1
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Li Y, Wang J, Gao Y, Pandey BK, Peralta Ogorek LL, Zhao Y, Quan R, Zhao Z, Jiang L, Huang R, Qin H. The OsEIL1-OsWOX11 transcription factor module controls rice crown root development in response to soil compaction. THE PLANT CELL 2024; 36:2393-2409. [PMID: 38489602 PMCID: PMC11132869 DOI: 10.1093/plcell/koae083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 02/20/2024] [Accepted: 03/11/2024] [Indexed: 03/17/2024]
Abstract
Optimizing the root architecture of crops is an effective strategy for improving crop yields. Soil compaction is a serious global problem that limits crop productivity by restricting root growth, but the underlying molecular mechanisms are largely unclear. Here, we show that ethylene stimulates rice (Oryza sativa) crown root development in response to soil compaction. First, we demonstrate that compacted soil promotes ethylene production and the accumulation of ETHYLENE INSENSITIVE 3-LIKE 1 (OsEIL1) in rice roots, stimulating crown root primordia initiation and development, thereby increasing crown root number in lower stem nodes. Through transcriptome profiling and molecular analyses, we reveal that OsEIL1 directly activates the expression of WUSCHEL-RELATED HOMEOBOX 11 (OsWOX11), an activator of crown root emergence and growth, and that OsWOX11 mutations delay crown root development, thus impairing the plant's response to ethylene and soil compaction. Genetic analysis demonstrates that OsWOX11 functions downstream of OsEIL1. In summary, our results demonstrate that the OsEIL1-OsWOX11 module regulates ethylene action during crown root development in response to soil compaction, providing a strategy for the genetic modification of crop root architecture and grain agronomic traits.
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Affiliation(s)
- Yuxiang Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Juan Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- National Key Facility of Crop Gene Resources and Genetic Improvement, Beijing 100081, China
| | - Yadi Gao
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Bipin K Pandey
- Plant and Crop Science Department, School of Biosciences, University of Nottingham, Loughborough LE12 5RD, United Kingdom
| | - Lucas León Peralta Ogorek
- Plant and Crop Science Department, School of Biosciences, University of Nottingham, Loughborough LE12 5RD, United Kingdom
| | - Yu Zhao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Ruidang Quan
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- National Key Facility of Crop Gene Resources and Genetic Improvement, Beijing 100081, China
| | - Zihan Zhao
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Lei Jiang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Rongfeng Huang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- National Key Facility of Crop Gene Resources and Genetic Improvement, Beijing 100081, China
| | - Hua Qin
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- National Key Facility of Crop Gene Resources and Genetic Improvement, Beijing 100081, China
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2
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Imran M, Junaid M, Shafiq S, Liu S, Chen X, Wang J, Tang X. Multiomics analysis reveals a substantial decrease in nanoplastics uptake and associated impacts by nano zinc oxide in fragrant rice (Oryza sativa L.). JOURNAL OF HAZARDOUS MATERIALS 2024; 474:134640. [PMID: 38810581 DOI: 10.1016/j.jhazmat.2024.134640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Revised: 04/28/2024] [Accepted: 05/16/2024] [Indexed: 05/31/2024]
Abstract
Nanoplastics (NPs) have emerged as global environmental pollutants with concerning implications for sustainable agriculture. Understanding the underlying mechanisms of NPs toxicity and devising strategies to mitigate their impact is crucial for crop growth and development. Here, we investigated the nanoparticles of zinc oxide (nZnO) to mitigate the adverse effects of 80 nm NPs on fragrant rice. Our results showed that optimized nZnO (25 mg L-1) concentration rescued root length and structural deficits by improving oxidative stress response, antioxidant defense mechanism and balanced nutrient levels, compared to seedlings subjected only to NPs stress (50 mg L-1). Consequently, microscopy observations, Zeta potential and Fourier transform infrared (FTIR) results revealed that NPs were mainly accumulated on the initiation joints of secondary roots and between cortical cells that blocks the nutrients uptake, while the supplementation of nZnO led to the formation of aggregates with NPs, which effectively impedes the uptake of NPs by the roots of fragrant rice. Transcriptomic analysis identified a total of 3973, 3513 and 3380 differentially expressed genes (DEGs) in response to NPs, nZnO and NPs+nZnO, respectively, compared to the control. Moreover, DEGs were significantly enriched in multiple pathways including biosynthesis of secondary metabolite, phenylpropanoid biosynthesis, amino sugar and nucleotide sugar metabolism, carotenoid biosynthesis, plant-pathogen interactions, MAPK signaling pathway, starch and sucrose metabolism, and plant hormone signal transduction. These pathways could play a significant role in alleviating NPs toxicity and restoring fragrant rice roots. Furthermore, metabolomic analysis demonstrated that nZnO application restored 2-acetyl-1-pyrroline (2-AP) pathways genes expression, enzymatic activities, and the content of essential precursors related to 2-AP biosynthesis under NPs toxicity, which ultimately led to the restoration of 2-AP content in the leaves. In conclusion, this study shows that optimized nZnO application effectively alleviates NPs toxic effects and restores both root structure and aroma production in fragrant rice leaves. This research offers a sustainable and practical strategy to enhance crop production under NPs toxicity while emphasizing the pivotal role of essential micronutrient nanomaterials in agriculture.
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Affiliation(s)
- Muhammad Imran
- Department of Crop Science and Technology, College of Agriculture, South China Agricultural University, Guangzhou 510642, China.
| | - Muhammad Junaid
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Sarfraz Shafiq
- Department of Crop Science and Technology, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Shulin Liu
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Xiaoyuan Chen
- Department of Crop Science and Technology, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Jun Wang
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Xiangru Tang
- Department of Crop Science and Technology, College of Agriculture, South China Agricultural University, Guangzhou 510642, China.
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3
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Isidra-Arellano MC, Singh J, Valdés-López O. Unraveling the potential of the strigolactones-NSP1/NSP2 friendship in crop improvement. TRENDS IN PLANT SCIENCE 2024; 29:501-503. [PMID: 38158302 DOI: 10.1016/j.tplants.2023.12.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 12/13/2023] [Accepted: 12/14/2023] [Indexed: 01/03/2024]
Abstract
Strigolactones (SLs) are fundamental to the ability of plants to cope with phosphate deficiency. A recent study by Yuan et al. indicates that the genetic module PHR2/NSP1/NSP2 is crucial in activating SL biosynthesis and signaling under inorganic phosphate (Pi) deficiency. Furthermore, this genetic module is essential for improving Pi and nitrogen homeostasis in rice.
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Affiliation(s)
| | - Jawahar Singh
- University of Cambridge, Sainsbury Laboratory (SLCU), Cambridge, UK
| | - Oswaldo Valdés-López
- Laboratorio de Genómica Funcional de Leguminosas, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla 54090, México.
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4
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Geng L, Tan M, Deng Q, Wang Y, Zhang T, Hu X, Ye M, Lian X, Zhou DX, Zhao Y. Transcription factors WOX11 and LBD16 function with histone demethylase JMJ706 to control crown root development in rice. THE PLANT CELL 2024; 36:1777-1790. [PMID: 38190205 PMCID: PMC11062443 DOI: 10.1093/plcell/koad318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 11/25/2023] [Indexed: 01/09/2024]
Abstract
Crown roots are the main components of root systems in cereals. Elucidating the mechanisms of crown root formation is instrumental for improving nutrient absorption, stress tolerance, and yield in cereal crops. Several members of the WUSCHEL-related homeobox (WOX) and lateral organ boundaries domain (LBD) transcription factor families play essential roles in controlling crown root development in rice (Oryza sativa). However, the functional relationships among these transcription factors in regulating genes involved in crown root development remain unclear. Here, we identified LBD16 as an additional regulator of rice crown root development. We showed that LBD16 is a direct downstream target of WOX11, a key crown root development regulator in rice. Our results indicated that WOX11 enhances LBD16 transcription by binding to its promoter and recruiting its interaction partner JMJ706, a demethylase that removes histone H3 lysine 9 dimethylation (H3K9me2) from the LBD16 locus. In addition, we established that LBD16 interacts with WOX11, thereby impairing JMJ706-WOX11 complex formation and repressing its own transcriptional activity. Together, our results reveal a feedback system regulating genes that orchestrate crown root development in rice, in which LBD16 acts as a molecular rheostat.
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Affiliation(s)
- Leping Geng
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Mingfang Tan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Qiyu Deng
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Yijie Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Ting Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaosong Hu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Miaomiao Ye
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Xingming Lian
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Dao-Xiu Zhou
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
- CNRS, INRAE, Institute of Plant Science Paris-Saclay (IPS2), University Paris-Saclay, Orsay 91405, France
| | - Yu Zhao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
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Mishra P, Roggen A, Ljung K, Albani MC, Vayssières A. Adventitious rooting in response to long-term cold: a possible mechanism of clonal growth in alpine perennials. FRONTIERS IN PLANT SCIENCE 2024; 15:1352830. [PMID: 38693930 PMCID: PMC11062184 DOI: 10.3389/fpls.2024.1352830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Accepted: 03/22/2024] [Indexed: 05/03/2024]
Abstract
Arctic alpine species experience extended periods of cold and unpredictable conditions during flowering. Thus, often, alpine plants use both sexual and asexual means of reproduction to maximize fitness and ensure reproductive success. We used the arctic alpine perennial Arabis alpina to explore the role of prolonged cold exposure on adventitious rooting. We exposed plants to 4°C for different durations and scored the presence of adventitious roots on the main stem and axillary branches. Our physiological studies demonstrated the presence of adventitious roots after 21 weeks at 4°C saturating the effect of cold on this process. Notably, adventitious roots on the main stem developing in specific internodes allowed us to identify the gene regulatory network involved in the formation of adventitious roots in cold using transcriptomics. These data and histological studies indicated that adventitious roots in A. alpina stems initiate during cold exposure and emerge after plants experience growth promoting conditions. While the initiation of adventitious root was not associated with changes of DR5 auxin response and free endogenous auxin level in the stems, the emergence of the adventitious root primordia was. Using the transcriptomic data, we discerned the sequential hormone responses occurring in various stages of adventitious root formation and identified supplementary pathways putatively involved in adventitious root emergence, such as glucosinolate metabolism. Together, our results highlight the role of low temperature during clonal growth in alpine plants and provide insights on the molecular mechanisms involved at distinct stages of adventitious rooting.
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Affiliation(s)
- Priyanka Mishra
- Institute for Plant Sciences, University of Cologne, Cologne, Germany
- Cluster of Excellence on Plant Sciences, “SMART Plants for Tomorrow’s Needs,” Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Department of Botany, Faculty of Science, University of Allahabad, Prayagraj, India
| | - Adrian Roggen
- Institute for Plant Sciences, University of Cologne, Cologne, Germany
- Cluster of Excellence on Plant Sciences, “SMART Plants for Tomorrow’s Needs,” Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Karin Ljung
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Maria C. Albani
- Institute for Plant Sciences, University of Cologne, Cologne, Germany
- Cluster of Excellence on Plant Sciences, “SMART Plants for Tomorrow’s Needs,” Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Rijk Zwaan, De Lier, Netherlands
| | - Alice Vayssières
- Institute for Plant Sciences, University of Cologne, Cologne, Germany
- Cluster of Excellence on Plant Sciences, “SMART Plants for Tomorrow’s Needs,” Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
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6
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Nguyen TT, Nguyen TC, Do PT, To HTM. Effect of gibberellin on crown root development in the mutant of the rice plasmodesmal Germin-like protein OsGER4. Funct Integr Genomics 2024; 24:59. [PMID: 38498207 DOI: 10.1007/s10142-024-01341-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 03/12/2024] [Accepted: 03/13/2024] [Indexed: 03/20/2024]
Abstract
Rice is an essential but highly stress-susceptible crop, whose root system plays an important role in plant development and stress adaptation. The rice root system architecture is controlled by gene regulatory networks involving different phytohormones including auxin, jasmonate, and gibberellin. Gibberellin is generally known as a molecular clock that interacts with different pathways to regulate root meristem development. The exogenous treatment of rice plantlets with Gibberellin reduced the number of crown roots, whilst the exogenous jasmonic acid treatment enhanced them by involving a Germin-like protein OsGER4. Due to those opposite effects, this study aims to investigate the effect of Gibberellin on crown root development in the rice mutant of the plasmodesmal Germin-like protein OsGER4. Under exogenous gibberellin treatment, the number of crown roots significantly increased in osger4 mutant lines and decreased in the OsGER4 overexpressed lines. GUS staining showed that OsGER4 was strongly expressed in rice root systems, particularly crown and lateral roots under GA3 application. Specifically, OsGER4 was strongly expressed from the exodermis, epidermis, sclerenchyma to the endodermis layers of the crown root, along the vascular bundle and throughout LR primordia. The plasmodesmal protein OsGER4 is suggested to be involved in crown root development by maintaining hormone homeostasis, including Gibberillin.
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Affiliation(s)
- Trang Thi Nguyen
- University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
- Agricultural Genetics Institute, PhamVan Dong, Bac Tu Liem, Ha Noi, Vietnam
| | - Thanh Chi Nguyen
- University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
| | - Phat Tien Do
- Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
| | - Huong Thi Mai To
- University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam.
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7
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Qin H, Xiao M, Li Y, Huang R. Ethylene Modulates Rice Root Plasticity under Abiotic Stresses. PLANTS (BASEL, SWITZERLAND) 2024; 13:432. [PMID: 38337965 PMCID: PMC10857340 DOI: 10.3390/plants13030432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 01/30/2024] [Accepted: 01/31/2024] [Indexed: 02/12/2024]
Abstract
Plants live in constantly changing environments that are often unfavorable or stressful. Root development strongly affects plant growth and productivity, and the developmental plasticity of roots helps plants to survive under abiotic stress conditions. This review summarizes the progress being made in understanding the regulation of the phtyohormone ethylene in rice root development in response to abiotic stresses, highlighting the complexity associated with the integration of ethylene synthesis and signaling in root development under adverse environments. Understanding the molecular mechanisms of ethylene in regulating root architecture and response to environmental signals can contribute to the genetic improvement of crop root systems, enhancing their adaptation to stressful environmental conditions.
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Affiliation(s)
- Hua Qin
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.L.); (R.H.)
