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Xu W, Cheng H, Cheng J, Zhu S, Cui Y, Wang C, Wu J, Lan X, Cheng Y. A COBRA family protein, PtrCOB3, contributes to gelatinous layer formation of tension wood fibers in poplar. PLANT PHYSIOLOGY 2024; 196:323-337. [PMID: 38850037 DOI: 10.1093/plphys/kiae328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 04/09/2024] [Accepted: 04/24/2024] [Indexed: 06/09/2024]
Abstract
Angiosperm trees usually develop tension wood (TW) in response to gravitational stimulation. TW comprises abundant gelatinous (G-) fibers with thick G-layers primarily composed of crystalline cellulose. Understanding the pivotal factors governing G-layer formation in TW fiber remains elusive. This study elucidates the role of a Populus trichocarpa COBRA family protein, PtrCOB3, in the G-layer formation of TW fibers. PtrCOB3 expression was upregulated, and its promoter activity was enhanced during TW formation. Comparative analysis with wild-type trees revealed that ptrcob3 mutants, mediated by Cas9/gRNA gene editing, were incapable of producing G-layers within TW fibers and showed severely impaired stem lift. Fluorescence immunolabeling data revealed a dearth of crystalline cellulose in the tertiary cell wall (TCW) of ptrcob3 TW fibers. The role of PtrCOB3 in G-layer formation is contingent upon its native promoter, as evidenced by the comparative phenotypic assessments of pCOB11::PtrCOB3, pCOB3::PtrCOB3, and pCOB3::PtrCOB11 transgenic lines in the ptrcob3 background. Overexpression of PtrCOB3 under the control of its native promoter expedited G-layer formation within TW fibers. We further identified 3 transcription factors that bind to the PtrCOB3 promoter and positively regulate its transcriptional levels. Alongside the primary TCW synthesis genes, these findings enable the construction of a 2-layer transcriptional regulatory network for the G-layer formation of TW fibers. Overall, this study uncovers mechanistic insight into TW formation, whereby a specific COB protein executes the deposition of cellulose, and consequently, G-layer formation within TW fibers.
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Affiliation(s)
- Wenjing Xu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- College of Life Sciences, Northeast Forestry University, Harbin 150040, China
| | - Hao Cheng
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Jiyao Cheng
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Siran Zhu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Yongyao Cui
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Chong Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Jianzhen Wu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Xingguo Lan
- College of Life Sciences, Northeast Forestry University, Harbin 150040, China
| | - Yuxiang Cheng
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
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2
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Shi J, Zhang J, Sun D, Zhao L, Chi Y, Gao C, Wang Y, Wang C. Protein profile analysis of tension wood development in response to artificial bending and gravitational stimuli in Betula platyphylla. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 339:111957. [PMID: 38122834 DOI: 10.1016/j.plantsci.2023.111957] [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: 08/30/2023] [Revised: 12/04/2023] [Accepted: 12/11/2023] [Indexed: 12/23/2023]
Abstract
Betula platyphylla Suk (birch) is an excellent short-term hardwood species with growth and wood characteristics well suited to wood industries. To investigate the molecular mechanism of wood development in birch, a tension wood (TW) induced system was used to explore the regulatory mechanism at the protein level and identify the key proteins involved in xylem development in birch. The results of dyeing with Safranin O-Fast Green indicated that the cellulose content of TW was significantly higher than that of opposite wood (OW) or normal wood (NW), and the lignin content in TW was significantly lower than that in OW and NW after artificial bending of birch stems. Protein profile analysis of TW, NW and OW by iTRAQ revealed that there were 639 and 460 differentially expressed proteins (DEPs) between TW/OW and TW/NW, respectively. The DEPs were mainly enriched in tyrosine metabolism, glycolysis/gluconeogenesis, phenylalanine and tyrosine metabolism, phenylpropanoid and pyruvate metabolism, the pentose phosphate pathway, the citrate cycle (TCA cycle), fructose and mannose metabolism, carbon fixation in photosynthetic organisms, fatty acid biosynthesis, photosynthesis proteins and other pathways. The proteins in the citrate cycle were upregulated. The expression levels of PGI, PGM and FRK proteins related to cellulose synthesis increased and the expression levels of PAL, 4CL and COMT related to lignin synthesis decreased, leading to an increase in cellulose content and decreased lignin levels in TW. PPI analysis revealed that key DEPs interact with each other, indicating that these proteins form complexes to implement this function, which may provide important insights for wood formation at the molecular level.
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Affiliation(s)
- Jingjing Shi
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Harbin 150040, China
| | - Jiawei Zhang
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Harbin 150040, China
| | - Dan Sun
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Harbin 150040, China
| | - Leifei Zhao
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Harbin 150040, China
| | - Yao Chi
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Harbin 150040, China
| | - Caiqiu Gao
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Harbin 150040, China
| | - Yucheng Wang
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Harbin 150040, China
| | - Chao Wang
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Harbin 150040, China.
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Song S, Ma D, Xu C, Guo Z, Li J, Song L, Wei M, Zhang L, Zhong YH, Zhang YC, Liu JW, Chi B, Wang J, Tang H, Zhu X, Zheng HL. In silico analysis of NAC gene family in the mangrove plant Avicennia marina provides clues for adaptation to intertidal habitats. PLANT MOLECULAR BIOLOGY 2023; 111:393-413. [PMID: 36645624 DOI: 10.1007/s11103-023-01333-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 12/29/2022] [Indexed: 06/17/2023]
Abstract
NAC (NAM, ATAF1/2, CUC2) transcription factors (TFs) constitute a plant-specific gene family. It is reported that NAC TFs play important roles in plant growth and developmental processes and in response to biotic/abiotic stresses. Nevertheless, little information is known about the functional and evolutionary characteristics of NAC TFs in mangrove plants, a group of species adapting coastal intertidal habitats. Thus, we conducted a comprehensive investigation for NAC TFs in Avicennia marina, one pioneer species of mangrove plants. We totally identified 142 NAC TFs from the genome of A. marina. Combined with NAC proteins having been functionally characterized in other organisms, we built a phylogenetic tree to infer the function of NAC TFs in A. marina. Gene structure and motif sequence analyses suggest the sequence conservation and transcription regulatory regions-mediated functional diversity. Whole-genome duplication serves as the driver force to the evolution of NAC gene family. Moreover, two pairs of NAC genes were identified as positively selected genes of which AmNAC010/040 may be imposed on less constraint toward neofunctionalization. Quite a few stress/hormone-related responsive elements were found in promoter regions indicating potential response to various external factors. Transcriptome data revealed some NAC TFs were involved in pneumatophore and leaf salt gland development and response to salt, flooding and Cd stresses. Gene co-expression analysis found a few NAC TFs participates in the special biological processes concerned with adaptation to intertidal environment. In summary, this study provides detailed functional and evolutionary information about NAC gene family in mangrove plant A. marina and new perspective for adaptation to intertidal habitats.
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Affiliation(s)
- Shiwei Song
- Key Laboratory of the Ministry of Education for Costal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361102, Fujian, China
| | - Dongna Ma
- Key Laboratory of the Ministry of Education for Costal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361102, Fujian, China
| | - Chaoqun Xu
- Key Laboratory of the Ministry of Education for Costal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361102, Fujian, China
| | - Zejun Guo
- Key Laboratory of the Ministry of Education for Costal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361102, Fujian, China
| | - Jing Li
- Key Laboratory of the Ministry of Education for Costal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361102, Fujian, China
| | - Lingyu Song
- Key Laboratory of the Ministry of Education for Costal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361102, Fujian, China
| | - Mingyue Wei
- Key Laboratory of the Ministry of Education for Costal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361102, Fujian, China
| | - Ludan Zhang
- Key Laboratory of the Ministry of Education for Costal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361102, Fujian, China
| | - You-Hui Zhong
- Key Laboratory of the Ministry of Education for Costal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361102, Fujian, China
| | - Yu-Chen Zhang
- Key Laboratory of the Ministry of Education for Costal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361102, Fujian, China
| | - Jing-Wen Liu
- Key Laboratory of the Ministry of Education for Costal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361102, Fujian, China
| | - Bingjie Chi
- Key Laboratory of the Ministry of Education for Costal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361102, Fujian, China
| | - Jicheng Wang
- Key Laboratory of the Ministry of Education for Costal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361102, Fujian, China
| | - Hanchen Tang
- Key Laboratory of the Ministry of Education for Costal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361102, Fujian, China
| | - Xueyi Zhu
- Key Laboratory of the Ministry of Education for Costal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361102, Fujian, China
| | - Hai-Lei Zheng
- Key Laboratory of the Ministry of Education for Costal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361102, Fujian, China.
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Kong L, Zhuo Y, Xu J, Meng X, Wang Y, Zhao W, Lai H, Chen J, Wang J. Identification of long non-coding RNAs and microRNAs involved in anther development in the tropical Camellia oleifera. BMC Genomics 2022; 23:596. [PMID: 35974339 PMCID: PMC9380326 DOI: 10.1186/s12864-022-08836-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 07/29/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Explored the molecular science of anther development is important for improving productivity and overall yield of crops. Although the role of regulatory RNAs, including long non-coding RNAs (lncRNAs) and microRNAs (miRNAs), in regulating anther development has been established, their identities and functions in Camellia oleifera, an important industrial crop, have yet not been clearly explored. Here, we report the identification and characterization of genes, lncRNAs and miRNAs during three stages of the tropical C. oleifera anther development by single-molecule real-time sequencing, RNA sequencing and small RNA sequencing, respectively. RESULTS These stages, viz. the pollen mother cells stage, tetrad stage and uninucleate pollen stage, were identified by analyzing paraffin sections of floral buds during rapid expansion periods. A total of 18,393 transcripts, 414 putative lncRNAs and 372 miRNAs were identified, of which 5,324 genes, 115 lncRNAs, and 44 miRNAs were differentially accumulated across three developmental stages. Of these, 44 and 92 genes were predicted be regulated by 37 and 30 differentially accumulated lncRNAs and miRNAs, respectively. Additionally, 42 differentially accumulated lncRNAs were predicted as targets of 27 miRNAs. Gene ontology enrichment indicated that potential target genes of lncRNAs were enriched in photosystem II, regulation of autophagy and carbohydrate phosphatase activity, which are essential for anther development. Functional annotation of genes targeted by miRNAs indicated that they are relevant to transcription and metabolic processes that play important roles in microspore development. An interaction network was built with 2 lncRNAs, 6 miRNAs and 10 mRNAs. Among these, miR396 and miR156 family were up-regulated, while their targets, genes (GROWTH REGULATING FACTORS and SQUAMOSA PROMOTER BINDING PROTEIN-LIKE genes) and lncRNAs, were down-regulated. Further, the trans-regulated targets of these lncRNAs, like wall-associated kinase2 and phosphomannose isomerase1, are involved in pollen wall formation during anther development. CONCLUSIONS This study unravels lncRNAs, miRNAs and miRNA-lncRNA-mRNA networks involved in development of anthers of the tropical C. oleifera lays a theoretical foundation for further elucidation of regulatory roles of lncRNAs and miRNAs in anther development.
