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Du J, Wei H, Song X, Zhang L, Hu J. PdRabG3f interfered with gibberellin-mediated internode elongation and xylem developing in poplar. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 343:112074. [PMID: 38548138 DOI: 10.1016/j.plantsci.2024.112074] [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: 01/17/2024] [Revised: 03/07/2024] [Accepted: 03/23/2024] [Indexed: 04/01/2024]
Abstract
As a member of the small GTPases family, Rab GTPases play a key role in specifying transport pathways in the intracellular membrane trafficking system and are involved in plant growth and development. By quantitative trait locus (QTL) mapping, PdRabG3f was identified as a candidate gene associated with shoot height in a hybrid offspring of Populus deltoides 'Danhong' × Populus simonii 'Tongliao1'. PdRabG3f localized to the nucleus, endoplasmic reticulum and tonoplast and was primarily expressed in the xylem and cambium. Overexpression of PdRabG3f in Populus alba × Populus glandulosa (84 K poplar) had inhibitory effects on vertical and radical growth. In the transgenic lines, there were evident changes in the levels of 15 gibberellin (GA) derivatives, and the application of exogenous GA3 partially restored the phenotypes mediated by GAs deficiency. The interaction between PdRabG3f and RIC4, which was the GA-responsive factor, provided additional explanation for PdRabG3f's inhibitory effect on poplar growth. RNA-seq analysis revealed differentially expressed genes (DEGs) associated with cell wall, xylem, and gibberellin response. PdRabG3f interfering endogenous GAs levels in poplar might involve the participation of MYBs and ultimately affected internode elongation and xylem development. This study provides a potential mechanism for gibberellin-mediated regulation of plant growth through Rab GTPases.
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Affiliation(s)
- Jiujun Du
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Hantian Wei
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Xueqin Song
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Lei Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu 210037, China.
| | - Jianjun Hu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu 210037, China.
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Zhang Q, Chu X, Gao Z, Ding Y, Que F, Ahmad Z, Yu F, Ramakrishnan M, Wei Q. Culm Morphological Analysis in Moso Bamboo Reveals the Negative Regulation of Internode Diameter and Thickness by Monthly Precipitation. PLANTS (BASEL, SWITZERLAND) 2024; 13:1484. [PMID: 38891293 PMCID: PMC11175016 DOI: 10.3390/plants13111484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 05/22/2024] [Accepted: 05/24/2024] [Indexed: 06/21/2024]
Abstract
The neglect of Moso bamboo's phenotype variations hinders its broader utilization, despite its high economic value globally. Thus, this study investigated the morphological variations of 16 Moso bamboo populations. The analysis revealed the culm heights ranging from 9.67 m to 17.5 m, with average heights under the first branch ranging from 4.91 m to 7.67 m. The total internode numbers under the first branch varied from 17 to 36, with internode lengths spanning 2.9 cm to 46.4 cm, diameters ranging from 5.10 cm to 17.2 cm, and wall thicknesses from 3.20 mm to 33.3 mm, indicating distinct attributes among the populations. Furthermore, strong positive correlations were observed between the internode diameter, thickness, length, and volume. The coefficient of variation of height under the first branch showed strong positive correlations with several parameters, indicating variability in their contribution to the total culm height. A regression analysis revealed patterns of covariation among the culm parameters, highlighting their influence on the culm height and structural characteristics. Both the diameter and thickness significantly contribute to the internode volume and culm height, and the culm parameters tend to either increase or decrease together, influencing the culm height. Moreover, this study also identified a significant negative correlation between monthly precipitation and the internode diameter and thickness, especially during December and January, impacting the primary thickening growth and, consequently, the internode size.
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Affiliation(s)
- Qianwen Zhang
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, School of Life Sciences, Nanjing Forestry University, Nanjing 210037, China; (Q.Z.); (Y.D.)
| | - Xue Chu
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, School of Life Sciences, Nanjing Forestry University, Nanjing 210037, China; (Q.Z.); (Y.D.)
| | - Zhipeng Gao
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, School of Life Sciences, Nanjing Forestry University, Nanjing 210037, China; (Q.Z.); (Y.D.)
| | - Yulong Ding
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, School of Life Sciences, Nanjing Forestry University, Nanjing 210037, China; (Q.Z.); (Y.D.)
| | - Feng Que
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, School of Life Sciences, Nanjing Forestry University, Nanjing 210037, China; (Q.Z.); (Y.D.)
| | - Zishan Ahmad
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, School of Life Sciences, Nanjing Forestry University, Nanjing 210037, China; (Q.Z.); (Y.D.)
| | - Fen Yu
- Jiangxi Provincial Key Laboratory for Bamboo Germplasm Resources and Utilization, Jiangxi Agriculture University, Nanchang 330045, China;
| | - Muthusamy Ramakrishnan
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, School of Life Sciences, Nanjing Forestry University, Nanjing 210037, China; (Q.Z.); (Y.D.)
| | - Qiang Wei
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, School of Life Sciences, Nanjing Forestry University, Nanjing 210037, China; (Q.Z.); (Y.D.)
- Jiangxi Provincial Key Laboratory for Bamboo Germplasm Resources and Utilization, Jiangxi Agriculture University, Nanchang 330045, China;
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Jiao Y, Tan J, Guo H, Huang B, Ying Y, Ramakrishnan M, Zhang Z. Genome-wide analysis of the KNOX gene family in Moso bamboo: insights into their role in promoting the rapid shoot growth. BMC PLANT BIOLOGY 2024; 24:213. [PMID: 38528453 DOI: 10.1186/s12870-024-04883-2] [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: 10/17/2023] [Accepted: 03/04/2024] [Indexed: 03/27/2024]
Abstract
BACKGROUND KNOTTED1-like homeobox (KNOX) genes, plant-specific homologous box transcription factors (TFs), play a central role in regulating plant growth, development, organ formation, and response to biotic and abiotic stresses. However, a comprehensive genome-wide identification of the KNOX genes in Moso bamboo (Phyllostachys edulis), the fastest growing plant, has not yet been conducted, and the specific biological functions of this family remain unknown. RESULTS The expression profiles of 24 KNOX genes, divided into two subfamilies, were determined by integrating Moso bamboo genome and its transcriptional data. The KNOX gene promoters were found to contain several light and stress-related cis-acting elements. Synteny analysis revealed stronger similarity with rice KNOX genes than with Arabidopsis KNOX genes. Additionally, several conserved structural domains and motifs were identified in the KNOX proteins. The expansion of the KNOX gene family was primarily regulated by tandem duplications. Furthermore, the KNOX genes were responsive to naphthaleneacetic acid (NAA) and gibberellin (GA) hormones, exhibiting distinct temporal expression patterns in four different organs of Moso bamboo. Short Time-series Expression Miner (STEM) analysis and quantitative real-time PCR (qRT-PCR) assays demonstrated that PeKNOX genes may play a role in promoting rapid shoot growth. Additionally, Gene Ontology (GO) and Protein-Protein Interaction (PPI) network enrichment analyses revealed several functional annotations for PeKNOXs. By regulating downstream target genes, PeKNOXs are involved in the synthesis of AUX /IAA, ultimately affecting cell division and elongation. CONCLUSIONS In the present study, we identified and characterized a total of 24 KNOX genes in Moso bamboo and investigated their physiological properties and conserved structural domains. To understand their functional roles, we conducted an analysis of gene expression profiles using STEM and RNA-seq data. This analysis successfully revealed regulatory networks of the KNOX genes, involving both upstream and downstream genes. Furthermore, the KNOX genes are involved in the AUX/IAA metabolic pathway, which accelerates shoot growth by influencing downstream target genes. These results provide a theoretical foundation for studying the molecular mechanisms underlying the rapid growth and establish the groundwork for future research into the functions and transcriptional regulatory networks of the KNOX gene family.
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Affiliation(s)
- Yang Jiao
- Bamboo Industry Institute, Zhejiang A&F University, Lin'an, Hangzhou, 311300, Zhejiang, China
| | - Jiaqi Tan
- Bamboo Industry Institute, Zhejiang A&F University, Lin'an, Hangzhou, 311300, Zhejiang, China
| | - Hui Guo
- Bamboo Industry Institute, Zhejiang A&F University, Lin'an, Hangzhou, 311300, Zhejiang, China
| | - Bin Huang
- Bamboo Industry Institute, Zhejiang A&F University, Lin'an, Hangzhou, 311300, Zhejiang, China
| | - Yeqing Ying
- Bamboo Industry Institute, Zhejiang A&F University, Lin'an, Hangzhou, 311300, Zhejiang, China
| | - Muthusamy Ramakrishnan
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, School of Life Sciences, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Zhijun Zhang
- Bamboo Industry Institute, Zhejiang A&F University, Lin'an, Hangzhou, 311300, Zhejiang, China.