- National Key Facility of Crop Gene Resources and Genetic Improvement, Beijing 100081, China
| | - Minggang Xiao
- Biotechnology Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150028, China;
| | - Yuxiang Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.L.); (R.H.)
| | - Rongfeng Huang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.L.); (R.H.)
- National Key Facility of Crop Gene Resources and Genetic Improvement, Beijing 100081, China
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8
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Kumar A, Verma K, Kashyap R, Joshi VJ, Sircar D, Yadav SR. Auxin-responsive ROS homeostasis genes display dynamic expression pattern during rice crown root primordia morphogenesis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 206:108307. [PMID: 38159549 DOI: 10.1016/j.plaphy.2023.108307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 12/15/2023] [Accepted: 12/22/2023] [Indexed: 01/03/2024]
Abstract
Reactive oxygen species (ROS) are generated continuously as a by-product of aerobic metabolism in plants. While excessive ROS cause oxidative stresses in cells, they act as signaling molecules when maintained at an optimum concentration through the dynamic equilibrium of ROS metabolizing mechanisms to regulate growth, development and response to environmental stress. Auxin and its crosstalk with other signaling cascades are crucial for maintaining ROS homeostasis and orchestrating root architecture but dissecting the underlying mechanism requires detailed investigation at the molecular level. Rice fibrous root system is primarily composed of shoot-derived adventitious roots (also called crown roots). Here, we uncover auxin-ROS cross-talk during initiation and growth of rice roots. Potassium iodide treatment changes ROS levels that results in an altered rice root architecture. We reveal that auxin induction recover root growth and development defects by recouping level of hydrogen peroxide. By comparing global datasets previously generated by auxin induction and laser capture microdissection-RNA sequencing, we identify the redox-related antioxidants genes from peroxidase, glutathione reductase, glutathione S-transferase, and thioredoxin reductase families whose expression is regulated by the auxin signaling and also display dynamic expression patterns during crown root primordia morphogenesis. The auxin-mediated differential transcriptome data were validated by quantifying expression levels of a set of genes upon auxin induction. Further, in-depth spatio-temporal expression pattern analysis by RNA in situ hybridization shows the spatially restricted expression of selected genes in the developing crown root primordia. Together, our findings uncover molecular components of auxin-ROS crosstalk involved in root organogenesis.
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Affiliation(s)
- Akshay Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Uttarakhand, India
| | - Komal Verma
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Uttarakhand, India
| | - Rohan Kashyap
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Uttarakhand, India
| | - Vedika Jayant Joshi
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Uttarakhand, India
| | - Debabrata Sircar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Uttarakhand, India
| | - Shri Ram Yadav
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Uttarakhand, India.
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9
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Kun Yuan, Zhang H, Yu C, Luo N, Yan J, Zheng S, Hu Q, Zhang D, Kou L, Meng X, Jing Y, Chen M, Ban X, Yan Z, Lu Z, Wu J, Zhao Y, Liang Y, Wang Y, Xiong G, Chu J, Wang E, Li J, Wang B. Low phosphorus promotes NSP1-NSP2 heterodimerization to enhance strigolactone biosynthesis and regulate shoot and root architecture in rice. MOLECULAR PLANT 2023; 16:1811-1831. [PMID: 37794682 DOI: 10.1016/j.molp.2023.09.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 08/18/2023] [Accepted: 09/28/2023] [Indexed: 10/06/2023]
Abstract
Phosphorus is an essential macronutrient for plant development and metabolism, and plants have evolved ingenious mechanisms to overcome phosphate (Pi) starvation. However, the molecular mechanisms underlying the regulation of shoot and root architecture by low phosphorus conditions and the coordinated utilization of Pi and nitrogen remain largely unclear. Here, we show that Nodulation Signaling Pathway 1 (NSP1) and NSP2 regulate rice tiller number by promoting the biosynthesis of strigolactones (SLs), a class of phytohormones with fundamental effects on plant architecture and environmental responses. We found that NSP1 and NSP2 are induced by Oryza sativa PHOSPHATE STARVATION RESPONSE2 (OsPHR2) in response to low-Pi stress and form a complex to directly bind the promoters of SL biosynthesis genes, thus markedly increasing SL biosynthesis in rice. Interestingly, the NSP1/2-SL signaling module represses the expression of CROWN ROOTLESS 1 (CRL1), a newly identified early SL-responsive gene in roots, to restrain lateral root density under Pi deficiency. We also demonstrated that GR244DO treatment under normal conditions inhibits the expression of OsNRTs and OsAMTs to suppress nitrogen absorption but enhances the expression of OsPTs to promote Pi absorption, thus facilitating the balance between nitrogen and phosphorus uptake in rice. Importantly, we found that NSP1p:NSP1 and NSP2p:NSP2 transgenic plants show improved agronomic traits and grain yield under low- and medium-phosphorus conditions. Taken together, these results revealed a novel regulatory mechanism of SL biosynthesis and signaling in response to Pi starvation, providing genetic resources for improving plant architecture and nutrient-use efficiency in low-Pi environments.
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Affiliation(s)
- Kun Yuan
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hao Zhang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chaoji Yu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Nan Luo
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jijun Yan
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Shuang Zheng
- University of Chinese Academy of Sciences, Beijing 100049, China; National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, SIBS, Chinese Academy of Sciences, Shanghai 200032, China
| | - Qingliang Hu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Dahan Zhang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liquan Kou
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiangbing Meng
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Yanhui Jing
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Mingjiang Chen
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Xinwei Ban
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zongyun Yan
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Zefu Lu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jian Wu
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Yu Zhao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Yan Liang
- College of Life Sciences, Shandong Agriculture University, Tai'an, Shandong 271018, China
| | - Yonghong Wang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; College of Life Sciences, Shandong Agriculture University, Tai'an, Shandong 271018, China
| | - Guosheng Xiong
- Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Jinfang Chu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ertao Wang
- University of Chinese Academy of Sciences, Beijing 100049, China; National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, SIBS, Chinese Academy of Sciences, Shanghai 200032, China
| | - Jiayang Li
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Yazhouwan National Laboratory, Sanya, Hainan 572024, China
| | - Bing Wang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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10
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Motte H, Parizot B, Xuan W, Chen Q, Maere S, Bensmihen S, Beeckman T. Interspecies co-expression analysis of lateral root development using inducible systems in rice, Medicago, and Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:1052-1063. [PMID: 37793018 DOI: 10.1111/tpj.16481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 08/30/2023] [Accepted: 09/13/2023] [Indexed: 10/06/2023]
Abstract
Lateral roots are crucial for plant growth and development, making them an important target for research aiming to improve crop yields and food security. However, their endogenous ontogeny and, as it were, stochastic appearance challenge their study. Lateral Root Inducible Systems (LRIS) can be used to overcome these challenges by inducing lateral roots massively and synchronously. The combination of LRISs with transcriptomic approaches significantly advanced our insights in the molecular control of lateral root formation, in particular for Arabidopsis. Despite this success, LRISs have been underutilized for other plant species or for lateral root developmental stages later than the initiation. In this study, we developed and/or adapted LRISs in rice, Medicago, and Arabidopsis to perform RNA-sequencing during time courses that cover different developmental stages of lateral root formation and primordium development. As such, our study provides three extensive datasets of gene expression profiles during lateral root development in three different plant species. The three LRISs are highly effective but timing and spatial distribution of lateral root induction vary among the species. Detailed characterization of the stages in time and space in the respective species enabled an interspecies co-expression analysis to identify conserved players involved in lateral root development, as illustrated for the AUX/IAA and LBD gene families. Overall, our results provide a valuable resource to identify potentially conserved regulatory mechanisms in lateral root development, and as such will contribute to a better understanding of the complex regulatory network underlying lateral root development.
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Affiliation(s)
- Hans Motte
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052, Ghent, Belgium
| | - Boris Parizot
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052, Ghent, Belgium
| | - Wei Xuan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qian Chen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052, Ghent, Belgium
| | - Steven Maere
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052, Ghent, Belgium
| | - Sandra Bensmihen
- INRAE, CNRS, LIPME, Université de Toulouse, F-31326, Castanet-Tolosan, France
| | - Tom Beeckman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052, Ghent, Belgium
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11
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Rahmati Ishka M, Julkowska M. Tapping into the plasticity of plant architecture for increased stress resilience. F1000Res 2023; 12:1257. [PMID: 38434638 PMCID: PMC10905174 DOI: 10.12688/f1000research.140649.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/24/2023] [Indexed: 03/05/2024] Open
Abstract
Plant architecture develops post-embryonically and emerges from a dialogue between the developmental signals and environmental cues. Length and branching of the vegetative and reproductive tissues were the focus of improvement of plant performance from the early days of plant breeding. Current breeding priorities are changing, as we need to prioritize plant productivity under increasingly challenging environmental conditions. While it has been widely recognized that plant architecture changes in response to the environment, its contribution to plant productivity in the changing climate remains to be fully explored. This review will summarize prior discoveries of genetic control of plant architecture traits and their effect on plant performance under environmental stress. We review new tools in phenotyping that will guide future discoveries of genes contributing to plant architecture, its plasticity, and its contributions to stress resilience. Subsequently, we provide a perspective into how integrating the study of new species, modern phenotyping techniques, and modeling can lead to discovering new genetic targets underlying the plasticity of plant architecture and stress resilience. Altogether, this review provides a new perspective on the plasticity of plant architecture and how it can be harnessed for increased performance under environmental stress.
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12
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Zhang Y, Du D, Wei H, Xie S, Tian X, Yang J, Xiao S, Tang Z, Li D, Liu Y. Transcriptomic and Hormone Analyses Provide Insight into the Regulation of Axillary Bud Outgrowth of Eucommia ulmoides Oliver. Curr Issues Mol Biol 2023; 45:7304-7318. [PMID: 37754246 PMCID: PMC10528246 DOI: 10.3390/cimb45090462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 08/30/2023] [Accepted: 08/31/2023] [Indexed: 09/28/2023] Open
Abstract
An essential indicator of Eucommia ulmoides Oliver (E. ulmoides) is the axillary bud; the growth and developmental capacity of axillary buds could be used to efficiently determine the structural integrity of branches and plant regeneration. We obtained axillary buds in different positions on the stem, including upper buds (CK), tip buds (T1), and bottom buds (T2), which provided optimal materials for the study of complicated regulatory networks that control bud germination. This study used transcriptomes to analyze the levels of gene expression in three different types of buds, and the results showed that 12,131 differentially expressed genes (DEGs) were discovered via the pairwise comparison of transcriptome data gathered from CK to T2, while the majority of DEGs (44.38%) were mainly found between CK and T1. These DEGs were closely related to plant hormone signal transduction and the amino acid biosynthesis pathway. We also determined changes in endogenous hormone contents during the process of bud germination. Interestingly, except for indole-3-acetic acid (IAA) content, which showed a significant upward trend (p < 0.05) in tip buds on day 4 compared with day 0, the other hormones showed no significant change during the process of germination. Then, the expression patterns of genes involved in IAA biosynthesis and signaling were examined through transcriptome analysis. Furthermore, the expression levels of genes related to IAA biosynthesis and signal transduction were upregulated in tip buds. Particularly, the expression of the IAA degradation gene Gretchen Hagen 3 (GH3.1) was downregulated on day 4, which may support the concept that endogenous IAA promotes bud germination. Based on these data, we propose that IAA synthesis and signal transduction lead to morphological changes in tip buds during the germination process. On this basis, suggestions to improve the efficiency of the production and application of E. ulmoides are put forward to provide guidance for future research.
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Affiliation(s)
- Ying Zhang
- College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin 150040, China; (Y.Z.); (D.D.); (H.W.); (S.X.); (X.T.); (J.Y.); (S.X.); (Z.T.)
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin 150040, China
- Heilongjiang Provincial Key Laboratory of Ecological Utilization of Forestry-Based Active Substances, Harbin 150040, China
| | - Dandan Du
- College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin 150040, China; (Y.Z.); (D.D.); (H.W.); (S.X.); (X.T.); (J.Y.); (S.X.); (Z.T.)
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin 150040, China
- Heilongjiang Provincial Key Laboratory of Ecological Utilization of Forestry-Based Active Substances, Harbin 150040, China
| | - Hongling Wei
- College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin 150040, China; (Y.Z.); (D.D.); (H.W.); (S.X.); (X.T.); (J.Y.); (S.X.); (Z.T.)
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin 150040, China
- Heilongjiang Provincial Key Laboratory of Ecological Utilization of Forestry-Based Active Substances, Harbin 150040, China
| | - Shengnan Xie
- College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin 150040, China; (Y.Z.); (D.D.); (H.W.); (S.X.); (X.T.); (J.Y.); (S.X.); (Z.T.)
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin 150040, China
- Heilongjiang Provincial Key Laboratory of Ecological Utilization of Forestry-Based Active Substances, Harbin 150040, China
| | - Xuchen Tian
- College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin 150040, China; (Y.Z.); (D.D.); (H.W.); (S.X.); (X.T.); (J.Y.); (S.X.); (Z.T.)
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin 150040, China
- Heilongjiang Provincial Key Laboratory of Ecological Utilization of Forestry-Based Active Substances, Harbin 150040, China
| | - Jing Yang
- College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin 150040, China; (Y.Z.); (D.D.); (H.W.); (S.X.); (X.T.); (J.Y.); (S.X.); (Z.T.)
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin 150040, China
- Heilongjiang Provincial Key Laboratory of Ecological Utilization of Forestry-Based Active Substances, Harbin 150040, China
| | - Siqiu Xiao
- College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin 150040, China; (Y.Z.); (D.D.); (H.W.); (S.X.); (X.T.); (J.Y.); (S.X.); (Z.T.)
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin 150040, China
- Heilongjiang Provincial Key Laboratory of Ecological Utilization of Forestry-Based Active Substances, Harbin 150040, China
| | - Zhonghua Tang
- College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin 150040, China; (Y.Z.); (D.D.); (H.W.); (S.X.); (X.T.); (J.Y.); (S.X.); (Z.T.)
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin 150040, China
- Heilongjiang Provincial Key Laboratory of Ecological Utilization of Forestry-Based Active Substances, Harbin 150040, China
| | - Dewen Li
- College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin 150040, China; (Y.Z.); (D.D.); (H.W.); (S.X.); (X.T.); (J.Y.); (S.X.); (Z.T.)