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Affiliation(s)
- Lingshan Kong
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, 572025, Sanya, P. R. China.,Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, School of Forestry, Hainan University, 570228, Haikou, P. R. China.,School of Horticulture, Hainan University, 570228, Haikou, P. R. China
| | - Yanjing Zhuo
- School of Public Administration, Hainan University, 570228, Haikou, P. R. China
| | - Jieru Xu
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, 572025, Sanya, P. R. China.,Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, School of Forestry, Hainan University, 570228, Haikou, P. R. China
| | - Xiangxu Meng
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, 572025, Sanya, P. R. China.,Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, School of Forestry, Hainan University, 570228, Haikou, P. R. China
| | - Yue Wang
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, 572025, Sanya, P. R. China.,Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, School of Forestry, Hainan University, 570228, Haikou, P. R. China
| | - Wenxiu Zhao
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, 572025, Sanya, P. R. China.,Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, School of Forestry, Hainan University, 570228, Haikou, P. R. China
| | - Hanggui Lai
- School of Tropical Crops, Hainan University, 570228, Haikou, P. R. China
| | - Jinhui Chen
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, 572025, Sanya, P. R. China. .,Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, School of Forestry, Hainan University, 570228, Haikou, P. R. China.
| | - Jian Wang
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, 572025, Sanya, P. R. China. .,School of Horticulture, Hainan University, 570228, Haikou, P. R. China.
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5
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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: 1.5] [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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Karannagoda N, Spokevicius A, Hussey S, Cassan-Wang H, Grima-Pettenati J, Bossinger G. Eucalyptus grandis AUX/INDOLE-3-ACETIC ACID 13 (EgrIAA13) is a novel transcriptional regulator of xylogenesis. PLANT MOLECULAR BIOLOGY 2022; 109:51-65. [PMID: 35292886 PMCID: PMC9072461 DOI: 10.1007/s11103-022-01255-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 02/16/2022] [Indexed: 06/14/2023]
Abstract
Our Induced Somatic Sector Analysis and protein-protein interaction experiments demonstrate that Eucalyptus grandis IAA13 regulates xylem fibre and vessel development, potentially via EgrIAA13 modules involving ARF2, ARF5, ARF6 and ARF19. Auxin is a crucial phytohormone regulating multiple aspects of plant growth and differentiation, including regulation of vascular cambium activity, xylogenesis and its responsiveness towards gravitropic stress. Although the regulation of these biological processes greatly depends on auxin and regulators of the auxin signalling pathway, many of their specific functions remain unclear. Therefore, the present study aims to functionally characterise Eucalyptus grandis AUX/INDOLE-3-ACETIC ACID 13 (EgrIAA13), a member of the auxin signalling pathway. In Eucalyptus and Populus, EgrIAA13 and its orthologs are preferentially expressed in the xylogenic tissues and downregulated in tension wood. Therefore, to further investigate EgrIAA13 and its function during xylogenesis, we conducted subcellular localisation and Induced Somatic Sector Analysis experiments using overexpression and RNAi knockdown constructs of EgrIAA13 to create transgenic tissue sectors on growing stems of Eucalyptus and Populus. Since Aux/IAAs interact with Auxin Responsive Factors (ARFs), in silico predictions of IAA13-ARF interactions were explored and experimentally validated via yeast-2-hybrid experiments. Our results demonstrate that EgrIAA13 localises to the nucleus and that downregulation of EgrIAA13 impedes Eucalyptus xylem fibre and vessel development. We also observed that EgrIAA13 interacts with Eucalyptus ARF2, ARF5, ARF6 and ARF19A. Based on these results, we conclude that EgrIAA13 is a regulator of Eucalyptus xylogenesis and postulate that the observed phenotypes are likely to result from alterations in the auxin-responsive transcriptome via IAA13-ARF modules such as EgrIAA13-EgrARF5. Our results provide the first insights into the regulatory role of EgrIAA13 during xylogenesis.
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Affiliation(s)
- Nadeeshani Karannagoda
- School of Ecosystem and Forest Sciences, The University of Melbourne, Creswick, VIC, 3363, Australia.
- Centre for AgriBioscience, Agriculture Victoria, AgriBio, Bundoora, Victoria, 3083, Australia.
| | - Antanas Spokevicius
- School of Ecosystem and Forest Sciences, The University of Melbourne, Creswick, VIC, 3363, Australia
| | - Steven Hussey
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa
| | - Hua Cassan-Wang
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse III, CNRS, UPS, UMR 5546, 24 Chemin de Borde Rouge, 31320, Castanet-Tolosan, France
| | - Jacqueline Grima-Pettenati
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse III, CNRS, UPS, UMR 5546, 24 Chemin de Borde Rouge, 31320, Castanet-Tolosan, France
| | - Gerd Bossinger
- School of Ecosystem and Forest Sciences, The University of Melbourne, Creswick, VIC, 3363, Australia
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7
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Zhao W, Meng X, Xu J, Liu Z, Hu Y, Li B, Chen J, Cao B. Integrated mRNA and Small RNA Sequencing Reveals microRNAs Associated With Xylem Development in Dalbergia odorifera. Front Genet 2022; 13:883422. [PMID: 35547261 PMCID: PMC9081728 DOI: 10.3389/fgene.2022.883422] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 03/23/2022] [Indexed: 11/13/2022] Open
Abstract
Dalbergia odorifera is a rare and precious rosewood specie, whose wood is a very high-quality material for valuable furniture and carving crafts. However, limited information is available about the process of wood formation in D. odorifera. To determine genes that might be closely associated with the xylem differentiation process, we analyzed the differentially expressed genes (DEGs) and microRNAs (miRNAs) from specific xylem tissues of D. odorifera by RNA sequencing (RNA-seq) and small RNA sequencing (small RNA-seq). In total, we obtained 134,221,955 clean reads from RNA-seq and 90,940,761 clean reads from small RNA-seq. By comparing the transition zone (Dotz) and sapwood (Dosw) samples, a total of 395 DEGs were identified. Further analysis revealed that DEGs encoded for WRKY transcription factors (eight genes), lignin synthesis (PER47, COMT, CCR2), cell wall composition (UXS2), gibberellin synthesis (KAO2, GA20OX1), jasmonic acid synthesis (OPR2, CYP74A), and synthesis of flavonoids (PAL2) and terpenoids (CYP71A1). Subsequently, a preliminary analysis by small RNA-seq showed that the expressions of 14 miRNAs (such as miR168a-5p, miR167f-5p, miR167h-5p, miR167e, miR390a, miR156g, novel_52, and novel_9) were significantly different between Dotz and Dosw. Further analysis revealed that the target genes of these differentially expressed miRNAs were enriched in the GO terms "amino acid binding," "cellulase activity," and "DNA beta-glucosyltransferase activity". Further, KEGG pathway annotation showed significant enrichment in "fatty acid elongation" and "biosynthesis of unsaturated fatty acids". These processes might be participating in the xylem differentiation of D. odorifera. Next, expression correlation analysis showed that nine differentially expressed miRNAs were significantly negatively associated with 21 target genes, which encoded for proteins such as pyrH, SPL6, SPL12, GCS1, and ARF8. Overall, this is the first study on miRNAs and their potential functions in the xylem development of D. odorifera, which provides a stepping stone for a detailed functional investigation of D. odorifera miRNAs.
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Affiliation(s)
- Wenxiu Zhao
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, School of Forestry, Hainan University, Haikou, China
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Xiangxu Meng
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, School of Forestry, Hainan University, Haikou, China
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Jiahong Xu
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, School of Forestry, Hainan University, Haikou, China
| | - Zijia Liu
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Yangyang Hu
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, School of Forestry, Hainan University, Haikou, China
| | - Bingyu Li
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, School of Forestry, Hainan University, Haikou, China
| | - Jinhui Chen
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, School of Forestry, Hainan University, Haikou, China
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Bing Cao
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, China
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8
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Zhang Z, Wang H, Wu J, Jin Y, Xiao S, Li T, Liu X, Zhang H, Zhang Z, Su J, Liu J, Wang X, Gao Y, Ma X, Gu L. Comprehensive Transcriptome Analysis of Stem-Differentiating Xylem Upon Compression Stress in Cunninghamia Lanceolata. Front Genet 2022; 13:843269. [PMID: 35309135 PMCID: PMC8927042 DOI: 10.3389/fgene.2022.843269] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Accepted: 01/11/2022] [Indexed: 11/21/2022] Open
Abstract
Compression wood (CW) in gymnosperm brings great difficulties to wood industry using wood as raw materials since CW presents special wood structure and have different physical and chemical properties from those of normal wood (NW). Chinese fir (Cunninghamia lanceolata) is widely distributed in China. However, global transcriptome profiling of coding and long non-coding RNA in response to compression stress has not been reported in the gymnosperm species. In this study, we revealed that CW in Chinese fir exhibited distinct morphology and cytology properties compared with those of NW, including high lignin content, thick and round tracheid cells. Furthermore, we combined both PacBio long-read SMRT sequencing (Iso-Seq) and Illumina short-read RNA-Seq to reveal the transcriptome in stem-differentiating xylem (SDX) under different time points (2, 26, and 74 h) upon compression stress in NW, CW, and OW (opposite wood), respectively. Iso-Seq was successfully assembled into 41,253 de-novo full-length transcriptome reference (average length 2,245 bp). Moreover, there were striking differences in expression upon compression stress, which were involved 13 and 7 key enzyme genes in the lignin and cellulose synthesis, respectively. Especially, we revealed 11 secondary growth-related transcription factors show differential expression under compression stress, which was further validated by qRT-PCR. Finally, the correlation between 6,533 differentially expressed coding genes and 372 differentially expressed long non-coding RNAs (lncRNAs) indicates that these lncRNAs may affect cell wall biogenesis and xyloglucan metabolism. In conclusion, our results provided comprehensive cytology properties and full-length transcriptome profiling of wood species upon compression stress. Especially we explored candidate genes, including both coding and long non-coding genes, and provided a theoretical basis for further research on the formation mechanism of CW in gymnosperm Chinese fir.