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Guo L, Chen T, Chu X, Sun K, Yu F, Que F, Ahmad Z, Wei Q, Ramakrishnan M. Anatomical and Transcriptome Analyses of Moso Bamboo Culm Neck Growth: Unveiling Key Insights. PLANTS (BASEL, SWITZERLAND) 2023; 12:3478. [PMID: 37836218 PMCID: PMC10574802 DOI: 10.3390/plants12193478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 09/24/2023] [Accepted: 09/26/2023] [Indexed: 10/15/2023]
Abstract
The Moso bamboo culm neck, connected with the rhizome and the shoot bud, is an important hub for connecting and transporting the aboveground and belowground systems of bamboo for the shoot bud development and rapid growth. Our previous study revealed that the culm neck generally undergoes six different developmental stages (CNS1-CNS6), according to the primary thickening growth of the underground shoot bud. However, the molecular mechanism of the culm neck development remains unknown. The present study focused on the developmental process of the CNS3-CNS5 stages, representing the early, middle, and late elongation stages, respectively. These stages are densely packed with vascular tissues and consist of epidermis, hypodermis, cortex, and ground tissue. Unlike the hollow structure of the culms, the culm necks are solid structures. As the culm neck continues to grow, the lignin deposition increases noticeably, contributing to its progressive strengthening. For the transcriptome analysis, a total of 161,160 transcripts with an average length of 2373 were obtained from these stages using both PacBio and Illumina sequencing. A total of 92.2% of the reads mapped to the Moso bamboo reference genome. Further analysis identified a total of 5524 novel genes and revealed a dynamic transcriptome. Secondary-metabolism- and transport-related genes were upregulated particularly with the growth of the culm neck. Further analysis revealed the molecular processes of lignin accumulation in the culm neck, which include differentially expressed genes (DEGs) related to cell wall loosening and remodeling and secondary metabolism. Moreover, the upregulations of transcription factors such as MYBH and RSM in the MYB family play crucial roles during critical transitions in the culm neck development, such as changes in the angle between the rhizome and the culm neck. Our new findings provide essential insights into the cellular roadmaps, transcriptional networks, and key genes involved in the culm neck development.
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Affiliation(s)
- Lin Guo
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, School of Life Sciences, Nanjing Forestry University, Nanjing 210037, China
| | - Tianguo Chen
- Changzhou Agricultural Technology Extension Center, Changzhou 213000, China
| | - Xue Chu
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, School of Life Sciences, Nanjing Forestry University, Nanjing 210037, China
| | - Kai Sun
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, School of Life Sciences, Nanjing Forestry University, Nanjing 210037, China
| | - Fen Yu
- Changzhou Agricultural Technology Extension Center, Changzhou 213000, China
| | - Feng Que
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, School of Life Sciences, Nanjing Forestry University, Nanjing 210037, China
| | - Zishan Ahmad
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, School of Life Sciences, Nanjing Forestry University, Nanjing 210037, China
| | - Qiang Wei
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, School of Life Sciences, Nanjing Forestry University, Nanjing 210037, China
- Jiangxi Provincial Key Laboratory for Bamboo Germplasm Resources and Utilization, Jiangxi Agriculture University, Nanchang 330045, China
| | - Muthusamy Ramakrishnan
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, School of Life Sciences, Nanjing Forestry University, Nanjing 210037, China
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Talha M, Shani MY, Ashraf MY, De Mastro F, Brunetti G, Khan MKR, Gillani SWUHS, Khan A, Abbas S, Cocozza C. Lead Toxicity-Mediated Growth and Metabolic Alterations at Early Seedling Stages of Maize ( Zea mays L.). PLANTS (BASEL, SWITZERLAND) 2023; 12:3335. [PMID: 37765499 PMCID: PMC10535917 DOI: 10.3390/plants12183335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 09/08/2023] [Accepted: 09/19/2023] [Indexed: 09/29/2023]
Abstract
To investigate the toxic effects of lead (Pb) on key metabolic activities essential for proper germination and seedling growth of maize seeds, experiments were carried out with different levels of Pb (0 to 120 mg of Pb L-1 as PbCl2) applied through growth medium to two maize hybrids H-3310S and H-6724. The research findings indicated that growth and metabolic activities were adversely affected by increased Pb contamination in growth medium; however, a slow increase in these parameters was recorded with increasing time from 0 to 120 h. Protease activity decreased with an increase in the level of Pb contamination but increased with time; consequently, a reduction in seed proteins and an increase in total free amino acids were observed with time. Similarly, α-amylase activity decreased with an increase in Pb concentration in growth medium while it increased with increasing time from 0 to 120 h; consequently, reducing and non-reducing sugars increased with time but decreased with exposure to lead. The roots of both maize hybrids had higher Pb contents than those of the shoot, which decreased the uptake of nitrogen, phosphorus, and potassium. All these nutrients are essential for optimal plant growth; therefore, the reduction in growth and biomass of maize seedlings could be due to Pb toxicity that altered metabolic processes, as sugar and amino acids are necessary for the synthesis of metabolic compounds, rapid cell division, and proper functioning of enzymes in the growing embryo, but all were dramatically reduced due to suppression of protease and α-amylase by toxicity of Pb. In general, hybrid H-3310S performed better in Pb-contaminated growth medium than H-6724.
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Affiliation(s)
- Muhammad Talha
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore 54000, Pakistan
| | - Muhammad Yousaf Shani
- Nuclear Institute for Agriculture and Biology (NIAB-C), Pakistan Institute of Engineering and Applied Sciences, Nilore, Islamabad 45650, Pakistan
- Plant Breeding and Genetics Division, Nuclear Institute for Agriculture and Biology (NIAB), Faisalabad 38000, Pakistan
| | - Muhammad Yasin Ashraf
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore 54000, Pakistan
| | - Francesco De Mastro
- Department of Soil, Plant, and Food Sciences, University of Bari “Aldo Moro”, 70126 Bari, Italy
| | - Gennaro Brunetti
- Department of Soil, Plant, and Food Sciences, University of Bari “Aldo Moro”, 70126 Bari, Italy
| | - Muhammad Kashif Riaz Khan
- Nuclear Institute for Agriculture and Biology (NIAB-C), Pakistan Institute of Engineering and Applied Sciences, Nilore, Islamabad 45650, Pakistan
- Plant Breeding and Genetics Division, Nuclear Institute for Agriculture and Biology (NIAB), Faisalabad 38000, Pakistan
| | - Syed Wajih ul Hassan Shah Gillani
- Nuclear Institute for Agriculture and Biology (NIAB-C), Pakistan Institute of Engineering and Applied Sciences, Nilore, Islamabad 45650, Pakistan
- Plant Breeding and Genetics Division, Nuclear Institute for Agriculture and Biology (NIAB), Faisalabad 38000, Pakistan
| | - Adeel Khan
- Nuclear Institute for Agriculture and Biology (NIAB-C), Pakistan Institute of Engineering and Applied Sciences, Nilore, Islamabad 45650, Pakistan
- Plant Breeding and Genetics Division, Nuclear Institute for Agriculture and Biology (NIAB), Faisalabad 38000, Pakistan
| | - Shahid Abbas
- Institute of Soil and Environmental Sciences, University of Agriculture, Faisalabad 38000, Pakistan
| | - Claudio Cocozza
- Department of Soil, Plant, and Food Sciences, University of Bari “Aldo Moro”, 70126 Bari, Italy
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Zha R, Chen T, Liu Q, Wei Q, Que F. Morphological and Anatomical Analysis of the Internodes of a New Dwarf Variant of Moso Bamboo, Phyllostachys edulis f. exaurita. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12091759. [PMID: 37176817 PMCID: PMC10180987 DOI: 10.3390/plants12091759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 04/19/2023] [Accepted: 04/24/2023] [Indexed: 05/15/2023]
Abstract
The lack of mutants due to the long periods between flowering of bamboo plants is one of the limiting factors inhibiting research progress in the culm development of bamboo plants. In this study, a stable new dwarf variant of Phyllostachys edulis (Moso bamboo), Phyllostachys edulis f. exaurita T. G. Chen, was discovered and was characterized morphologically, anatomically, and physiologically. The height, diameter at breast height, number of internodes, length and wall thickness of internodes, length, width and number of parenchyma cells of internodes, and morphology of the wide-type (WT) and dwarf variant vascular bundles were compared. The height of the variant was only 49% that of the WT Moso bamboo. It was concluded that the decrease in internode number and length was the cause of dwarfism in P. edulis f. exaurita. The decreased internode length was the result of a decrease in cell number and cell length in the internode. In addition, the laws of change of internode length, internode thickness, cell length, and cell number differed between the WT Moso bamboo and the variant. Furthermore, lower IAA and zeatin concentrations were detected in the buds of the variant. These results suggest that P. edulis f. exaurita is a variant with inhibited primary thickening growth, which is valuable for interpretating the molecular mechanisms underlying the primary thickening growth of bamboo that are still largely unknown.