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin 150040, China
- Heilongjiang Provincial Key Laboratory of Ecological Utilization of Forestry-Based Active Substances, Harbin 150040, China
| | - Ying Liu
- College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin 150040, China; (Y.Z.); (D.D.); (H.W.); (S.X.); (X.T.); (J.Y.); (S.X.); (Z.T.)
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin 150040, China
- Heilongjiang Provincial Key Laboratory of Ecological Utilization of Forestry-Based Active Substances, Harbin 150040, China
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13
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Nguyen TT, Pham DT, Nguyen NH, Do PT, To HTM. The Germin-like protein gene OsGER4 is involved in heat stress response in rice root development. Funct Integr Genomics 2023; 23:271. [PMID: 37561192 DOI: 10.1007/s10142-023-01201-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 08/02/2023] [Accepted: 08/02/2023] [Indexed: 08/11/2023]
Abstract
Rice (Oryza sativa L.) is one of the most important dietary carbohydrate sources for half of the world's population. However, it is not well adapted to environmental stress conditions, necessitating to create new and improved varieties to help ensure sufficient rice production in the face of rising populations and shrinking arable land. Recently, the development of the CRISPR/Cas9 gene editing system has allowed researchers to study functional genomics and engineer new rice varieties with great efficiency compared to conventional methods. In this study, we investigate the involvement of OsGER4, a germin-like protein identified by a genome-wide association study that is associated with rice root development under a stress hormone jasmonic acids treatment. Analysis of the OsGER4 promoter region revealed a series of regulatory elements that connect this gene to ABA signaling and water stress response. Under heat stress, osger4 mutant lines produce a significantly lower crown root than wild-type Kitaake rice. The loss of OsGER4 also led to the reduction of lateral root development. Using the GUS promoter line, OsGER4 expression was detected in the epidermis of the crown root primordial, in the stele of the crown root, and subsequently in the primordial of the lateral root. Taken together, these results illustrated the involvement of OsGER4 in root development under heat stress by regulating auxin transport through plasmodesmata, under control by both ABA and auxin signaling.
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Affiliation(s)
- Trang Thi Nguyen
- University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology. 100000, Hanoi, Vietnam
| | - Dan The Pham
- University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology. 100000, Hanoi, Vietnam
| | - Nhung Hong Nguyen
- University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology. 100000, Hanoi, Vietnam
- Institute of Biotechnology, Vietnam Academy of Science and Technology. 100000, Hanoi, Vietnam
| | - Phat Tien Do
- Institute of Biotechnology, Vietnam Academy of Science and Technology. 100000, Hanoi, Vietnam
| | - Huong Thi Mai To
- University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology. 100000, Hanoi, Vietnam.
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14
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Garg T, Yadav M, Mushahary KKK, Kumar A, Pal V, Singh H, Jain M, Yadav SR. Spatially activated conserved auxin-transcription factor regulatory module controls de novo root organogenesis in rice. PLANTA 2023; 258:52. [PMID: 37491477 DOI: 10.1007/s00425-023-04210-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 07/19/2023] [Indexed: 07/27/2023]
Abstract
MAIN CONCLUSION This study reveals that the process of crown root development and auxin-induced de novo root organogenesis during in vitro plantlet regeneration share a common auxin-OsWOX10 regulatory module in rice. In the fibrous-type root system of rice, the crown roots (CR) are developed naturally from the shoot tissues. Generation of robust auxin response, followed by activation of downstream cell fate determinants and signaling pathways at the onset of crown root primordia (CRP) establishment is essential for new root initiation. During rice tissue culture, embryonic calli are induced to regenerate shoots in vitro which undergo de novo root organogenesis on an exogenous auxin-supplemented medium, but the mechanism underlying spatially restricted root organogenesis remains unknown. Here, we reveal the dynamics of progressive activation of genes involved in auxin homeostasis and signaling during initiation and outgrowth of rice crown root primordia. By comparative global dataset analysis, we identify the crown root primordia-expressed genes whose expression is also regulated by auxin signaling. In-depth spatio-temporal expression pattern analysis shows that the exogenous application of auxin induces a set of key transcription factors exclusively in the spatially positioned CRP. Further, functional analysis of rice WUSCHEL-RELATED HOMEOBOX 10 (OsWOX10) during in vitro plantlet regeneration from embryogenic calli shows that it promotes de novo root organogenesis from regenerated shoots. Expression of rice OsWOX10 also induces adventitious roots (AR) in Arabidopsis, independent of homologous endogenous Arabidopsis genes. Together, our findings reveal that a common auxin-transcription factor regulatory module is involved in root organogenesis under different conditions.
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Affiliation(s)
- Tushar Garg
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, Uttarakhand, 247667, India
- Department of Plant Biology, University of California, Davis, CA, USA
| | - Manoj Yadav
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, Uttarakhand, 247667, India
- Department of Biochemistry, All India Institute of Medical Sciences, Raebareli, Uttar Pradesh, India
| | | | - Akshay Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, Uttarakhand, 247667, India
| | - Vivek Pal
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Harshita Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, Uttarakhand, 247667, India
- Center for Organismal Studies, University of Heidelberg, 69120, Heidelberg, Germany
| | - Mukesh Jain
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Shri Ram Yadav
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, Uttarakhand, 247667, India.
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15
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Kettenburg AT, Lopez MA, Yogendra K, Prior MJ, Rose T, Bimson S, Heuer S, Roy SJ, Bailey-Serres J. PHOSPHORUS-STARVATION TOLERANCE 1 (OsPSTOL1) is prevalent in upland rice and enhances root growth and hastens low phosphate signaling in wheat. PLANT, CELL & ENVIRONMENT 2023; 46:2187-2205. [PMID: 36946067 DOI: 10.1111/pce.14588] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 03/07/2023] [Accepted: 03/19/2023] [Indexed: 06/08/2023]
Abstract
PHOSPHORUS-STARVATION TOLERANCE 1 (OsPSTOL1) is a variably present gene that benefits crown root growth and phosphorus (P) sufficiency in rice (Oryza sativa). To explore the ecophysiological importance of this gene, we performed a biogeographic survey of landraces and cultivars, confirming that functional OsPSTOL1 alleles prevail in low nutrient and drought-prone rainfed ecosystems, whereas loss-of-function and absence haplotypes predominate in control-irrigated paddy varieties of east Asia. An evolutionary history analysis of OsPSTOL1 and related genes in cereal, determined it and other genes are kinase-only domain derivatives of membrane-associated receptor like kinases. Finally, to evaluate the potential value of this kinase of unknown function in another Gramineae, wheat (Triticum aestivum) lines overexpressing OsPSTOL1 were evaluated under field and controlled low P conditions. OsPSTOL1 enhances growth, crown root number, and overall root plasticity under low P in wheat. Survey of root and shoot crown transcriptomes at two developmental stages identifies transcription factors that are differentially regulated in OsPSTOL1 wheat that are similarly controlled by the gene in rice. In wheat, OsPSTOL1 alters the timing and amplitude of regulators of root development in dry soils and hastens induction of the core P-starvation response. OsPSTOL1 and related genes may aid more sustainable cultivation of cereal crops.
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Affiliation(s)
- Alek T Kettenburg
- Botany and Plant Sciences Department, Center for Plant Cell Biology, University of California, Riverside, California, USA
| | - Miguel A Lopez
- Botany and Plant Sciences Department, Center for Plant Cell Biology, University of California, Riverside, California, USA
| | - Kalenahalli Yogendra
- School of Agriculture, Food and Wine & Waite Research Institute, The University of Adelaide, Adelaide, South Australia, Australia
- ARC Industrial Transformation Research Hub for Wheat in a Hot and Dry Climate, The University of Adelaide, Adelaide, South Australia, Australia
| | - Matthew J Prior
- Botany and Plant Sciences Department, Center for Plant Cell Biology, University of California, Riverside, California, USA
| | - Teresa Rose
- Department of Plant Science, Rothamsted Research, Harpenden, Hertfordshire, UK
| | - Sabrina Bimson
- Botany and Plant Sciences Department, Center for Plant Cell Biology, University of California, Riverside, California, USA
| | - Sigrid Heuer
- School of Agriculture, Food and Wine & Waite Research Institute, The University of Adelaide, Adelaide, South Australia, Australia
- Department of Plant Science, Rothamsted Research, Harpenden, Hertfordshire, UK
| | - Stuart J Roy
- School of Agriculture, Food and Wine & Waite Research Institute, The University of Adelaide, Adelaide, South Australia, Australia
- ARC Industrial Transformation Research Hub for Wheat in a Hot and Dry Climate, The University of Adelaide, Adelaide, South Australia, Australia
| | - Julia Bailey-Serres
- Botany and Plant Sciences Department, Center for Plant Cell Biology, University of California, Riverside, California, USA
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16
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Wang Z, Li Z, Wu D, Tian Q, Su S, Cheng C, Nie J, Yuan Y, Wang Y, Xu X. DNA methylation variation is crucial to restore adventitious rooting ability during in vitro shoot culture-induced rejuvenation in apple rootstock. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:554-569. [PMID: 36799443 DOI: 10.1111/tpj.16153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 02/02/2023] [Accepted: 02/07/2023] [Indexed: 05/10/2023]
Abstract
In vitro shoot culture has been widely used for restoring adventitious rooting ability in rooting recalcitrant woody perennial species for the past few decades, but its molecular mechanism is largely uncovered. DNA methylation is an essential epigenetic mark that participates in many biological processes. Recent reports suggested a role of DNA methylation in vitro culture in plants. In this study, we characterized the single-base resolution DNA methylome and transcriptome of adult and in vitro shoot culture-induced rejuvenation cuttings of apple rootstock M9T337. We found a global decrease in DNA methylation during rejuvenation, which may be correlated with increased expression of DNA demethylase genes and decreased expression of DNA methyltransferase genes. We additionally documented DNA hypomethylation in 'T337'_R in gene protomer associated with higher transcript levels of several adventitious rooting-related genes. The application of a DNA methylation inhibitor (5-azacytidine) enhanced the adventitious rooting ability and the expression level of adventitious rooting-related genes, such as, MdANT, MdMPK3, MdABCB21, MdCDC48, MdKIN8B, pri-MdMIR156a5 and pri-MdMIR156a12. Together, the DNA hypomethylation is critical for the rejuvenation-dependent adventitious rooting ability in apple rootstock. In addition, increased DNA methylation was also found in thousands of genes in 'T337'_R. We additionally documented that DNA hypermethylation is required for inhibition of adventitious rooting-repressed genes, such as MdGAD5a, encoding glutamate decarboxylase, which can catalyze glutamate decarboxylated to form γ-aminobutyric acid (GABA). Our results revealed that in vitro shoot culture-dependent DNA methylation variation plays important roles in adventitious rooting in apple rootstock.
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Affiliation(s)
- Zhe Wang
- College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China
| | - Zhengnan Li
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Dongchen Wu
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, Qingdao Agricultural University, Qingdao, 266109, China
| | - Qiuye Tian
- College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China
| | - Shenghui Su
- College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China
| | - Chenxia Cheng
- College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China
| | - Jiyun Nie
- Laboratory of Quality & Safety Risk Assessment for Fruit (Qingdao), Ministry of Agriculture and Rural Affairs, Qingdao Agricultural University, Qingdao, 266109, China
| | - Yongbing Yuan
- College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China
| | - Yongzhang Wang
- College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China
| | - Xiaozhao Xu
- College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China
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17
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Lin C, Ogorek LLP, Liu D, Pedersen O, Sauter M. A quantitative trait locus conferring flood tolerance to deepwater rice regulates the formation of two distinct types of aquatic adventitious roots. THE NEW PHYTOLOGIST 2023; 238:1403-1419. [PMID: 36519256 DOI: 10.1111/nph.18678] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 12/02/2022] [Indexed: 06/17/2023]
Abstract
A key trait conferring flood tolerance is the ability to grow adventitious roots as a response to submergence. The genetic traits of deepwater rice determining the development and characteristics of aquatic adventitious roots (AAR) had not been evaluated. We used near-isogenic lines introgressed to test the hypothesis that the impressive shoot elongation ability of deepwater rice linked to quantitative trait loci 1 and 12 also promote the development of AAR. The deepwater rice genotype NIL-12 possessed expanded regions at the stem nodes where numerous AAR developed as a response to submergence. Two types (AR1 and AR2) of roots with distinct timing of emergence and large differences in morphological and anatomical traits formed within 3 (AR1) to 7 (AR2) d of submergence. The mechanical impedance provided by the leaf sheath caused AR2 to emerge later promoting thicker roots, higher elongation capacity and higher desiccation tolerance. Upregulation of key genes suggests a joint contribution in activating the meristem in AAR enhancing the development of these in response to submergence. The morphological and anatomical traits suggested that AR2 is better adapted to long-term flooding than AR1. We therefore propose that AR2 in deepwater rice functions as an evolutionary defence strategy to tackle periodic submergence.
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Affiliation(s)
- Chen Lin
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
- Plant Developmental Biology and Plant Physiology, University of Kiel, Am Botanischen Garten 5, 24118, Kiel, Germany
| | - Lucas León Peralta Ogorek
- Freshwater Biological Laboratory, Department of Biology, University of Copenhagen, Universitetsparken 4, 3rd floor, 2100, Copenhagen, Denmark
| | - Dan Liu
- Plant Developmental Biology and Plant Physiology, University of Kiel, Am Botanischen Garten 5, 24118, Kiel, Germany
| | - Ole Pedersen
- Freshwater Biological Laboratory, Department of Biology, University of Copenhagen, Universitetsparken 4, 3rd floor, 2100, Copenhagen, Denmark
- School of Agriculture and Environment, The University of Western Australia, Crawley, WA, 6009, Australia
| | - Margret Sauter
- Plant Developmental Biology and Plant Physiology, University of Kiel, Am Botanischen Garten 5, 24118, Kiel, Germany
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18
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Gao J, Zhao Y, Zhao Z, Liu W, Jiang C, Li J, Zhang Z, Zhang H, Zhang Y, Wang X, Sun X, Li Z. RRS1 shapes robust root system to enhance drought resistance in rice. THE NEW PHYTOLOGIST 2023; 238:1146-1162. [PMID: 36862074 DOI: 10.1111/nph.18775] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Accepted: 01/20/2023] [Indexed: 06/18/2023]
Abstract
A strong root system facilitates the absorption of water and nutrients from the soil, to improve the growth of crops. However, to date, there are still very few root development regulatory genes that can be used in crop breeding for agriculture. In this study, we cloned a negative regulator gene of root development, Robust Root System 1 (RRS1), which encodes an R2R3-type MYB family transcription factor. RRS1 knockout plants showed enhanced root growth, including longer root length, longer lateral root length, and larger lateral root density. RRS1 represses root development by directly activating the expression of OsIAA3 which is involved in the auxin signaling pathway. A natural variation in the coding region of RRS1 changes the transcriptional activity of its protein. RRS1T allele, originating from wild rice, possibly increases root length by means of weakening regulation of OsIAA3. Knockout of RRS1 enhances drought resistance by promoting water absorption and improving water use efficiency. This study provides a new gene resource for improving root systems and cultivating drought-resistant rice varieties with important values in agricultural applications.