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Affiliation(s)
- Zekun Zhang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Huiyuan Wang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ji Wu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yandong Jin
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shengwu Xiao
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Tao Li
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xuqinq Liu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Hangxiao Zhang
- College of Forestry, Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zeyu Zhang
- College of Forestry, Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jun Su
- College of Forestry, Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jingzao Liu
- Taining State-owned Forest Farm, Taining, China
| | | | - Yubang Gao
- College of Forestry, Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, China
- *Correspondence: Xiangqing Ma, ; Yubang Gao, ; Lianfeng Gu,
| | - Xiangqing Ma
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- *Correspondence: Xiangqing Ma, ; Yubang Gao, ; Lianfeng Gu,
| | - Lianfeng Gu
- College of Forestry, Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, China
- *Correspondence: Xiangqing Ma, ; Yubang Gao, ; Lianfeng Gu,
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9
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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: 4.0] [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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10
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Patturaj M, Munusamy A, Kannan N, Ramasamy Y. Biologia Futura: progress and future perspectives of long non-coding RNAs in forest trees. Biol Futur 2021; 73:43-53. [PMID: 34843103 DOI: 10.1007/s42977-021-00108-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 11/16/2021] [Indexed: 10/19/2022]
Abstract
Forest trees are affected by climate change, anthropogenic pressure, as well as abiotic and biotic stresses. Conventional tree breeding has so far been limited to enhance overall productivity, and our understanding of the genetic basis of quantitative traits is still inadequate. Quantum leaps in next-generation sequencing technologies and bioinformatics have permitted the exploration and identification of various non-coding regions of the genome other than protein coding genes. These genomic regions produce various types of non-coding RNAs and regulate myriads of biological functions at epigenetic, transcriptional and translational levels. Recently, long non-coding RNAs (lncRNAs) which act as molecular switch have been identified to be pivotal molecules in forest trees. This review focuses on progress made in regulatory mechanisms in various developmental phases like wood formation, adventitious rooting and flowering and stress responses. It was predicted that complex regulatory interactions among lncRNA, miRNA and gene exist. LncRNAs can function as a sponge for miRNAs, reducing the suppressive effect of miRNAs on target mRNAs and perhaps adding a new layer of regulatory interactions among non-coding RNA classes in trees. Furthermore, network analysis revealed the interactions of lncRNA and genes during the expression of several important genes. The insights generated about lncRNAs in forest trees would enable improvement of economically important traits including the devastating abiotic and biotic stresses. In addition, solid understanding on the wide range of regulatory functions of lncRNAs on traits influencing biomass productivity and adaptation would aid the applications of biotechnology in genetic improvement of forest trees.
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Affiliation(s)
- Maheswari Patturaj
- Division of Plant Biotechnology and Cytogenetics, Institute of Forest Genetics and Tree Breeding, R.S. Puram, Coimbatore, 641002, India
| | - Aiswarya Munusamy
- Division of Plant Biotechnology and Cytogenetics, Institute of Forest Genetics and Tree Breeding, R.S. Puram, Coimbatore, 641002, India
| | - Nithishkumar Kannan
- Division of Plant Biotechnology and Cytogenetics, Institute of Forest Genetics and Tree Breeding, R.S. Puram, Coimbatore, 641002, India
| | - Yasodha Ramasamy
- Division of Plant Biotechnology and Cytogenetics, Institute of Forest Genetics and Tree Breeding, R.S. Puram, Coimbatore, 641002, India.
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11
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Dasgupta MG, Parveen AM, Rajasugunasekar D, Ulaganathan K. Wood transcriptome analysis and expression variation of lignin biosynthetic pathway transcripts in Ailanthus excelsa Roxb., a multi-purpose tropical tree species. J Biosci 2021. [DOI: 10.1007/s12038-021-00218-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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12
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Meng X, Wang Y, Li J, Jiao N, Zhang X, Zhang Y, Chen J, Tu Z. RNA Sequencing Reveals Phenylpropanoid Biosynthesis Genes and Transcription Factors for Hevea brasiliensis Reaction Wood Formation. Front Genet 2021; 12:763841. [PMID: 34777481 PMCID: PMC8585928 DOI: 10.3389/fgene.2021.763841] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 10/08/2021] [Indexed: 11/13/2022] Open
Abstract
Given the importance of wood in many industrial applications, much research has focused on wood formation, especially lignin biosynthesis. However, the mechanisms governing the regulation of lignin biosynthesis in the rubber tree (Hevea brasiliensis) remain to be elucidated. Here, we gained insight into the mechanisms of rubber tree lignin biosynthesis using reaction wood (wood with abnormal tissue structure induced by gravity or artificial mechanical treatment) as an experimental model. We performed transcriptome analysis of rubber tree mature xylem from tension wood (TW), opposite wood (OW), and normal wood (NW) using RNA sequencing (RNA-seq). A total of 214, 1,280, and 32 differentially expressed genes (DEGs) were identified in TW vs. NW, OW vs. NW, and TW vs. OW, respectively. GO and KEGG enrichment analysis of DEGs from different comparison groups showed that zeatin biosynthesis, plant hormone signal transduction, phenylpropanoid biosynthesis, and plant-pathogen interaction pathways may play important roles in reaction wood formation. Sixteen transcripts involved in phenylpropanoid biosynthesis and 129 transcripts encoding transcription factors (TFs) were used to construct a TF-gene regulatory network for rubber tree lignin biosynthesis. Among them, MYB, C2H2, and NAC TFs could regulate all the DEGs involved in phenylpropanoid biosynthesis. Overall, this study identified candidate genes and TFs likely involved in phenylpropanoid biosynthesis and provides novel insights into the mechanisms regulating rubber tree lignin biosynthesis.
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Affiliation(s)
- Xiangxu Meng
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, School of Forestry, Hainan University, Haikou, China.,Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, Institute of Tropical Agriculture and Forestry, School of Forestry, Hainan University, Haikou, China
| | - Yue Wang
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, School of Forestry, Hainan University, Haikou, China.,Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, Institute of Tropical Agriculture and Forestry, School of Forestry, Hainan University, Haikou, China
| | - Jia Li
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, School of Forestry, Hainan University, Haikou, China.,Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, Institute of Tropical Agriculture and Forestry, School of Forestry, Hainan University, Haikou, China
| | - Nanbo Jiao
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, School of Forestry, Hainan University, Haikou, China.,Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, Institute of Tropical Agriculture and Forestry, School of Forestry, Hainan University, Haikou, China
| | - Xiujie Zhang
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, School of Forestry, Hainan University, Haikou, China.,Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, Institute of Tropical Agriculture and Forestry, School of Forestry, Hainan University, Haikou, China
| | - Yuanyuan Zhang
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China.,State Centre for Rubber Breeding, Haikou, China
| | - Jinhui Chen
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, School of Forestry, Hainan University, Haikou, China.,Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, Institute of Tropical Agriculture and Forestry, School of Forestry, Hainan University, Haikou, China
| | - Zhihua Tu
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, School of Forestry, Hainan University, Haikou, China.,Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, Institute of Tropical Agriculture and Forestry, School of Forestry, Hainan University, Haikou, China
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13
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Xiao Y, Ling J, Yi F, Ma W, Lu N, Zhu T, Wang J, Zhao K, Yun H. Transcriptomic, Proteomic, and Metabolic Profiles of Catalpa bungei Tension Wood Reveal New Insight Into Lignin Biosynthesis Involving Transcription Factor Regulation. FRONTIERS IN PLANT SCIENCE 2021; 12:704262. [PMID: 34868103 PMCID: PMC8634757 DOI: 10.3389/fpls.2021.704262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Accepted: 10/12/2021] [Indexed: 06/13/2023]
Abstract
Lignin is a complex polymer in plant cell walls whose proportion is second only to that of cellulose and plays an important role in the mechanical properties of wood and stress resistance of plants. Here, we induced tension wood (TW) formation in Catalpa bungei by artificial bending and analyzed the lignin metabolism of the TW. LC-MS analysis showed that a significantly higher content of coniferyl aldehyde was observed in the TW cell wall than in the opposite wood (OW) and normal wood (NW) cell walls. TW had significantly lower contents of coniferyl alcohol than OW and NW. Raman spectroscopy results indicated that TW had lower total lignin than OW and NW. The transcription and translation levels of most of the differentially expressed genes (DEGs) involved in lignin monomer biosynthesis indicated upregulation in TW/OW and TW/NW. We found no significant difference in the transcription levels of three collision gases (CADs) between TW and OW or between NW, but their translation levels were significantly downregulated in TW, suggesting post-transcriptional control for CAD. We predicted and analyzed transcription factors that could target DEGs involved in lignin monomer biosynthesis in TW. Based on the analysis of the relationships of targeting and coexpression, we found that NAC (evm.model.group1.695) could potentially target 4CLs and CCoAOMT, that HD-Zip (evm.model.group7.1157) had potential targeting relationships with CCoAOMT, F5H, and CCR, and that their expression levels were significantly positive. It is speculated that the upregulation of NAC and HD-ZIP transcription factors activates the expression of downstream target genes, which leads to a significant increase in coniferyl aldehyde in TW. However, the decrease in total lignin in TW may be caused by the significant downregulation of CAD translation and the significant decrease in precursors (coniferyl alcohol). Whether the expression of CAD genes is regulated by post-transcriptional control and affects TW lignin metabolism needs further study.
