inclination while TAC1 partially takes part in it, and both genes promote tiller inclination in Asian wild rice. Asian wild rice (Oryza rufipogon), the ancestor of cultivated rice (O. sativa), has a prostrate architecture, with tillers branching from near the ground. The main culm of each plant grows upward and then tilts during the vegetative stage. Genes controlling tiller angle have been reported; however, their genetic contributions to the culm movement have not been quantified. Here, we quantified their genetic contributions to angular kinematics in the main culm and tillers. For the main culm inclination, one major QTL surrounding the PROG1 region was found. In cultivated rice, tillers firstly inclined and lately rose, while it kept inclining in wild rice. It was suggested that PROG1 affected the tiller elevation angle in the later kinematics, whereas TAC1 was weakly associated with the tiller angle in the whole vegetative stage. Micro-computed tomography (micro-CT) suggested that these angular changes are produced by the bending of culm bases. Because near-isogenic lines (NILs) of wild rice-type Prog1 and Tac1 alleles in the genetic background of cultivated rice did not show the prostrate architecture, the involvement of another gene(s) for inclination of the main culm was suggested. Our findings will not only contribute to the understanding of the morphological transition during domestication but also be used in plant breeding to precisely reproduce the ideal plant architecture by combining the effects of multiple genes.
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Affiliation(s)
- Yoshiki Tokuyama
- Research Faculty of Agriculture, Hokkaido University, Sapporo-Shi, Hokkaido, 060-8589, Japan
| | - Miku Omachi
- Research Faculty of Agriculture, Hokkaido University, Sapporo-Shi, Hokkaido, 060-8589, Japan
| | - Shiori Kushida
- Research Faculty of Agriculture, Hokkaido University, Sapporo-Shi, Hokkaido, 060-8589, Japan
| | - Kiwamu Hikichi
- Research Faculty of Agriculture, Hokkaido University, Sapporo-Shi, Hokkaido, 060-8589, Japan
| | - Shuhei Okada
- Research Faculty of Agriculture, Hokkaido University, Sapporo-Shi, Hokkaido, 060-8589, Japan
| | - Kazumitsu Onishi
- Research Department of Agro-Environmental Science, Obihiro University of Agriculture and Veterinary Medicine, Obihiro-Shi, Hokkaido, 080-8555, Japan
| | - Takashige Ishii
- Graduate School of Agricultural Science, Kobe University, Kobe-Shi, Hyogo, 657-8501, Japan
| | - Yuji Kishima
- Research Faculty of Agriculture, Hokkaido University, Sapporo-Shi, Hokkaido, 060-8589, Japan
| | - Yohei Koide
- Research Faculty of Agriculture, Hokkaido University, Sapporo-Shi, Hokkaido, 060-8589, Japan.
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Wang X, Zhang Z, Peng W, Huang J, Yan X, Yao W, Ouyang J, Li S. Inositolphosphorylceramide synthases, OsIPCSs, regulate plant height in rice. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 335:111798. [PMID: 37467787 DOI: 10.1016/j.plantsci.2023.111798] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 07/14/2023] [Accepted: 07/16/2023] [Indexed: 07/21/2023]
Abstract
Inositolphosphorylceramide synthase (IPCS) catalyses ceramides and phosphatidylinositol (PI) into inositolphosphorylceramide (IPC), which is involved in the regulation of plant growth and development. A total of three OsIPCS family genes have been identified in rice. However, most of their functions remain unknown. Here, the functions of OsIPCSs were analyzed by CRISPR/Cas9 technology, lipidomics analysis, and transcriptomics analysis. Single-gene mutation of OsIPCSs resulted in dwarf phenotype. Among them, the phenotype of osipcs3 mutant was more severe. Multi-gene mutation of OsIPCS genes led to more severe phenotypes, indicating the additive effects of OsIPCSs. We further determined that a significant decrease in epidermal cell elongation of internode in the mutants. There was a significant decrease in the content of IPC detected in the osipcs2/3 and osipcs1/2/3 mutants. The contents of glycosyl inositol phosphoryl ceramide (GIPC) were also decreased by 20% and 10% in osipcs2/3 and osipcs1/2/3, respectively. The results of RNA-seq showed that numerous DEGs found to be associated with cellular component organization, anatomical structure morphogenesis, and cell growth in the osipcs2, osipcs2/3, and osipcs1/2/3. Taken together, OsIPCSs may be involved in the regulation of plant height through affecting cell growth and sphingolipid metabolism in rice.
