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Luo X, Zhou H, Cao D, Yan F, Chen P, Wang J, Woeste K, Chen X, Fei Z, An H, Malvolti M, Ma K, Liu C, Ebrahimi A, Qiao C, Ye H, Li M, Lu Z, Xu J, Cao S, Zhao P. Domestication and selection footprints in Persian walnuts (Juglans regia). PLoS Genet 2022; 18:e1010513. [PMID: 36477175 PMCID: PMC9728896 DOI: 10.1371/journal.pgen.1010513] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 11/07/2022] [Indexed: 12/12/2022] Open
Abstract
Walnut (Juglans) species are economically important hardwood trees cultivated worldwide for both edible nuts and high-quality wood. Broad-scale assessments of species diversity, evolutionary history, and domestication are needed to improve walnut breeding. In this study, we sequenced 309 walnut accessions from around the world, including 55 Juglans relatives, 98 wild Persian walnuts (J. regia), 70 J. regia landraces, and 86 J. regia cultivars. The phylogenetic tree indicated that J. regia samples (section Dioscaryon) were monophyletic within Juglans. The core areas of genetic diversity of J. regia germplasm were southwestern China and southern Asia near the Qinghai-Tibet Plateau and the Himalayas, and the uplift of the Himalayas was speculated to be the main factor leading to the current population dynamics of Persian walnut. The pattern of genomic variation in terms of nucleotide diversity, linkage disequilibrium, single nucleotide polymorphisms, and insertions/deletions revealed the domestication and selection footprints in Persian walnut. Selective sweep analysis, GWAS, and expression analysis further identified two transcription factors, JrbHLH and JrMYB6, that influence the thickness of the nut diaphragm as loci under selection during domestication. Our results elucidate the domestication and selection footprints in Persian walnuts and provide a valuable resource for the genomics-assisted breeding of this important crop.
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Affiliation(s)
- Xiang Luo
- College of Agriculture, Henan University, Kaifeng, Henan, China
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, Shaanxi, China
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Huijuan Zhou
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, Shaanxi, China
- Xi’an Botanical Garden of Shaanxi Province, Xi’an, China
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, China
| | - Da Cao
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
- Laboratory of Functional Plant Biology, Department of Biology, Ghent University, Ghent, Belgium
| | - Feng Yan
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, Shaanxi, China
| | - Pengpeng Chen
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, Shaanxi, China
| | - Jiangtao Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, Shaanxi, China
| | - Keith Woeste
- USDA Forest Service Hardwood Tree Improvement and Regeneration Center (HTIRC), Department of Forestry and Natural Resources, Purdue University, West Lafayette, Indiana, United States of America
| | - Xin Chen
- Shandong Institute of Pomology, National Germplasm Repository of Walnut and Chestnut, Tai’an, China
| | - Zhangjun Fei
- Boyce Thompson Institute for Plant Research, US Department of Agriculture (USDA) Robert W. Holley Center for Agriculture and Health, Cornell University, Ithaca, New York, United States of America
| | - Hong An
- Bioinformatics and Analytics Core, University of Missouri, Columbia, Missouri, United States of America
| | - Maria Malvolti
- Research Institute on Terrestrial Ecosystems, National Research Council, Porano, Terni, Italy
| | - Kai Ma
- Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Chaobin Liu
- Laboratory of Functional Plant Biology, Department of Biology, Ghent University, Ghent, Belgium
| | - Aziz Ebrahimi
- USDA Forest Service Hardwood Tree Improvement and Regeneration Center (HTIRC), Department of Forestry and Natural Resources, Purdue University, West Lafayette, Indiana, United States of America
| | - Chengkui Qiao
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Hang Ye
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, Shaanxi, China
| | - Mengdi Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, Shaanxi, China
| | - Zhenhua Lu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Jiabao Xu
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
- * E-mail: (JX); (SC); (PZ)
| | - Shangying Cao
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
- * E-mail: (JX); (SC); (PZ)
| | - Peng Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, Shaanxi, China
- * E-mail: (JX); (SC); (PZ)
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2
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Sousa-Baena MS, Onyenedum JG. Bouncing back stronger: Diversity, structure, and molecular regulation of gelatinous fiber development. CURRENT OPINION IN PLANT BIOLOGY 2022; 67:102198. [PMID: 35286861 DOI: 10.1016/j.pbi.2022.102198] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 01/18/2022] [Accepted: 02/01/2022] [Indexed: 06/14/2023]
Abstract
Gelatinous fibers (G-fibers) are specialized contractile cells found in a diversity of vascular plant tissues, where they provide mechanical support and/or facilitate plant mobility. G-fibers are distinct from typical fibers by the presence of an innermost thickened G-layer, comprised mainly of axially oriented cellulose microfibrils. Despite the disparate developmental origins-tension wood fibers from the vascular cambium or primary phloem fibers from the procambium-G-fiber development, composition, and molecular signatures are remarkably similar; however, important distinctions do exist. Here, we synthesize current knowledge of the phylogenetic diversity, compositional makeup, and the molecular profiles that characterize G-fiber development and highlight open questions for future investigation.
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Affiliation(s)
- Mariane S Sousa-Baena
- School of Integrative Plant Sciences, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, NY, USA.
| | - Joyce G Onyenedum
- School of Integrative Plant Sciences, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, NY, USA
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3
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Zhang M, Shi Y, Liu Z, Zhang Y, Yin X, Liang Z, Huang Y, Grierson D, Chen K. An EjbHLH14-EjHB1-EjPRX12 module is involved in methyl jasmonate alleviation of chilling-induced lignin deposition in loquat fruit. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:1668-1682. [PMID: 34893804 DOI: 10.1093/jxb/erab511] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 12/04/2021] [Indexed: 06/14/2023]
Abstract
Loquat fruit are susceptible to chilling injuries induced by postharvest storage at low temperature. The major symptoms are increased lignin content and flesh firmness, which cause a leathery texture. Pretreatment with methyl jasmonate (MeJA) can alleviate this low-temperature-induced lignification, but the mechanism is not understood. In this study, we characterized a novel class III peroxidase, EjPRX12, and studied its relationship to lignification. Transcript levels of EjPRX12 were attenuated following MeJA pretreatment, consistent with the reduced lignin content in fruit. In vitro enzyme activity assay indicated that EjPRX12 polymerized sinapyl alcohol, and overexpression of EjPRX12 in Arabidopsis promoted lignin accumulation, indicating that it plays a functional role in lignin polymerization. We also identified an HD-ZIP transcription factor, EjHB1, repressed by MeJA pretreatment, which directly bound to and significantly activated the EjPRX12 promoter. Overexpression of EjHB1 in Arabidopsis promoted lignin accumulation with induced expression of lignin-related genes, especially AtPRX64. Furthermore, a JAZ-interacting repressor, EjbHLH14, was characterized, and it is proposed that MeJA pretreatment caused EjbHLH14 to be released to repress the expression of EjHB1. These results identified a novel regulatory pathway involving EjbHLH14-EjHB1-EjPRX12 and revealed the molecular mechanism whereby MeJA alleviated lignification of loquat fruit at low temperature.