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Affiliation(s)
- Ruofei Zha
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing 210037, China
| | - Tianguo Chen
- Changzhou Agricultural Comprehensive Technology Extension Center, Changzhou 213022, China
| | - Qingnan Liu
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing 210037, China
| | - Qiang Wei
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing 210037, China
| | - Feng Que
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing 210037, China
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Li L, Zhou B, Liu D, Wu H, Shi Q, Lin S, Yao W. Transcriptomic Complexity of Culm Growth and Development in Different Types of Moso Bamboo. Int J Mol Sci 2023; 24:ijms24087425. [PMID: 37108588 PMCID: PMC10138756 DOI: 10.3390/ijms24087425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 04/03/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
Moso bamboo is capable of both sexual and asexual reproduction during natural growth, resulting in four distinct types of culms: the bamboo shoot-culm, the seedling stem, the leptomorph rhizome, and a long-ignored culm-the outward-rhizome. Sometimes, when the outward rhizomes break through the soil, they continue to grow longitudinally and develop into a new individual. However, the roles of alternative transcription start sites (aTSS) or termination sites (aTTS) as well as alternative splicing (AS) have not been comprehensively studied for their development. To re-annotate the moso bamboo genome and identify genome-wide aTSS, aTTS, and AS in growing culms, we utilized single-molecule long-read sequencing technology. In total, 169,433 non-redundant isoforms and 14,840 new gene loci were identified. Among 1311 lncRNAs, most of which showed a positive correlation with their target mRNAs, one-third of these IncRNAs were preferentially expressed in winter bamboo shoots. In addition, the predominant AS type observed in moso bamboo was intron retention, while aTSS and aTTS events occurred more frequently than AS. Notably, most genes with AS events were also accompanied by aTSS and aTTS events. Outward rhizome growth in moso bamboo was associated with a significant increase in intron retention, possibly due to changes in the growth environment. As different types of moso bamboo culms grow and develop, a significant number of isoforms undergo changes in their conserved domains due to the regulation of aTSS, aTTS, and AS. As a result, these isoforms may play different roles than their original functions. These isoforms then performed different functions from their original roles, contributing to the transcriptomic complexity of moso bamboo. Overall, this study provided a comprehensive overview of the transcriptomic changes underlying different types of moso bamboo culm growth and development.
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Affiliation(s)
- Long Li
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing 210037, China
| | - Binao Zhou
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing 210037, China
| | - Dong Liu
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing 210037, China
| | - Hongyu Wu
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing 210037, China
| | - Qianqian Shi
- College of Landscape Architecture and Art, Northwest A&F University, Xianyang 712100, China
| | - Shuyan Lin
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing 210037, China
| | - Wenjing Yao
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing 210037, China
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Li T, Wang H, Zhang Y, Wang H, Zhang Z, Liu X, Zhang Z, Liu K, Yang D, Zhang H, Gu L. Comprehensive profiling of epigenetic modifications in fast-growing Moso bamboo shoots. PLANT PHYSIOLOGY 2023; 191:1017-1035. [PMID: 36417282 PMCID: PMC9922427 DOI: 10.1093/plphys/kiac525] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 10/10/2022] [Accepted: 11/17/2022] [Indexed: 05/13/2023]
Abstract
The fast growth of Moso bamboo (Phyllostachys edulis) shoots is caused by the rapid elongation of each internode. However, the key underlying cellular processes and epigenetic mechanisms remain largely unexplored. We used microscopy and multi-omics approaches to investigate two regions (bottom and middle) of the 18th internode from shoots of two different heights (2 and 4 m). We observed that internode cells become longer, and that lignin biosynthesis and glycosyltransferase family 43 (GT43) genes are substantially upregulated with shoot height. Nanopore direct RNA sequencing (DRS) revealed a higher N6-methyladenine (m6A) modification rate in 2-m shoots than in 4-m shoots. In addition, different specific m6A modification sites were enriched at different growth stages. Global DNA methylation profiling indicated that DNA methylation levels are higher in 4-m shoots than in 2-m shoots. We also detected shorter poly(A) tail lengths (PALs) in 4-m shoots compared with 2-m shoots. Genes showing differential PAL were mainly enriched in the functional terms of protein translation and vesicle fusion. An association analysis between PALs and DNA methylation strongly suggested that gene body CG methylation levels are positively associated with PAL. This study provides valuable information to better understand post-transcriptional regulations responsible for fast-growing shoots in Moso bamboo.
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Affiliation(s)
- Tao Li
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Huihui Wang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yaxin Zhang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Huiyuan Wang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zeyu Zhang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xuqing Liu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zekun Zhang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Kai Liu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Deming Yang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Hangxiao Zhang
- Basic Forestry and Proteomics Research Center, College of Forestry, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Lianfeng Gu
- Basic Forestry and Proteomics Research Center, College of Forestry, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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9
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Le L, Guo W, Du D, Zhang X, Wang W, Yu J, Wang H, Qiao H, Zhang C, Pu L. A spatiotemporal transcriptomic network dynamically modulates stalk development in maize. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:2313-2331. [PMID: 36070002 PMCID: PMC9674325 DOI: 10.1111/pbi.13909] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 04/19/2022] [Accepted: 08/12/2022] [Indexed: 06/15/2023]
Abstract
Maize (Zea mays) is an important cereal crop with suitable stalk formation which is beneficial for acquiring an ideal agronomic trait to resist lodging and higher planting density. The elongation pattern of stalks arises from the variable growth of individual internodes driven by cell division and cell expansion comprising the maize stalk. However, the spatiotemporal dynamics and regulatory network of the maize stalk development and differentiation process remain unclear. Here, we report spatiotemporally resolved transcriptomes using all internodes of the whole stalks from developing maize at the elongation and maturation stages. We identified four distinct groups corresponding to four developmental zones and nine specific clusters with diverse spatiotemporal expression patterns among individual internodes of the stalk. Through weighted gene coexpression network analysis, we constructed transcriptional regulatory networks at a fine spatiotemporal resolution and uncovered key modules and candidate genes involved in internode maintenance, elongation, and division that determine stalk length and thickness in maize. Further CRISPR/Cas9-mediated knockout validated the function of a cytochrome P450 gene, ZmD1, in the regulation of stalk length and thickness as predicted by the WGCN. Collectively, these results provide insights into the high genetic complexity of stalk development and the potentially valuable resources with ideal stalk lengths and widths for genetic improvements in maize.