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Affiliation(s)
- Xin Wang
- Key Laboratory of Molecular Biology and Genetic Engineering of Jiangxi Province, School of Life Sciences, Nanchang University, Nanchang 330031, China; Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Zongfei Zhang
- Key Laboratory of Molecular Biology and Genetic Engineering of Jiangxi Province, School of Life Sciences, Nanchang University, Nanchang 330031, China
| | - Wei Peng
- Key Laboratory of Molecular Biology and Genetic Engineering of Jiangxi Province, School of Life Sciences, Nanchang University, Nanchang 330031, China
| | - Jinqiu Huang
- Key Laboratory of Molecular Biology and Genetic Engineering of Jiangxi Province, School of Life Sciences, Nanchang University, Nanchang 330031, China
| | - Xin Yan
- Key Laboratory of Molecular Biology and Genetic Engineering of Jiangxi Province, School of Life Sciences, Nanchang University, Nanchang 330031, China
| | - Wen Yao
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China
| | - Jiexiu Ouyang
- Key Laboratory of Molecular Biology and Genetic Engineering of Jiangxi Province, School of Life Sciences, Nanchang University, Nanchang 330031, China.
| | - Shaobo Li
- Key Laboratory of Molecular Biology and Genetic Engineering of Jiangxi Province, School of Life Sciences, Nanchang University, Nanchang 330031, China.
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Wang H, Ouyang J, Jian W, Li M, Zhong J, Yan X, Gao J, Wang X, Li S. Rice miR5504 regulates plant height by affecting cell proliferation and expansion. PHYSIOLOGIA PLANTARUM 2023; 175:e14023. [PMID: 37882316 DOI: 10.1111/ppl.14023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 08/26/2023] [Accepted: 08/29/2023] [Indexed: 10/27/2023]
Abstract
miRNAs play critical roles in the regulation of plant growth and development by cleaving mRNA or repressing transcription. In our previous study, miR5504 with unknown functions was captured by small RNA sequencing. Here, the function and characters of miR5504 were extensively analyzed using CRISPR/Cas9, overexpression strategy, Northern blot, cytological analysis, and transcriptomics analysis. We found that the dwarf phenotype of mir5504 mutants (mir5504-1 and mir5504-2) appeared on 35-day seedlings and became more apparent at the mature stage. The cytological results showed a substantial decrease in the vascular bundle number, cell number and cell length in the mir5504 mutant compared with NIP. In addition, we found that miR5504 regulated plant height by targeting LOC_Os08g16914. The results of RNA-seq revealed that numerous biological processes were mainly enriched, including DNA-binding transcription factor activity, transferase activity, regulation of transcription, metabolic process, and protein binding. Meanwhile, KEEG analysis showed that numerous proteins were associated with cellular processes and metabolism pathways. Taken together, miR5504 may be involved in the regulation of plant height by affecting cell expansion and division of internode in rice.