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Affiliation(s)
- Mengxue Zhang
- College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
| | - Yanna Shi
- College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
- State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
| | - Zimeng Liu
- College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
| | - Yijin Zhang
- College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
| | - Xueren Yin
- College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
- State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
| | - Zihao Liang
- College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
| | - Yiqing Huang
- College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
| | - Donald Grierson
- State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | - Kunsong Chen
- College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
- State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
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4
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Yu J, Zhou C, Li D, Li S, Jimmy Lin YC, Wang JP, Chiang VL, Li W. A PtrLBD39-mediated transcriptional network regulates tension wood formation in Populus trichocarpa. PLANT COMMUNICATIONS 2022; 3:100250. [PMID: 35059630 PMCID: PMC8760142 DOI: 10.1016/j.xplc.2021.100250] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 09/10/2021] [Accepted: 10/19/2021] [Indexed: 05/29/2023]
Abstract
Tension wood (TW) is a specialized xylem tissue formed in angiosperm trees under gravitational stimulus or mechanical stresses (e.g., bending). The genetic regulation that underlies this important mechanism remains poorly understood. Here, we used laser capture microdissection of stem xylem cells coupled with full transcriptome RNA-sequencing to analyze TW formation in Populus trichocarpa. After tree bending, PtrLBD39 was the most significantly induced transcription factor gene; it has a phylogenetically paired homolog, PtrLBD22. CRISPR-based knockout of PtrLBD39/22 severely inhibited TW formation, reducing cellulose and increasing lignin content. Transcriptomic analyses of CRISPR-based PtrLBD39/22 double mutants showed that these two genes regulate a set of TW-related genes. Chromatin immunoprecipitation sequencing (ChIP-seq) was used to identify direct targets of PtrLBD39. We integrated transcriptomic analyses and ChIP-seq assays to construct a transcriptional regulatory network (TRN) mediated by PtrLBD39. In this TRN, PtrLBD39 directly regulates 26 novel TW-responsive transcription factor genes. Our work suggests that PtrLBD39 and PtrLBD22 specifically control TW formation by mediating a TW-specific TRN in Populus.
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Affiliation(s)
- Jing Yu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Chenguang Zhou
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Danning Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Shuang Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Ying-Chung Jimmy Lin
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- Department of Life Sciences and Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei, Taiwan 10617, China
| | - Jack P. Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- Department of Forestry and Environmental Resources, Forest Biotechnology Group, North Carolina State University, Raleigh, NC 27695, USA
| | - Vincent L. Chiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- Department of Forestry and Environmental Resources, Forest Biotechnology Group, North Carolina State University, Raleigh, NC 27695, USA
| | - Wei Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
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5
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Liu B, Liu J, Yu J, Wang Z, Sun Y, Li S, Lin YCJ, Chiang VL, Li W, Wang JP. Transcriptional reprogramming of xylem cell wall biosynthesis in tension wood. PLANT PHYSIOLOGY 2021; 186:250-269. [PMID: 33793955 PMCID: PMC8154086 DOI: 10.1093/plphys/kiab038] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 01/04/2021] [Indexed: 05/02/2023]
Abstract
Tension wood (TW) is a specialized xylem tissue developed under mechanical/tension stress in angiosperm trees. TW development involves transregulation of secondary cell wall genes, which leads to altered wood properties for stress adaptation. We induced TW in the stems of black cottonwood (Populus trichocarpa, Nisqually-1) and identified two significantly repressed transcription factor (TF) genes: class B3 heat-shock TF (HSFB3-1) and MYB092. Transcriptomic analysis and chromatin immunoprecipitation (ChIP) were used to identify direct TF-DNA interactions in P. trichocarpa xylem protoplasts overexpressing the TFs. This analysis established a transcriptional regulatory network in which PtrHSFB3-1 and PtrMYB092 directly activate 8 and 11 monolignol genes, respectively. The TF-DNA interactions were verified for their specificity and transactivator roles in 35 independent CRISPR-based biallelic mutants and overexpression transgenic lines of PtrHSFB3-1 and PtrMYB092 in P. trichocarpa. The gene-edited trees (mimicking the repressed PtrHSFB3-1 and PtrMYB092 under tension stress) have stem wood composition resembling that of TW during normal growth and under tension stress (i.e., low lignin and high cellulose), whereas the overexpressors showed an opposite effect (high lignin and low cellulose). Individual overexpression of the TFs impeded lignin reduction under tension stress and restored high levels of lignin biosynthesis in the TW. This study offers biological insights to further uncover how metabolism, growth, and stress adaptation are coordinately regulated in trees.
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Affiliation(s)
- Baoguang Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- Department of Forestry, Beihua University, Jilin 132013, China
| | - Juan Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Jing Yu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Zhifeng Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Yi Sun
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Shuang Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Ying-Chung Jimmy Lin
- Department of Life Sciences, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
| | - Vincent L Chiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina 27695
| | - Wei Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Jack P Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina 27695
- Author for communication:
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6
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Jin Y, Yu C, Jiang C, Guo X, Li B, Wang C, Kong F, Zhang H, Wang H. PtiCYP85A3, a BR C-6 Oxidase Gene, Plays a Critical Role in Brassinosteroid-Mediated Tension Wood Formation in Poplar. FRONTIERS IN PLANT SCIENCE 2020; 11:468. [PMID: 32391036 PMCID: PMC7193022 DOI: 10.3389/fpls.2020.00468] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 03/30/2020] [Indexed: 05/21/2023]
Abstract
In angiosperm trees, the gelatinous layer (G-layer) takes a great part of the fiber cell wall in the tension wood (TW). However, the mechanism underlying G-layer formation in poplar is largely unknown. In this work, we demonstrate that G-layer formation in poplar TW cells is regulated by brassinosteroid (BR) and its signaling. PtiCYP85A3, a key BR biosynthesis gene, was predominantly expressed in the xylem of TW, accompanied with a relatively higher castasterone (CS) accumulation, than in the xylem of opposite wood (OW). A wider expression zone of BZR1, a key transcriptional factor in BR singling pathway, was also observed in G-fiber cells on TW side than in wood fiber cells on the OW side, as indicated by immunohistochemistry assays. Transgenic poplar plants overexpressing PtiCYP85A3 produced thicker G-layer with higher cellulose proportion, and accumulated more BZR1 protein in the xylem of TW than did the wild type (WT) plants. Expression of most TW-associated CesAs, which were induced by 2, 4-epibrassinolide, an active BR, and inhibited by brassinazole, a BR biosynthesis inhibitor, were also up-regulated in the xylem of TW in transgenic plants compared to that in WT plants. Further studies with dual-luciferase assays demonstrated that the promoters of PtiCesAs were activated by PtiMYB128, a TW specific transcription factor, which was then regulated by BZR1. All these results indicate that BR plays a crucial role in the G-layer formation of TW fiber cells by regulating the expression of BZR1, PtiMYB128, and PtiCesAs in poplar.