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Affiliation(s)
- Liang Le
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijingChina
- National Nanfan Research Institute (Sanya)Chinese Academy of Agricultural SciencesSanyaChina
| | - Weijun Guo
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijingChina
| | - Danyao Du
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijingChina
| | - Xiaoyuan Zhang
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijingChina
| | - Weixuan Wang
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijingChina
| | - Jia Yu
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijingChina
| | - Huan Wang
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijingChina
| | - Hong Qiao
- Institute for Cellular and Molecular Biology, The University of Texas at AustinAustinTXUSA
- Department of Molecular BiosciencesThe University of Texas at AustinAustinTXUSA
| | - Chunyi Zhang
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijingChina
- Sanya InstituteHainan Academy of Agricultural SciencesSanyaChina
| | - Li Pu
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijingChina
- National Nanfan Research Institute (Sanya)Chinese Academy of Agricultural SciencesSanyaChina
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10
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Zheng H, Bai Y, Li X, Song H, Cai M, Cheng Z, Mu S, Li J, Gao J. Photosynthesis, Phytohormone Signaling and Sugar Catabolism in the Culm Sheaths of Phyllostachys edulis. PLANTS (BASEL, SWITZERLAND) 2022; 11:2866. [PMID: 36365317 PMCID: PMC9655093 DOI: 10.3390/plants11212866] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 10/17/2022] [Accepted: 10/25/2022] [Indexed: 06/16/2023]
Abstract
Culm sheaths play an important role in supporting and protecting bamboo shoots during the growth and development period. The physiological and molecular functions of bamboo sheaths during the growth of bamboo shoots remain unclear. In this study, we investigated the morphological anatomy of culm sheaths, photosynthesis in sheath blades, storage and distribution of sugars, and the transcriptome of the sheath. Respiration in the base of the culm sheath was higher than that in the sheath blades; chloroplasts matured with the development of the sheath blades, the fluorescence efficiency Fv/Fm value increased from 0.3 to 0.82; and sucrose and hexose accumulated in the sheath blade and the culm sheath. The sucrose, glucose, and fructose contents of the middle sheath blades were 10.66, 5.73, and 8.84 mg/g FW, respectively. Starches accumulated in parenchymal cells close to vascular bundles. Genes related to the plant hormone signaling pathway and sugar catabolism were highly expressed in the culm sheath base. These findings provide a research basis for further understanding the possible role of bamboo sheaths in the growth and development of bamboo shoots.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Jian Gao
- Correspondence: ; Tel.: +86-010-8478-9801
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11
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Liu L, Liu S, Lu H, Tian Z, Zhao H, Wei D, Wang S, Huang Z. Integration of transcriptome and metabolome analyses reveals key lodging-resistance-related genes and metabolic pathways in maize. Front Genet 2022; 13:1001195. [PMID: 36299597 PMCID: PMC9588961 DOI: 10.3389/fgene.2022.1001195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 09/20/2022] [Indexed: 11/28/2022] Open
Abstract
Stalk lodging, or breakage of the stalk at or below the ear, is one of the vital factors causing substantial yield losses in maize (Zea mays. L). Lodging affects maize plants’ physiological and molecular processes, eventually impacting plant growth and productivity. Despite this known fact, few researchers have investigated the genetic architecture underlying lodging in maize. Herein, through integrated transcriptome, metabolome, and phenotypic analyses of stalks of three diverse hybrid cultivars (highly resistant JNK738, mildly resistant JNK728, and lowly resistant XY335) at the tasseling (10 days to silking, 10 DTS) stage, we identified key genes and metabolic pathways modulating lodging resistance in maize. Based on the RNA-Seq analysis, a total of 10093 differentially expressed genes (DEGs) were identified from the comparison of the three varieties in pairs. Additionally, key lodging resistance–related metabolic pathways were obtained by KEGG enrichment analysis, and the DEGs were found predominantly enriched in phenylpropanoid and secondary metabolites biosynthesis pathways in the L_vs._H and M_vs._H comparison groups. Moreover, K-means analysis clustered the DEGs into clear and distinct expression profiles for each cultivar, with several functional and regulatory genes involved in the cell wall assembly, lignin biosynthetic process and hormone metabolic process being identified in the special clusters related to lodging resistance. Subsequently, integrating metabolome and transcriptome analyses revealed nine key lignin-associated metabolites that showed different expression trends in the three hybrid cultivars, among which L-phenylalanine and p-coumaric acid were regarded as differentially changed metabolites (DCMs). These two DCMs belonged to phenylalanine metabolism and biosynthesis pathways and were also supported by the RNA-Seq data. Furthermore, plant hormone signal transduction pathway–related genes encoding auxin, abscisic acid, jasmonates, and salicylic acid were differentially expressed in the three comparisons of lodging resistance, indicating these DEGs were valuable potential targets for improving maize lodging resistance. Finally, comparative physiological and qRT-PCR analyses results supported our transcriptome-based findings. Our research not only provides a preliminary theoretical basis and experimental ideas for an in-depth study of the regulatory networks involved in maize lodging resistance regulation but also opens up new avenues for molecular maize stalk lodging resistance breeding.
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Affiliation(s)
- Lei Liu
- Hebei Key Laboratory of Quality and Safety Analysis-Testing for Agro-Products and Food, Hebei North University, Zhangjiakou, China
| | - Songtao Liu
- Hebei Key Laboratory of Quality and Safety Analysis-Testing for Agro-Products and Food, Hebei North University, Zhangjiakou, China
| | - Haibo Lu
- Hebei Key Laboratory of Quality and Safety Analysis-Testing for Agro-Products and Food, Hebei North University, Zhangjiakou, China
| | - Zaimin Tian
- Hebei Key Laboratory of Quality and Safety Analysis-Testing for Agro-Products and Food, Hebei North University, Zhangjiakou, China
| | - Haichao Zhao
- Hebei Key Laboratory of Quality and Safety Analysis-Testing for Agro-Products and Food, Hebei North University, Zhangjiakou, China
| | - Dong Wei
- Hebei Key Laboratory of Quality and Safety Analysis-Testing for Agro-Products and Food, Hebei North University, Zhangjiakou, China
| | - Shuo Wang
- School of Medicine, Nankai University, Tianjin, China
| | - Zhihong Huang
- Hebei Key Laboratory of Quality and Safety Analysis-Testing for Agro-Products and Food, Hebei North University, Zhangjiakou, China
- *Correspondence: Zhihong Huang,
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12
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Chen M, Guo L, Ramakrishnan M, Fei Z, Vinod KK, Ding Y, Jiao C, Gao Z, Zha R, Wang C, Gao Z, Yu F, Ren G, Wei Q. Rapid growth of Moso bamboo (Phyllostachys edulis): Cellular roadmaps, transcriptome dynamics, and environmental factors. THE PLANT CELL 2022; 34:3577-3610. [PMID: 35766883 PMCID: PMC9516176 DOI: 10.1093/plcell/koac193] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 06/24/2022] [Indexed: 05/09/2023]
Abstract
Moso bamboo (Phyllostachys edulis) shows remarkably rapid growth (114.5 cm/day), but the underlying biological mechanisms remain unclear. After examining more than 12,750 internodes from more than 510 culms from 17 Moso populations, we identified internode 18 as a representative internode for rapid growth. This internode includes a 2-cm cell division zone (DZ), a cell elongation zone up to 12 cm, and a secondary cell wall (SCW) thickening zone. These zones elongated 11.8 cm, produced approximately 570,000,000 cells, and deposited ∼28 mg g-1 dry weight (DW) lignin and ∼44 mg g-1 DW cellulose daily, far exceeding vegetative growth observed in other plants. We used anatomical, mathematical, physiological, and genomic data to characterize development and transcriptional networks during rapid growth in internode 18. Our results suggest that (1) gibberellin may directly trigger the rapid growth of Moso shoots, (2) decreased cytokinin and increased auxin accumulation may trigger cell DZ elongation, and (3) abscisic acid and mechanical pressure may stimulate rapid SCW thickening via MYB83L. We conclude that internode length involves a possible tradeoff mediated by mechanical pressure caused by rapid growth, possibly influenced by environmental temperature and regulated by genes related to cell division and elongation. Our results provide insight into the rapid growth of Moso bamboo.
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Affiliation(s)
- Ming Chen
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Lin Guo
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Muthusamy Ramakrishnan
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Zhangjun Fei
- Boyce Thompson Institute, Cornell University, Ithaca, New York 14853, USA
| | - Kunnummal K Vinod
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Yulong Ding
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | | | - Zhipeng Gao
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Ruofei Zha
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Chunyue Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Zhimin Gao
- Key Laboratory of National Forestry and Grassland Administration, Beijing for Bamboo & Rattan Science and Technology, Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Fen Yu
- Jiangxi Provincial Key Laboratory for Bamboo Germplasm Resources and Utilization, Jiangxi Agriculture University, Nanchang, Jiangxi 330045, China
| | - Guodong Ren
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China
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13
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Identification of the 14-3-3 Gene Family in Bamboo and Characterization of Pe14-3-3b Reveals Its Potential Role in Promoting Growth. Int J Mol Sci 2022; 23:ijms231911221. [PMID: 36232520 PMCID: PMC9569445 DOI: 10.3390/ijms231911221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 09/18/2022] [Accepted: 09/20/2022] [Indexed: 11/16/2022] Open
Abstract
The 14-3-3 protein family plays an important role in regulating plant growth and development. The genes of the 14-3-3 family have been reported in multiple species. However, little is known about the 14-3-3 gene family in bamboo. In this study, a total of 58 genes belonging to the 14-3-3 family were identified in three representative bamboo species, i.e., Olyra latifolia, Phyllostachys edulis, and Bonia amplexicaulis, whose encoding proteins were grouped into ε and non-ε groups by phylogeny analysis with 14-3-3 proteins from Arabidopsis thaliana and Oryza sativa. The 14-3-3s had diverse gene structures and motif characteristics among the three bamboo species. Collinearity analysis suggested that the genes of the 14-3-3 family in bamboo had undergone a strong purification selection during evolution. Tissue-specific expression analysis showed the expression of Pe14-3-3s varied in different tissues of P. edulis, suggesting that they had functional diversity during growth and development. Co-expression analysis showed that four Pe14-3-3s co-expressed positively with eight ribosomal genes. Yeast two-hybrid (Y2H) assays showed that Pe14-3-3b/d could interact with Pe_ribosome-1/5/6, and qPCR results demonstrated that Pe14-3-3b/d and Pe_ribosome-1/5/6 had similar expression trends with the increase in shoot height, which further confirmed that they would work together to participate in the shoot growth and development of bamboo. Additionally, the transgenic Arabidopsis plants overexpressing Pe14-3-3b had longer roots, a larger stem diameter, an earlier bolting time and a faster growth rate than wild-type Arabidopsis, indicating that Pe14-3-3b acted as a growth promoter. Our results provide comprehensive information on 14-3-3 genes in bamboo and highlight Pe14-3-3b as a potential target for bamboo improvement.