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Affiliation(s)
- Yao Xiao
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, National Innovation Alliance of Catalpa bungei, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Juanjuan Ling
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, National Innovation Alliance of Catalpa bungei, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Fei Yi
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, National Innovation Alliance of Catalpa bungei, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Wenjun Ma
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, National Innovation Alliance of Catalpa bungei, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Nan Lu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, National Innovation Alliance of Catalpa bungei, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Tianqing Zhu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, National Innovation Alliance of Catalpa bungei, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Junhui Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, National Innovation Alliance of Catalpa bungei, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Kun Zhao
- Luoyang Academy of Agriculture and Forestry Sciences, Luoyang, China
| | - Huiling Yun
- Xiaolongshan Research Institute of Forest Science and Technology, Tianshui, China
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14
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Kerwin RE. Under pressure: transcriptional regulation of tension wood in Populus trichocarpa (California poplar). PLANT PHYSIOLOGY 2021; 186:212-214. [PMID: 33822214 PMCID: PMC8154089 DOI: 10.1093/plphys/kiab096] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 02/10/2021] [Indexed: 06/12/2023]
Affiliation(s)
- Rachel E Kerwin
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, United States
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15
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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: 7.3] [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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16
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Lopez D, Franchel J, Venisse JS, Drevet JR, Label P, Coutand C, Roeckel-Drevet P. Early transcriptional response to gravistimulation in poplar without phototropic confounding factors. AOB PLANTS 2021; 13:plaa071. [PMID: 33542802 PMCID: PMC7850117 DOI: 10.1093/aobpla/plaa071] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 12/30/2020] [Indexed: 05/30/2023]
Abstract
In response to gravistimulation under anisotropic light, tree stems showing an active cambium produce reaction wood that redirects the axis of the trees. Several studies have described transcriptomic or proteomic models of reaction wood relative to the opposite wood. However, the mechanisms leading to the formation of reaction wood are difficult to decipher because so many environmental factors can induce various signalling pathways leading to this developmental reprogramming. Using an innovative isotropic device where the phototropic response does not interfere with gravistimulation we characterized the early molecular responses occurring in the stem of poplar after gravistimulation in an isotropic environment, and without deformation of the stem. After 30 min tilting at 35° under anisotropic light, we collected the upper and lower xylems from the inclined stems. Controls were collected from vertical stems. We used a microarray approach to identify differentially expressed transcripts. High-throughput real-time PCR allowed a kinetic experiment at 0, 30, 120 and 180 min after tilting at 35°, with candidate genes. We identified 668 differentially expressed transcripts, from which we selected 153 candidates for additional Fluidigm qPCR assessment. Five candidate co-expression gene clusters have been identified after the kinetic monitoring of the expression of candidate genes. Gene ontology analyses indicate that molecular reprogramming of processes such as 'wood cell expansion', 'cell wall reorganization' and 'programmed cell death' occur as early as 30 min after gravistimulation. Of note is that the change in the expression of different genes involves a fine regulation of gibberellin and brassinosteroid pathways as well as flavonoid and phosphoinositide pathways. Our experimental set-up allowed the identification of genes regulated in early gravitropic response without the bias introduced by phototropic and stem bending responses.
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Affiliation(s)
- David Lopez
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Jérôme Franchel
- Université Clermont Auvergne, INRAE, PIAF, Campus Universitaire des Cézeaux, 1 Impasse Amélie Murat, TSA, Aubière Cedex, France
| | - Jean-Stéphane Venisse
- Université Clermont Auvergne, INRAE, PIAF, Campus Universitaire des Cézeaux, 1 Impasse Amélie Murat, TSA, Aubière Cedex, France
| | - Joël R Drevet
- Université Clermont Auvergne, GReD INSERM U1103-CNRS UMR 6293, Faculté de Médecine, CRBC (Centre de Recherche Bio-Clinique), Clermont-Ferrand, France
| | - Philippe Label
- Université Clermont Auvergne, INRAE, PIAF, Campus Universitaire des Cézeaux, 1 Impasse Amélie Murat, TSA, Aubière Cedex, France
| | - Catherine Coutand
- INRAE, UR 115 PSH, Centre de recherche PACA, 228, route de l’aérodrome, CS, Avignon Cedex, France
| | - Patricia Roeckel-Drevet
- Université Clermont Auvergne, INRAE, PIAF, Campus Universitaire des Cézeaux, 1 Impasse Amélie Murat, TSA, Aubière Cedex, France
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17
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Wu Q, Zang F, Xie X, Ma Y, Zheng Y, Zang D. Full-length transcriptome sequencing analysis and development of EST-SSR markers for the endangered species Populus wulianensis. Sci Rep 2020; 10:16249. [PMID: 33004908 PMCID: PMC7530656 DOI: 10.1038/s41598-020-73289-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 09/14/2020] [Indexed: 02/07/2023] Open
Abstract
Populus wulianensis is an endangered species endemic to Shandong Province, China. Despite the economic and ornamental value of this species, few genomics and genetic studies have been performed. In this study, we performed a relevant analysis of the full-length transcriptome sequencing data of P. wulianensis and obtained expressed sequence tag (EST)-simple sequence repeat (SSR) markers with polymorphisms that can be used for further genetic research. In total, 8.18 Gb (3,521,665) clean reads with an average GC content of 42.12% were obtained. From the corrected 64,737 high-quality isoforms, 42,323 transcript sequences were obtained after redundancy analysis with CD-HIT. Among these transcript sequences, 41,876 sequences were annotated successfully. A total of 23,539 potential EST-SSRs were identified from 16,057 sequences. Excluding mononucleotides, the most abundant motifs were trinucleotide SSRs (47.80%), followed by di- (46.80%), tetra- (2.98%), hexa- (1.58%) and pentanucleotide SSRs (0.84%). Among the 100 designed EST-SSRs, 18 were polymorphic with high PIC values (0.721 and 0.683) and could be used for analyses of the genetic diversity and population structure of P. wulianensis. These full-length transcriptome sequencing data will facilitate gene discovery and functional genomics research in P. wulianensis, and the novel EST-SSRs developed in our study will promote molecular-assisted breeding, genetic diversity and conservation biology research in this species.
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Affiliation(s)
- Qichao Wu
- College of Forestry, Key Laboratory of State Forestry Administration for Silviculture of the Lower Yellow River, Shandong Agricultural University, Tai'an, 271018, People's Republic of China
| | - Fengqi Zang
- Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, People's Republic of China
| | - Xiaoman Xie
- Center for Forest Genetic Resources of Shandong Province, Jinan, 250014, People's Republic of China
| | - Yan Ma
- College of Forestry, Key Laboratory of State Forestry Administration for Silviculture of the Lower Yellow River, Shandong Agricultural University, Tai'an, 271018, People's Republic of China.
| | - Yongqi Zheng
- Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, People's Republic of China
| | - Dekui Zang
- College of Forestry, Key Laboratory of State Forestry Administration for Silviculture of the Lower Yellow River, Shandong Agricultural University, Tai'an, 271018, People's Republic of China
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18
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Xiao Y, Yi F, Ling J, Yang G, Lu N, Jia Z, Wang J, Zhao K, Wang J, Ma W. Genome-wide analysis of lncRNA and mRNA expression and endogenous hormone regulation during tension wood formation in Catalpa bungei. BMC Genomics 2020; 21:609. [PMID: 32891118 PMCID: PMC7487903 DOI: 10.1186/s12864-020-07044-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 09/01/2020] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Phytohormones are the key factors regulating vascular development in plants, and they are also involved in tension wood (TW) formation. Although the theory of hormone distribution in TW formation is widely supported, the effects of endogenous hormones on TW formation have not yet been assessed. In this study, TW formation was induced in Catalpa bungei by artificial bending. The phytohormone content of TW, opposite wood (OW) and normal wood (NW) was determined using liquid chromatography-mass spectrometry (LC-MS), and transcriptome sequencing was performed. The hormone content and related gene expression data were comprehensively analyzed. RESULTS The results of analyses of the plant hormone contents indicated significantly higher levels of cis-zeatin (cZ), indoleacetic acid (IAA) and abscisic acid (ABA) in TW than in OW. Genes involved in the IAA and ABA synthesis pathways, such as ALDH (evm. MODEL group5.1511) and UGT (evm. MODEL scaffold36.20), were significantly upregulated in TW. and the expression levels of ARF (evm. MODEL group5.1332), A-ARR (evm. MODEL group0.1600), and TCH4 (evm. MODEL group2.745), which participate in IAA, cZ and Brassinolide (BR) signal transduction, were significantly increased in TW. In particular, ARF expression may be regulated by long noncoding RNAs (lncRNAs) and the HD-ZIP transcription factor ATHB-15. CONCLUSIONS We constructed a multiple hormone-mediated network of C. bungei TW formation based on hormone levels and transcriptional expression profiles were identified during TW formation.
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Affiliation(s)
- Yao Xiao
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, PR China
| | - Fei Yi
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, PR China
| | - Juanjuan Ling
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, PR China
| | - Guijuan Yang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, PR China
| | - Na Lu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, PR China
| | - Zirui Jia
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, PR China
| | - Junchen Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, PR China
| | - Kun Zhao
- Luoyang Academy of Agriculture and Forestry Science, Luoyang, 471002, Henan Province, China
| | - Junhui Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, PR China
| | - Wenjun Ma
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, PR China.