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Affiliation(s)
- Yanli Jin
- College of Agriculture, Ludong University, Yantai, China
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- The Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in the Universities of Shandong, Institute for Advanced Study of Coastal Ecology, Ludong University, Yantai, China
| | - Chunyan Yu
- College of Agriculture, Ludong University, Yantai, China
- The Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in the Universities of Shandong, Institute for Advanced Study of Coastal Ecology, Ludong University, Yantai, China
| | - Chunmei Jiang
- College of Agriculture, Ludong University, Yantai, China
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, College of Life Sciences, Hubei University, Wuhan, China
| | - Xiaotong Guo
- College of Agriculture, Ludong University, Yantai, China
- The Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in the Universities of Shandong, Institute for Advanced Study of Coastal Ecology, Ludong University, Yantai, China
| | - Bei Li
- College of Agriculture, Ludong University, Yantai, China
- The Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in the Universities of Shandong, Institute for Advanced Study of Coastal Ecology, Ludong University, Yantai, China
| | - Cuiting Wang
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Fanjing Kong
- Ministry of Natural Resources Key Laboratory of Saline Lake Resources and Environments, Institute of Mineral Resources, Chinese Academy of Geological Sciences, Beijing, China
| | - Hongxia Zhang
- College of Agriculture, Ludong University, Yantai, China
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- The Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in the Universities of Shandong, Institute for Advanced Study of Coastal Ecology, Ludong University, Yantai, China
| | - Haihai Wang
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
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7
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Gao J, Yu M, Zhu S, Zhou L, Liu S. Effects of exogenous 24-epibrassinolide and brassinazole on negative gravitropism and tension wood formation in hybrid poplar (Populus deltoids × Populus nigra). PLANTA 2019; 249:1449-1463. [PMID: 30689054 DOI: 10.1007/s00425-018-03074-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 12/19/2018] [Indexed: 06/09/2023]
Abstract
Exogenous 24-epibrassinolide (BL) and brassinazole (BRZ) have regulatory roles in G-fiber cell wall development and secondary xylem cell wall carbohydrate biosynthesis during tension wood formation in hybrid poplar. Brassinosteroids (BRs) play important roles in regulating gravitropism and vasculature development. Here, we report the effect of brassinosteroids on negative gravitropism and G-fiber cell wall development of the stem in woody angiosperms. We applied exogenous 24-epibrassinolide (BL) or its biosynthesis inhibitor brassinazole (BRZ) to slanted hybrid poplar trees (Populus deltoids × Populus nigra) and measured the morphology of gravitropic stems, anatomy and chemistry of secondary cell wall. We furthermore analyzed the expression levels of auxin transport and cellulose biosynthetic genes after 24-epibrassinolide (BL) or brassinazole (BRZ) application. The BL-treated seedlings showed no negative gravitropism bending, whereas application of BRZ dramatically enhanced negative gravitropic bending. BL treatment stimulated secondary xylem fiber elongation and G-fiber formation on the upper side of stems but delayed G-fiber maturation. BRZ inhibited xylem fiber elongation but induced the production of more mature G-fibers on the upper side of stems. Wood chemistry analyses and immunolocalization demonstrated that BL and BRZ treatments increased the cellulose content and modified the deposition of cell wall carbohydrates including arabinose, galactose and rhamnose in the secondary xylem. The expression of cellulose biosynthetic genes, especially those related to cellulose microfibril deposition (PtFLA12 and PtCOBL4) was significantly upregulated in BL- and BRZ-treated TW stems compared with control stems. The significant differences of G-fibers development and negative gravitropism bending between 24-epibrassinolide (BL) and brassinazole (BRZ) application suggest that brassinosteroids are important for secondary xylem development during tension wood formation. Our findings provide potential insights into the mechanism by which BRs regulate G-fiber cell wall development to accomplish negative gravitropism in TW formation.
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Affiliation(s)
- Junlan Gao
- School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, Anhui, People's Republic of China
| | - Min Yu
- School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, Anhui, People's Republic of China
| | - Shiliu Zhu
- School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, Anhui, People's Republic of China
| | - Liang Zhou
- School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, Anhui, People's Republic of China
| | - Shengquan Liu
- School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, Anhui, People's Republic of China.
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8
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Park J, Kim Y, Kwon M. The complete mitochondrial genome of tulip tree, Liriodendron tulipifera L. (Magnoliaceae): intra-species variations on mitochondrial genome. Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2019.1591242] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Jongsun Park
- InfoBoss Co., Ltd., Seoul, Republic of Korea
- InfoBoss Research Center, Seoul, Republic of Korea
| | - Yongsung Kim
- InfoBoss Co., Ltd., Seoul, Republic of Korea
- InfoBoss Research Center, Seoul, Republic of Korea
| | - Mi Kwon
- InfoBoss Co., Ltd., Seoul, Republic of Korea
- InfoBoss Research Center, Seoul, Republic of Korea
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9
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Ma J, Wei L, Li J, Li H. The Analysis of Genes and Phytohormone Metabolic Pathways Associated with Leaf Shape Development in Liriodendron chinense via De Novo Transcriptome Sequencing. Genes (Basel) 2018; 9:E577. [PMID: 30486397 PMCID: PMC6316054 DOI: 10.3390/genes9120577] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 11/10/2018] [Accepted: 11/16/2018] [Indexed: 11/16/2022] Open
Abstract
The leaf, a photosynthetic organ that plays an indispensable role in plant development and growth, has a certain ability to adapt to the environment and exhibits tremendous diversity among angiosperms. Liriodendron chinense, an ancestral angiosperm species, is very popular in landscaping. The leaf of this species has two lobes and resembles a Qing Dynasty Chinese robe; thus, leaf shape is the most valuable ornamental trait of the tree. In this work, to determine the candidate genes associated with leaf development in L. chinense, scanning electron microscopy (SEM) was employed to distinguish the developmental stages of tender leaves. Four stages were clearly separated, and transcriptome sequencing was performed for two special leaf stages. Altogether, there were 48.23 G clean reads in the libraries of the two leaf developmental stages, and 48,107 assembled unigenes were annotated with five databases. Among four libraries, 3118 differentially expressed genes (DEGs) were enriched in expression profiles. We selected ten DEGs associated with leaf development and validated their expression patterns via quantitative real-time PCR (qRT-PCR) assays. Most validation results were closely correlated with the RNA-sequencing data. Taken together, we examined the dynamic process of leaf development and indicated that several transcription factors and phytohormone metabolism genes may participate in leaf shape development. The transcriptome data analysis presented in this work aims to provide basic insights into the mechanisms mediating leaf development, and the results serve as a reference for the genetic breeding of ornamental traits in L. chinense.
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Affiliation(s)
- Jikai Ma
- College of Forestry, Nanjing Forestry University, Nanjing 210037, China.
| | - Lingmin Wei
- College of Forestry, Nanjing Forestry University, Nanjing 210037, China.
| | - Jiayu Li
- College of Forestry, Nanjing Forestry University, Nanjing 210037, China.
| | - Huogen Li
- College of Forestry, Nanjing Forestry University, Nanjing 210037, China.
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China.
