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Yang T, Lu X, Duan L, Wang L, Yan S. Clathrin is required for DNA damage repair. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2025. [PMID: 40183342 DOI: 10.1111/jipb.13910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2025] [Accepted: 03/18/2025] [Indexed: 04/05/2025]
Abstract
Genetic screening in Arabidopsis reveals that clathrin, a well-known regulator of endocytosis, is required for homologous recombination, a precise mechanism for repairing DNA double- strand breaks. Notably, CLATHRIN LIGHT CHAIN 2 localizes in the nucleus, suggesting that clathrin has non-canonical functions in the nucleus.
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Affiliation(s)
- Tongbin Yang
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen, 518000, China
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen, 518000, China
| | - Xuerui Lu
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen, 518000, China
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen, 518000, China
| | - Leilei Duan
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen, 518000, China
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen, 518000, China
| | - Lili Wang
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen, 518000, China
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen, 518000, China
| | - Shunping Yan
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen, 518000, China
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen, 518000, China
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2
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Wu J, Liu B, Dong A. Interplay between histone variants and chaperones in plants. CURRENT OPINION IN PLANT BIOLOGY 2024; 80:102551. [PMID: 38776573 DOI: 10.1016/j.pbi.2024.102551] [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: 03/18/2024] [Revised: 04/25/2024] [Accepted: 04/28/2024] [Indexed: 05/25/2024]
Abstract
Histone chaperones and histone variants play crucial roles in DNA replication, gene transcription, and DNA repair in eukaryotes. Histone chaperones reversibly promote nucleosome assembly and disassembly by incorporating or evicting histones and histone variants to modulate chromatin accessibility, thereby altering the chromatin states and modulating DNA-related biological processes. Cofactors assist histone chaperones to target specific chromatin regions to regulate the exchange of histones and histone variants. In this review, we summarize recent progress in the interplay between histone variants and chaperones in plants. We discuss the structural basis of chaperone-histone complexes and the mechanisms of their cooperation in regulating gene transcription and plant development.
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Affiliation(s)
- Jiabing Wu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, PR China; Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai, 200438, PR China
| | - Bing Liu
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Aiwu Dong
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, PR China.
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Kutashev K, Meschichi A, Reeck S, Fonseca A, Sartori K, White CI, Sicard A, Rosa S. Differences in RAD51 transcriptional response and cell cycle dynamics reveal varying sensitivity to DNA damage among Arabidopsis thaliana root cell types. THE NEW PHYTOLOGIST 2024; 243:966-980. [PMID: 38840557 DOI: 10.1111/nph.19875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 05/11/2024] [Indexed: 06/07/2024]
Abstract
Throughout their lifecycle, plants are subjected to DNA damage from various sources, both environmental and endogenous. Investigating the mechanisms of the DNA damage response (DDR) is essential to unravel how plants adapt to the changing environment, which can induce varying amounts of DNA damage. Using a combination of whole-mount single-molecule RNA fluorescence in situ hybridization (WM-smFISH) and plant cell cycle reporter lines, we investigated the transcriptional activation of a key homologous recombination (HR) gene, RAD51, in response to increasing amounts of DNA damage in Arabidopsis thaliana roots. The results uncover consistent variations in RAD51 transcriptional response and cell cycle arrest among distinct cell types and developmental zones. Furthermore, we demonstrate that DNA damage induced by genotoxic stress results in RAD51 transcription throughout the whole cell cycle, dissociating its traditional link with S/G2 phases. This work advances the current comprehension of DNA damage response in plants by demonstrating quantitative differences in DDR activation. In addition, it reveals new associations with the cell cycle and cell types, providing crucial insights for further studies of the broader response mechanisms in plants.