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14
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Sah SK, Jumaa S, Li J, Reddy KR. Proteomic analysis response of rice ( Oryza sativa) leaves to ultraviolet-B radiation stress. FRONTIERS IN PLANT SCIENCE 2022; 13:871331. [PMID: 36212327 PMCID: PMC9536139 DOI: 10.3389/fpls.2022.871331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 08/05/2022] [Indexed: 06/16/2023]
Abstract
Rice (Oryza sativa) is a human staple food and serves as a model organism for genetic and molecular studies. Few studies have been conducted to determine the effects of ultraviolet-B (UV-B) stress on rice. UV-B stress triggers morphological and physiological changes in plants. However, the underlying mechanisms governing these integrated responses are unknown. In this study, we conducted a proteomic response of rice leaves to UV-B stress using two-dimensional gel electrophoresis and identified the selected proteins by mass spectrometry analysis. Four levels of daily biologically effective UV-B radiation intensities were imposed to determine changes in protein accumulation in response to UV-B stress: 0 (control), 5, 10, and 15 kJ m-2 d-1in two cultivars, i.e., IR6 and REX. To mimic the natural environment, we conducted this experiment in Sunlit Soil-Plant-Atmosphere-Research (SPAR) chambers. Among the identified proteins, 11% of differentially expressed proteins were found in both cultivars. In the Rex cultivar, only 45% of proteins are differentially expressed, while only 27.5% were expressed in IR6. The results indicate that REX is more affected by UV-B stress than IR6 cultivars. The identified protein TSJT1 (spot 16) in both cultivars plays a crucial role in plant growth and development during stress treatment. Additionally, we found that UV-B stress altered many antioxidant enzymes associated with redox homeostasis and cell defense response. Another enzyme, the glyceraldehyde-3-phosphate dehydrogenase (GAPDH), has been identified as spot 15, which plays an essential role in glycolysis and cellular energy production. Another vital protein identified is glycosyl hydrolase (GH) as spot 9, which catalyzes the hydrolysis of glycosidic bonds in cell wall polymers and significantly affects cell wall architecture. Some identified proteins are related to photosynthesis, protein biosynthesis, signal transduction, and stress response. The findings of our study provide new insights into understanding how rice plants are tailored to UV-B stress via modulating the expression of UV-B responsive proteins, which will help develop superior rice breeds in the future to combat UV-B stress. Data are available via ProteomeXchange with identifier PXD032163.
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Affiliation(s)
- Saroj Kumar Sah
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Mississippi State, MS, United States
| | - Salah Jumaa
- Department of Plant and Soil Sciences, Mississippi State University, Mississippi State, MS, United States
| | - Jiaxu Li
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Mississippi State, MS, United States
| | - K. Raja Reddy
- Department of Plant and Soil Sciences, Mississippi State University, Mississippi State, MS, United States
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15
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Guo L, Wang C, Chen J, Ju Y, Yu F, Jiao C, Fei Z, Ding Y, Wei Q. Cellular differentiation, hormonal gradient, and molecular alternation between the division zone and the elongation zone of bamboo internodes. PHYSIOLOGIA PLANTARUM 2022; 174:e13774. [PMID: 36050899 DOI: 10.1111/ppl.13774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 08/20/2022] [Accepted: 08/26/2022] [Indexed: 06/15/2023]
Abstract
Bamboo differentiates a cell division zone (DZ) and a cell elongation zone (EZ) to promote internode elongation during rapid growth. However, the biological mechanisms underlying this sectioned growth behavior are still unknown. Using histological, physiological, and genomic data, we found that the cell wall and other subcellular organelles such as chloroplasts are more developed in the EZ. Abundant hydrogen peroxide accumulated in the pith cells of the EZ, and stomata formed completely in the EZ. In contrast, most cells in the DZ were in an undifferentiated state with wrinkled cell walls and dense cytoplasm. Hormone detection revealed that the levels of gibberellin, auxin, cytokinin, and brassinosteroid were higher in the DZ than in the EZ. However, the levels of salicylic acid and jasmonic acid were higher in the EZ than in the DZ. Transcriptome analysis with qRT-PCR quantification revealed that the transcripts for cell division and primary metabolism had higher expression in the DZ, whereas the genes for photosynthesis, cell wall growth, and secondary metabolism were dramatically upregulated in the EZ. Overexpression of a MYB transcription factor, BmMYB83, promotes cell wall lignification in transgenic plants. BmMYB83 is specifically expressed in cells that may have lignin deposits, such as protoxylem vessels and fiber cells. Our results indicate that hormone gradient and transcriptome reprogramming, as well as specific expression of key genes such as BmMYB83, may lead to differentiation of cell growth in the bamboo internode.
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Affiliation(s)
- Lin Guo
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Chunyue Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Jin Chen
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Ye Ju
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Fen Yu
- Jiangxi Provincial Key Laboratory for Bamboo Germplasm Resources and Utilization, Jiangxi Agriculture University, Nanchang, Jiangxi, China
| | - Chen Jiao
- Boyce Thompson Institute, Cornell University, Ithaca, New York, USA
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Zhangjun Fei
- Boyce Thompson Institute, Cornell University, Ithaca, New York, USA
| | - Yulong Ding
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Qiang Wei
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, China
- Jiangxi Provincial Key Laboratory for Bamboo Germplasm Resources and Utilization, Jiangxi Agriculture University, Nanchang, Jiangxi, China
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16
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Niu LZ, Xu W, Ma PF, Guo ZH, Li DZ. Single-base methylome analysis reveals dynamic changes of genome-wide DNA methylation associated with rapid stem growth of woody bamboos. PLANTA 2022; 256:53. [PMID: 35913571 DOI: 10.1007/s00425-022-03962-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 07/14/2022] [Indexed: 06/15/2023]
Abstract
CG and CHG methylation levels in the rapid shoot growth stages (ST2-ST4) of woody bamboos were obviously decreased, which might regulate the internode elongation during rapid shoot growth, while CHH methylation was strongly associated with shoot developmental time or age. DNA methylation plays a critical role in the regulation of plant growth and development. Woody bamboos have a unique trait of rapid stem growth resulted from internode elongation at the shooting period. However, it is still unclear whether DNA methylation significantly controls the bamboo rapid stem growth. Here we present whole-genome DNA methylation profiles of the paleotropical woody bamboo Bonia amplexicaulis at five newly defined stages of shoot growth, named ST1-ST5. We found that CG and CHG methylation levels in the rapid shoot growth stages (ST2-ST4) were significantly lower than in the incubation (ST1) and plateau stages (ST5). The changes in methylation levels mainly occurred in flanking regions of genes and gene body regions, and 23647 differentially methylated regions (DMRs) were identified between ST1 and rapid shoot growth stages (ST2-ST4). Combined with transcriptome analysis, we found that DMR-related genes enriched in the auxin and jasmonic acid (JA) signal transduction, and other pathways closely related to plant growth. Intriguingly, CHH methylation was not involved in the rapid shoot growth, but strongly associated with shoot developmental time by gradually accumulating in transposable elements (TEs) regions. Overall, our results reveal the importance of DNA methylation in regulating the bamboo rapid shoot growth and suggest a role of DNA methylation associated with development time or age in woody bamboos.