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Zinkgraf M, Gerttula S, Zhao S, Filkov V, Groover A. Transcriptional and temporal response of Populus stems to gravi-stimulation. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2018; 60:578-590. [PMID: 29480544 DOI: 10.1111/jipb.12645] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 02/24/2018] [Indexed: 05/12/2023]
Abstract
Plants modify development in response to external stimuli, to produce new growth that is appropriate for environmental conditions. For example, gravi-stimulation of leaning branches in angiosperm trees results in modifications of wood development, to produce tension wood that pulls leaning stems upright. Here, we use gravi-stimulation and tension wood response to dissect the temporal changes in gene expression underlying wood formation in Populus stems. Using time-series analysis of seven time points over a 14-d experiment, we identified 8,919 genes that were differentially expressed between tension wood (upper) and opposite wood (lower) sides of leaning stems. Clustering of differentially expressed genes showed four major transcriptional responses, including gene clusters whose transcript levels were associated with two types of tissue-specific impulse responses that peaked at about 24-48 h, and gene clusters with sustained changes in transcript levels that persisted until the end of the 14-d experiment. Functional enrichment analysis of those clusters suggests they reflect temporal changes in pathways associated with hormone regulation, protein localization, cell wall biosynthesis and epigenetic processes. Time-series analysis of gene expression is an underutilized approach for dissecting complex developmental responses in plants, and can reveal gene clusters and mechanisms influencing development.
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Affiliation(s)
- Matthew Zinkgraf
- USDA Forest Service, Pacific Southwest Research Station, 1731 Research Park Drive, Davis, CA 95618, USA
- Department of Computer Science, University of California Davis, One Shields Avenue, Davis, CA 95618, USA
| | - Suzanne Gerttula
- USDA Forest Service, Pacific Southwest Research Station, 1731 Research Park Drive, Davis, CA 95618, USA
- Department of Computer Science, University of California Davis, One Shields Avenue, Davis, CA 95618, USA
| | - Shutang Zhao
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Vladimir Filkov
- Department of Computer Science, University of California Davis, One Shields Avenue, Davis, CA 95618, USA
| | - Andrew Groover
- USDA Forest Service, Pacific Southwest Research Station, 1731 Research Park Drive, Davis, CA 95618, USA
- Department of Plant Biology, University of California Davis, One Shields Avenue, Davis, CA 95618, USA
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11
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Gorshkov O, Mokshina N, Ibragimova N, Ageeva M, Gogoleva N, Gorshkova T. Phloem fibres as motors of gravitropic behaviour of flax plants: level of transcriptome. FUNCTIONAL PLANT BIOLOGY : FPB 2018; 45:203-214. [PMID: 32291034 DOI: 10.1071/fp16348] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2016] [Accepted: 01/16/2017] [Indexed: 05/25/2023]
Abstract
Restoration of stem vertical position after plant inclination is a widely spread version of plant orientation in accordance with gravity vector direction. Gravitropic behaviour of flax plants involves the formation of curvature in stem region that has ceased elongation long in advance of stem inclination. The important participants of such behaviour are phloem fibres with constitutively formed tertiary cell wall (G-layer). We performed the large-scale transcriptome profiling of phloem fibres isolated from pulling and opposite sides of gravitropic curvature and compared with control plant fibres. Significant changes in transcript abundance take place for genes encoding proteins of several ion channels, transcription factors and other regulating elements. The largest number of upregulated genes belonged to the cell wall category; many of those were specifically upregulated in fibres of pulling stem side. The obtained data permit to suggest the mechanism of fibre participation in gravitropic reaction that involves the increase of turgor pressure and the rearrangements of cell wall structure in order to improve contractile properties, and to identify the regulatory elements that operate specifically in the fibres of the pulling stem side making gelatinous phloem fibres an important element of gravitropic response in herbaceous plants.
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Affiliation(s)
- Oleg Gorshkov
- Kazan Institute of Biochemistry and Biophysics of Kazan Scientific Centre of the Russian Academy of Sciences, Lobachevsky str., 2/31, Kazan, 420111, Russia
| | - Natalia Mokshina
- Kazan Institute of Biochemistry and Biophysics of Kazan Scientific Centre of the Russian Academy of Sciences, Lobachevsky str., 2/31, Kazan, 420111, Russia
| | - Nadezda Ibragimova
- Kazan Institute of Biochemistry and Biophysics of Kazan Scientific Centre of the Russian Academy of Sciences, Lobachevsky str., 2/31, Kazan, 420111, Russia
| | - Marina Ageeva
- Kazan Institute of Biochemistry and Biophysics of Kazan Scientific Centre of the Russian Academy of Sciences, Lobachevsky str., 2/31, Kazan, 420111, Russia
| | - Natalia Gogoleva
- Kazan Institute of Biochemistry and Biophysics of Kazan Scientific Centre of the Russian Academy of Sciences, Lobachevsky str., 2/31, Kazan, 420111, Russia
| | - Tatyana Gorshkova
- Kazan Institute of Biochemistry and Biophysics of Kazan Scientific Centre of the Russian Academy of Sciences, Lobachevsky str., 2/31, Kazan, 420111, Russia
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12
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Bygdell J, Srivastava V, Obudulu O, Srivastava MK, Nilsson R, Sundberg B, Trygg J, Mellerowicz EJ, Wingsle G. Protein expression in tension wood formation monitored at high tissue resolution in Populus. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:3405-3417. [PMID: 28633298 PMCID: PMC5853651 DOI: 10.1093/jxb/erx186] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2017] [Accepted: 05/30/2017] [Indexed: 05/18/2023]
Abstract
Tension wood (TW) is a specialized tissue with contractile properties that is formed by the vascular cambium in response to gravitational stimuli. We quantitatively analysed the proteomes of Populus tremula cambium and its xylem cell derivatives in stems forming normal wood (NW) and TW to reveal the mechanisms underlying TW formation. Phloem-, cambium-, and wood-forming tissues were sampled by tangential cryosectioning and pooled into nine independent samples. The proteomes of TW and NW samples were similar in the phloem and cambium samples, but diverged early during xylogenesis, demonstrating that reprogramming is an integral part of TW formation. For example, 14-3-3, reactive oxygen species, ribosomal and ATPase complex proteins were found to be up-regulated at early stages of xylem differentiation during TW formation. At later stages of xylem differentiation, proteins involved in the biosynthesis of cellulose and enzymes involved in the biosynthesis of rhamnogalacturonan-I, rhamnogalacturonan-II, arabinogalactan-II and fasciclin-like arabinogalactan proteins were up-regulated in TW. Surprisingly, two isoforms of exostosin family proteins with putative xylan xylosyl transferase function and several lignin biosynthesis proteins were also up-regulated, even though xylan and lignin are known to be less abundant in TW than in NW. These data provided new insight into the processes behind TW formation.
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Affiliation(s)
- Joakim Bygdell
- Department of Chemistry, Umeå University, Umeå, Sweden
- Computational life science cluster (CLiC), Umeå University, Sweden
| | - Vaibhav Srivastava
- Division of Glycoscience, School of Biotechnology, Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden
| | - Ogonna Obudulu
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Manoj K Srivastava
- Crop Improvement Division, Indian Grassland and Fodder Research Institute, Jhansi, UP, India
| | - Robert Nilsson
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Björn Sundberg
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Johan Trygg
- Department of Chemistry, Umeå University, Umeå, Sweden
- Computational life science cluster (CLiC), Umeå University, Sweden
| | - Ewa J Mellerowicz
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Gunnar Wingsle
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
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13
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Gorshkov O, Mokshina N, Gorshkov V, Chemikosova S, Gogolev Y, Gorshkova T. Transcriptome portrait of cellulose-enriched flax fibres at advanced stage of specialization. PLANT MOLECULAR BIOLOGY 2017; 93:431-449. [PMID: 27981388 DOI: 10.1007/s11103-016-0571-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 12/02/2016] [Indexed: 05/13/2023]
Abstract
Functional specialization of cells is among the most fundamental processes of higher organism ontogenesis. The major obstacle to studying this phenomenon in plants is the difficulty of isolating certain types of cells at defined stages of in planta development for in-depth analysis. A rare opportunity is given by the developed model system of flax (Linum usitatissimum L.) phloem fibres that can be purified from the surrounding tissues at the stage of the tertiary cell wall deposition. The performed comparison of the whole transcriptome profile in isolated fibres and other portions of the flax stem, together with fibre metabolism characterization, helped to elucidate the general picture of the advanced stage of plant cell specialization and to reveal novel participants potentially involved in fibre metabolism regulation and cell wall formation. Down-regulation of all genes encoding proteins involved in xylan and lignin synthesis and up-regulation of genes for the specific set of transcription factors transcribed during tertiary cell wall formation were revealed. The increased abundance of transcripts for several glycosyltransferases indicated the enzymes that may be involved in synthesis of fibre-specific version of rhamnogalacturonan I.