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Zhang L, Wan X, Xu Y, Niyitanga S, Qi J, Zhang L. De novo assembly of transcriptome and genome-wide identification reveal GA 3 stress-responsive WRKY transcription factors involved in fiber formation in jute (Corchorus capsularis). BMC PLANT BIOLOGY 2020; 20:403. [PMID: 32867682 PMCID: PMC7460746 DOI: 10.1186/s12870-020-02617-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 08/23/2020] [Indexed: 05/28/2023]
Abstract
BACKGROUND WRKY is a group of transcription factors (TFs) that play a vital role in plant growth, development, and stress tolerance. To date, none of jute WRKY (CcWRKY) genes have been identified, even if jute (Corchorus capsularis) is one of the most important natural fiber crops in the world. Little information about the WRKY genes in jute is far from sufficient to understand the molecular mechanism of bast fiber biosynthesis. RESULTS A total of 244,489,479 clean reads were generated using Illumina paired-end sequencing. De novo assembly yielded 90,982 unigenes with an average length of 714 bp. By sequence similarity searching for known proteins, 48,896 (53.74%) unigenes were annotated. To mine the CcWRKY TFs and identify their potential function, the search for CcWRKYs against the transcriptome data of jute was performed, and a total of 43 CcWRKYs were identified in this study. The gene structure, phylogeny, conserved domain and three-dimensional structure of protein were analyzed by bioinformatics tools of GSDS2.0, MEGA7.0, DNAMAN5.0, WebLogo 3 and SWISS-MODEL respectively. Phylogenetic analysis showed that 43 CcWRKYs were divided into three groups: I, II and III, containing 9, 28, and 6 members respectively, according to the WRKY conserved domain features and the evolution analysis with Arabidopsis thaliana. Gene structure analysis indicated that the number of exons of these CcWRKYs varied from 3 to 11. Among the 43 CcWRKYs, 10, 2, 2, and 14 genes showed higher expression in leaves, stem sticks, stem barks, and roots at the vigorous vegetative growth stage, respectively. Moreover, the expression of 21 of 43 CcWRKYs was regulated significantly with secondary cell wall biosynthesis genes using FPKM and RT-qPCR by GA3 stress to a typical GA3 sensitive dwarf germplasm in comparison to an elite cultivar in jute. The Cis-element analysis showed that promoters of these 21 CcWRKYs had 1 to 4 cis-elements involved in gibberellin-responsiveness, suggesting that they might regulate the development of bast fiber in response to GA3 stress. CONCLUSIONS A total of 43 CcWRKYs were identified in jute for the first time. Analysis of phylogenetic relationship and gene structure revealed that these CcWRKYs might have a functional diversity. Expression analysis showed 21 TFs as GA3 stress responsive genes. The identification of these CcWRKYs and the characterization of their expression pattern will provide a basis for future clarification of their functions in bast fiber development in jute.
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Affiliation(s)
- Lilan Zhang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops / Fujian Key Laboratory for Crop Breeding by Design / College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Experiment Station of Ministry of Agriculture and Rural Affairs for Jute and Kenaf in Southeast China / Fujian Public Platform for Germplasm Resources of Bast Fiber Crops / Fujian International Science and Technology Cooperation Base for Genetics, Breeding and Multiple Utilization Development of Southern Economic Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Xuebei Wan
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops / Fujian Key Laboratory for Crop Breeding by Design / College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Experiment Station of Ministry of Agriculture and Rural Affairs for Jute and Kenaf in Southeast China / Fujian Public Platform for Germplasm Resources of Bast Fiber Crops / Fujian International Science and Technology Cooperation Base for Genetics, Breeding and Multiple Utilization Development of Southern Economic Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
| | - Yi Xu
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops / Fujian Key Laboratory for Crop Breeding by Design / College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Experiment Station of Ministry of Agriculture and Rural Affairs for Jute and Kenaf in Southeast China / Fujian Public Platform for Germplasm Resources of Bast Fiber Crops / Fujian International Science and Technology Cooperation Base for Genetics, Breeding and Multiple Utilization Development of Southern Economic Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Sylvain Niyitanga
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops / Fujian Key Laboratory for Crop Breeding by Design / College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Jianmin Qi
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops / Fujian Key Laboratory for Crop Breeding by Design / College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Liwu Zhang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops / Fujian Key Laboratory for Crop Breeding by Design / College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Experiment Station of Ministry of Agriculture and Rural Affairs for Jute and Kenaf in Southeast China / Fujian Public Platform for Germplasm Resources of Bast Fiber Crops / Fujian International Science and Technology Cooperation Base for Genetics, Breeding and Multiple Utilization Development of Southern Economic Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
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Xu J, Fang M, Li Z, Zhang M, Liu X, Peng Y, Wan Y, Chen J. Third-Generation Sequencing Reveals LncRNA-Regulated HSP Genes in the Populus x canadensis Moench Heat Stress Response. Front Genet 2020; 11:249. [PMID: 32457788 PMCID: PMC7221187 DOI: 10.3389/fgene.2020.00249] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Accepted: 03/02/2020] [Indexed: 11/13/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) regulate plant responses to abiotic stresses. However, the short reads produced by second-generation sequencing technology make it difficult to accurately explore full-length transcripts, limiting the study of lncRNAs. In this study, we used third-generation long-read sequencing technology with the PacBio Sequel and Illumina platform to explore the role of lncRNAs in the heat stress response of Populus x canadensis Moench trees. We using 382,034,416 short reads to correct 4,297,179 long reads by resulted in 66,657 full-length transcripts, representing 33,840 genes. Then, 753 putative lncRNAs were identified, including 658 sense lncRNAs (87.38%), 41 long intervening/intergenic non-coding RNAs (lincRNAs) (5.44%), 12 antisense lncRNAs (1.59%), and 42 sense intronic lncRNAs (5.58%). Using the criteria | log2FC| ≥ 1 and q-value < 0.05, 3,493 genes and 78 lncRNAs were differentially expressed under the heat treatment. Furthermore, 923 genes were detected as targets of 43 differently expressed lncRNAs by cis regulation. Functional annotation demonstrated that these target genes were related to unfolded protein binding, response to stress, protein folding, and response to stimulus. Lastly, we identified a lncRNA–gene interaction network consisting of four lncRNAs and six genes [Heat Shock Protein 82 (HSP82), HSP83, Disease Resistance Protein 27 (DRL27), DnaJ family protein (DNJH), and two other predicted protein-coding genes], which showed that lncRNAs could regulate HSP family genes in response to heat stress in Populus. Therefore, our third-generation sequencing has improved the description of the P. canadensis transcriptome. The potential lncRNAs and HSP family genes identified here present a genetic resource to improve our understanding of the heat-adaptation mechanisms of trees.
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Affiliation(s)
- Jiahong Xu
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, College of Forestry, Hainan University, Haikou, China.,Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, College of Forestry, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China.,Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, China
| | - Meng Fang
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, College of Forestry, Hainan University, Haikou, China.,Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, College of Forestry, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China.,School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Zhihao Li
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, College of Forestry, Hainan University, Haikou, China.,Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, College of Forestry, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China.,Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, China
| | - Maoning Zhang
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, College of Forestry, Hainan University, Haikou, China.,Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, College of Forestry, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China.,Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, China
| | - Xiaoyu Liu
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, College of Forestry, Hainan University, Haikou, China.,Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, College of Forestry, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China.,Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, China
| | - Yuanyuan Peng
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, College of Forestry, Hainan University, Haikou, China.,Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, College of Forestry, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China.,Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, China
| | - Yinglang Wan
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, China
| | - Jinhui Chen
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, College of Forestry, Hainan University, Haikou, China.,Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, College of Forestry, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China.,Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, China
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21
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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: 1.8] [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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22
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Xiao Y, Yi F, Ling J, Wang Z, Zhao K, Lu N, Qu G, Kong L, Ma W, Wang J. Transcriptomics and Proteomics Reveal the Cellulose and Pectin Metabolic Processes in the Tension Wood (Non-G-Layer) of Catalpa bungei. Int J Mol Sci 2020; 21:E1686. [PMID: 32121503 PMCID: PMC7084593 DOI: 10.3390/ijms21051686] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 02/25/2020] [Accepted: 02/26/2020] [Indexed: 12/23/2022] Open
Abstract
: Catalpa bungei is an economically important tree with high-quality wood and highly valuable to the study of wood formation. In this work, the xylem microstructure of C. bungei tension wood (TW) was observed, and we performed transcriptomics, proteomics and Raman spectroscopy of TW, opposite wood (OW) and normal wood (NW). The results showed that there was no obvious gelatinous layer (G-layer) in the TW of C. bungei and that the secondary wall deposition in the TW was reduced compared with that in the OW and NW. We found that most of the differentially expressed mRNAs and proteins were involved in carbohydrate polysaccharide synthesis. Raman spectroscopy results indicated that the cellulose and pectin content and pectin methylation in the TW were lower than those in the OW and NW, and many genes and proteins involved in the metabolic pathways of cellulose and pectin, such as galacturonosyltransferase (GAUT), polygalacturonase (PG), endoglucanase (CLE) and β-glucosidase (BGLU) genes, were significantly upregulated in TW. In addition, we found that the MYB2 transcription factor may regulate the pectin degradation genes PG1 and PG3, and ARF, ERF, SBP and MYB1 may be the key transcription factors regulating the synthesis and decomposition of cellulose. In contrast to previous studies on TW with a G-layer, our results revealed a change in metabolism in TW without a G-layer, and we inferred that the change in the pectin type, esterification and cellulose characteristics in the TW of C. bungei may contribute to high tensile stress. These results will enrich the understanding of the mechanism of TW formation.
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Affiliation(s)
- Yao Xiao
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; (Y.X.); (F.Y.); (J.L.); (Z.W.); (N.L.); (W.M.)
| | - Fei Yi
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; (Y.X.); (F.Y.); (J.L.); (Z.W.); (N.L.); (W.M.)
| | - Juanjuan Ling
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; (Y.X.); (F.Y.); (J.L.); (Z.W.); (N.L.); (W.M.)
| | - Zhi Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; (Y.X.); (F.Y.); (J.L.); (Z.W.); (N.L.); (W.M.)
| | - Kun Zhao
- Luoyang Academy of Agriculture and Forestry Science, Luoyang 471002, China;
| | - Nan Lu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; (Y.X.); (F.Y.); (J.L.); (Z.W.); (N.L.); (W.M.)
| | - Guanzheng Qu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China;
| | - Lisheng Kong
- Department of Biology, Centre for Forest Biology, University of Victoria, 3800 Finnerty Road, Victoria, BC V8P5C2, Canada;
| | - Wenjun Ma
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; (Y.X.); (F.Y.); (J.L.); (Z.W.); (N.L.); (W.M.)
| | - Junhui Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; (Y.X.); (F.Y.); (J.L.); (Z.W.); (N.L.); (W.M.)