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Affiliation(s)
- Konstantin Kutashev
- Plant Biology Department, Swedish University of Agricultural Sciences, Almas allé 5, Uppsala, 756 51, Sweden
| | - Anis Meschichi
- Department of Biology, Institute of Molecular Plant Biology, Swiss Federal Institute of Technology Zürich, Zürich, 8092, Switzerland
| | - Svenja Reeck
- Department of Cell and Developmental Biology, John Innes Centre, Research Park, Norwich, NR4 7UH, UK
| | - Alejandro Fonseca
- Plant Biology Department, Swedish University of Agricultural Sciences, Almas allé 5, Uppsala, 756 51, Sweden
| | - Kevin Sartori
- Plant Biology Department, Swedish University of Agricultural Sciences, Almas allé 5, Uppsala, 756 51, Sweden
| | - Charles I White
- Institut Génétique Reproduction et Développement (iGReD), Université Clermont Auvergne, UMR 6293, CNRS, U1103 INSERM, Clermont-Ferrand, 63001, France
| | - Adrien Sicard
- Plant Biology Department, Swedish University of Agricultural Sciences, Almas allé 5, Uppsala, 756 51, Sweden
| | - Stefanie Rosa
- Plant Biology Department, Swedish University of Agricultural Sciences, Almas allé 5, Uppsala, 756 51, Sweden
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4
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Mahapatra K, Roy S. SOG1 and BRCA1 Interdependently Regulate RAD54 Expression for Repairing Salinity-Induced DNA Double-Strand Breaks in Arabidopsis. PLANT & CELL PHYSIOLOGY 2024; 65:708-728. [PMID: 38242160 DOI: 10.1093/pcp/pcae008] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 12/04/2023] [Accepted: 01/16/2024] [Indexed: 01/21/2024]
Abstract
As sessile organisms, land plants experience various forms of environmental stresses throughout their life span. Therefore, plants have developed extensive and complicated defense mechanisms, including a robust DNA damage response (DDR) and DNA repair systems for maintaining genome integrity. In Arabidopsis, the NAC [NO APICAL MERISTEM (NAM), ARABIDOPSIS TRANSCRIPTION ACTIVATION FACTOR (ATAF), CUP-SHAPED COTYLEDON (CUC)] domain family transcription factor SUPPRESSOR OF GAMMA RESPONSE 1 (SOG1) plays an important role in regulating DDR. Here, we show that SOG1 plays a key role in regulating the repair of salinity-induced DNA double-strand breaks (DSBs) via the homologous recombination (HR) pathway in Arabidopsis. The sog1-1 mutant seedlings display a considerably slower rate of repair of salinity-induced DSBs. Accumulation of SOG1 protein increases in wild-type Arabidopsis under salinity stress, and it enhances the expression of HR pathway-related genes, including RAD51, RAD54 and BReast CAncer gene 1 (BRCA1), respectively, as found in SOG1 overexpression lines. SOG1 binds specifically to the AtRAD54 promoter at the 5'-(N)4GTCAA(N)3C-3' consensus sequence and positively regulates its expression under salinity stress. The phenotypic responses of sog1-1/atrad54 double mutants suggest that SOG1 functions upstream of RAD54, and both these genes are essential in regulating DDR under salinity stress. Furthermore, SOG1 interacts directly with BRCA1, an important component of the HR-mediated DSB repair pathway in plants, where BRCA1 appears to facilitate the binding of SOG1 to the RAD54 promoter. At the genetic level, SOG1 and BRCA1 function interdependently in modulating RAD54 expression under salinity-induced DNA damage. Together, our results suggest that SOG1 regulates the repair of salinity-induced DSBs via the HR-mediated pathway through genetic interactions with RAD54 and BRCA1 in Arabidopsis.