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Affiliation(s)
- Oleg Gorshkov
- Kazan Institute of Biochemistry and Biophysics, Kazan Scientific Centre, Russian Academy of Science, Lobachevsky str., 2/31, Kazan, 420111, Russia
| | - Natalia Mokshina
- Kazan Institute of Biochemistry and Biophysics, Kazan Scientific Centre, Russian Academy of Science, Lobachevsky str., 2/31, Kazan, 420111, Russia
| | - Vladimir Gorshkov
- Kazan Institute of Biochemistry and Biophysics, Kazan Scientific Centre, Russian Academy of Science, Lobachevsky str., 2/31, Kazan, 420111, Russia
| | - Svetlana Chemikosova
- Kazan Institute of Biochemistry and Biophysics, Kazan Scientific Centre, Russian Academy of Science, Lobachevsky str., 2/31, Kazan, 420111, Russia
| | - Yuri Gogolev
- Kazan Institute of Biochemistry and Biophysics, Kazan Scientific Centre, Russian Academy of Science, Lobachevsky str., 2/31, Kazan, 420111, Russia
| | - Tatyana Gorshkova
- Kazan Institute of Biochemistry and Biophysics, Kazan Scientific Centre, Russian Academy of Science, Lobachevsky str., 2/31, Kazan, 420111, Russia.
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14
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Groover A. Gravitropisms and reaction woods of forest trees - evolution, functions and mechanisms. THE NEW PHYTOLOGIST 2016; 211:790-802. [PMID: 27111862 DOI: 10.1111/nph.13968] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Accepted: 03/15/2016] [Indexed: 05/03/2023]
Abstract
Contents 790 I. 790 II. 792 III. 795 IV. 797 V. 798 VI. 800 VII. 800 800 References 800 SUMMARY: The woody stems of trees perceive gravity to determine their orientation, and can produce reaction woods to reinforce or change their position. Together, graviperception and reaction woods play fundamental roles in tree architecture, posture control, and reorientation of stems displaced by wind or other environmental forces. Angiosperms and gymnosperms have evolved strikingly different types of reaction wood. Tension wood of angiosperms creates strong tensile force to pull stems upward, while compression wood of gymnosperms creates compressive force to push stems upward. In this review, the general features and evolution of tension wood and compression wood are presented, along with descriptions of how gravitropisms and reaction woods contribute to the survival and morphology of trees. An overview is presented of the molecular and genetic mechanisms underlying graviperception, initial graviresponse and the regulation of tension wood development in the model angiosperm, Populus. Critical research questions and new approaches are discussed.
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Affiliation(s)
- Andrew Groover
- Pacific Southwest Research Station, US Forest Service, Davis, CA, 95618, USA
- Department of Plant Biology, University of California Davis, Davis, CA, 95616, USA
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15
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Park EJ, Kim HT, Choi YI, Lee C, Nguyen VP, Jeon HW, Cho JS, Funada R, Pharis RP, Kurepin LV, Ko JH. Overexpression of gibberellin 20-oxidase1 from Pinus densiflora results in enhanced wood formation with gelatinous fiber development in a transgenic hybrid poplar. TREE PHYSIOLOGY 2015; 35:1264-77. [PMID: 26433020 DOI: 10.1093/treephys/tpv099] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 08/22/2015] [Indexed: 05/21/2023]
Abstract
Gibberellins (GAs) are important regulators of plant shoot biomass growth, and GA 20-oxidase (GA20ox) is one of the major regulatory enzymes in the GA biosynthetic pathway. Previously, we showed that the expression levels of a putative GA20ox1 (i.e., PdGA20ox1) in stem tissue of 3-month-old seedlings of 12 families of Pinus densiflora were positively correlated with stem diameter growth across those same families growing in an even-aged 32-year-old pine forest (Park EJ, Lee WY, Kurepin LV, Zhang R, Janzen L, Pharis RP (2015) Plant hormone-assisted early family selection in Pinus densiflora via a retrospective approach. Tree Physiol 35:86-94). To further investigate the molecular function of this gene in the stem wood growth of forest trees, we produced transgenic poplar lines expressing PdGA20ox1 under the control of the 35S promoter (designated as 35S::PdGA20ox1). By age 3 months, most of the 35S::PdGA20ox1 poplar trees were showing an exceptional enhancement of stem wood growth, i.e., up to fourfold increases in stem dry weight, compared with the nontransformed control poplar plants. Significant increases in endogenous GA1, its immediate precursor (GA20) and its catabolite (GA8) in elongating internode tissue accompanied the increased stem growth in the transgenic lines. Additionally, the development of gelatinous fibers occurred in vertically grown stems of the 35S::PdGA20ox1 poplars. An analysis of the cell wall monosaccharide composition of the 35S::PdGA20ox1 poplars showed significant increases in xylose and glucose contents, indicating a qualitative increase in secondary wall depositions. Microarray analyses led us to find a total of 276 probe sets that were upregulated (using threefold as a threshold) in the stem tissues of 35S::PdGA20ox1 poplars relative to the controls. 'Cell organization or biogenesis'- and 'cell wall'-related genes were overrepresented, including many of genes that are involved in cell wall modification. Several transcriptional regulators, which positively regulate cell elongation through GA signaling, were also upregulated. In contrast, genes involved in defense signaling were appreciably downregulated in the 35S::PdGA20ox1 stem tissues, suggesting a growth versus defense trade-off. Taken together, our results suggest that PdGA20ox1 functions to promote stem growth and wood formation in poplar, probably by activating GA signaling while coincidentally depressing defense signaling.