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Affiliation(s)
- Jie Gao
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Yong Zhao
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Zhikun Zhao
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Wei Liu
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
- Sanya Institute of China Agricultural University, Sanya, 572025, China
| | - Conghui Jiang
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
- Shandong Rice Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100, Shandong, China
| | - Jinjie Li
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Zhanying Zhang
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Hongliang Zhang
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Yage Zhang
- Sanya Institute, Hainan Academy of Agricultural Sciences, Sanya, 572025, China
| | - Xiaoning Wang
- Sanya Institute, Hainan Academy of Agricultural Sciences, Sanya, 572025, China
| | - Xingming Sun
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Zichao Li
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
- Sanya Institute of China Agricultural University, Sanya, 572025, China
- Sanya Institute, Hainan Academy of Agricultural Sciences, Sanya, 572025, China
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19
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Guo F, Wang H, Lian G, Cai G, Liu W, Zhang H, Li D, Zhou C, Han N, Zhu M, Su Y, Seo PJ, Xu L, Bian H. Initiation of scutellum-derived callus is regulated by an embryo-like developmental pathway in rice. Commun Biol 2023; 6:457. [PMID: 37100819 PMCID: PMC10130139 DOI: 10.1038/s42003-023-04835-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 04/12/2023] [Indexed: 04/28/2023] Open
Abstract
In rice (Oryza sativa) tissue culture, callus can be induced from the scutellum in embryo or from the vasculature of non-embryonic organs such as leaves, nodes, or roots. Here we show that the auxin signaling pathway triggers cell division in the epidermis of the scutellum to form an embryo-like structure, which leads to callus formation. Our transcriptome data show that embryo-, stem cell-, and auxin-related genes are upregulated during scutellum-derived callus initiation. Among those genes, the embryo-specific gene OsLEC1 is activated by auxin and involved in scutellum-derived callus initiation. However, OsLEC1 is not required for vasculature-derived callus initiation from roots. In addition, OsIAA11 and OsCRL1, which are involved in root development, are required for vasculature-derived callus formation but not for scutellum-derived callus formation. Overall, our data indicate that scutellum-derived callus initiation is regulated by an embryo-like development program, and this is different from vasculature-derived callus initiation which borrows a root development program.
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Affiliation(s)
- Fu Guo
- Institute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
- Hainan Institute, Zhejiang University, Yazhou Bay Science and Technology City, Sanya, 572025, China
- Yazhou Bay Seed Laboratory, Yazhou Bay Science and Technology City, Yazhou District, Sanya, 572025, China
| | - Hua Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China
| | - Guiwei Lian
- Institute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Gui Cai
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, China
| | - Wu Liu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China
| | - Haidao Zhang
- Institute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
- Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
| | - Dandan Li
- Hainan Institute, Zhejiang University, Yazhou Bay Science and Technology City, Sanya, 572025, China
| | - Chun Zhou
- Institute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Ning Han
- Institute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Muyuan Zhu
- Institute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yinghua Su
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, China
| | - Pil Joon Seo
- Department of Chemistry, Seoul National University, Seoul, 08826, Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826, Korea
| | - Lin Xu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China.
| | - Hongwu Bian
- Institute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.
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20
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Wang J, Li C, Mao X, Wang J, Li L, Li J, Fan Z, Zhu Z, He L, Jing R. The wheat basic helix-loop-helix gene TabHLH123 positively modulates the formation of crown roots and is associated with plant height and 1000-grain weight under various conditions. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:2542-2555. [PMID: 36749713 DOI: 10.1093/jxb/erad051] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 02/03/2023] [Indexed: 06/06/2023]
Abstract
Crown roots are the main components of the fibrous root system in cereal crops and play critical roles in plant adaptation; however, the molecular mechanisms underlying their formation in wheat (Triticum aestivum) have not been fully elucidated. In this study, we identified a wheat basic helix-loop-helix (bHLH) protein, TabHLH123, that interacts with the essential regulator of crown root initiation, MORE ROOT in wheat (TaMOR). TabHLH123 is expressed highly in shoot bases and roots. Ectopic expression of TabHLH123 in rice resulted in more roots compared with the wild type. TabHLH123 regulates the expression of genes controlling crown-root development and auxin metabolism, responses, and transport. In addition, we analysed the nucleotide sequence polymorphisms of TabHLH123s in the wheat genome and identified a superior haplotype, TabHLH123-6B, that is associated with high root dry weight and 1000-grain weight, and short plant height. Our study reveals the role of TabHLH123 in controlling the formation of crown roots and provides beneficial insights for molecular marker-assisted breeding in wheat.
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Affiliation(s)
- Jinping Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- College of Agronomy, Shanxi Agricultural University, Taigu 030031, China
| | - Chaonan Li
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xinguo Mao
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jingyi Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Long Li
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jialu Li
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zipei Fan
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhi Zhu
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Liheng He
- College of Agronomy, Shanxi Agricultural University, Taigu 030031, China
| | - Ruilian Jing
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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21
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Li K, Wei Y, Wang Y, Tan B, Chen S, Li H. Genome-Wide Identification of LBD Genes in Foxtail Millet ( Setaria italica) and Functional Characterization of SiLBD21. Int J Mol Sci 2023; 24:ijms24087110. [PMID: 37108274 PMCID: PMC10138450 DOI: 10.3390/ijms24087110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/05/2023] [Accepted: 04/09/2023] [Indexed: 04/29/2023] Open
Abstract
Plant-specific lateral organ boundaries domain (LBD) proteins play important roles in plant growth and development. Foxtail millet (Setaria italica) is one new C4 model crop. However, the functions of foxtail millet LBD genes are unknown. In this study, a genome-wide identification of foxtail millet LBD genes and a systematical analysis were conducted. A total of 33 SiLBD genes were identified. They are unevenly distributed on nine chromosomes. Among these SiLBD genes, six segmental duplication pairs were detected. The thirty-three encoded SiLBD proteins could be classified into two classes and seven clades. Members in the same clade have similar gene structure and motif composition. Forty-seven kinds of cis-elements were found in the putative promoters, and they are related to development/growth, hormone, and abiotic stress response, respectively. Meanwhile, the expression pattern was investigated. Most SiLBD genes are expressed in different tissues, while several genes are mainly expressed in one or two kinds of tissues. In addition, most SiLBD genes respond to different abiotic stresses. Furthermore, the function of SiLBD21, which is mainly expressed in roots, was characterized by ectopic expression in Arabidopsis and rice. Compared to controls, transgenic plants generated shorter primary roots and more lateral roots, indicating the function of SiLBD21 in root development. Overall, our study laid the foundation for further functional elucidation of SiLBD genes.
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Affiliation(s)
- Kunjie Li
- College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Yaning Wei
- College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Yimin Wang
- College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Bin Tan
- College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Shoukun Chen
- College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Haifeng Li
- College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China
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22
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Tao GY, Xie YH, Li WF, Li KP, Sun C, Wang HM, Sun XM. LkARF7 and LkARF19 overexpression promote adventitious root formation in a heterologous poplar model by positively regulating LkBBM1. Commun Biol 2023; 6:372. [PMID: 37020138 PMCID: PMC10076273 DOI: 10.1038/s42003-023-04731-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 03/17/2023] [Indexed: 04/07/2023] Open
Abstract
Cuttage propagation involves adventitious root formation induced by auxin. In our previous study, Larix kaempferi BABY BOOM 1 (LkBBM1), which is known to regulate adventitious root formation, was affected by auxin. However, the relationship between LkBBM1 and auxin remains unclear. Auxin response factors (ARFs) are a class of important transcription factors in the auxin signaling pathway and modulate the expression of early auxin-responsive genes by binding to auxin response elements. In the present study, we identified 14 L. kaempferi ARFs (LkARFs), and found LkARF7 and LkARF19 bound to LkBBM1 promoter and enhanced its transcription using yeast one-hybrid, ChIP-qPCR, and dual-luciferase assays. In addition, the treatment with naphthalene acetic acid promoted the expression of LkARF7 and LkARF19. We also found that overexpression of these two genes in poplar promoted adventitious root formation. Furthermore, LkARF19 interacted with the DEAD-box ATP-dependent RNA helicase 53-like protein to form a heterodimer to regulate adventitious root formation. Altogether, our results reveal an additional regulatory mechanism underlying the control of adventitious root formation by auxin.
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Affiliation(s)
- Gui-Yun Tao
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Yun-Hui Xie
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Wan-Feng Li
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Kui-Peng Li
- Guangxi Forestry Research Institute, Guangxi, 530009, China
| | - Chao Sun
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Hong-Ming Wang
- College of Bioengineering and Biotechnology, Tianshui Normal University, Gansu, 741000, China
| | - Xiao-Mei Sun
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China.
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23
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Song X, Xiong Y, Kong X, Huang G. Roles of auxin response factors in rice development and stress responses. PLANT, CELL & ENVIRONMENT 2023; 46:1075-1086. [PMID: 36397176 DOI: 10.1111/pce.14494] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 11/07/2022] [Accepted: 11/13/2022] [Indexed: 06/16/2023]
Abstract
Auxin signalling plays a key role in various developmental processes ranging from embryogenesis to senescence in plants. Auxin response factor (ARF), a key component of auxin signalling, functions by binding to auxin response element within promoter of auxin response genes, activating or repressing the target genes. Increasing evidences show that ARFs are crucial for plant response to stresses. This review summarises the recent advance on the functions and their regulatory pathways of rice ARFs in development and responding to stresses. The importance of OsARFs is demonstrated by their roles in triggering various physiological, biochemical and molecular reactions to resist adverse environmental conditions. We also describe the transcriptional and post-transcriptional regulation of OsARFs, and discuss the major challenges in this area.
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Affiliation(s)
- Xiaoyun Song
- Joint International Research Laboratory of Metabolic & Developmental Sciences, SJTU-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yali Xiong
- Joint International Research Laboratory of Metabolic & Developmental Sciences, SJTU-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiuzhen Kong
- Joint International Research Laboratory of Metabolic & Developmental Sciences, SJTU-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Guoqiang Huang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, SJTU-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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24
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Transcriptome and Co-Expression Network Analysis Reveals the Molecular Mechanism of Rice Root Systems in Response to Low-Nitrogen Conditions. Int J Mol Sci 2023; 24:ijms24065290. [PMID: 36982364 PMCID: PMC10048922 DOI: 10.3390/ijms24065290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/03/2023] [Accepted: 03/07/2023] [Indexed: 03/12/2023] Open
Abstract
Nitrogen is an important nutrient for plant growth and essential metabolic processes. Roots integrally obtain nutrients from soil and are closely related to the growth and development of plants. In this study, the morphological analysis of rice root tissues collected at different time points under low-nitrogen and normal nitrogen conditions demonstrated that, compared with normal nitrogen treatment, the root growth and nitrogen use efficiency (NUE) of rice under low-nitrogen treatment were significantly improved. To better understand the molecular mechanisms of the rice root system’s response to low-nitrogen conditions, a comprehensive transcriptome analysis of rice seedling roots under low-nitrogen and control conditions was conducted in this study. As a result, 3171 differentially expressed genes (DEGs) were identified. Rice seedling roots enhance NUE and promote root development by regulating the genes related to nitrogen absorption and utilization, carbon metabolism, root growth and development, and phytohormones, thereby adapting to low-nitrogen conditions. A total of 25,377 genes were divided into 14 modules using weighted gene co-expression network analysis (WGCNA). Two modules were significantly associated with nitrogen absorption and utilization. A total of 8 core genes and 43 co-expression candidates related to nitrogen absorption and utilization were obtained in these two modules. Further studies on these genes will contribute to the understanding of low-nitrogen adaptation and nitrogen utilization mechanisms in rice.
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25
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Tanaka W, Yamauchi T, Tsuda K. Genetic basis controlling rice plant architecture and its modification for breeding. BREEDING SCIENCE 2023; 73:3-45. [PMID: 37168811 PMCID: PMC10165344 DOI: 10.1270/jsbbs.22088] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 12/25/2022] [Indexed: 05/13/2023]
Abstract
The shoot and root system architectures are fundamental for crop productivity. During the history of artificial selection of domestication and post-domestication breeding, the architecture of rice has significantly changed from its wild ancestor to fulfil requirements in agriculture. We review the recent studies on developmental biology in rice by focusing on components determining rice plant architecture; shoot meristems, leaves, tillers, stems, inflorescences and roots. We also highlight natural variations that affected these structures and were utilized in cultivars. Importantly, many core regulators identified from developmental mutants have been utilized in breeding as weak alleles moderately affecting these architectures. Given a surge of functional genomics and genome editing, the genetic mechanisms underlying the rice plant architecture discussed here will provide a theoretical basis to push breeding further forward not only in rice but also in other crops and their wild relatives.
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Affiliation(s)
- Wakana Tanaka
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-4-4 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8528, Japan
| | - Takaki Yamauchi
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi 464-8601, Japan
| | - Katsutoshi Tsuda
- National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
- Department of Genetics, School of Life Science, Graduate University for Advanced Studies, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
- Corresponding author (e-mail: )
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26
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Li Y, Luo J, Chen R, Zhou Y, Yu H, Chu Z, Lu Y, Gu X, Wu S, Wang P, Kuang H, Ouyang B. Folate shapes plant root architecture by affecting auxin distribution. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 113:969-985. [PMID: 36587293 DOI: 10.1111/tpj.16093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 11/26/2022] [Accepted: 12/24/2022] [Indexed: 06/17/2023]
Abstract
Folate (vitamin B9) is important for plant root development, but the mechanism is largely unknown. Here we characterized a root defective mutant, folb2, in Arabidopsis, which has severe developmental defects in the primary root. The root apical meristem of the folb2 mutant is impaired, and adventitious roots are frequently found at the root-hypocotyl junction. Positional cloning revealed that a 61-bp deletion is present in the predicted junction region of the promoter and the 5' untranslated region of AtFolB2, a gene encoding a dihydroneopterin aldolase that functions in folate biosynthesis. This mutation leads to a significant reduction in the transcript level of AtFolB2. Liquid chromatography-mass spectrometry analysis showed that the contents of the selected folate compounds were decreased in folb2. Arabidopsis AtFolB2 knockdown lines phenocopy the folb2 mutant. On the other hand, the application of exogenous 5-formyltetrahydrofolic acid could rescue the root phenotype of folb2, indicating that the root phenotype is indeed related to the folate level. Further analysis revealed that folate could promote rootward auxin transport through auxin transporters and that folate may affect particular auxin/indole-3-acetic acid proteins and auxin response factors. Our findings provide new insights into the important role of folic acid in shaping root structure.