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Affiliation(s)
- Liang-Zhong Niu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, 650201, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wei Xu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, 650201, Yunnan, China
| | - Peng-Fei Ma
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, 650201, Yunnan, China
| | - Zhen-Hua Guo
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, 650201, Yunnan, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, 650201, Yunnan, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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17
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Li J, Liu Z, Gao C, Miao Y, Cui K. Overexpression of DsEXLA2 gene from Dendrocalamus sinicus accelerates the plant growth rate of Arabidopsis. PHYTOCHEMISTRY 2022; 199:113178. [PMID: 35385712 DOI: 10.1016/j.phytochem.2022.113178] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 03/23/2022] [Accepted: 03/25/2022] [Indexed: 06/14/2023]
Abstract
Expansins play crucial roles in cell wall loosening and a range of life activities involving cell wall modification. Nevertheless, the biological functions of expansin genes during fast growth of bamboo remain unclear. In this study, Dendrocalamus sinicus, the largest and fastest growing bamboo species in the world, was used as the research material, and the full length of DsEXLA2 was cloned. Bioinformatics analysis revealed that DsEXLA2 contained expansin family typical domains (DPBB_1 and Pollen_allerg_1, CDRC motif) and amino acid sequence was highly conserved among different species. The expression level of DsEXLA2 increased from top section to basal section in different internodes. Subcellular localization verified that DsEXLA2 protein was located in the cell wall. Further genetic transformation studies in Arabidopsis indicated that compared with the wild type, DsEXLA2 overexpressed transgenic plants exhibited higher plant height, thicker stem, larger leaf, and less epidermal hair number and smaller stomatal aperture in the prophase and metaphase of growth. In addition, the cellulose content in the stem of transgenic plants was increased, and cell wall was thickened significantly. Moreover, a total of 1656 differentially expressed genes (DEGs) were identified by RNA-seq. The upregulated genes were predominantly enriched in the plant-pathogen interaction, MAPK signaling pathway-plant, plant hormone signal transduction, lipid metabolism and amino acid metabolism, while the downregulated genes were mainly enriched in energy metabolism, carbohydrate metabolism, plant hormone signal transduction and ribosome. These data implied that overexpression of DsEXLA2 gene accelerates the plant growth rate of Arabidopsis. This study is helpful to reveal the molecular mechanism of DsEXLA2 in culm growth and development of D. sinicus, and to understand the rapid growth of bamboos.
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Affiliation(s)
- Jin Li
- State Key Laboratory of Tree Genetics and Breeding, Institute of Highland Forest Science, Chinese Academy of Forestry, Kunming, 650233, PR China
| | - Zirui Liu
- State Key Laboratory of Tree Genetics and Breeding, Institute of Highland Forest Science, Chinese Academy of Forestry, Kunming, 650233, PR China
| | - Chengjie Gao
- State Key Laboratory of Tree Genetics and Breeding, Institute of Highland Forest Science, Chinese Academy of Forestry, Kunming, 650233, PR China
| | - Yingchun Miao
- State Key Laboratory of Tree Genetics and Breeding, Institute of Highland Forest Science, Chinese Academy of Forestry, Kunming, 650233, PR China
| | - Kai Cui
- State Key Laboratory of Tree Genetics and Breeding, Institute of Highland Forest Science, Chinese Academy of Forestry, Kunming, 650233, PR China.
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18
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Total and Mitochondrial Transcriptomic and Proteomic Insights into Regulation of Bioenergetic Processes for Shoot Fast-Growth Initiation in Moso Bamboo. Cells 2022; 11:cells11071240. [PMID: 35406802 PMCID: PMC8997719 DOI: 10.3390/cells11071240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 04/02/2022] [Accepted: 04/04/2022] [Indexed: 11/16/2022] Open
Abstract
As a fast-growing, woody grass plant, Moso bamboo (Phyllostachys edulis) can supply edible shoots, building materials, fibrous raw material, raw materials for crafts and furniture and so on within a relatively short time. Rapid growth of Moso bamboo occurs after the young bamboo shoots are covered with a shell and emerge from the ground. However, the molecular reactions of bioenergetic processes essential for fast growth remain undefined. Herein, total and mitochondrial transcriptomes and proteomes were compared between spring and winter shoots. Numerous key genes and proteins responsible for energy metabolism were significantly upregulated in spring shoots, including those involved in starch and sucrose catabolism, glycolysis, the pentose phosphate pathway, the tricarboxylic acid cycle and oxidative phosphorylation. Accordingly, significant decreases in starch and soluble sugar, higher ATP content and higher rates of respiration and glycolysis were identified in spring shoots. Further, the upregulated genes and proteins related to mitochondrial fission significantly increased the number of mitochondria, indirectly promoting intracellular energy metabolism. Moreover, enhanced alternate-oxidase and uncoupled-protein pathways in winter shoots showed that an efficient energy-dissipating system was important for winter shoots to adapt to the low-temperature environment. Heterologous expression of PeAOX1b in Arabidopsis significantly affected seedling growth and enhanced cold-stress tolerance. Overall, this study highlights the power of comparing total and mitochondrial omics and integrating physiochemical data to understand how bamboo initiates fast growth through modulating bioenergetic processes.
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Li L, Xia T, Li B, Yang H. Hormone and carbohydrate metabolism associated genes play important roles in rhizome bud full-year germination of Cephalostachyum pingbianense. PHYSIOLOGIA PLANTARUM 2022; 174:e13674. [PMID: 35306669 DOI: 10.1111/ppl.13674] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 03/06/2022] [Accepted: 03/14/2022] [Indexed: 06/14/2023]
Abstract
Cephalostachyum pingbianense is the only woody bamboo species that can produce bamboo shoots in four seasons under natural conditions. So far, the regulatory mechanism of shoot bud differentiation and development is unknown. In the present study, indole-3-acetic acid (IAA), zeatin riboside (ZR), gibberellin A3 (GA3 ) and abscisic acid (ABA) contents determination, RNA sequencing and differentially expressed gene analysis were performed on dormant rhizome bud (DR), growing rhizome bud (GR), and germinative bud (GB) in each season. The results showed that the contents of IAA and ZR increased while ABA content decreased, and GA3 content was stable during bud transition from dormancy to germination in each season. Moreover, rhizome bud germination was cooperatively regulated by multiple pathways such as carbohydrate metabolism, hormone signal transduction, cell wall biogenesis, temperature response, and water transport. The inferred hub genes among these candidates were identified by protein-protein interaction network analyses, most of which were involved in hormone and carbohydrate metabolism, such as HK and BGLU4 in spring, IDH and GH3 in winter, GPI and talA/talB in summer and autumn. It is speculated that dynamic phytohormone changes and differential expression of these genes promote the release of rhizome bud dormancy and contribute to the phenological characteristics of full-year shooting. Moreover, the rhizome buds of C. pingbianense may not suffer from ecodormancy in winter. These findings would help accumulate knowledge on shooting mechanisms in woody bamboos and provide a physiological insight into germplasm conservation and forest management of C. pingbianense.
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Affiliation(s)
- Lushuang Li
- Institute of Highland Forest Science, Chinese Academy of Forestry, Kunming, Yunnan, China
| | - Tize Xia
- Institute of Highland Forest Science, Chinese Academy of Forestry, Kunming, Yunnan, China
| | - Bin Li
- Institute of Highland Forest Science, Chinese Academy of Forestry, Kunming, Yunnan, China
| | - Hanqi Yang
- Institute of Highland Forest Science, Chinese Academy of Forestry, Kunming, Yunnan, China
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20
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Ashraf MF, Hou D, Hussain Q, Imran M, Pei J, Ali M, Shehzad A, Anwar M, Noman A, Waseem M, Lin X. Entailing the Next-Generation Sequencing and Metabolome for Sustainable Agriculture by Improving Plant Tolerance. Int J Mol Sci 2022; 23:651. [PMID: 35054836 PMCID: PMC8775971 DOI: 10.3390/ijms23020651] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 12/23/2021] [Accepted: 12/29/2021] [Indexed: 02/07/2023] Open
Abstract
Crop production is a serious challenge to provide food for the 10 billion individuals forecasted to live across the globe in 2050. The scientists' emphasize establishing an equilibrium among diversity and quality of crops by enhancing yield to fulfill the increasing demand for food supply sustainably. The exploitation of genetic resources using genomics and metabolomics strategies can help generate resilient plants against stressors in the future. The innovation of the next-generation sequencing (NGS) strategies laid the foundation to unveil various plants' genetic potential and help us to understand the domestication process to unmask the genetic potential among wild-type plants to utilize for crop improvement. Nowadays, NGS is generating massive genomic resources using wild-type and domesticated plants grown under normal and harsh environments to explore the stress regulatory factors and determine the key metabolites. Improved food nutritional value is also the key to eradicating malnutrition problems around the globe, which could be attained by employing the knowledge gained through NGS and metabolomics to achieve suitability in crop yield. Advanced technologies can further enhance our understanding in defining the strategy to obtain a specific phenotype of a crop. Integration among bioinformatic tools and molecular techniques, such as marker-assisted, QTLs mapping, creation of reference genome, de novo genome assembly, pan- and/or super-pan-genomes, etc., will boost breeding programs. The current article provides sequential progress in NGS technologies, a broad application of NGS, enhancement of genetic manipulation resources, and understanding the crop response to stress by producing plant metabolites. The NGS and metabolomics utilization in generating stress-tolerant plants/crops without deteriorating a natural ecosystem is considered a sustainable way to improve agriculture production. This highlighted knowledge also provides useful research that explores the suitable resources for agriculture sustainability.