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Affiliation(s)
- Eung-Jun Park
- Division of Forest Biotechnology, Korea Forest Research Institute, Suwon 441-847, Republic of Korea
| | - Hyun-Tae Kim
- Division of Forest Biotechnology, Korea Forest Research Institute, Suwon 441-847, Republic of Korea
| | - Young-Im Choi
- Division of Forest Biotechnology, Korea Forest Research Institute, Suwon 441-847, Republic of Korea
| | - Chanhui Lee
- Department of Plant and Environmental New Resources, Kyung Hee University, Yongin 446-701, Republic of Korea
| | - Van Phap Nguyen
- Department of Plant and Environmental New Resources, Kyung Hee University, Yongin 446-701, Republic of Korea
| | - Hyung-Woo Jeon
- Department of Plant and Environmental New Resources, Kyung Hee University, Yongin 446-701, Republic of Korea
| | - Jin-Seong Cho
- Division of Forest Biotechnology, Korea Forest Research Institute, Suwon 441-847, Republic of Korea Department of Plant and Environmental New Resources, Kyung Hee University, Yongin 446-701, Republic of Korea
| | - Ryo Funada
- Faculty of Agriculture, Tokyo University of Agriculture and Technology, Fuchu-Tokyo 183-8509, Japan
| | - Richard P Pharis
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada T2N 1N4
| | - Leonid V Kurepin
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada T2N 1N4 Present address: Department of Biology, Western University, London, ON, Canada N6A 5B7
| | - Jae-Heung Ko
- Department of Plant and Environmental New Resources, Kyung Hee University, Yongin 446-701, Republic of Korea
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16
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Mizrachi E, Maloney VJ, Silberbauer J, Hefer CA, Berger DK, Mansfield SD, Myburg AA. Investigating the molecular underpinnings underlying morphology and changes in carbon partitioning during tension wood formation in Eucalyptus. THE NEW PHYTOLOGIST 2015; 206:1351-63. [PMID: 25388807 DOI: 10.1111/nph.13152] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Accepted: 09/25/2014] [Indexed: 05/13/2023]
Abstract
Tension wood has distinct physical and chemical properties, including altered fibre properties, cell wall composition and ultrastructure. It serves as a good system for investigating the genetic regulation of secondary cell wall biosynthesis and wood formation. The reference genome sequence for Eucalyptus grandis allows investigation of the global transcriptional reprogramming that accompanies tension wood formation in this global wood fibre crop. We report the first comprehensive analysis of physicochemical wood property changes in tension wood of Eucalyptus measured in a hybrid (E. grandis × Eucalyptus urophylla) clone, as well as genome-wide gene expression changes in xylem tissues 3 wk post-induction using RNA sequencing. We found that Eucalyptus tension wood in field-grown trees is characterized by an increase in cellulose, a reduction in lignin, xylose and mannose, and a marked increase in galactose. Gene expression profiling in tension wood-forming tissue showed corresponding down-regulation of monolignol biosynthetic genes, and differential expression of several carbohydrate active enzymes. We conclude that alterations of cell wall traits induced by tension wood formation in Eucalyptus are a consequence of a combination of down-regulation of lignin biosynthesis and hemicellulose remodelling, rather than the often proposed up-regulation of the cellulose biosynthetic pathway.
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Affiliation(s)
- Eshchar Mizrachi
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20, Pretoria, 0028, South Africa
| | - Victoria J Maloney
- Department of Wood Science, University of British Columbia, 4030-2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Janine Silberbauer
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20, Pretoria, 0028, South Africa
| | - Charles A Hefer
- Bioinformatics and Computational Biology Unit, Department of Biochemistry, University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa
| | - Dave K Berger
- Department of Plant Science, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa
| | - Shawn D Mansfield
- Department of Wood Science, University of British Columbia, 4030-2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Alexander A Myburg
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20, Pretoria, 0028, South Africa
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17
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Chen J, Chen B, Zhang D. Transcript profiling of Populus tomentosa genes in normal, tension, and opposite wood by RNA-seq. BMC Genomics 2015; 16:164. [PMID: 25886950 PMCID: PMC4372042 DOI: 10.1186/s12864-015-1390-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2014] [Accepted: 02/24/2015] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Wood formation affects the chemical and physical properties of wood, and thus affects its utility as a building material or a feedstock for biofuels, pulp and paper. To obtain genome-wide insights on the transcriptome changes and regulatory networks in wood formation, we used high-throughput RNA sequencing to characterize cDNA libraries of mature xylem from tension wood (TW), opposite wood (OW), and normal wood (NW), in the industrial tree species Populus tomentosa. RESULTS Our sequencing generated 140,978,316 (TW), 128,972,228 (OW), and 117,672,362 (NW) reads, corresponding to 10,127 (TW), 10,129 (OW), and 10,129 (NW) unique genes. Of these, 361 genes were differentially transcribed between TW and OW (log2FC ≥ 1 or ≤ -1, FDR < 0.05), 2,658 differed between OW and NW, and 2,417 differed between TW and NW. This indicates that NW differs significantly from the wood in branches; GO term analysis also indicated that OW experienced more transcriptome remodeling. The differentially expressed genes included 97 encoding transcription factors (TFs), 40 involved in hormone signal transduction, 33 in lignin biosynthesis, 21 in flavonoid biosynthesis, and 43 in cell wall metabolism, including cellulose synthase, sucrose synthase, and COBRA. More than half of the differentially expressed TF showed more than 4-fold lower transcript levels in NW compared with TW or OW, indicating that TF abundances differed dramatically in different wood types and may have important roles in the formation of reaction wood. In addition, transcripts of most of the genes involved in lignin biosynthesis were more abundant in OW compared with TW, consistent with the higher lignin content of OW. We constructed two transcriptomic networks for the regulation of lignin and cellulose biosynthesis, including TFs, based on the co-expression patterns of different genes. Lastly, we used reverse transcription quantitative PCR to validate the differentially expressed genes identified. CONCLUSIONS Here, we identified the global patterns and differences in gene expression among TW, OW, and NW, and constructed two transcriptomic regulatory networks involved in TW formation in P. tomentosa. We also identified candidate genes for molecular breeding of wood quality, and provided a starting point to decipher the molecular mechanisms of wood formation in Populus.
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Affiliation(s)
- Jinhui Chen
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, P. R. China.
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, P. R. China.
| | - Beibei Chen
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, P. R. China.
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, P. R. China.
| | - Deqiang Zhang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, P. R. China.
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, P. R. China.
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18
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Yu H, Soler M, Mila I, San Clemente H, Savelli B, Dunand C, Paiva JAP, Myburg AA, Bouzayen M, Grima-Pettenati J, Cassan-Wang H. Genome-wide characterization and expression profiling of the AUXIN RESPONSE FACTOR (ARF) gene family in Eucalyptus grandis. PLoS One 2014; 9:e108906. [PMID: 25269088 PMCID: PMC4182523 DOI: 10.1371/journal.pone.0108906] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 08/27/2014] [Indexed: 12/27/2022] Open
Abstract
Auxin is a central hormone involved in a wide range of developmental processes including the specification of vascular stem cells. Auxin Response Factors (ARF) are important actors of the auxin signalling pathway, regulating the transcription of auxin-responsive genes through direct binding to their promoters. The recent availability of the Eucalyptus grandis genome sequence allowed us to examine the characteristics and evolutionary history of this gene family in a woody plant of high economic importance. With 17 members, the E. grandis ARF gene family is slightly contracted, as compared to those of most angiosperms studied hitherto, lacking traces of duplication events. In silico analysis of alternative transcripts and gene truncation suggested that these two mechanisms were preeminent in shaping the functional diversity of the ARF family in Eucalyptus. Comparative phylogenetic analyses with genomes of other taxonomic lineages revealed the presence of a new ARF clade found preferentially in woody and/or perennial plants. High-throughput expression profiling among different organs and tissues and in response to environmental cues highlighted genes expressed in vascular cambium and/or developing xylem, responding dynamically to various environmental stimuli. Finally, this study allowed identification of three ARF candidates potentially involved in the auxin-regulated transcriptional program underlying wood formation.