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Affiliation(s)
- Kalyan Mahapatra
- Department of Botany, UGC Center for Advanced Studies, The University of Burdwan, Golapbag Campus, Burdwan, 713 104 West Bengal, India
| | - Sujit Roy
- Department of Botany, UGC Center for Advanced Studies, The University of Burdwan, Golapbag Campus, Burdwan, 713 104 West Bengal, India
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Herbst J, Li QQ, De Veylder L. Mechanistic insights into DNA damage recognition and checkpoint control in plants. NATURE PLANTS 2024; 10:539-550. [PMID: 38503962 DOI: 10.1038/s41477-024-01652-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 02/18/2024] [Indexed: 03/21/2024]
Abstract
The plant DNA damage response (DDR) pathway safeguards genomic integrity by rapid recognition and repair of DNA lesions that, if unrepaired, may cause genome instability. Most frequently, DNA repair goes hand in hand with a transient cell cycle arrest, which allows cells to repair the DNA lesions before engaging in a mitotic event, but consequently also affects plant growth and yield. Through the identification of DDR proteins and cell cycle regulators that react to DNA double-strand breaks or replication defects, it has become clear that these proteins and regulators form highly interconnected networks. These networks operate at both the transcriptional and post-transcriptional levels and include liquid-liquid phase separation and epigenetic mechanisms. Strikingly, whereas the upstream DDR sensors and signalling components are well conserved across eukaryotes, some of the more downstream effectors are diverged in plants, probably to suit unique lifestyle features. Additionally, DDR components display functional diversity across ancient plant species, dicots and monocots. The observed resistance of DDR mutants towards aluminium toxicity, phosphate limitation and seed ageing indicates that gaining knowledge about the plant DDR may offer solutions to combat the effects of climate change and the associated risk for food security.
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Affiliation(s)
- Josephine Herbst
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
- Center for Plant Systems Biology, VIB, Gent, Belgium
| | - Qian-Qian Li
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
- Center for Plant Systems Biology, VIB, Gent, Belgium
| | - Lieven De Veylder
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium.
- Center for Plant Systems Biology, VIB, Gent, Belgium.
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Lorković ZJ, Klingenbrunner M, Cho CH, Berger F. Identification of plants' functional counterpart of the metazoan mediator of DNA Damage checkpoint 1. EMBO Rep 2024; 25:1936-1961. [PMID: 38438802 PMCID: PMC11014961 DOI: 10.1038/s44319-024-00107-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 02/13/2024] [Accepted: 02/19/2024] [Indexed: 03/06/2024] Open
Abstract
Induction of DNA damage triggers rapid phosphorylation of the histone H2A.X (γH2A.X). In animals, mediator of DNA damage checkpoint 1 (MDC1) binds γH2A.X through a tandem BRCA1 carboxyl-terminal (tBRCT) domain and mediates recruitment of downstream effectors of DNA damage response (DDR). However, readers of this modification in plants have remained elusive. We show that from the Arabidopsis BRCT domain proteome, BCP1-4 proteins with tBRCT domains are involved in DDR. Through its tBRCT domain BCP4 binds γH2A.X in vitro and localizes to DNA damage-induced foci in an H2A.X-dependent manner. BCP4 also contains a domain that interacts directly with NBS1 and thus acts as a functional counterpart of MDC1. We also show that BCP1, that contains two tBRCT domains, co-localizes with γH2A.X but it does not bind γH2A.X suggesting functional similarity with human PAXIP1. A phylogenetic analysis supports that PAXIP1 and MDC1 in metazoa and their plant counterparts evolved independently from common ancestors with tBRCT domains. Collectively, our study reveals missing components and provides mechanistic and evolutionary insights into plant DDR.
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Affiliation(s)
- Zdravko J Lorković
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria.
| | - Michael Klingenbrunner
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Chung Hyun Cho
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
| | - Frédéric Berger
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria.