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Affiliation(s)
- Muhammad Furqan Ashraf
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, 666 Wusu Street, Lin’An, Hangzhou 311300, China; (M.F.A.); (D.H.); (Q.H.); (J.P.)
| | - Dan Hou
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, 666 Wusu Street, Lin’An, Hangzhou 311300, China; (M.F.A.); (D.H.); (Q.H.); (J.P.)
| | - Quaid Hussain
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, 666 Wusu Street, Lin’An, Hangzhou 311300, China; (M.F.A.); (D.H.); (Q.H.); (J.P.)
| | - Muhammad Imran
- Colleges of Agriculture and Horticulture, South China Agricultural University, Guangzhou 510642, China; (M.I.); (M.W.)
| | - Jialong Pei
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, 666 Wusu Street, Lin’An, Hangzhou 311300, China; (M.F.A.); (D.H.); (Q.H.); (J.P.)
| | - Mohsin Ali
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China;
| | - Aamar Shehzad
- Maize Research Station, AARI, Faisalabad 38000, Pakistan;
| | - Muhammad Anwar
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Key Laboratory of Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, China;
| | - Ali Noman
- Department of Botany, Government College University, Faisalabad 38000, Pakistan;
| | - Muhammad Waseem
- Colleges of Agriculture and Horticulture, South China Agricultural University, Guangzhou 510642, China; (M.I.); (M.W.)
| | - Xinchun Lin
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, 666 Wusu Street, Lin’An, Hangzhou 311300, China; (M.F.A.); (D.H.); (Q.H.); (J.P.)
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21
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Zhang J, Ma R, Ding X, Huang M, Shen K, Zhao S, Xiao Z, Xiu C. Association among starch storage, metabolism, related genes and growth of Moso bamboo (Phyllostachys heterocycla) shoots. BMC PLANT BIOLOGY 2021; 21:477. [PMID: 34670492 PMCID: PMC8527747 DOI: 10.1186/s12870-021-03257-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 10/08/2021] [Indexed: 05/14/2023]
Abstract
BACKGROUND Both underground rhizomes/buds and above-ground Moso bamboo (Phyllostachys heterocycla) shoots/culms/branches are connected together into a close inter-connecting system in which nutrients are transported and shared among each organ. However, the starch storage and utilization mechanisms during bamboo shoot growth remain unclear. This study aimed to reveal in which organs starch was stored, how carbohydrates were transformed among each organ, and how the expression of key genes was regulated during bamboo shoot growth and developmental stages which should lay a foundation for developing new theoretical techniques for bamboo cultivation. RESULTS Based on changes of the NSC content, starch metabolism-related enzyme activity and gene expression from S0 to S3, we observed that starch grains were mainly elliptical in shape and proliferated through budding and constriction. Content of both soluble sugar and starch in bamboo shoot peaked at S0, in which the former decreased gradually, and the latter initially decreased and then increased as shoots grew. Starch synthesis-related enzymes (AGPase, GBSS and SBE) and starch hydrolase (α-amylase and β-amylase) activities exhibited the same dynamic change patterns as those of the starch content. From S0 to S3, the activity of starch synthesis-related enzyme and starch amylase in bamboo rhizome was significantly higher than that in bamboo shoot, while the NSC content in rhizomes was obviously lower than that in bamboo shoots. It was revealed by the comparative transcriptome analysis that the expression of starch synthesis-related enzyme-encoding genes were increased at S0, but reduced thereafter, with almost the same dynamic change tendency as the starch content and metabolism-related enzymes, especially during S0 and S1. It was revealed by the gene interaction analysis that AGPase and SBE were core genes for the starch and sucrose metabolism pathway. CONCLUSIONS Bamboo shoots were the main organ in which starch was stored, while bamboo rhizome should be mainly functioned as a carbohydrate transportation channel and the second carbohydrate sink. Starch metabolism-related genes were expressed at the transcriptional level during underground growth, but at the post-transcriptional level during above-ground growth. It may be possible to enhance edible bamboo shoot quality for an alternative starch source through genetic engineering.
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Affiliation(s)
- Jiajia Zhang
- China National Bamboo Research Center, Hangzhou, 310012, Zhejiang Province, China
- Chinese Academy of Forestry, Beijing, 100089, China
| | - Ruixiang Ma
- China National Bamboo Research Center, Hangzhou, 310012, Zhejiang Province, China
- Chinese Academy of Forestry, Beijing, 100089, China
| | - Xingcui Ding
- China National Bamboo Research Center, Hangzhou, 310012, Zhejiang Province, China.
- Chinese Academy of Forestry, Beijing, 100089, China.
| | - Manchang Huang
- China National Bamboo Research Center, Hangzhou, 310012, Zhejiang Province, China
- Chinese Academy of Forestry, Beijing, 100089, China
| | - Kai Shen
- China National Bamboo Research Center, Hangzhou, 310012, Zhejiang Province, China
- Chinese Academy of Forestry, Beijing, 100089, China
| | - Siqi Zhao
- China National Bamboo Research Center, Hangzhou, 310012, Zhejiang Province, China
- Chinese Academy of Forestry, Beijing, 100089, China
| | - Zizhang Xiao
- China National Bamboo Research Center, Hangzhou, 310012, Zhejiang Province, China
- Chinese Academy of Forestry, Beijing, 100089, China
| | - Chengming Xiu
- China National Bamboo Research Center, Hangzhou, 310012, Zhejiang Province, China
- Chinese Academy of Forestry, Beijing, 100089, China
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22
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Yang K, Li L, Lou Y, Zhu C, Li X, Gao Z. A regulatory network driving shoot lignification in rapidly growing bamboo. PLANT PHYSIOLOGY 2021; 187:900-916. [PMID: 34608957 PMCID: PMC8491019 DOI: 10.1093/plphys/kiab289] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 05/31/2021] [Indexed: 05/24/2023]
Abstract
Woody bamboo is environmentally friendly, abundant, and an alternative to conventional timber. Degree of lignification and lignin content and deposition affect timber properties. However, the lignification regulatory network in monocots is poorly understood. To elucidate the regulatory mechanism of lignification in moso bamboo (Phyllostachys edulis), we conducted integrated analyses using transcriptome, small RNA, and degradome sequencing followed by experimental verification. The lignification degree and lignin content increased with increased bamboo shoot height, whereas phenylalanine ammonia-lyase and Laccase activities first increased and then decreased with shoot growth. Moreover, we identified 11,504 differentially expressed genes (DEGs) in different portions of the 13th internodes of different height shoots; most DEGs associated with cell wall and lignin biosynthesis were upregulated, whereas some DEGs related to cell growth were downregulated. We identified a total of 1,502 miRNAs, of which 687 were differentially expressed. Additionally, in silico and degradome analyses indicated that 5,756 genes were targeted by 691 miRNAs. We constructed a regulatory network of lignification, including 11 miRNAs, 22 transcription factors, and 36 enzyme genes, in moso bamboo. Furthermore, PeLAC20 overexpression increased lignin content in transgenic Arabidopsis (Arabidopsis thaliana) plants. Finally, we proposed a reliable miRNA-mediated "MYB-PeLAC20" module for lignin monomer polymerization. Our findings provide definite insights into the genetic regulation of bamboo lignification. In addition to providing a platform for understanding related mechanisms in other monocots, these insights could be used to develop strategies to improve bamboo timber properties.
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Affiliation(s)
- Kebin Yang
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo and Rattan Science and Technology, Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Lichao Li
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo and Rattan Science and Technology, Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Yongfeng Lou
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo and Rattan Science and Technology, Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Beijing 100102, China
- Jiangxi Academy of Forestry, Jiangxi Provincial Key Laboratory of Plant Biotechnology, Nanchang 330013, China
| | - Chenglei Zhu
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo and Rattan Science and Technology, Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Xueping Li
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo and Rattan Science and Technology, Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Zhimin Gao
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo and Rattan Science and Technology, Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Beijing 100102, China
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23
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Cao Y, Sun G, Zhai X, Xu P, Ma L, Deng M, Zhao Z, Yang H, Dong Y, Shang Z, Lv Y, Yan L, Liu H, Cao X, Li B, Wang Z, Zhao X, Yu H, Wang F, Ma W, Huang J, Fan G. Genomic insights into the fast growth of paulownias and the formation of Paulownia witches' broom. MOLECULAR PLANT 2021; 14:1668-1682. [PMID: 34214658 DOI: 10.1016/j.molp.2021.06.021] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 01/18/2021] [Accepted: 06/24/2021] [Indexed: 06/13/2023]
Abstract
Paulownias are among the fastest growing trees in the world, but they often suffer tremendous loss of wood production due to infection by Paulownia witches' broom (PaWB) phytoplasmas. In this study, we have sequenced and assembled a high-quality nuclear genome of Paulownia fortunei, a commonly cultivated paulownia species. The assembled genome of P. fortunei is 511.6 Mb in size, with 93.2% of its sequences anchored to 20 pseudo-chromosomes, and it contains 31 985 protein-coding genes. Phylogenomic analyses show that the family Paulowniaceae is sister to a clade composed of Phrymaceae and Orobanchaceae. Higher photosynthetic efficiency is achieved by integrating C3 photosynthesis and the crassulacean acid metabolism pathway, which may contribute to the extremely fast growth habit of paulownia trees. Comparative transcriptome analyses reveal modules related to cambial growth and development, photosynthesis, and defense responses. Additional genome sequencing of PaWB phytoplasma, combined with functional analyses, indicates that the effector PaWB-SAP54 interacts directly with Paulownia PfSPLa, which in turn causes the degradation of PfSPLa by the ubiquitin-mediated pathway and leads to the formation of witches' broom. Taken together, these results provide significant insights into the biology of paulownias and the regulatory mechanism for the formation of PaWB.