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23
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Tobias LM, Spokevicius AV, McFarlane HE, Bossinger G. The Cytoskeleton and Its Role in Determining Cellulose Microfibril Angle in Secondary Cell Walls of Woody Tree Species. PLANTS (BASEL, SWITZERLAND) 2020; 9:E90. [PMID: 31936868 PMCID: PMC7020502 DOI: 10.3390/plants9010090] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 01/06/2020] [Accepted: 01/10/2020] [Indexed: 12/28/2022]
Abstract
Recent advances in our understanding of the molecular control of secondary cell wall (SCW) formation have shed light on molecular mechanisms that underpin domestication traits related to wood formation. One such trait is the cellulose microfibril angle (MFA), an important wood quality determinant that varies along tree developmental phases and in response to gravitational stimulus. The cytoskeleton, mainly composed of microtubules and actin filaments, collectively contribute to plant growth and development by participating in several cellular processes, including cellulose deposition. Studies in Arabidopsis have significantly aided our understanding of the roles of microtubules in xylem cell development during which correct SCW deposition and patterning are essential to provide structural support and allow for water transport. In contrast, studies relating to SCW formation in xylary elements performed in woody trees remain elusive. In combination, the data reviewed here suggest that the cytoskeleton plays important roles in determining the exact sites of cellulose deposition, overall SCW patterning and more specifically, the alignment and orientation of cellulose microfibrils. By relating the reviewed evidence to the process of wood formation, we present a model of microtubule participation in determining MFA in woody trees forming reaction wood (RW).
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Affiliation(s)
- Larissa Machado Tobias
- School of Ecosystem and Forest Sciences, The University of Melbourne, Creswick, Victoria 3363, Australia; (A.V.S.); (G.B.)
| | - Antanas V. Spokevicius
- School of Ecosystem and Forest Sciences, The University of Melbourne, Creswick, Victoria 3363, Australia; (A.V.S.); (G.B.)
| | - Heather E. McFarlane
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON M5S 3B2, Canada
| | - Gerd Bossinger
- School of Ecosystem and Forest Sciences, The University of Melbourne, Creswick, Victoria 3363, Australia; (A.V.S.); (G.B.)
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24
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Seyfferth C, Wessels BA, Gorzsás A, Love JW, Rüggeberg M, Delhomme N, Vain T, Antos K, Tuominen H, Sundberg B, Felten J. Ethylene Signaling Is Required for Fully Functional Tension Wood in Hybrid Aspen. FRONTIERS IN PLANT SCIENCE 2019; 10:1101. [PMID: 31611886 PMCID: PMC6775489 DOI: 10.3389/fpls.2019.01101] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 08/12/2019] [Indexed: 06/01/2023]
Abstract
Tension wood (TW) in hybrid aspen trees forms on the upper side of displaced stems to generate a strain that leads to uplifting of the stem. TW is characterized by increased cambial growth, reduced vessel frequency and diameter, and the presence of gelatinous, cellulose-rich (G-)fibers with its microfibrils oriented parallel to the fiber cell axis. Knowledge remains limited about the molecular regulators required for the development of this special xylem tissue with its characteristic morphological, anatomical, and chemical features. In this study, we use transgenic, ethylene-insensitive (ETI) hybrid aspen trees together with time-lapse imaging to show that functional ethylene signaling is required for full uplifting of inclined stems. X-ray diffraction and Raman microspectroscopy of TW in ETI trees indicate that, although G-fibers form, the cellulose microfibril angle in the G-fiber S-layer is decreased, and the chemical composition of S- and G-layers is altered than in wild-type TW. The characteristic asymmetric growth and reduction of vessel density is suppressed during TW formation in ETI trees. A genome-wide transcriptome profiling reveals ethylene-dependent genes in TW, related to cell division, cell wall composition, vessel differentiation, microtubule orientation, and hormone crosstalk. Our results demonstrate that ethylene regulates transcriptional responses related to the amount of G-fiber formation and their properties (chemistry and cellulose microfibril angle) during TW formation. The quantitative and qualitative changes in G-fibers are likely to contribute to uplifting of stems that are displaced from their original position.
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Affiliation(s)
- Carolin Seyfferth
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
| | - Bernard A. Wessels
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
| | | | | | - Markus Rüggeberg
- Institute for Building Materials, Swiss Federal Institute of Technology Zurich (ETH Zurich), Zurich, Switzerland
- Laboratory of Wood Materials, Swiss Federal Laboratories of Materials Science and Technology, Dubendorf, Switzerland
| | - Nicolas Delhomme
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Thomas Vain
- DIADE, Univ Montpellier, IRD, Montpellier, France
| | - Kamil Antos
- Department of Integrative Medical Biology, Umeå University, Umeå, Sweden
| | - Hannele Tuominen
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
| | - Björn Sundberg
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
- Stora Enso AB, Nacka, Sweden
| | - Judith Felten
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
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25
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Lu N, Ma W, Han D, Liu Y, Wang Z, Wang N, Yang G, Qu G, Wang Q, Zhao K, Wang J. Genome-wide analysis of the Catalpa bungei caffeic acid O-methyltransferase (COMT) gene family: identification and expression profiles in normal, tension, and opposite wood. PeerJ 2019; 7:e6520. [PMID: 30886769 PMCID: PMC6421059 DOI: 10.7717/peerj.6520] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 01/22/2019] [Indexed: 01/12/2023] Open
Abstract
Caffeic acid O-methyltransferase (COMT) is an important protein that participates in lignin synthesis and is associated with the ratio of G-/S-type lignin in plants. COMTs are associated with the wood properties of forest trees; however, little known about the COMT family in Catalpa bungei, a valuable timber tree species in China . We performed a comprehensive analysis of COMT genes in the C. bungei genome by describing the gene structure and phylogenetic relationships of each family member using bioinformatics-based methods. A total of 23 putative COMT genes were identified using the conserved domain sequences and amino acid sequences of COMTs from Arabidopsis thaliana and Populus trichocarpa as probes. Phylogenetic analysis showed that 23 CbuCOMTs can be divided into three groups based on their structural characteristics; five conserved domains were found in the COMT family. Promoter analysis indicated that the CbuCOMT promoters included various cis-acting elements related to growth and development. Real-time quantitative polymerase chain reaction (PCR) analysis showed differential expression among CbuCOMTs. CbuCOMT2, 7, 8, 9, 10, 12, 13, 14, 21, and 23 were mainly expressed in xylem. Only CbuCOMT23 was significantly downregulated in tension wood and upregulated in opposite wood compared to normal wood. Our study provides new information about the CbuCOMT gene family and will facilitate functional characterisation in further research.
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Affiliation(s)
- Nan Lu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Wenjun Ma
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Donghua Han
- College of Landscape Architecture, Nanjing Forestry University, Nanjing, China
| | - Ying Liu
- College of Forestry, Northwest A&F University, Yangling, China
| | - Zhi Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Nan Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Guijuan Yang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Guanzheng Qu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Qiuxia Wang
- Nanyang Research Institute of Forestry, Nanyang, China
| | - Kun Zhao
- Luoyang Academy of Agriculture and Forestry, Luoyang, China
| | - Junhui Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
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Exogenous Application of Phytohormones Promotes Growth and Regulates Expression of Wood Formation-Related Genes in Populus simonii × P. nigra. Int J Mol Sci 2019; 20:ijms20030792. [PMID: 30759868 PMCID: PMC6387376 DOI: 10.3390/ijms20030792] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Revised: 02/06/2019] [Accepted: 02/11/2019] [Indexed: 02/06/2023] Open
Abstract
Although phytohormones are known to be important signal molecules involved in wood formation, their roles are still largely unclear. Here, Populus simonii × P. nigra seedlings were treated with different concentrations of exogenous phytohormones, indole-3-acetic acid (IAA), gibberellin (GA3), and brassinosteroid (BR), and the effects of phytohormones on growth were investigated. Next, 27 genes with known roles in wood formation were selected for qPCR analysis to determine tissue-specificity and timing of responses to phytohormone treatments. Compared to the control, most IAA, GA3, and BR concentrations significantly increased seedling height. Meanwhile, IAA induced significant seedling stem diameter and cellulose content increases that peaked at 3 and 30 mg·L−1, respectively. Significant increase in cellulose content was also observed in seedlings treated with 100 mg·L−1 GA3. Neither stem diameter nor cellulose content of seedlings were affected by BR treatment significantly, although slight effects were observed. Anatomical measurements demonstrated improved xylem, but not phloem, development in IAA- and BR-treated seedlings. Most gene expression patterns induced by IAA, GA3, and BR differed among tissues. Many IAA response genes were also regulated by GA3, while BR-induced transcription was weaker and slower in Populus than for IAA and GA3. These results reveal the roles played by phytohormones in plant growth and lay the foundation for exploring molecular regulatory mechanisms of wood formation in Populus.
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Chao Q, Gao Z, Zhang D, Zhao B, Dong F, Fu C, Liu L, Wang B. The developmental dynamics of the Populus stem transcriptome. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:206-219. [PMID: 29851301 PMCID: PMC6330540 DOI: 10.1111/pbi.12958] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 05/23/2018] [Accepted: 05/27/2018] [Indexed: 05/20/2023]
Abstract
The Populus shoot undergoes primary growth (longitudinal growth) followed by secondary growth (radial growth), which produces biomass that is an important source of energy worldwide. We adopted joint PacBio Iso-Seq and RNA-seq analysis to identify differentially expressed transcripts along a developmental gradient from the shoot apex to the fifth internode of Populus Nanlin895. We obtained 87 150 full-length transcripts, including 2081 new isoforms and 62 058 new alternatively spliced isoforms, most of which were produced by intron retention, that were used to update the Populus annotation. Among these novel isoforms, there are 1187 long non-coding RNAs and 356 fusion genes. Using this annotation, we found 15 838 differentially expressed transcripts along the shoot developmental gradient, of which 1216 were transcription factors (TFs). Only a few of these genes were reported previously. The differential expression of these TFs suggests that they may play important roles in primary and secondary growth. AP2, ARF, YABBY and GRF TFs are highly expressed in the apex, whereas NAC, bZIP, PLATZ and HSF TFs are likely to be important for secondary growth. Overall, our findings provide evidence that long-read sequencing can complement short-read sequencing for cataloguing and quantifying eukaryotic transcripts and increase our understanding of the vital and dynamic process of shoot development.