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Affiliation(s)
- Ying Li
- Key Laboratory of Horticultural Plant Biology, MOE, and Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- College of Horticulture, Henan Agricultural University, Zhengzhou, Henan, 450002, China
| | - Jinying Luo
- Key Laboratory of Horticultural Plant Biology, MOE, and Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Rong Chen
- Key Laboratory of Horticultural Plant Biology, MOE, and Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Yuhong Zhou
- Key Laboratory of Horticultural Plant Biology, MOE, and Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Huiyang Yu
- Key Laboratory of Horticultural Plant Biology, MOE, and Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Zhuannan Chu
- Key Laboratory of Horticultural Plant Biology, MOE, and Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Yongen Lu
- Key Laboratory of Horticultural Plant Biology, MOE, and Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Xiaofeng Gu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Shuang Wu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Pengwei Wang
- Key Laboratory of Horticultural Plant Biology, MOE, and Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Hanhui Kuang
- Key Laboratory of Horticultural Plant Biology, MOE, and Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Bo Ouyang
- Key Laboratory of Horticultural Plant Biology, MOE, and Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
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27
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Li Y, Han S, Qi Y. Advances in structure and function of auxin response factor in plants. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:617-632. [PMID: 36263892 DOI: 10.1111/jipb.13392] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 10/18/2022] [Indexed: 06/16/2023]
Abstract
Auxin is a crucial phytohormone that has various effects on the regulators of plant growth and development. Auxin signal transduction is mainly controlled by two gene families: auxin response factor (ARF) and auxin/indole-3-acetic acid (Aux/IAA). ARFs are plant-specific transcription factors that bind directly to auxin response elements in the promoters of auxin-responsive genes. ARF proteins contain three conserved regions: a conserved N-terminal B3 DNA-binding domain, a variable intermediate middle region domain that functions in activation or repression, and a C-terminal domain including the Phox and Bem1p region for dimerization, similar to the III and IV elements of Aux/IAA, which facilitate protein-protein interaction through homodimerization of ARF proteins or heterodimerization of ARF and Aux/IAA proteins. In the two decades following the identification of the first ARF, 23 ARF members have been identified and characterized in Arabidopsis. Using whole-genome sequencing, 22, 25, 23, 25, and 36 ARF genes have been identified in tomato, rice, wheat, sorghum, and maize, respectively, in addition to which the related biofunctions of some ARFs have been reported. ARFs play crucial roles in regulating the growth and development of roots, leaves, flowers, fruits, seeds, responses to biotic and abiotic stresses, and phytohormone signal crosstalk. In this review, we summarize the research progress on the structures and functions of ARFs in Arabidopsis, tomato, and cereal crops, to provide clues for future basic research on phytohormone signaling and the molecular design breeding of crops.
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Affiliation(s)
- Yonghui Li
- Key Laboratory of Herbage & Endemic Crop Biology of Ministry of Education, Inner Mongolia Key Laboratory of Herbage & Endemic Crop Biotechnology, School of Life Sciences, Inner Mongolia University, Hohhot, 010000, China
| | - Shaqila Han
- Key Laboratory of Herbage & Endemic Crop Biology of Ministry of Education, Inner Mongolia Key Laboratory of Herbage & Endemic Crop Biotechnology, School of Life Sciences, Inner Mongolia University, Hohhot, 010000, China
| | - Yanhua Qi
- Key Laboratory of Herbage & Endemic Crop Biology of Ministry of Education, Inner Mongolia Key Laboratory of Herbage & Endemic Crop Biotechnology, School of Life Sciences, Inner Mongolia University, Hohhot, 010000, China
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
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28
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Li L, Chen X. Auxin regulation on crop: from mechanisms to opportunities in soybean breeding. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:16. [PMID: 37313296 PMCID: PMC10248601 DOI: 10.1007/s11032-023-01361-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 02/10/2023] [Indexed: 06/15/2023]
Abstract
Breeding crop varieties with high yield and ideal plant architecture is a desirable goal of agricultural science. The success of "Green Revolution" in cereal crops provides opportunities to incorporate phytohormones in crop breeding. Auxin is a critical phytohormone to determine nearly all the aspects of plant development. Despite the current knowledge regarding auxin biosynthesis, auxin transport and auxin signaling have been well characterized in model Arabidopsis (Arabidopsis thaliana) plants, how auxin regulates crop architecture is far from being understood, and the introduction of auxin biology in crop breeding stays in the theoretical stage. Here, we give an overview on molecular mechanisms of auxin biology in Arabidopsis, and mainly summarize auxin contributions for crop plant development. Furthermore, we propose potential opportunities to integrate auxin biology in soybean (Glycine max) breeding.
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Affiliation(s)
- Linfang Li
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
- Haixia Institute of Science and Technology, Horticultural Plant Biology and Metabolomics Center, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
| | - Xu Chen
- Haixia Institute of Science and Technology, Horticultural Plant Biology and Metabolomics Center, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
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Han Y, Zhang C, Sha H, Wang X, Yu Y, Liu J, Zhao G, Wang J, Qiu G, Xu X, Fang J. Ubiquitin-Conjugating Enzyme OsUBC11 Affects the Development of Roots via Auxin Pathway. RICE (NEW YORK, N.Y.) 2023; 16:9. [PMID: 36808375 PMCID: PMC9941415 DOI: 10.1186/s12284-023-00626-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 02/11/2023] [Indexed: 06/01/2023]
Abstract
Rice has 48 ubiquitin-conjugating enzymes, and the functions of most of these enzymes have not been elucidated. In the present study, a T-DNA insertional mutant named R164, which exhibited a significant decrease in the length of primary and lateral roots, was used as the experimental material to explore the potential function of OsUBC11. Analysis using the SEFA-PCR method showed that the T-DNA insertion was present in the promoter region of OsUBC11 gene, which encodes ubiquitin-conjugating enzyme (E2), and activates its expression. Biochemical experiments showed that OsUBC11 is a lysine-48-linked ubiquitin chain-forming conjugase. OsUBC11 overexpression lines showed the same root phenotypes. These results demonstrated that OsUBC11 was involved in root development. Further analyses showed that the IAA content of R164 mutant and OE3 line were significantly lower compared with wild-type Zhonghua11. Application of exogenous NAA restored the length of lateral and primary roots in R164 and OsUBC11 overexpression lines. Expression of the auxin synthesis regulating gene OsYUCCA4/6/7/9, the auxin transport gene OsAUX1, auxin/indole-3-acetic acid (Aux/IAA) family gene OsIAA31, auxin response factor OsARF16 and root regulator key genes, including OsWOX11, OsCRL1, OsCRL5 was significantly down-regulated in OsUBC11 overexpressing plants. Collectively, these results indicate that OsUBC11 modulates auxin signaling, ultimately affecting root development at the rice seedling stage.
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Affiliation(s)
- Yunfei Han
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chuanzhong Zhang
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Hanjing Sha
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Xiaojing Wang
- Hinggan League Institute of Agricultural and Animal Husbandry Sciences, Hinggan League, 137400, Inner Mongolia, China
| | - Yue Yu
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
- Northeast Agricultural University, Harbin, China
| | - Jia Liu
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Guangxin Zhao
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jingying Wang
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Guankai Qiu
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xingjian Xu
- Hinggan League Institute of Agricultural and Animal Husbandry Sciences, Hinggan League, 137400, Inner Mongolia, China.
| | - Jun Fang
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China.
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Singh H, Singh Z, Zhu T, Xu X, Waghmode B, Garg T, Yadav S, Sircar D, De Smet I, Yadav SR. Auxin-Responsive (Phospho)proteome Analysis Reveals Key Biological Processes and Signaling Associated with Shoot-Borne Crown Root Development in Rice. PLANT & CELL PHYSIOLOGY 2023; 63:1968-1979. [PMID: 34679169 DOI: 10.1093/pcp/pcab155] [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: 07/17/2021] [Revised: 09/13/2021] [Accepted: 10/21/2021] [Indexed: 06/13/2023]
Abstract
The rice root system is primarily composed of shoot-borne adventitious/crown roots (ARs/CRs) that develop from the coleoptile base, and therefore, it is an excellent model system for studying shoot-to-root trans-differentiation process. We reveal global changes in protein and metabolite abundance and protein phosphorylation in response to an auxin stimulus during CR development. The liquid chromatography-tandem mass spectrometry (LC-MS/MS) and gas chromatography-mass spectrometry (GC-MS) analyses of developing crown root primordia (CRP) and emerged CRs identified 334 proteins and 12 amino acids, respectively, that were differentially regulated upon auxin treatment. Gene ontology enrichment analysis of global proteome data uncovered the biological processes associated with chromatin conformational change, gene expression and cell cycle that were regulated by auxin signaling. Spatial gene expression pattern analysis of differentially abundant proteins disclosed their stage-specific dynamic expression pattern during CRP development. Further, our tempo-spatial gene expression and functional analyses revealed that auxin creates a regulatory module during CRP development and activates ethylene biosynthesis exclusively during CRP initiation. Further, the phosphoproteome analysis identified 8,220 phosphosites, which could be mapped to 1,594 phosphoproteins and of which 66 phosphosites were differentially phosphorylated upon auxin treatment. Importantly, we observed differential phosphorylation of the cyclin-dependent kinase G-2 (OsCDKG;2) and cell wall proteins, in response to auxin signaling, suggesting that auxin-dependent phosphorylation may be required for cell cycle activation and cell wall synthesis during root organogenesis. Thus, our study provides evidence for the translational and post-translational regulation during CR development downstream of the auxin signaling pathway.
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Affiliation(s)
- Harshita Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, Uttarakhand 247667, India
| | - Zeenu Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, Uttarakhand 247667, India
| | - Tingting Zhu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent 9052, Belgium
| | - Xiangyu Xu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent 9052, Belgium
| | - Bhairavnath Waghmode
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, Uttarakhand 247667, India
| | - Tushar Garg
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, Uttarakhand 247667, India
| | - Shivani Yadav
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, Uttarakhand 247667, India
| | - Debabrata Sircar
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, Uttarakhand 247667, India
| | - Ive De Smet
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent 9052, Belgium
| | - Shri Ram Yadav
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, Uttarakhand 247667, India
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31
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Singh Z, Singh H, Garg T, Mushahary KKK, Yadav SR. Genetic and Hormonal Blueprint of Shoot-Borne Adventitious Root Development in Rice and Maize. PLANT & CELL PHYSIOLOGY 2023; 63:1806-1813. [PMID: 35713294 DOI: 10.1093/pcp/pcac084] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 05/05/2022] [Accepted: 06/14/2022] [Indexed: 06/15/2023]
Abstract
The evolution of root architecture in plants was a prerequisite for the absorption of water and minerals from the soil, and thus a major determinant of terrestrial plant colonization. Cereals have a remarkably complex root system consisting of embryonic primary roots and post-embryonic lateral roots and shoot-borne adventitious roots. Among grass species, rice adventitious roots (also called crown roots) are developed from compressed nodes at the stem base, whereas in maize, besides crown roots, several aboveground brace roots are also formed, thus adventitious root types display species-specific diversity. Despite being the backbone for the adult root system in monocots, adventitious roots are the least studied of all the plant organs. In recent times, molecular genetics, genomics and proteomics-based approaches have been utilized to dissect the mechanism of post-embryonic meristem formation and tissue patterning. Adventitious root development is a cumulative effect of the actions and interactions of crucial genetic and hormonal regulators. In this review, we provide a comprehensive view of the key regulators involved during the different stages of adventitious root development in two important crop plants, rice and maize. We have reviewed the roles of major phytohormones, microRNAs and transcription factors and their crosstalk during adventitious root development in these cereal crops.
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Affiliation(s)
- Zeenu Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand 247667, India
| | - Harshita Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand 247667, India
| | - Tushar Garg
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand 247667, India
| | | | - Shri Ram Yadav
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand 247667, India
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Liu H, Huang J, Zhang X, Liu G, Liang W, Zhu G, Dong M, Li M, Zhang J, Yang W, Xiao W, Cheung AY, Tao LZ. The RAC/ROP GTPase activator OsRopGEF10 functions in crown root development by regulating cytokinin signaling in rice. THE PLANT CELL 2023; 35:453-468. [PMID: 36190337 PMCID: PMC9806555 DOI: 10.1093/plcell/koac297] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 09/28/2022] [Indexed: 05/26/2023]
Abstract
RAC/Rho of plant (ROP) GTPases are major molecular switches that control diverse signaling cascades for plant growth, development, and defense. Here, we discovered a signaling node that connects RAC/ROPs to cytokinins. Rice (Oryza sativa) plants develop a fibrous root system mainly composed of crown roots. Cytokinin signaling via a phosphorelay system is critical for crown root development. We show that OsRopGEF10, which activates RAC/ROPs, acts upstream of the cytoplasmic-nuclear shuttling phosphotransfer proteins AHPs of the cytokinin signaling pathway to promote crown root development. Mutations of OsRopGEF10 induced hypersensitivity to cytokinin, whereas overexpressing this gene reduced the cytokinin response. Loss of OsRopGEF10 function reduced the expression of the response regulator gene OsRR6, a repressor of cytokinin signaling, and impaired crown root development. Mutations in OsAHP1/2 led to increased crown root production and rescued the crown root defect of Osropgef10. Furthermore, auxin activates the ROP GTPase OsRAC3, which attenuates cytokinin signaling for crown root initiation. Molecular interactions between OsRopGEF10, OsRAC3, and OsAHP1/2 implicate a mechanism whereby OsRopGEF10-activated OsRAC3 recruits OsAHP1/2 to the cortical cytoplasm, sequestering them from their phosphorelay function in the nucleus. Together, our findings uncover the OsRopGEF10-OsRAC3-OsAHP1/2 signaling module, establish a link between RAC/ROPs and cytokinin, and reveal molecular crosstalk between auxin and cytokinin during crown root development.