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Affiliation(s)
- Hong Yu
- LRSV Laboratoire de Recherche en Sciences Végétales, UMR5546, Université Toulouse III/CNRS, Castanet Tolosan, France
| | - Marçal Soler
- LRSV Laboratoire de Recherche en Sciences Végétales, UMR5546, Université Toulouse III/CNRS, Castanet Tolosan, France
| | - Isabelle Mila
- Université de Toulouse, Institut National Polytechnique-Ecole Nationale Supérieure Agronomique de Toulouse, Laboratoire de Génomique et Biotechnologie des Fruits, Castanet-Tolosan, France
| | - Hélène San Clemente
- LRSV Laboratoire de Recherche en Sciences Végétales, UMR5546, Université Toulouse III/CNRS, Castanet Tolosan, France
| | - Bruno Savelli
- LRSV Laboratoire de Recherche en Sciences Végétales, UMR5546, Université Toulouse III/CNRS, Castanet Tolosan, France
| | - Christophe Dunand
- LRSV Laboratoire de Recherche en Sciences Végétales, UMR5546, Université Toulouse III/CNRS, Castanet Tolosan, France
| | - Jorge A. P. Paiva
- Instituto de Investigação Científica e Tropical (IICT/MCTES), Lisboa, Portugal
- Instituto de Biologia Experimental e Tecnológica (IBET), Oeiras, Portugal
| | - Alexander A. Myburg
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), University of Pretoria, Pretoria, South Africa
| | - Mondher Bouzayen
- Université de Toulouse, Institut National Polytechnique-Ecole Nationale Supérieure Agronomique de Toulouse, Laboratoire de Génomique et Biotechnologie des Fruits, Castanet-Tolosan, France
| | - Jacqueline Grima-Pettenati
- LRSV Laboratoire de Recherche en Sciences Végétales, UMR5546, Université Toulouse III/CNRS, Castanet Tolosan, France
| | - Hua Cassan-Wang
- LRSV Laboratoire de Recherche en Sciences Végétales, UMR5546, Université Toulouse III/CNRS, Castanet Tolosan, France
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19
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Jin H, Do J, Shin SJ, Choi JW, Choi YI, Kim W, Kwon M. Exogenously applied 24-epi brassinolide reduces lignification and alters cell wall carbohydrate biosynthesis in the secondary xylem of Liriodendron tulipifera. PHYTOCHEMISTRY 2014; 101:40-51. [PMID: 24582278 DOI: 10.1016/j.phytochem.2014.02.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Revised: 12/30/2013] [Accepted: 02/03/2014] [Indexed: 05/06/2023]
Abstract
The roles of brassinosteroids (BRs) in vasculature development have been implicated based on an analysis of Arabidopsis BR mutants and suspension cells of Zinnia elegans. However, the effects of BRs in vascular development of a woody species have not been demonstrated. In this study, 24-epi brassinolide (BL) was applied to the vascular cambium of a vertical stem of a 2-year-old Liriodendron, and the resulting chemical and anatomical phenotypes were characterized to uncover the roles of BRs in secondary xylem formation of a woody species. The growth in xylary cells was clearly promoted when treated with BL. Statistical analysis indicated that the length of both types of xylary cells (fiber and vessel elements) increased significantly after BL application. Histochemical analysis demonstrated that BL-induced growth promotion involved the acceleration of cell division and cell elongation. Histochemical and expression analysis of several lignin biosynthetic genes indicated that most genes in the phenylpropanoid pathway were significantly down-regulated in BL-treated stems compared to that in control stems. Chemical analysis of secondary xylem demonstrated that BL treatment induced significant modification in the cell wall carbohydrates, including biosynthesis of hemicellulose and cellulose. Lignocellulose crystallinity decreased significantly, and the hemicellulose composition changed with significant increases in galactan and arabinan. Thus, BL has regulatory roles in the biosynthesis and modification of secondary cell wall components and cell wall assembly during secondary xylem development in woody plants.
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Affiliation(s)
- Hyunjung Jin
- Department of Biosystems Engineering, Korea University, Seoul 136-701, Republic of Korea
| | - Jihye Do
- Department of Biotechnology, Korea University, Seoul 136-701, Republic of Korea
| | - Soo-Jeong Shin
- Department of Wood and Paper Science, Chungbuk National University, Cheongju 361-763, Republic of Korea
| | - Joon Weon Choi
- Department of Forest Sciences, Seoul National University, Seoul 151-742, Republic of Korea
| | - Young Im Choi
- Division of Forest Biotechnology, Korea Forest Research Institute, Suwon 441-350, Republic of Korea
| | - Wook Kim
- Department of Biotechnology, Korea University, Seoul 136-701, Republic of Korea
| | - Mi Kwon
- Department of Biotechnology, Korea University, Seoul 136-701, Republic of Korea.
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Wang C, Zhang N, Gao C, Cui Z, Sun D, Yang C, Wang Y. Comprehensive transcriptome analysis of developing xylem responding to artificial bending and gravitational stimuli in Betula platyphylla. PLoS One 2014; 9:e87566. [PMID: 24586282 PMCID: PMC3930542 DOI: 10.1371/journal.pone.0087566] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Accepted: 12/21/2013] [Indexed: 11/18/2022] Open
Abstract
Betula platyphylla Suk (birch) is a fast-growing woody species that is important in pulp industries and the biofuels. However, as an important pulp species, few studies had been performed on its wood formation. In the present study, we investigated the molecular responses of birch xylem to artificial bending and gravitational stimuli. After trunks of birch trees were subjected to bending for 8 weeks, the cellulose content was significantly greater in tension wood (TW) than in opposite wood (OW) or normal wood (NW), whereas the lignin content in TW was significantly lower than that in OW and NW. In addition, TW grew more rapidly than OW and generated TW-specific fibers with an additional G-layer. Three transcriptome libraries were constructed from TW, OW and NW of B. platyphylla, respectively, after the plants were subjected to artificial bending. Overall, 80,909 nonredundant unigenes with a mean size of 768 nt were assembled. Expression profiles were generated, and 9,684 genes were found to be significantly differentially expressed among the TW, OW and NW libraries. These included genes involved in secondary cell wall structure, wood composition, and cellulose or lignin biosynthesis. Our study showed that during TW formation, genes involved in cellulose synthesis were induced, while the expression of lignin synthesis-related genes decreased, resulting in increased cellulose content and decreased lignin levels in TW. In addition, fasciclin-like arabinogalactan proteins play important role in TW formation. These findings may provide important insights into wood formation at the molecular level.