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Affiliation(s)
- Qing Chao
- Key Laboratory of PhotobiologyPhotosynthesis Research CenterInstitute of BotanyChinese Academy of SciencesBeijingChina
| | - Zhi‐Fang Gao
- Key Laboratory of PhotobiologyPhotosynthesis Research CenterInstitute of BotanyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Dong Zhang
- Biomarker Technologies CorporationBeijingChina
| | - Biligen‐Gaowa Zhao
- Key Laboratory of PhotobiologyPhotosynthesis Research CenterInstitute of BotanyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Feng‐Qin Dong
- The Key Laboratory of Plant Molecular PhysiologyInstitute of BotanyChinese Academy of SciencesBeijingChina
| | - Chun‐Xiang Fu
- Key Laboratory of BiofuelsQingdao Engineering Research Center of Biomass Resources and EnvironmentQingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdaoShandongChina
| | - Li‐Jun Liu
- College of ForestryShandong Agricultural UniversityTai‐AnShandongChina
| | - Bai‐Chen Wang
- Key Laboratory of PhotobiologyPhotosynthesis Research CenterInstitute of BotanyChinese Academy of SciencesBeijingChina
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Van de Wouwer D, Boerjan W, Vanholme B. Plant cell wall sugars: sweeteners for a bio-based economy. PHYSIOLOGIA PLANTARUM 2018; 164:27-44. [PMID: 29430656 DOI: 10.1111/ppl.12705] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 02/07/2018] [Accepted: 02/07/2018] [Indexed: 05/23/2023]
Abstract
Global warming and the consequent climate change is one of the major environmental challenges we are facing today. The driving force behind the rise in temperature is our fossil-based economy, which releases massive amounts of the greenhouse gas carbon dioxide into the atmosphere. In order to reduce greenhouse gas emission, we need to scale down our dependency on fossil resources, implying that we need other sources for energy and chemicals to feed our economy. Here, plants have an important role to play; by means of photosynthesis, plants capture solar energy to split water and fix carbon derived from atmospheric carbon dioxide. A significant fraction of the fixed carbon ends up as polysaccharides in the plant cell wall. Fermentable sugars derived from cell wall polysaccharides form an ideal carbon source for the production of bio-platform molecules. However, a major limiting factor in the use of plant biomass as feedstock for the bio-based economy is the complexity of the plant cell wall and its recalcitrance towards deconstruction. To facilitate the release of fermentable sugars during downstream biomass processing, the composition and structure of the cell wall can be engineered. Different strategies to reduce cell wall recalcitrance will be described in this review. The ultimate goal is to obtain a tailor-made biomass, derived from plants with a cell wall optimized for particular industrial or agricultural applications, without affecting plant growth and development.
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Affiliation(s)
- Dorien Van de Wouwer
- Ghent University, Department of Plant Biotechnology and Bioinformatics, (Technologiepark 927), 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, (Technologiepark 927), 9052, Ghent, Belgium
| | - Wout Boerjan
- Ghent University, Department of Plant Biotechnology and Bioinformatics, (Technologiepark 927), 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, (Technologiepark 927), 9052, Ghent, Belgium
| | - Bartel Vanholme
- Ghent University, Department of Plant Biotechnology and Bioinformatics, (Technologiepark 927), 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, (Technologiepark 927), 9052, Ghent, Belgium
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Cai M, Huang H, Ni F, Tong Z, Lin E, Zhu M. RNA-Seq analysis of differential gene expression in Betula luminifera xylem during the early stages of tension wood formation. PeerJ 2018; 6:e5427. [PMID: 30155351 PMCID: PMC6108316 DOI: 10.7717/peerj.5427] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 07/20/2018] [Indexed: 01/09/2023] Open
Abstract
Background Betula luminifera H. Winkler, which is widely distributed in southern China, is an economically important broadleaf tree species. However, little genomic information of B. luminifera is available, and little is known about the molecular mechanisms of wood formation in this species. Meanwhile, few efforts have focused on investigating the early transcriptional changes during tension wood formation in woody plants. Results A reference transcriptome dataset was first generated containing 45,700 Unigenes, and 35,135 (76.9%) Unigenes were annotated by a BLAST similarity search against four public databases. Then, based on an anatomical investigation, the global gene expression changes during the early stages of tension wood formation were analyzed. Gene expression profiling showed that a total of 13,273 Unigenes were differentially regulated during the early stages of tension wood formation. Most genes involved in cellulose and lignin biosynthesis were highlighted to reveal their biological importance in tension wood formation. In addition, the transcription levels of many genes involved in the auxin response pathway were significantly changed during the early stages of tension wood formation. Furthermore, 18 TFs co-expressed with key enzymes of cellulose synthesis were identified. Conclusions Our results revealed the transcriptional changes associated with TW formation and identified potential key genes in the regulation of this process. These results will help to dissect the molecular mechanism of wood formation and provide key candidate genes for marker-assisted selection in B. luminifera.
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Affiliation(s)
- Miaomiao Cai
- The State Key Laboratory of Subtropical Silviculture, Institute of Biotechnology, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
| | - Huahong Huang
- The State Key Laboratory of Subtropical Silviculture, Institute of Biotechnology, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
| | - Fei Ni
- The State Key Laboratory of Subtropical Silviculture, Institute of Biotechnology, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
| | - Zaikang Tong
- The State Key Laboratory of Subtropical Silviculture, Institute of Biotechnology, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
| | - Erpei Lin
- The State Key Laboratory of Subtropical Silviculture, Institute of Biotechnology, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
| | - Muyuan Zhu
- Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Institute of Genetics, College of Life Sciences, Zhejiang University, Hangzhou, 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: 1.8] [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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Wang J, Tian Y, Li J, Yang K, Xing S, Han X, Xu D, Wang Y. Transcriptome sequencing of active buds from Populus deltoides CL. and Populus × zhaiguanheibaiyang reveals phytohormones involved in branching. Genomics 2018; 111:700-709. [PMID: 29660475 DOI: 10.1016/j.ygeno.2018.04.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 02/22/2018] [Accepted: 04/10/2018] [Indexed: 10/17/2022]
Abstract
Branching in woody plants affects their ecological benefits and impacts wood formation. To obtain genome-wide insights into the transcriptome changes and regulatory mechanisms associated with branching, we performed high-throughput RNA sequencing to characterize cDNA libraries generated from active buds of Populus deltoides CL. 'zhonglin2025' (BC) and Populus × zhaiguanheibaiyang (NC). NC has more branches than BC and rapid growth. We obtained a total of 198.2 million high-quality clean reads from the NC and BC libraries. We detected 3543 differentially expressed genes (DEGs) between the NC and BC libraries; 1418 were down-regulated and 2125 were up-regulated. Gene ontology functional classification of the DEGs indicated that they included 89 genes that encoded proteins related to hormone biosynthesis, 364 genes related to hormone signaling transduction, and 104 related to the auxin efflux transmembrane transporter. We validated the expression profiles of 16° by real-time quantitative PCR and found that their expression patterns were similar to those obtained from the high-throughput RNA sequencing data. We also measured the hormone content in young buds of BC and NC by high-pressure liquid chromatography. In this study, we identified global hormone regulatory patterns and differences in gene expression between NC and BC, and constructed a hormone regulatory network to explain branching in Populus buds. In addition, candidate genes that may be useful for molecular breeding of particular plant types were identified. Our results will provide a starting point for future investigations into the molecular mechanisms of branching in Populus.
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Affiliation(s)
- Jinnan Wang
- Key Laboratory of Agricultural Ecology and Environment, College of Forestry, Shandong Agricultural University, Tai'an, Shandong 271018, PR China; Silviculture Key Lab of Shandong Province Forestry, College of Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Yanting Tian
- Key Laboratory of Agricultural Ecology and Environment, College of Forestry, Shandong Agricultural University, Tai'an, Shandong 271018, PR China; Silviculture Key Lab of Shandong Province Forestry, College of Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Jihong Li
- Key Laboratory of Agricultural Ecology and Environment, College of Forestry, Shandong Agricultural University, Tai'an, Shandong 271018, PR China; Silviculture Key Lab of Shandong Province Forestry, College of Shandong Agricultural University, Tai'an, Shandong 271018, PR China.
| | - Keqiang Yang
- Key Laboratory of Agricultural Ecology and Environment, College of Forestry, Shandong Agricultural University, Tai'an, Shandong 271018, PR China; Silviculture Key Lab of Shandong Province Forestry, College of Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Shiyan Xing
- Key Laboratory of Agricultural Ecology and Environment, College of Forestry, Shandong Agricultural University, Tai'an, Shandong 271018, PR China; Silviculture Key Lab of Shandong Province Forestry, College of Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Xiaojiao Han
- Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, PR China.
| | - Dong Xu
- Key Laboratory of Agricultural Ecology and Environment, College of Forestry, Shandong Agricultural University, Tai'an, Shandong 271018, PR China; Silviculture Key Lab of Shandong Province Forestry, College of Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Yiwei Wang
- Key Laboratory of Agricultural Ecology and Environment, College of Forestry, Shandong Agricultural University, Tai'an, Shandong 271018, PR China; Silviculture Key Lab of Shandong Province Forestry, College of Shandong Agricultural University, Tai'an, Shandong 271018, PR China
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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: 1.1] [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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Gong C, Du Q, Xie J, Quan M, Chen B, Zhang D. Dissection of Insertion-Deletion Variants within Differentially Expressed Genes Involved in Wood Formation in Populus. FRONTIERS IN PLANT SCIENCE 2017; 8:2199. [PMID: 29403506 PMCID: PMC5778123 DOI: 10.3389/fpls.2017.02199] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 12/14/2017] [Indexed: 05/02/2023]
Abstract
Short insertions and deletions (InDels) are one of the major genetic variants and are distributed widely across the genome; however, few investigations of InDels have been conducted in long-lived perennial plants. Here, we employed a combination of RNA-seq and population resequencing to identify InDels within differentially expressed (DE) genes underlying wood formation in a natural population of Populus tomentosa (435 individuals) and utilized InDel-based association mapping to detect the causal variants under additive, dominance, and epistasis underlying growth and wood properties. In the present paper, 5,482 InDels detected from 629 DE genes showed uneven distributions throughout all 19 chromosomes, and 95.9% of these loci were diallelic InDels. Seventy-four InDels (positive false discovery rate q ≤ 0.10) from 68 genes exhibited significant additive/dominant effects on 10 growth and wood-properties, with an average of 14.7% phenotypic variance explained. Potential pleiotropy was observed in one-third of the InDels (representing 24 genes). Seven genes exhibited significantly differential expression among the genotypic classes of associated InDels, indicating possible important roles for these InDels. Epistasis analysis showed that overlapping interacting genes formed unique interconnected networks for each trait, supporting the putative biochemical links that control quantitative traits. Therefore, the identification and utilization of InDels in trees will be recognized as an effective marker system for molecular marker-assisted breeding applications, and further facilitate our understanding of quantitative genomics.