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Affiliation(s)
- Huili Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Jiaqing Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Xiaojing Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Guolan Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Wei Liang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Guangqi Zhu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Mengge Dong
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Ming Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Jie Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Weiyuan Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Wu Xiao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Alice Y Cheung
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Massachusetts 01003, USA
| | - Li-Zhen Tao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
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33
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Geng L, Li Q, Jiao L, Xiang Y, Deng Q, Zhou DX, Zhao Y. WOX11 and CRL1 act synergistically to promote crown root development by maintaining cytokinin homeostasis in rice. THE NEW PHYTOLOGIST 2023; 237:204-216. [PMID: 36208055 DOI: 10.1111/nph.18522] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 09/22/2022] [Indexed: 06/16/2023]
Abstract
Crown root (CR) morphogenesis is critical for normal growth and nutrition absorption in cereals. In rice, WUSCHEL-RELATED HOMEOBOX11 (WOX11) and CROWN ROOTLESS1 (CRL1) play vital roles in controlling CR development. Despite their importance, whether and how the two regulators coordinate CR formation remains unclear. Electrophoretic mobility shift assays, transient expression, and chromatin immunoprecipitation qPCR suggested that WOX11 and CRL1 directly bind to OsCKX4 to regulate its expression during CR development. CRL1 enhances OsCKX4 activation through direct interaction with WOX11 at root emergence and elongation stages. Genetic dissection showed that the wox11/crl1 double mutant exhibits a more severe root phenotype. OsCKX4 knockout plants generated by CRISPR/Cas9 exhibited fewer CRs and higher cytokinin levels in the root meristem. Increased expression of OsCKX4 could partially complement the CR phenotypes of both crl1 and wox11 mutants. Furthermore, cytokinin can promote WOX11 protein accumulation in the root meristem. Together, these findings show that cytokinin accumulation is tightly regulated by the WOX11-CRL1 complex during CR elongation by counteracting the negative regulatory effects of cytokinin on root development. Importantly, these results reveal an intrinsic link between WOX11 protein accumulation and cytokinin to maintain CR growth.
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Affiliation(s)
- Leping Geng
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qi Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Lele Jiao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yimeng Xiang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qiyu Deng
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Dao-Xiu Zhou
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
- Institute of Plant Science Paris-Saclay (IPS2), CNRS, INRAE, University Paris-Saclay, Orsay, 91405, France
| | - Yu Zhao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
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Li Y, Wu L, Ren M, Zhu J, Xu J, Hu H, Quan X, Huang C, Mao C. Functional redundancy of OsPIN1 paralogous genes in regulating plant growth and development in rice. PLANT SIGNALING & BEHAVIOR 2022; 17:2065432. [PMID: 35442849 PMCID: PMC9037464 DOI: 10.1080/15592324.2022.2065432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 04/06/2022] [Accepted: 04/06/2022] [Indexed: 06/14/2023]
Abstract
The OsPIN1 paralogous genes (OsPIN1a-1d) are important for root and panicle development in rice (Oryza sativa L.). However, the specific role of OsPIN1 paralogous genes is still not clear. To understand the specific roles of PIN1 paralogs in rice, we generated pin1 triple and quadruple mutants by crossing the pin1a pin1b and pin1c pin1d double mutants which we previously created. Compared with the 7-day-old wild type, the pin1a pin1c pin1d and pin1b pin1c pin1d triple mutants showed no obvious phenotype variation except that the pin1a pin1c pin1d triple mutant had shorter primary root and shoot. The pin1a pin1b pin1c and pin1a pin1b pin1d triple mutants exhibited a series of developmental abnormalities, including shorter primary roots, longer root hairs, fewer crown roots and lateral roots, shorter and curved shoots. Furthermore, the pin1a pin1b pin1c pin1d quadruple mutant displayed more severe phenotypic defects which was lethal. In addition, the expression levels of some hormone signal transduction and crown root development related genes, such as OsIAAs, OsARFs, OsRRs, and OsCRLs, were significantly altered in the stem base of all examined pin1 multiple mutants. Taken together, our results demonstrated that the four OsPIN1 paralogous genes function redundantly in regulating rice growth and development.
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Affiliation(s)
- Yong Li
- Institute of Plant Biology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Lingling Wu
- Institute of Plant Biology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Meiyan Ren
- Institute of Plant Biology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jianshu Zhu
- Institute of Plant Biology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jiming Xu
- Institute of Plant Biology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Han Hu
- Agricultural Experiment Station of Zhejiang University, Hangzhou, Zhejiang, China
| | - Xiaokang Quan
- Agricultural Experiment Station of Zhejiang University, Hangzhou, Zhejiang, China
| | - Chongping Huang
- Agricultural Experiment Station of Zhejiang University, Hangzhou, Zhejiang, China
| | - Chuanzao Mao
- Institute of Plant Biology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
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Zhou X, Zhu T, Fang W, Yu R, He Z, Chen D. Systematic annotation of conservation states provides insights into regulatory regions in rice. J Genet Genomics 2022; 49:1127-1137. [PMID: 35470092 DOI: 10.1016/j.jgg.2022.04.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 04/08/2022] [Accepted: 04/12/2022] [Indexed: 01/14/2023]
Abstract
Plant genomes contain a large fraction of noncoding sequences. The discovery and annotation of conserved noncoding sequences (CNSs) in plants is an ongoing challenge. Here we report the application of comparative genomics to systematically identify CNSs in 50 well-annotated Gramineae genomes using rice (Oryza sativa) as the reference. We conduct multiple-way whole-genome alignments to the rice genome. The rice genome is annotated as 20 conservation states (CSs) at single-nucleotide resolution using a multivariate hidden Markov model (ConsHMM) based on the multiple-genome alignments. Different states show distinct enrichments for various genomic features, and the conservation scores of CSs are highly correlated with the level of associated chromatin accessibility. We find that at least 33.5% of the rice genome is highly under selection, with more than 70% of the sequence lying outside of coding regions. A catalog of 855,366 regulatory CNSs is generated, and they significantly overlapped with putative active regulatory elements such as promoters, enhancers, and transcription factor binding sites. Collectively, our study provides a resource for elucidating functional noncoding regions of the rice genome and an evolutionary aspect of regulatory sequences in higher plants.
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Affiliation(s)
- Xinkai Zhou
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Tao Zhu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Wen Fang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Ranran Yu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Zhaohui He
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Dijun Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210023, China.
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36
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To HTM, Pham DT, Le Thi VA, Nguyen TT, Tran TA, Ta AS, Chu HH, Do PT. The Germin-like protein OsGER4 is involved in promoting crown root development under exogenous jasmonic acid treatment in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:860-874. [PMID: 36134434 DOI: 10.1111/tpj.15987] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 09/13/2022] [Accepted: 09/15/2022] [Indexed: 06/16/2023]
Abstract
In rice (Oryza sativa L.), crown roots (CRs) have many important roles in processes such as root system expansion, water and mineral uptake, and adaptation to environmental stresses. Phytohormones such as auxin, cytokinin, and ethylene are known to control CR initiation and development in rice. However, the role of jasmonic acid (JA) in CR development remained elusive. Here, we report that JA promotes CR development by regulating OsGER4, a rice Germin-like protein. Root phenotyping analysis revealed that exogenous JA treatment induced an increase in CR number in a concentration-dependent manner. A subsequent genome-wide association study and gene expression analyses pinpointed a strong association between the Germin-like protein OsGER4 and the increase in CR number under exogenous JA treatment. The ProGER4::GUS reporter line showed that OsGER4 is a hormone-responsive gene involved in various stress responses, mainly confined to epidermal and vascular tissues during CR primordia development and to vascular bundles of mature crown and lateral roots. Notable changes in OsGER4 expression patterns caused by the polar auxin transport inhibitor NPA support its connection to auxin signaling. Phenotyping experiments with OsGER4 knockout mutants confirmed that this gene is required for CR development under exogenous JA treatment. Overall, our results provide important insights into JA-mediated regulation of CR development in rice.
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Affiliation(s)
- Huong Thi Mai To
- University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, 100000, Vietnam
| | - Dan The Pham
- University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, 100000, Vietnam
| | - Van Anh Le Thi
- University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, 100000, Vietnam
| | - Trang Thi Nguyen
- University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, 100000, Vietnam
| | - Tuan Anh Tran
- University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, 100000, Vietnam
| | - Anh Son Ta
- School of Applied Mathematics and Informatics, University of Science and Technology of Hanoi, 1 Dai Co Viet, Hai Ba Trung, Hanoi, Vietnam
| | - Ha Hoang Chu
- Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, 100000, Vietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, 100000, Vietnam
| | - Phat Tien Do
- Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, 100000, Vietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, 100000, Vietnam
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37
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Genomic insights into local adaptation and future climate-induced vulnerability of a keystone forest tree in East Asia. Nat Commun 2022; 13:6541. [PMID: 36319648 PMCID: PMC9626627 DOI: 10.1038/s41467-022-34206-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 10/17/2022] [Indexed: 11/19/2022] Open
Abstract
Rapid global climate change is posing a substantial threat to biodiversity. The assessment of population vulnerability and adaptive capacity under climate change is crucial for informing conservation and mitigation strategies. Here we generate a chromosome-scale genome assembly and re-sequence genomes of 230 individuals collected from 24 populations for Populus koreana, a pioneer and keystone tree species in temperate forests of East Asia. We integrate population genomics and environmental variables to reveal a set of climate-associated single-nucleotide polymorphisms, insertion/deletions and structural variations, especially numerous adaptive non-coding variants distributed across the genome. We incorporate these variants into an environmental modeling scheme to predict a highly spatiotemporal shift of this species in response to future climate change. We further identify the most vulnerable populations that need conservation priority and many candidate genes and variants that may be useful for forest tree breeding with special aims. Our findings highlight the importance of integrating genomic and environmental data to predict adaptive capacity of a key forest to rapid climate change in the future.
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Wang H, Han X, Fu X, Sun X, Chen H, Wei X, Cui S, Liu Y, Guo W, Li X, Xing J, Zhang Y. Overexpression of TaLBD16-4D alters plant architecture and heading date in transgenic wheat. FRONTIERS IN PLANT SCIENCE 2022; 13:911993. [PMID: 36212357 PMCID: PMC9533090 DOI: 10.3389/fpls.2022.911993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 09/02/2022] [Indexed: 06/16/2023]
Abstract
Lateral organ boundaries domain (LBD) proteins, a class of plant-specific transcription factors with a special domain of lateral organ boundaries (LOB), play essential roles in plant growth and development. However, there is little known about the functions of these genes in wheat to date. Our previous study demonstrated that TaLBD16-4D is conducive to increasing lateral root number in wheat. In the present work, we further examined important agronomical traits of the aerial part of transgenic wheat overexpressing TaLBD16-4D. Interestingly, it was revealed that overexpressing TaLBD16-4D could lead to early heading and multiple alterations of plant architecture, including decreased plant height, increased flag leaf size and stem diameter, reduced spike length and tillering number, improved spike density and grain width, and decreased grain length. Moreover, auxin-responsive experiments demonstrated that the expression of TaLBD16-4D in wild-type (WT) wheat plants showed a significant upregulation through 2,4-D treatment. TaLBD16-4D-overexpression lines displayed a hyposensitivity to 2,4-D treatment and reduced shoot gravitropic response. The expressions of a set of auxin-responsive genes were markedly different between WT and transgenic plants. In addition, overexpressing TaLBD16-4D affected the transcript levels of flowering-related genes (TaGI, TaCO1, TaHd1, TaVRN1, TaVRN2, and TaFT1). Notably, the expression of TaGI, TaCO1, TaHd1, TaVRN1, and TaFT1 displayed significant upregulation under IAA treatment. Collectively, our observations indicated that overexpressing TaLBD16-4D could affect aerial architecture and heading time possibly though participating in the auxin pathway.
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Affiliation(s)
- Huifang Wang
- Shandong Provincial Key Laboratory of Dryland Farming Technology, Qingdao Agricultural University, Qingdao, China
| | - Xiaofan Han
- Shandong Provincial Key Laboratory of Dryland Farming Technology, Qingdao Agricultural University, Qingdao, China
| | - Xiaofeng Fu
- Shandong Provincial Key Laboratory of Dryland Farming Technology, Qingdao Agricultural University, Qingdao, China
| | - Xinling Sun
- Shandong Provincial Key Laboratory of Dryland Farming Technology, Qingdao Agricultural University, Qingdao, China
| | - Hailong Chen
- Shandong Provincial Key Laboratory of Dryland Farming Technology, Qingdao Agricultural University, Qingdao, China
| | - Xirui Wei
- Shandong Provincial Key Laboratory of Dryland Farming Technology, Qingdao Agricultural University, Qingdao, China
| | - Shubin Cui
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Yiguo Liu
- Shandong Provincial Key Laboratory of Dryland Farming Technology, Qingdao Agricultural University, Qingdao, China
| | - Weiwei Guo
- Shandong Provincial Key Laboratory of Dryland Farming Technology, Qingdao Agricultural University, Qingdao, China
| | - Ximei Li
- Shandong Provincial Key Laboratory of Dryland Farming Technology, Qingdao Agricultural University, Qingdao, China
| | - Jiewen Xing
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Yumei Zhang
- Shandong Provincial Key Laboratory of Dryland Farming Technology, Qingdao Agricultural University, Qingdao, China
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Adu BG, Argete AYS, Egawa S, Nagano AJ, Shimizu A, Ohmori Y, Fujiwara T. A Koshihikari X Oryza rufipogon Introgression Line with a High Capacity to Take up Nitrogen to Maintain Growth and Panicle Development under Low Nitrogen Conditions. PLANT & CELL PHYSIOLOGY 2022; 63:1215-1229. [PMID: 35791818 DOI: 10.1093/pcp/pcac097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 06/15/2022] [Accepted: 07/05/2022] [Indexed: 06/15/2023]
Abstract
Nitrogen (N) is an important macronutrient for plant growth and development. Currently, N fertilizers are required for the efficient production of modern crops such as rice due to their limited capacity to take up N when present at low concentrations. Wild rice represents a useful genetic resource for improving crop responses to low nutrient stress. Here, we describe the isolation and characterization of an introgression line, KRIL37, that carries a small region of the Oryza rufipogon genome in the Oryza sativa L. cv Koshihikari (KH) background. This line was found to grow better under low N conditions and have similar or lower C/N ratios in aerial portions compared to those in the parental KH cultivar, suggesting that KRIL37 has a higher capacity to take up and assimilate N when present at low concentrations. KRIL37 performance in the field was also better than that of KH cultivated without N and fertilizer (-F). Transcriptome analyses of 3-week-old seedlings based on RNA-sequencing revealed that KH induced a wider suite of genes than the tolerant line KRIL37 in response to low N conditions. Some ammonium transporters and N assimilation genes were found to be induced under low N in KRIL37, but not in KH. Our findings suggest that the superior growth performance of KRIL37 under limited N conditions could be due to the expression of wild alleles influencing N uptake and assimilation. Our study demonstrates the potential to use wild rice genomes to improve modern crops for low nutrient tolerance.