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Han TT, Tang JX, Fang M, Zhang P, Han PY, Yin ZN, Ma Y, Zhang J, Lu QY. Two genes encoded by mulberry crinkle leaf virus (MCLV): The V4 gene enhances viral replication, and the V5 gene is needed for MCLV infection in Nicotiana benthamiana. Virus Res 2024; 339:199288. [PMID: 38043724 PMCID: PMC10751690 DOI: 10.1016/j.virusres.2023.199288] [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: 05/06/2023] [Revised: 11/21/2023] [Accepted: 11/26/2023] [Indexed: 12/05/2023]
Abstract
Mulberry crinkle leaf virus (MCLV) is a member of the genus Mulcrilevirus, family Geminiviridae. The expression and functions of the V4 and V5 genes encoded by the MCLV genome remain unknown. Here, we confirmed the expression of V4 and V5 by analyzing the V4 and V5 mRNAs and the promoter activity of individual ORFs upstream sequences. The functions of V4 and V5 were investigated by constructing Agrobacterium-mediated infectious clones of wild-type MCLV variant П (MCLV vII), MCLVwt and MCLV vП mutants, such as MCLVmV4 (start codon of V4 ORF mutated), MCLVdV4 (5'-end partial deletion of V4 ORF sequence) and MCLVmV5 (V5 ORF start codon mutated). Although MCLVwt, MCLVmV4, and MCLVdV4 could infect natural host mulberry and experimental tomato plants systematically, the replication of the MCLVmV4 and MCLVdV4 genomes was obviously reduced compared to MCLVwt in both mulberry and tomato plants. MCLV vП expressing V5 could infect Nicotiana benthamiana plants systematically, but MCLVmV5 could not, implying that V5 is needed for MCLV vП to infect N. benthamiana plants. Taken together, V4 is involved in replication of the MCLV genome in host plants, and V5 potentially might extend the host range. Our findings lay a foundation for in-depth insight into the functions of MCLV-encoded proteins and provide a novel perspective for the subsequent study of MCLV-host plant interactions.
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Affiliation(s)
- Tao-Tao Han
- College of Biotechnology, Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu 212100, China
| | - Jia-Xuan Tang
- College of Biotechnology, Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu 212100, China
| | - Miao Fang
- College of Biotechnology, Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu 212100, China
| | - Peng Zhang
- College of Biotechnology, Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu 212100, China
| | - Pei-Yu Han
- College of Biotechnology, Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu 212100, China
| | - Zhen-Ni Yin
- College of Biotechnology, Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu 212100, China
| | - Yu Ma
- College of Biotechnology, Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu 212100, China
| | - Jian Zhang
- College of Biotechnology, Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu 212100, China; Key Laboratory of Genetic Improvement of Silkworm and Mulberry, Ministry of Agriculture and Rural Affairs, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, Jiangsu 212100, China
| | - Quan-You Lu
- College of Biotechnology, Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu 212100, China; Key Laboratory of Genetic Improvement of Silkworm and Mulberry, Ministry of Agriculture and Rural Affairs, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, Jiangsu 212100, China.
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Xiang X, Zhou X, Zi H, Wei H, Cao D, Zhang Y, Zhang L, Hu J. Populus cathayana genome and population resequencing provide insights into its evolution and adaptation. HORTICULTURE RESEARCH 2024; 11:uhad255. [PMID: 38274646 PMCID: PMC10809908 DOI: 10.1093/hr/uhad255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 11/20/2023] [Indexed: 01/27/2024]
Abstract
Populus cathayana Rehder, an indigenous poplar species of ecological and economic importance, is widely distributed in a high-elevation range from southwest to northeast China. Further development of this species as a sustainable poplar resource has been hindered by a lack of genome information the at the population level. Here, we produced a chromosome-level genome assembly of P. cathayana, covering 406.55 Mb (scaffold N50 = 20.86 Mb) and consisting of 19 chromosomes, with 35 977 protein-coding genes. Subsequently, we made a genomic variation atlas of 438 wild individuals covering 36 representative geographic areas of P. cathayana, which were divided into four geographic groups. It was inferred that the Northwest China regions served as the genetic diversity centers and a population bottleneck happened during the history of P. cathayana. By genotype-environment association analysis, 947 environment-association loci were significantly associated with temperature, solar radiation, precipitation, and altitude variables. We identified local adaptation genes involved in DNA repair and UV radiation response, among which UVR8, HY5, and CUL4 had key roles in high-altitude adaptation of P. cathayana. Predictions of adaptive potential under future climate conditions showed that P. cathayana populations in areas with drastic climate change were anticipated to have greater maladaptation risk. These results provide comprehensive insights for understanding wild poplar evolution and optimizing adaptive potential in molecular breeding.
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Affiliation(s)
- Xiaodong Xiang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Xinglu Zhou
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Hailing Zi
- Novogene Bioinformatics Institute, Beijing 100083, China
| | - Hantian Wei
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Demei Cao
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Yahong Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Lei Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Jianjun Hu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
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