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Affiliation(s)
- Chenrui Gong
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 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, Beijing, China
- College of Forestry, Henan Agricultural University, Zhengzhou, China
| | - Qingzhang Du
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 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, Beijing, China
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
| | - Jianbo Xie
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 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, Beijing, China
| | - Mingyang Quan
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 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, Beijing, China
| | - Beibei Chen
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 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, Beijing, China
| | - Deqiang Zhang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 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, Beijing, China
- *Correspondence: Deqiang Zhang,
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34
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Badenes ML, Fernández I Martí A, Ríos G, Rubio-Cabetas MJ. Application of Genomic Technologies to the Breeding of Trees. Front Genet 2016; 7:198. [PMID: 27895664 PMCID: PMC5109026 DOI: 10.3389/fgene.2016.00198] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 10/31/2016] [Indexed: 12/22/2022] Open
Abstract
The recent introduction of next generation sequencing (NGS) technologies represents a major revolution in providing new tools for identifying the genes and/or genomic intervals controlling important traits for selection in breeding programs. In perennial fruit trees with long generation times and large sizes of adult plants, the impact of these techniques is even more important. High-throughput DNA sequencing technologies have provided complete annotated sequences in many important tree species. Most of the high-throughput genotyping platforms described are being used for studies of genetic diversity and population structure. Dissection of complex traits became possible through the availability of genome sequences along with phenotypic variation data, which allow to elucidate the causative genetic differences that give rise to observed phenotypic variation. Association mapping facilitates the association between genetic markers and phenotype in unstructured and complex populations, identifying molecular markers for assisted selection and breeding. Also, genomic data provide in silico identification and characterization of genes and gene families related to important traits, enabling new tools for molecular marker assisted selection in tree breeding. Deep sequencing of transcriptomes is also a powerful tool for the analysis of precise expression levels of each gene in a sample. It consists in quantifying short cDNA reads, obtained by NGS technologies, in order to compare the entire transcriptomes between genotypes and environmental conditions. The miRNAs are non-coding short RNAs involved in the regulation of different physiological processes, which can be identified by high-throughput sequencing of RNA libraries obtained by reverse transcription of purified short RNAs, and by in silico comparison with known miRNAs from other species. All together, NGS techniques and their applications have increased the resources for plant breeding in tree species, closing the former gap of genetic tools between trees and annual species.
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Affiliation(s)
- Maria L Badenes
- Instituto Valenciano de Investigaciones Agrarias Valencia, Spain
| | - Angel Fernández I Martí
- Hortofruticulture Department, Agrifood Research and Technology Centre of AragonZaragoza, Spain; Genome Center, University of California, Davis, Davis, CAUSA
| | - Gabino Ríos
- Instituto Valenciano de Investigaciones Agrarias Valencia, Spain
| | - María J Rubio-Cabetas
- Hortofruticulture Department, Agrifood Research and Technology Centre of Aragon Zaragoza, Spain
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Chen J, Xie J, Chen B, Quan M, Li Y, Li B, Zhang D. Genetic variations and miRNA-target interactions contribute to natural phenotypic variations in Populus. THE NEW PHYTOLOGIST 2016; 212:150-60. [PMID: 27265357 DOI: 10.1111/nph.14040] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 04/28/2016] [Indexed: 05/22/2023]
Abstract
Variation in regulatory factors, including microRNAs (miRNAs), contributes to variation in quantitative and complex traits. However, in plants, variants in miRNAs and their target genes that contribute to natural phenotypic variation, and the underlying regulatory networks, remain poorly characterized. We investigated the associations and interactions of single-nucleotide polymorphisms (SNPs) in miRNAs and their target genes with phenotypes in 435 individuals from a natural population of Populus. We used RNA-seq to identify 217 miRNAs differentially expressed in a tension wood system, and identified 1196 candidate target genes; degradome sequencing confirmed 60 of the target sites. In addition, 72 miRNA-target pairs showed significant co-expression. Gene ontology (GO) term analysis showed that most of the genes in the co-regulated pairs participate in biological regulation. Genome resequencing found 5383 common SNPs (frequency ≥ 0.05) in 139 miRNAs and 31 037 SNPs in 819 target genes. Single-SNP association analyses identified 232 significant associations between wood traits (P ≤ 0.05) and SNPs in 102 miRNAs and 1387 associations with 478 target genes. Among these, 102 miRNA-target pairs associated with the same traits. Multi-SNP associations found 102 epistatic pairs associated with traits. Furthermore, a reconstructed regulatory network contained 12 significantly co-expressed pairs, including eight miRNAs and nine targets associated with traits. Lastly, both expression and genetic association showed that miR156i, miR156j, miR396a and miR6445b were involved in the formation of tension wood. This study shows that variants in miRNAs and target genes contribute to natural phenotypic variation and annotated roles and interactions of miRNAs and their target genes by genetic association analysis.
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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, 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, China
| | - Jianbo Xie
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, 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, 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, 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, China
| | - Mingyang Quan
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, 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, China
| | - Ying Li
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, 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, China
| | - Bailian Li
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, 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, China
- Department of Forestry, North Carolina State University, Raleigh, NC, 27695-8203, USA
| | - Deqiang Zhang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, 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, China
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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: 1.6] [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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Zhao H, Dong L, Sun H, Li L, Lou Y, Wang L, Li Z, Gao Z. Comprehensive analysis of multi-tissue transcriptome data and the genome-wide investigation of GRAS family in Phyllostachys edulis. Sci Rep 2016; 6:27640. [PMID: 27325361 PMCID: PMC4914925 DOI: 10.1038/srep27640] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 05/19/2016] [Indexed: 11/28/2022] Open
Abstract
GRAS family is one of plant specific transcription factors and plays diverse roles in the regulation of plant growth and development as well as in the plant disease resistance and abiotic stress responses. However, the investigation of GRAS family and multi-tissue gene expression profiles still remains unavailable in bamboo (Phyllostachys edulis). Here, we applied RNA-Seq analysis to monitor global transcriptional changes and investigate expression patterns in the five tissues of Ph. edulis, and analyzed a large-scale transcriptional events and patterns. Moreover, the tissue-specific genes and DEGs in different tissues were detected. For example, DEGs in panicle and leaf tissues were abundant in photosynthesis, glutathione, porphyrin and chlorophyll metabolism, whereas those in shoot and rhizome were majority in glycerophospholipid metabolism. In the portion of Ph. edulis GRAS (PeGRAS) analyses, we performed the analysis of phylogenetic, gene structure, conserved motifs, and analyzed the expression profiles of PeGRASs in response to high light and made a co-expression analysis. Additionally, the expression profiles of PeGRASs were validated using quantitative real-time PCR. Thus, PeGRASs based on dynamics profiles of gene expression is helpful in uncovering the specific biological functions which might be of critical values for bioengineering to improve bamboo breeding in future.
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Affiliation(s)
- Hansheng Zhao
- State Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Lili Dong
- State Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Huayu Sun
- State Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Lichao Li
- State Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Yongfeng Lou
- State Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Lili Wang
- State Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Zuyao Li
- Jiangxi Agricultural University, Nanchang 330045, China
| | - Zhimin Gao
- State Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, International Center for Bamboo and Rattan, Beijing 100102, China
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Zhang L, Ming R, Zhang J, Tao A, Fang P, Qi J. De novo transcriptome sequence and identification of major bast-related genes involved in cellulose biosynthesis in jute (Corchorus capsularis L.). BMC Genomics 2015; 16:1062. [PMID: 26666317 PMCID: PMC4678609 DOI: 10.1186/s12864-015-2256-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 11/30/2015] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Jute fiber, extracted from stem bast, is called golden fiber. It is essential for fiber improvement to discover the genes associated with jute development at the vegetative growth stage. However, only 858 EST sequences of jute were deposited in the GenBank database. Obviously, the public available data is far from sufficient to understand the molecular mechanism of the fiber biosynthesis. It is imperative to conduct transcriptomic sequence for jute, which can be used for the discovery of a number of new genes, especially genes involved in cellulose biosynthesis. RESULTS A total of 79,754,600 clean reads (7.98 Gb) were generated using Illumina paired-end sequencing. De novo assembly yielded 48,914 unigenes with an average length of 903 bp. By sequence similarity searching for known proteins, 27,962 (57.16 %) unigenes were annotated for their function. Out of these annotated unigenes, 21,856 and 11,190 unigenes were assigned to gene ontology (GO) and euKaryotic Ortholog Groups (KOG), respectively. Searching against the Kyoto Encyclopedia of Genes and Genomes Pathway database (KEGG) indicated that 14,216 unigenes were mapped to 268 KEGG pathways. Moreover, 5 Susy, 3 UGPase, 9 CesA, 18 CSL, 2 Kor (Korrigan), and 12 Cobra unigenes involving in cellulose biosynthesis were identified. Among these unigenes, the unigenes of comp11264_c0 (SuSy), comp24568_c0 (UGPase), comp11363_c0 (CesA), comp11363_c1 (CesA), comp24217_c0 (CesA), and comp23531_c0 (CesA), displayed relatively high expression level in stem bast using FPKM and RT-qPCR, indicating that they may have potential value of dissecting mechanism on cellulose biosynthesis in jute. In addition, a total of 12,518 putative gene-associate SNPs were called from these assembled uingenes. CONCLUSION We characterized the transcriptome of jute, discovered a broad survey of unigenes associated with vegetative growth and development, developed large-scale SNPs, and analyzed the expression patterns of genes involved in cellulose biosynthesis for bast fiber. All these provides a valuable genomics resource, which will accelerate the understanding of the mechanism of fiber development in jute.
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Affiliation(s)
- Liwu Zhang
- Key Laboratory for Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education / College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- Department of Plant Biology, University of Illlinois at Urbana-Champaign, Urbana, IL, 61801, USA.
| | - Ray Ming
- Department of Plant Biology, University of Illlinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Jisen Zhang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Aifen Tao
- Key Laboratory for Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education / College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Pingping Fang
- Key Laboratory for Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education / College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Jianmin Qi
- Key Laboratory for Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education / College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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