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Affiliation(s)
- Huihui Wang
- Key Laboratory of Molecular Biology and Genetic Engineering of Jiangxi Province, School of Life Sciences, Nanchang University, Nanchang, China
| | - Jiexiu Ouyang
- Key Laboratory of Molecular Biology and Genetic Engineering of Jiangxi Province, School of Life Sciences, Nanchang University, Nanchang, China
| | - Wenjia Jian
- Key Laboratory of Molecular Biology and Genetic Engineering of Jiangxi Province, School of Life Sciences, Nanchang University, Nanchang, China
| | - Meng Li
- Key Laboratory of Molecular Biology and Genetic Engineering of Jiangxi Province, School of Life Sciences, Nanchang University, Nanchang, China
| | - Jiancong Zhong
- Key Laboratory of Molecular Biology and Genetic Engineering of Jiangxi Province, School of Life Sciences, Nanchang University, Nanchang, China
| | - Xin Yan
- Key Laboratory of Molecular Biology and Genetic Engineering of Jiangxi Province, School of Life Sciences, Nanchang University, Nanchang, China
| | - Jiadong Gao
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Guangzhou, China
- Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Xin Wang
- Key Laboratory of Molecular Biology and Genetic Engineering of Jiangxi Province, School of Life Sciences, Nanchang University, Nanchang, China
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Shaobo Li
- Key Laboratory of Molecular Biology and Genetic Engineering of Jiangxi Province, School of Life Sciences, Nanchang University, Nanchang, China
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Cortés AJ, Barnaby JY. Editorial: Harnessing genebanks: High-throughput phenotyping and genotyping of crop wild relatives and landraces. FRONTIERS IN PLANT SCIENCE 2023; 14:1149469. [PMID: 36968416 PMCID: PMC10036837 DOI: 10.3389/fpls.2023.1149469] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Accepted: 01/26/2023] [Indexed: 06/18/2023]
Affiliation(s)
- Andrés J. Cortés
- Corporación Colombiana de Investigación Agropecuaria – AGROSAVIA, C.I. La Selva, Rionegro, Colombia
| | - Jinyoung Y. Barnaby
- U.S. Department of Agriculture, U.S. National Arboretum, Floral and Nursery Plants Research Unit, Beltsville, MD, United States
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Kawamoto N, Morita MT. Gravity sensing and responses in the coordination of the shoot gravitropic setpoint angle. THE NEW PHYTOLOGIST 2022; 236:1637-1654. [PMID: 36089891 PMCID: PMC9828789 DOI: 10.1111/nph.18474] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 08/13/2022] [Indexed: 06/15/2023]
Abstract
Gravity is one of the fundamental environmental cues that affect plant development. Indeed, the plant architecture in the shoots and roots is modulated by gravity. Stems grow vertically upward, whereas lateral organs, such as the lateral branches in shoots, tend to grow at a specific angle according to a gravity vector known as the gravitropic setpoint angle (GSA). During this process, gravity is sensed in specialised gravity-sensing cells named statocytes, which convert gravity information into biochemical signals, leading to asymmetric auxin distribution and driving asymmetric cell division/expansion in the organs to achieve gravitropism. As a hypothetical offset mechanism against gravitropism to determine the GSA, the anti-gravitropic offset (AGO) has been proposed. According to this concept, the GSA is a balance of two antagonistic growth components, that is gravitropism and the AGO. Although the nature of the AGO has not been clarified, studies have suggested that gravitropism and the AGO share a common gravity-sensing mechanism in statocytes. This review discusses the molecular mechanisms underlying gravitropism as well as the hypothetical AGO in the control of the GSA.
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Affiliation(s)
- Nozomi Kawamoto
- Division of Plant Environmental ResponsesNational Institute for Basic BiologyMyodaijiOkazaki444‐8556Japan
| | - Miyo Terao Morita
- Division of Plant Environmental ResponsesNational Institute for Basic BiologyMyodaijiOkazaki444‐8556Japan
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Tirnaz S, Zandberg J, Thomas WJW, Marsh J, Edwards D, Batley J. Application of crop wild relatives in modern breeding: An overview of resources, experimental and computational methodologies. FRONTIERS IN PLANT SCIENCE 2022; 13:1008904. [PMID: 36466237 PMCID: PMC9712971 DOI: 10.3389/fpls.2022.1008904] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 10/25/2022] [Indexed: 06/01/2023]
Abstract
Global agricultural industries are under pressure to meet the future food demand; however, the existing crop genetic diversity might not be sufficient to meet this expectation. Advances in genome sequencing technologies and availability of reference genomes for over 300 plant species reveals the hidden genetic diversity in crop wild relatives (CWRs), which could have significant impacts in crop improvement. There are many ex-situ and in-situ resources around the world holding rare and valuable wild species, of which many carry agronomically important traits and it is crucial for users to be aware of their availability. Here we aim to explore the available ex-/in- situ resources such as genebanks, botanical gardens, national parks, conservation hotspots and inventories holding CWR accessions. In addition we highlight the advances in availability and use of CWR genomic resources, such as their contribution in pangenome construction and introducing novel genes into crops. We also discuss the potential and challenges of modern breeding experimental approaches (e.g. de novo domestication, genome editing and speed breeding) used in CWRs and the use of computational (e.g. machine learning) approaches that could speed up utilization of CWR species in breeding programs towards crop adaptability and yield improvement.