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Affiliation(s)
- Bright G Adu
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, 113-8657 Japan
| | - Aizelle Y S Argete
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, 113-8657 Japan
| | - Sakiko Egawa
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, 113-8657 Japan
| | - Atsushi J Nagano
- Faculty of Agriculture, Ryukoku University, Otsu, 520-2194, Japan
- Institute of Advanced Biosciences, Keio University, Tsuruoka, 997-0017, Japan
| | - Akifumi Shimizu
- School of Environmental Science, The University of Shiga Prefecture, Hassaka-cho, Hikone-City, Shiga 522-8533 Japan
| | - Yoshihiro Ohmori
- Agricultural Bioinformatics Research Unit, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, 113-8657 Japan
| | - Toru Fujiwara
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, 113-8657 Japan
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Zhao J, Jiang L, Bai H, Dai Y, Li K, Li S, Wang X, Wu L, Fu Q, Yang Y, Dong Q, Yu S, Wang M, Liu H, Peng Z, Zhu H, Zhang X, He X, Lei Y, Liang Y, Guo L, Zhang H, Yu D, Liu Y, Huang H, Liu C, Peng S, Du Y. Characteristics of members of IGT family genes in controlling rice root system architecture and tiller development. FRONTIERS IN PLANT SCIENCE 2022; 13:961658. [PMID: 36147240 PMCID: PMC9487910 DOI: 10.3389/fpls.2022.961658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Accepted: 07/27/2022] [Indexed: 06/16/2023]
Abstract
Root system architecture (RSA) and tiller are important agronomic traits. However, the mechanisms of the IGT family genes regulate RSA and tiller development in different rice varieties remain unclear. In this study, we demonstrated that 38 rice varieties obtained from Yuanyang Hani's terraced fields with different RSA and could be classified into six groups based on the ratio of root length and width. We found a positive correlation between RSA (including root width, length, and area) and tiller number in most of rice varieties. Furthermore, the IGT family genes Deeper Rooting 1 (DRO1), LAZY1, TAC1, and qSOR1 showed different expression patterns when rice grown under irrigation and drought conditions. Moreover, the qSOR1 gene had higher levels in the roots and tillers, and accompanied with higher levels of PIN1b gene in roots when rice grown under drought environmental condition. DRO1 gene had two single nucleotide polymorphisms (SNPs) in the exon 3 sequences and showed different expression patterns in the roots and tillers of the 38 rice varieties. Overexpression of DRO1 with a deletion of exon 5 caused shorter root length, less lateral roots and lower levels of LAZY1, TAC1, and qSOR1. Further protein interaction network, microRNA targeting and co-expression analysis showed that DRO1 plays a critical role in the root and tiller development associated with auxin transport. These data suggest that the RSA and tiller development are regulated by the IGT family genes in an intricate network way, which is tightly related to rice genetic background in rice adapting to different environmental conditions.
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Affiliation(s)
- Jianping Zhao
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, China
| | - Lihui Jiang
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, China
| | - Hanrui Bai
- Division of Life Sciences and Medicine, College of Life Sciences, University of Science and Technology of China, Hefei, China
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, China
| | - Yuliang Dai
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
| | - Kuixiu Li
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
| | - Saijie Li
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
| | - Xiaoran Wang
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
| | - Lixia Wu
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, China
| | - Qijing Fu
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, China
| | - Yanfen Yang
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, China
| | - Qian Dong
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
| | - Si Yu
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
| | - Meixian Wang
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
| | - Haiyan Liu
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
| | - Ziai Peng
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, China
| | - Haiyan Zhu
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, China
| | - Xiaoyan Zhang
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, China
| | - Xie He
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, China
| | - Yan Lei
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, China
| | - Yan Liang
- Yuguopu District Agricultural Comprehensive Service Center, Mengzi, China
| | - Liwei Guo
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, China
| | - Hongji Zhang
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, China
| | - Decai Yu
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, China
| | - Yixiang Liu
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, China
| | - Huichuan Huang
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, China
| | - Changning Liu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, China
| | - Sheng Peng
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, China
| | - Yunlong Du
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, China
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The Pyramiding of Three Key Root Traits Aid Breeding of Flood-Tolerant Rice. PLANTS 2022; 11:plants11152033. [PMID: 35956512 PMCID: PMC9370703 DOI: 10.3390/plants11152033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 08/02/2022] [Accepted: 08/02/2022] [Indexed: 11/17/2022]
Abstract
Flooding is constantly threatening the growth and yield of crops worldwide. When flooding kicks in, the soil becomes water-saturated and, therefore, the roots are the first organs to be exposed to excess water. Soon after flooding, the soil turns anoxic and the roots can no longer obtain molecular oxygen for respiration from the rhizosphere, rendering the roots dysfunctional. Rice, however, is a semi-aquatic plant and therefore relatively tolerant to flooding due to adaptive traits developed during evolution. In the present review, we have identified three key root traits, viz. cortical aerenchyma formation, a barrier to radial oxygen loss and adventitious root growth. The understanding of the physiological function, the molecular mechanisms, and the genetic regulation of these three traits has grown substantially and therefore forms the backbone of this review. Our synthesis of the recent literature shows each of the three key root traits contributes to flood tolerance in rice. One trait, however, is generally insufficient to enhance plant tolerance to flooding. Consequently, we suggest comprehensive use of all three adaptive traits in a pyramiding approach in order to improve tolerance to flooding in our major crops, in general, and in rice, in particular.
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Gonin M, Jeong K, Coudert Y, Lavarenne J, Hoang GT, Bes M, To HTM, Thiaw MN, Do TV, Moukouanga D, Guyomarc'h S, Bellande K, Brossier J, Parizot B, Nguyen HT, Beeckman T, Bergougnoux V, Rouster J, Sallaud C, Laplaze L, Champion A, Gantet P. CROWN ROOTLESS1 binds DNA with a relaxed specificity and activates OsROP and OsbHLH044 genes involved in crown root formation in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:546-566. [PMID: 35596715 PMCID: PMC9542200 DOI: 10.1111/tpj.15838] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 04/14/2022] [Accepted: 05/01/2022] [Indexed: 06/15/2023]
Abstract
In cereals, the root system is mainly composed of post-embryonic shoot-borne roots, named crown roots. The CROWN ROOTLESS1 (CRL1) transcription factor, belonging to the ASYMMETRIC LEAVES2-LIKE/LATERAL ORGAN BOUNDARIES DOMAIN (ASL/LBD) family, is a key regulator of crown root initiation in rice (Oryza sativa). Here, we show that CRL1 can bind, both in vitro and in vivo, not only the LBD-box, a DNA sequence recognized by several ASL/LBD transcription factors, but also another not previously identified DNA motif that was named CRL1-box. Using rice protoplast transient transactivation assays and a set of previously identified CRL1-regulated genes, we confirm that CRL1 transactivates these genes if they possess at least a CRL1-box or an LBD-box in their promoters. In planta, ChIP-qPCR experiments targeting two of these genes that include both a CRL1- and an LBD-box in their promoter show that CRL1 binds preferentially to the LBD-box in these promoter contexts. CRISPR/Cas9-targeted mutation of these two CRL1-regulated genes, which encode a plant Rho GTPase (OsROP) and a basic helix-loop-helix transcription factor (OsbHLH044), show that both promote crown root development. Finally, we show that OsbHLH044 represses a regulatory module, uncovering how CRL1 regulates specific processes during crown root formation.
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Affiliation(s)
- Mathieu Gonin
- UMR DIADEUniversité de Montpellier, IRD, CIRAD911 Avenue Agropolis34394Montpellier cedex 5France
| | - Kwanho Jeong
- UMR DIADEUniversité de Montpellier, IRD, CIRAD911 Avenue Agropolis34394Montpellier cedex 5France
| | - Yoan Coudert
- Laboratoire Reproduction et Développement des PlantesUniversité de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, INRIALyon69007France
| | - Jeremy Lavarenne
- UMR DIADEUniversité de Montpellier, IRD, CIRAD911 Avenue Agropolis34394Montpellier cedex 5France
| | - Giang Thi Hoang
- National Key Laboratory for Plant Cell Biotechnology, LMI RICE2Agricultural Genetic Institute11300HanoiVietnam
| | - Martine Bes
- CIRAD, UMR AGAPF‐34398MontpellierFrance
- UMR AGAPUniversité de Montpellier, CIRAD, INRA, Montpellier SupAgroMontpellierFrance
| | - Huong Thi Mai To
- University of Science and Technology of Hanoi, LMIRICE2Vietnam Academy of Science and Technology11300HanoiVietnam
| | - Marie‐Rose Ndella Thiaw
- UMR DIADEUniversité de Montpellier, IRD, CIRAD911 Avenue Agropolis34394Montpellier cedex 5France
| | - Toan Van Do
- National Key Laboratory for Plant Cell Biotechnology, LMI RICE2Agricultural Genetic Institute11300HanoiVietnam
| | - Daniel Moukouanga
- UMR DIADEUniversité de Montpellier, IRD, CIRAD911 Avenue Agropolis34394Montpellier cedex 5France
| | - Soazig Guyomarc'h
- UMR DIADEUniversité de Montpellier, IRD, CIRAD911 Avenue Agropolis34394Montpellier cedex 5France
| | - Kevin Bellande
- UMR DIADEUniversité de Montpellier, IRD, CIRAD911 Avenue Agropolis34394Montpellier cedex 5France
| | - Jean‐Rémy Brossier
- UMR DIADEUniversité de Montpellier, IRD, CIRAD911 Avenue Agropolis34394Montpellier cedex 5France
| | - Boris Parizot
- Department of Plant Biotechnology and BioinformaticsGhent UniversityB‐9052GhentBelgium
- VIB Center for Plant Systems Biology9052GhentBelgium
| | - Hieu Trang Nguyen
- UMR DIADEUniversité de Montpellier, IRD, CIRAD911 Avenue Agropolis34394Montpellier cedex 5France
| | - Tom Beeckman
- Department of Plant Biotechnology and BioinformaticsGhent UniversityB‐9052GhentBelgium
- VIB Center for Plant Systems Biology9052GhentBelgium
| | - Véronique Bergougnoux
- Czech Advanced Technology and Research Institute, Centre of Region Haná for Biotechnological and Agricultural ResearchPalacký University OlomoucOlomoucCzech Republic
| | - Jacques Rouster
- Limagrain Field Seeds, Traits and Technologies, Groupe Limagrain—Centre de RechercheRoute d'EnnezatChappesFrance
| | - Christophe Sallaud
- Limagrain Field Seeds, Traits and Technologies, Groupe Limagrain—Centre de RechercheRoute d'EnnezatChappesFrance
| | - Laurent Laplaze
- UMR DIADEUniversité de Montpellier, IRD, CIRAD911 Avenue Agropolis34394Montpellier cedex 5France
| | - Antony Champion
- UMR DIADEUniversité de Montpellier, IRD, CIRAD911 Avenue Agropolis34394Montpellier cedex 5France
| | - Pascal Gantet
- UMR DIADEUniversité de Montpellier, IRD, CIRAD911 Avenue Agropolis34394Montpellier cedex 5France
- Czech Advanced Technology and Research Institute, Centre of Region Haná for Biotechnological and Agricultural ResearchPalacký University OlomoucOlomoucCzech Republic
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Luo L, Zhu M, Jia L, Xie Y, Wang Z, Xuan W. Ammonium transporters cooperatively regulate rice crown root formation responding to ammonium nitrogen. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:3671-3685. [PMID: 35176162 DOI: 10.1093/jxb/erac059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 02/16/2022] [Indexed: 06/14/2023]
Abstract
Crown roots (CRs) are major components of the rice root system. They form at the basal node of the shoot, and their development is greatly influenced by environmental factors. Ammonium nitrogen is known to impact plant root development through ammonium transporters (AMTs), but it remains unclear whether ammonium and AMTs play roles in rice CR formation. In this study, we revealed a significant role of ammonium, rather than nitrate, in regulating rice CR development. High ammonium supply increases CR formation but inhibits CR elongation. Genetic evidence showed that ammonium regulation of CR development relies on ammonium uptake mediated jointly by ammonium transporters OsAMT1;1, OsAMT1;2; OsAMT1;3, and OsAMT2;1, but not on root acidification which was the result of ammonium uptake. OsAMTs are also needed for glutamine-induced CR formation. Furthermore, we showed that polar auxin transport dependent on the PIN auxin efflux carriers acts downstream of ammonium uptake and assimilation to activate local auxin signaling at CR primordia, in turn promoting CR formation. Taken together, our results highlight a critical role for OsAMTs in cooperatively regulating CR formation through regulating auxin transport under nitrogen-rich conditions.