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Affiliation(s)
- Chao Wang
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Harbin, China
| | - Nan Zhang
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Harbin, China
| | - Caiqiu Gao
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Harbin, China
| | - Zhiyuan Cui
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Harbin, China
| | - Dan Sun
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Harbin, China
| | - Chuanping Yang
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Harbin, China
| | - Yucheng Wang
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Harbin, China
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Yang Y, Xu M, Luo Q, Wang J, Li H. De novo transcriptome analysis of Liriodendron chinense petals and leaves by Illumina sequencing. Gene 2013; 534:155-62. [PMID: 24239772 DOI: 10.1016/j.gene.2013.10.073] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Revised: 09/21/2013] [Accepted: 10/27/2013] [Indexed: 12/31/2022]
Abstract
Liriodendron chinense (Hemsl.) Sarg is an endangered species and occupies a pivotal position in phylogenetic studies of flowering plants, while its genomic resources are limited. In this study, we performed transcriptome sequencing for L. chinense petals and leaves using the Illumina paired-end sequencing technique. Approximately 17.02-Gb clean reads were obtained, and de novo assembly generated 87,841 unigenes, with an average length of 778 bp. Of these, there were 65,535 (74.61%) unigenes with significant similarity to publically available plant protein sequences. There were 3386 genes identified as significant differentially expressed between petals and leaves, among them 2969 (87.68%) were up-regulated and 417 (12.31%) down-regulated in petals. Metabolic pathway analysis revealed that 25 unigenes were predicted to be responsible for the biosynthesis of carotenoids, with 7 genes differentially expressed between these two tissues. This report is the first to identify genes associated with carotenoid biosynthesis in Liriodendron and represents a valuable resource for future genomic studies on the endangered species L. chinense.
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Affiliation(s)
- Ying Yang
- Key Laboratory of Forest Genetics & Gene Engineering of the Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
| | - Meng Xu
- Key Laboratory of Forest Genetics & Gene Engineering of the Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
| | - Qunfeng Luo
- Key Laboratory of Forest Genetics & Gene Engineering of the Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
| | - Jie Wang
- Key Laboratory of Forest Genetics & Gene Engineering of the Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
| | - Huogen Li
- Key Laboratory of Forest Genetics & Gene Engineering of the Ministry of Education, Nanjing Forestry University, Nanjing 210037, China.
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Wullschleger SD, Weston DJ, DiFazio SP, Tuskan GA. Revisiting the sequencing of the first tree genome: Populus trichocarpa. TREE PHYSIOLOGY 2013; 33:357-364. [PMID: 23100257 DOI: 10.1093/treephys/tps081] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Ten years ago, it was announced that the Joint Genome Institute with funds provided by the Department of Energy, Office of Science, Biological and Environmental Research would sequence the black cottonwood (Populus trichocarpa Torr. & Gray) genome. This landmark decision was the culmination of work by the forest science community to develop Populus as a model system. Since its public release in late 2006, the availability of the Populus genome has spawned research in plant biology, morphology, genetics and ecology. Here we address how the tree physiologist has used this resource. More specifically, we revisit our earlier contention that the rewards of sequencing the Populus genome would depend on how quickly scientists working with woody perennials could adopt molecular approaches to investigate the mechanistic underpinnings of basic physiological processes. Several examples illustrate the integration of functional and comparative genomics into the forest sciences, especially in areas that target improved understanding of the developmental differences between woody perennials and herbaceous annuals (e.g., phase transitions). Sequencing the Populus genome and the availability of genetic and genomic resources has also been instrumental in identifying candidate genes that underlie physiological and morphological traits of interest. Genome-enabled research has advanced our understanding of how phenotype and genotype are related and provided insights into the genetic mechanisms whereby woody perennials adapt to environmental stress. In the future, we anticipate that low-cost, high-throughput sequencing will continue to facilitate research in tree physiology and enhance our understanding at scales of individual organisms and populations. A challenge remains, however, as to how genomic resources, including the Populus genome, can be used to understand ecosystem function. Although examples are limited, progress in this area is encouraging and will undoubtedly improve as future research targets the many unique aspects of Populus as a keystone species in terrestrial ecosystems.
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Affiliation(s)
- Stan D Wullschleger
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6301, USA.
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Nugroho WD, Yamagishi Y, Nakaba S, Fukuhara S, Begum S, Marsoem SN, Ko JH, Jin HO, Funada R. Gibberellin is required for the formation of tension wood and stem gravitropism in Acacia mangium seedlings. ANNALS OF BOTANY 2012; 110:887-95. [PMID: 22843341 PMCID: PMC3423806 DOI: 10.1093/aob/mcs148] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2012] [Accepted: 05/01/2012] [Indexed: 05/03/2023]
Abstract
BACKGROUND AND AIMS Angiosperm trees generally form tension wood on the upper sides of leaning stems. The formation of tension wood is an important response to gravitational stimulus. Gibberellin appears to be involved in the differentiation of secondary xylem, but it remains unclear whether gibberellin plays a key role in the formation of tension wood and plant gravitropism. Therefore, a study was designed to investigate the effects of gibberellin and of inhibitors of the synthesis of gibberellin, namely paclobutrazole and uniconazole-P, on the formation of tension wood and negative stem gravitropism in Acacia mangium seedlings. METHODS Gibberellic acid (GA(3)), paclobutrazole and uniconazole-P were applied to seedlings via the soil in which they were growing. Distilled water was applied similarly as a control. Three days after such treatment, seedlings were tilted at an angle of 45° from the vertical, and samples of stems were collected for analysis 2 weeks, 2 months and 6 months after tilting. The effects of treatments on the stem recovery degree (Rº) were analysed as an index of the negative gravitropism of seedlings, together the width of the region of tension wood in the upper part of inclined stems. KEY RESULTS It was found that GA(3) stimulated the negative gravitropism of tilted seedling stems of A. mangium, while paclobutrazole and uniconazole-P inhibited recovery to vertical growth. Moreover, GA(3) stimulated the formation of tension wood in tilted A. mangium seedlings, while paclobutrazole and uniconazole-P strongly suppressed the formation of tension wood, as assessed 2 weeks after tilting. CONCLUSIONS The results suggest that gibberellin plays an important role at the initial stages of formation of tension wood and in stem gravitropism in A. mangium seedlings in response to a gravitational stimulus.
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Affiliation(s)
- Widyanto Dwi Nugroho
- Tokyo University of Agriculture and Technology, Fuchu-Tokyo 183-8509, Japan
- Faculty of Forestry, Universitas Gadjah Mada, Jalan Agro No. 1 Bulaksumur, Yogyakarta, 55281, Indonesia
| | - Yusuke Yamagishi
- Tokyo University of Agriculture and Technology, Fuchu-Tokyo 183-8509, Japan
| | - Satoshi Nakaba
- Tokyo University of Agriculture and Technology, Fuchu-Tokyo 183-8509, Japan
| | - Shiori Fukuhara
- Tokyo University of Agriculture and Technology, Fuchu-Tokyo 183-8509, Japan
| | - Shahanara Begum
- Tokyo University of Agriculture and Technology, Fuchu-Tokyo 183-8509, Japan
- Faculty of Agriculture, Bangladesh Agricultural University, Mymensingh-2202, Bangladesh
| | - Sri Nugroho Marsoem
- Faculty of Forestry, Universitas Gadjah Mada, Jalan Agro No. 1 Bulaksumur, Yogyakarta, 55281, Indonesia
| | - Jae-Heung Ko
- College of Life Science, Kyung Hee University, Yongin 446-701, Korea
| | - Hyun-O Jin
- College of Life Science, Kyung Hee University, Yongin 446-701, Korea
| | - Ryo Funada
- Tokyo University of Agriculture and Technology, Fuchu-Tokyo 183-8509, Japan
- College of Life Science, Kyung Hee University, Yongin 446-701, Korea
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