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Tanaka M, Keira M, Yoon DK, Mae T, Ishida H, Makino A, Ishiyama K. Photosynthetic Enhancement, Lifespan Extension, and Leaf Area Enlargement in Flag Leaves Increased the Yield of Transgenic Rice Plants Overproducing Rubisco Under Sufficient N Fertilization. RICE (NEW YORK, N.Y.) 2022; 15:10. [PMID: 35138458 PMCID: PMC8828814 DOI: 10.1186/s12284-022-00557-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 01/31/2022] [Indexed: 06/07/2023]
Abstract
BACKGROUND Improvement in photosynthesis is one of the most promising approaches to increase grain yields. Transgenic rice plants overproducing Rubisco by 30% (RBCS-sense rice plants) showed up to 28% increase in grain yields under sufficient nitrogen (N) fertilization using an isolated experimental paddy field (Yoon et al. in Nat Food 1:134-139, 2020). The plant N contents above-ground sections and Rubisco contents of the flag leaves were higher in the RBCS-sense plants than in the wild-type rice plants during the ripening period, which may be reasons for the increased yields. However, some imprecise points were left in the previous research, such as contributions of photosynthesis of leaves below the flag leaves to the yield, and maintenance duration of high photosynthesis of RBCS-sense rice plants during ripening periods. RESULT In this research, the photosynthetic capacity and canopy architecture were analyzed to explore factors for the increased yields of RBCS-sense rice plants. It was found that N had already been preferentially distributed into the flag leaves at the early ripening stage, contributing to maintaining higher Rubisco content levels in the enlarged flag leaves and extending the lifespan of the flag leaves of RBCS-sense rice plants throughout ripening periods under sufficient N fertilization. The higher amounts of Rubisco also improved the photosynthetic activity in the flag leaves throughout the ripening period. Although the enlarged flag leaves of the RBCS-sense rice plants occupied large spatial areas of the uppermost layer in the canopy, no significant prevention of light penetration to leaves below the flag leaves was observed. Additionally, since the CO2 assimilation rates of lower leaves between wild-type and RBCS-sense rice plants were the same at the early ripening stage, the lower leaves did not contribute to an increase in yields of the RBCS-sense rice plants. CONCLUSION We concluded that improvements in the photosynthetic capacity by higher leaf N and Rubisco contents, enlarged leaf area and extended lifespan of flag leaves led to an increase in grain yields of RBCS-sense rice plants grown under sufficient N fertilization.
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Affiliation(s)
- Marin Tanaka
- Graduate School of Agricultural Science, Tohoku University, 468-1 Aramaki-Aoba, Aoba-ku, Sendai, 980-8572, Japan
| | - Mamoru Keira
- Graduate School of Agricultural Science, Tohoku University, 468-1 Aramaki-Aoba, Aoba-ku, Sendai, 980-8572, Japan
| | - Dong-Kyung Yoon
- Graduate School of Agricultural Science, Tohoku University, 468-1 Aramaki-Aoba, Aoba-ku, Sendai, 980-8572, Japan
| | - Tadahiko Mae
- Graduate School of Agricultural Science, Tohoku University, 468-1 Aramaki-Aoba, Aoba-ku, Sendai, 980-8572, Japan
| | - Hiroyuki Ishida
- Graduate School of Agricultural Science, Tohoku University, 468-1 Aramaki-Aoba, Aoba-ku, Sendai, 980-8572, Japan
| | - Amane Makino
- Graduate School of Agricultural Science, Tohoku University, 468-1 Aramaki-Aoba, Aoba-ku, Sendai, 980-8572, Japan
| | - Keiki Ishiyama
- Graduate School of Agricultural Science, Tohoku University, 468-1 Aramaki-Aoba, Aoba-ku, Sendai, 980-8572, Japan.
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