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Affiliation(s)
- Long Luo
- MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River and State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Ming Zhu
- MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River and State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Letian Jia
- MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River and State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Yuanming Xie
- MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River and State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Ziniu Wang
- MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River and State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Wei Xuan
- MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River and State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
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Ji XL, Li HL, Qiao ZW, Zhang JC, Sun WJ, You CX, Hao YJ, Wang XF. The BTB protein MdBT2 recruits auxin signaling components to regulate adventitious root formation in apple. PLANT PHYSIOLOGY 2022; 189:1005-1020. [PMID: 35218363 PMCID: PMC9157121 DOI: 10.1093/plphys/kiac084] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 01/28/2022] [Indexed: 05/27/2023]
Abstract
Ubiquitination is an important post-translational protein modification. Although BROAD-COMPLEX, TRAMTRACK AND BRIC A BRAC and TRANSCRIPTION ADAPTOR PUTATIVE ZINC FINGER domain protein 2 (BT2) is involved in many biological processes, its role in apple (Malus domestic) root formation remains unclear. Here, we revealed that MdBT2 inhibits adventitious root (AR) formation through interacting with AUXIN RESPONSE FACTOR8 (MdARF8) and INDOLE-3-ACETIC ACID INDUCIBLE3 (MdIAA3). MdBT2 facilitated MdARF8 ubiquitination and degradation through the 26S proteasome pathway and negatively regulated GRETCHEN HAGEN 3.1 (MdGH3.1) and MdGH3.6 expression. MdARF8 regulates AR formation through inducing transcription of MdGH3s (MdGH3.1, MdGH3.2, MdGH3.5, and MdGH3.6). In addition, MdBT2 facilitated MdIAA3 stability and slightly promoted its interaction with MdARF8. MdIAA3 inhibited AR formation by forming heterodimers with MdARF8 as well as other MdARFs (MdARF5, MdARF6, MdARF7, and MdARF19). Our findings reveal that MdBT2 acts as a negative regulator of AR formation in apple.
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Affiliation(s)
- Xing-Long Ji
- State Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center of Fruit and Vegetable Quality and Efficient Production, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An 271018, China
- Institute of Grape Science and Engineering, College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
| | - Hong-Liang Li
- State Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center of Fruit and Vegetable Quality and Efficient Production, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An 271018, China
| | - Zhi-Wen Qiao
- State Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center of Fruit and Vegetable Quality and Efficient Production, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An 271018, China
| | - Jiu-Cheng Zhang
- State Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center of Fruit and Vegetable Quality and Efficient Production, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An 271018, China
| | - Wei-Jian Sun
- State Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center of Fruit and Vegetable Quality and Efficient Production, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An 271018, China
| | - Chun-Xiang You
- State Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center of Fruit and Vegetable Quality and Efficient Production, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An 271018, China
| | - Yu-Jin Hao
- State Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center of Fruit and Vegetable Quality and Efficient Production, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An 271018, China
| | - Xiao-Fei Wang
- State Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center of Fruit and Vegetable Quality and Efficient Production, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An 271018, China
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Xiong J, Zhang W, Zheng D, Xiong H, Feng X, Zhang X, Wang Q, Wu F, Xu J, Lu Y. ZmLBD5 Increases Drought Sensitivity by Suppressing ROS Accumulation in Arabidopsis. PLANTS (BASEL, SWITZERLAND) 2022; 11:1382. [PMID: 35631807 PMCID: PMC9144968 DOI: 10.3390/plants11101382] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 05/17/2022] [Accepted: 05/18/2022] [Indexed: 06/15/2023]
Abstract
Drought stress is known to significantly limit crop growth and productivity. Lateral organ boundary domain (LBD) transcription factors-particularly class-I members-play essential roles in plant development and biotic stress. However, little information is available on class-II LBD genes related to abiotic stress in maize. Here, we cloned a maize class-II LBD transcription factor, ZmLBD5, and identified its function in drought stress. Transient expression, transactivation, and dimerization assays demonstrated that ZmLBD5 was localized in the nucleus, without transactivation, and could form a homodimer or heterodimer. Promoter analysis demonstrated that multiple drought-stress-related and ABA response cis-acting elements are present in the promoter region of ZmLBD5. Overexpression of ZmLBD5 in Arabidopsis promotes plant growth under normal conditions, and suppresses drought tolerance under drought conditions. Furthermore, the overexpression of ZmLBD5 increased the water loss rate, stomatal number, and stomatal apertures. DAB and NBT staining demonstrated that the reactive oxygen species (ROS) decreased in ZmLBD5-overexpressed Arabidopsis. A physiological index assay also revealed that SOD and POD activities in ZmLBD5-overexpressed Arabidopsis were higher than those in wild-type Arabidopsis. These results revealed the role of ZmLBD5 in drought stress by regulating ROS levels.
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Affiliation(s)
- Jing Xiong
- Maize Research Institute, Sichuan Agricultural University, Wenjiang 611130, China; (J.X.); (W.Z.); (D.Z.); (H.X.); (X.F.); (X.Z.); (Q.W.); (F.W.); (J.X.)
| | - Weixiao Zhang
- Maize Research Institute, Sichuan Agricultural University, Wenjiang 611130, China; (J.X.); (W.Z.); (D.Z.); (H.X.); (X.F.); (X.Z.); (Q.W.); (F.W.); (J.X.)
| | - Dan Zheng
- Maize Research Institute, Sichuan Agricultural University, Wenjiang 611130, China; (J.X.); (W.Z.); (D.Z.); (H.X.); (X.F.); (X.Z.); (Q.W.); (F.W.); (J.X.)
| | - Hao Xiong
- Maize Research Institute, Sichuan Agricultural University, Wenjiang 611130, China; (J.X.); (W.Z.); (D.Z.); (H.X.); (X.F.); (X.Z.); (Q.W.); (F.W.); (J.X.)
| | - Xuanjun Feng
- Maize Research Institute, Sichuan Agricultural University, Wenjiang 611130, China; (J.X.); (W.Z.); (D.Z.); (H.X.); (X.F.); (X.Z.); (Q.W.); (F.W.); (J.X.)
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Wenjiang 611130, China
| | - Xuemei Zhang
- Maize Research Institute, Sichuan Agricultural University, Wenjiang 611130, China; (J.X.); (W.Z.); (D.Z.); (H.X.); (X.F.); (X.Z.); (Q.W.); (F.W.); (J.X.)
| | - Qingjun Wang
- Maize Research Institute, Sichuan Agricultural University, Wenjiang 611130, China; (J.X.); (W.Z.); (D.Z.); (H.X.); (X.F.); (X.Z.); (Q.W.); (F.W.); (J.X.)
| | - Fengkai Wu
- Maize Research Institute, Sichuan Agricultural University, Wenjiang 611130, China; (J.X.); (W.Z.); (D.Z.); (H.X.); (X.F.); (X.Z.); (Q.W.); (F.W.); (J.X.)
| | - Jie Xu
- Maize Research Institute, Sichuan Agricultural University, Wenjiang 611130, China; (J.X.); (W.Z.); (D.Z.); (H.X.); (X.F.); (X.Z.); (Q.W.); (F.W.); (J.X.)
| | - Yanli Lu
- Maize Research Institute, Sichuan Agricultural University, Wenjiang 611130, China; (J.X.); (W.Z.); (D.Z.); (H.X.); (X.F.); (X.Z.); (Q.W.); (F.W.); (J.X.)
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Wenjiang 611130, China
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Tian Y, Han X, Qu Y, Zhang Y, Rong H, Wu K, Xu L. Genome-Wide Identification of the Ginkgo ( Ginkgo biloba L.) LBD Transcription Factor Gene and Characterization of Its Expression. Int J Mol Sci 2022; 23:ijms23105474. [PMID: 35628284 PMCID: PMC9141976 DOI: 10.3390/ijms23105474] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/24/2022] [Accepted: 05/10/2022] [Indexed: 11/16/2022] Open
Abstract
Lateral organ boundaries domain (LBD) proteins are plant-specific transcription factors involved in various transcriptional regulation processes. We identified a total of 37 GbLBD genes in ginkgo, and based on gene structure and phylogenetic analysis, the GbLBD gene family was classified into class I (33, with the largest number of Id genes (16)) and class II (4). The ginkgo LBD gene was also analyzed regarding its chromosomal distributions, gene duplications, promoters, and introns/exons. In addition, gene expression profiling and real-time quantitative PCR analysis showed that the expression of 14 GbLBD genes differed in six different tissues and three developmental stages. The GbLBD gene of class II were highly expressed relative to the class I gene in all tissues and developmental stages, while class Id gene were generally at low levels or were not expressed, especially in seed developmental stages. The expression pattern analysis of cold/drought treatment and IAA/ABA hormone treatment showed that abiotic stress treatment could significantly induce the expression of GbLBD gene, of which class II genes played a key role in stress treatment. Our study provides a solid foundation for further evolutionary and functional analysis of the ginkgo LBD gene family.
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Affiliation(s)
| | | | | | | | | | | | - Li’an Xu
- Correspondence: ; Tel.: +86-25-8542-7882
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Li C, Wang J, Li L, Li J, Zhuang M, Li B, Li Q, Huang J, Du Y, Wang J, Fan Z, Mao X, Jing R. TaMOR is essential for root initiation and improvement of root system architecture in wheat. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:862-875. [PMID: 34890129 PMCID: PMC9055823 DOI: 10.1111/pbi.13765] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/25/2021] [Accepted: 12/07/2021] [Indexed: 05/13/2023]
Abstract
Optimal root system architecture is beneficial for water-fertilizer use efficiency, stress tolerance and yield improvement of crops. However, because of the complexity of root traits and difficulty in phenotyping deep roots, the study on mechanisms of root development is rarely reported in wheat (Triticum aestivum L.). In this study, we identified that the LBD (LATERAL ORGAN BOUNDARIES DOMAIN) gene TaMOR (MORE ROOT in wheat) determines wheat crown root initiation. The mor mutants exhibited less or even no crown root, dwarfism, less grain number and lodging caused by few roots. The observation of cross sections showed that crown root initiation is inhibited in the mor mutants. Molecular assays revealed that TaMOR interacts with the auxin response factor ARF5 to directly induce the expression of the auxin transporter gene PIN2 (PIN-FORMED 2) in the root base to regulate crown root initiation. In addition, a 159-bp MITE (miniature inverted-repeat transposable element) insertion causing DNA methylation and lower expression of TaMOR-B was identified in TaMOR-B promoter, which is associated with lower root dry weight and shorter plant height. The results bring new light into regulation mechanisms of crown root initiation and offer a new target for the improvement of root system architecture in wheat.
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Affiliation(s)
- Chaonan Li
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Jingyi Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Long Li
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Jialu Li
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Mengjia Zhuang
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Bo Li
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Qiaoru Li
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Junfang Huang
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Yan Du
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Jinping Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Zipei Fan
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Xinguo Mao
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Ruilian Jing
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
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Ashraf MA, Nan Q. Evolutionarily conserved shoot-borne root developmental circuit. MOLECULAR PLANT 2022; 15:S1674-2052(22)00119-8. [PMID: 35440407 DOI: 10.1016/j.molp.2022.04.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 04/11/2022] [Accepted: 04/12/2022] [Indexed: 06/14/2023]
Affiliation(s)
- M Arif Ashraf
- Department of Biology, University of Massachusetts Amherst, Amherst, MA, USA.
| | - Qiong Nan
- Department of Biology, University of Massachusetts Amherst, Amherst, MA, USA.
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Maqbool S, Hassan MA, Xia X, York LM, Rasheed A, He Z. Root system architecture in cereals: progress, challenges and perspective. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:23-42. [PMID: 35020968 DOI: 10.1111/tpj.15669] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 12/31/2021] [Accepted: 01/06/2022] [Indexed: 06/14/2023]
Abstract
Roots are essential multifunctional plant organs involved in water and nutrient uptake, metabolite storage, anchorage, mechanical support, and interaction with the soil environment. Understanding of this 'hidden half' provides potential for manipulation of root system architecture (RSA) traits to optimize resource use efficiency and grain yield in cereal crops. Unfortunately, root traits are highly neglected in breeding due to the challenges of phenotyping, but could have large rewards if the variability in RSA traits can be fully exploited. Until now, a plethora of genes have been characterized in detail for their potential role in improving RSA. The use of forward genetics approaches to find sequence variations in genes underpinning desirable RSA would be highly beneficial. Advances in computer vision applications have allowed image-based approaches for high-throughput phenotyping of RSA traits that can be used by any laboratory worldwide to make progress in understanding root function and dissection of the genetics. At the same time, the frontiers of root measurement include non-invasive methods like X-ray computer tomography and magnetic resonance imaging that facilitate new types of temporal studies. Root physiology and ecology are further supported by spatiotemporal root simulation modeling. The discovery of component traits providing improved resilience and yield advantage in target environments is a key necessity for mainstreaming root-based cereal breeding. The integrated use of pan-genome resources, now available in most cereals, coupled with new in-field phenotyping platforms has the potential for precise selection of superior genotypes with improved RSA.
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Affiliation(s)
- Saman Maqbool
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Muhammad Adeel Hassan
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Xianchun Xia
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Larry M York
- Biosciences Division and Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Awais Rasheed
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
- International Wheat and Maize Improvement Center (CIMMYT) China Office, c/o CAAS, 12 Zhongguancun South Street, Beijing, 100081, China
| | - Zhonghu He
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
- International Wheat and Maize Improvement Center (CIMMYT) China Office, c/o CAAS, 12 Zhongguancun South Street, Beijing, 100081, China
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50
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Omary M, Gil-Yarom N, Yahav C, Steiner E, Hendelman A, Efroni I. A conserved superlocus regulates above- and belowground root initiation. Science 2022; 375:eabf4368. [PMID: 35239373 DOI: 10.1126/science.abf4368] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Plants continuously form new organs in different developmental contexts in response to environmental cues. Underground lateral roots initiate from prepatterned cells in the main root, but cells can also bypass the root-shoot trajectory separation and generate shoot-borne roots through an unknown mechanism. We mapped tomato (Solanum lycopersicum) shoot-borne root development at single-cell resolution and showed that these roots initiate from phloem-associated cells through a unique transition state. This state requires the activity of a transcription factor that we named SHOOTBORNE ROOTLESS (SBRL). Evolutionary analysis reveals that SBRL's function and cis regulation are conserved in angiosperms and that it arose as an ancient duplication, with paralogs controlling wound-induced and lateral root initiation. We propose that the activation of a common transition state by context-specific regulators underlies the plasticity of plant root systems.
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Affiliation(s)
- Moutasem Omary
- The Institute of Plant Science and Genetics in Agriculture, Faculty of Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Naama Gil-Yarom
- The Institute of Plant Science and Genetics in Agriculture, Faculty of Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Chen Yahav
- The Institute of Plant Science and Genetics in Agriculture, Faculty of Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Evyatar Steiner
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Anat Hendelman
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Idan Efroni
- The Institute of Plant Science and Genetics in Agriculture, Faculty of Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
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