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Affiliation(s)
- Yabing Cao
- Institute of Paulownia, Henan Agricultural University, Zhengzhou, Henan 450002, China; College of Forestry, Henan Agricultural University, Zhengzhou, Henan 450002, China
| | - Guiling Sun
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, Henan 475004, China
| | - Xiaoqiao Zhai
- Henan Academy of Forestry, Zhengzhou, Henan 450002, China
| | - Pingluo Xu
- Institute of Paulownia, Henan Agricultural University, Zhengzhou, Henan 450002, China; College of Forestry, Henan Agricultural University, Zhengzhou, Henan 450002, China
| | - Liming Ma
- Biomarker Technologies Corporation, Beijing 101399, China
| | - Minjie Deng
- Institute of Paulownia, Henan Agricultural University, Zhengzhou, Henan 450002, China; College of Forestry, Henan Agricultural University, Zhengzhou, Henan 450002, China
| | - Zhenli Zhao
- Institute of Paulownia, Henan Agricultural University, Zhengzhou, Henan 450002, China; College of Forestry, Henan Agricultural University, Zhengzhou, Henan 450002, China
| | - Haibo Yang
- Institute of Paulownia, Henan Agricultural University, Zhengzhou, Henan 450002, China; College of Forestry, Henan Agricultural University, Zhengzhou, Henan 450002, China
| | - Yanpeng Dong
- Institute of Paulownia, Henan Agricultural University, Zhengzhou, Henan 450002, China; College of Forestry, Henan Agricultural University, Zhengzhou, Henan 450002, China
| | - Zhonghai Shang
- Henan Academy of Forestry, Zhengzhou, Henan 450002, China
| | - Yujie Lv
- Institute of Paulownia, Henan Agricultural University, Zhengzhou, Henan 450002, China; College of Forestry, Henan Agricultural University, Zhengzhou, Henan 450002, China
| | - Lijun Yan
- Institute of Paulownia, Henan Agricultural University, Zhengzhou, Henan 450002, China; College of Forestry, Henan Agricultural University, Zhengzhou, Henan 450002, China
| | - Haifang Liu
- Institute of Paulownia, Henan Agricultural University, Zhengzhou, Henan 450002, China; College of Forestry, Henan Agricultural University, Zhengzhou, Henan 450002, China
| | - Xibing Cao
- Institute of Paulownia, Henan Agricultural University, Zhengzhou, Henan 450002, China; College of Forestry, Henan Agricultural University, Zhengzhou, Henan 450002, China
| | - Bingbing Li
- Institute of Paulownia, Henan Agricultural University, Zhengzhou, Henan 450002, China; College of Forestry, Henan Agricultural University, Zhengzhou, Henan 450002, China
| | - Zhe Wang
- Institute of Paulownia, Henan Agricultural University, Zhengzhou, Henan 450002, China; College of Forestry, Henan Agricultural University, Zhengzhou, Henan 450002, China
| | - Xiaogai Zhao
- Institute of Paulownia, Henan Agricultural University, Zhengzhou, Henan 450002, China; College of Forestry, Henan Agricultural University, Zhengzhou, Henan 450002, China
| | - Haiyan Yu
- Biomarker Technologies Corporation, Beijing 101399, China
| | - Fan Wang
- Biomarker Technologies Corporation, Beijing 101399, China
| | - Wen Ma
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, Henan 475004, China
| | - Jinling Huang
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, Henan 475004, China; Department of Biology, East Carolina University, Greenville, NC 27858, USA.
| | - Guoqiang Fan
- Institute of Paulownia, Henan Agricultural University, Zhengzhou, Henan 450002, China; College of Forestry, Henan Agricultural University, Zhengzhou, Henan 450002, China.
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24
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Jin G, Ma PF, Wu X, Gu L, Long M, Zhang C, Li DZ. New Genes Interacted with Recent Whole Genome Duplicates in the Fast Stem Growth of Bamboos. Mol Biol Evol 2021; 38:5752-5768. [PMID: 34581782 PMCID: PMC8662795 DOI: 10.1093/molbev/msab288] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
As drivers of evolutionary innovations, new genes allow organisms to explore new niches. However, clear examples of this process remain scarce. Bamboos, the unique grass lineage diversifying into the forest, have evolved with a key innovation of fast growth of woody stem, reaching up to 1 m/day. Here, we identify 1,622 bamboo-specific orphan genes that appeared in recent 46 million years, and 19 of them evolved from noncoding ancestral sequences with entire de novo origination process reconstructed. The new genes evolved gradually in exon−intron structure, protein length, expression specificity, and evolutionary constraint. These new genes, whether or not from de novo origination, are dominantly expressed in the rapidly developing shoots, and make transcriptomes of shoots the youngest among various bamboo tissues, rather than reproductive tissue in other plants. Additionally, the particularity of bamboo shoots has also been shaped by recent whole-genome duplicates (WGDs), which evolved divergent expression patterns from ancestral states. New genes and WGDs have been evolutionarily recruited into coexpression networks to underline fast-growing trait of bamboo shoot. Our study highlights the importance of interactions between new genes and genome duplicates in generating morphological innovation.
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Affiliation(s)
- Guihua Jin
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Peng-Fei Ma
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Xiaopei Wu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Lianfeng Gu
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Manyuan Long
- Department of Ecology and Evolution, The University of Chicago, Chicago, Illinois, 60637, USA
| | - Chengjun Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
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25
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Lan Y, Wu L, Wu M, Liu H, Gao Y, Zhang K, Xiang Y. Transcriptome analysis reveals key genes regulating signaling and metabolic pathways during the growth of moso bamboo (Phyllostachys edulis) shoots. PHYSIOLOGIA PLANTARUM 2021; 172:91-105. [PMID: 33280114 DOI: 10.1111/ppl.13296] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 11/22/2020] [Accepted: 11/30/2020] [Indexed: 06/12/2023]
Abstract
Moso bamboo (Phyllostachys edulis), a high-value bamboo used to produce food (young shoots), building, and industrial goods. To explore key candidate genes regulating signal transduction and metabolic processes during the initiation of stem elongation in moso bamboo, a transcriptome analysis of the shoots during three successive early elongation stages was performed. From cluster and differential expression analyses, 2984 differentially expressed genes (DEGs) were selected for an enrichment analysis. The DEGs were significantly enriched in the plant hormone signal transduction, sugar and starch metabolism, and energy metabolism pathways. Consequently, the DEG expression patterns of these pathways were analyzed, and the plant endogenous hormone and carbon metabolite (including sucrose, total soluble sugar, and starch) contents for each growth stage, of the shoot, were determined. The cytokinin-signaling pathway was continuously active in the three successive elongation stages, in which several cytokinin-signaling genes played indispensable roles. Additionally, many key DEGs regulating sugar, starch metabolism, and energy conversion, which are actively involved in energy production and substrate synthesis during the continuous growth of the shoots, were found. In summary, our study lays a foundation for understanding the mechanisms of moso bamboo growth and provides useful gene resources for breeding through genetic engineering.
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Affiliation(s)
- Yangang Lan
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, China
| | - Lin Wu
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, China
| | - Min Wu
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, China
| | - Huanlong Liu
- College of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Yameng Gao
- College of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Kaimei Zhang
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, China
| | - Yan Xiang
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, China
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26
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Ren Z, Wang X, Tao Q, Guo Q, Zhou Y, Yi F, Huang G, Li Y, Zhang M, Li Z, Duan L. Transcriptome dynamic landscape underlying the improvement of maize lodging resistance under coronatine treatment. BMC PLANT BIOLOGY 2021; 21:202. [PMID: 33906598 PMCID: PMC8077928 DOI: 10.1186/s12870-021-02962-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 04/07/2021] [Indexed: 05/17/2023]
Abstract
BACKGROUND Lodging is one of the important factors causing maize yield. Plant height is an important factor in determining plant architecture in maize (Zea mays L.), which is closely related to lodging resistance under high planting density. Coronatine (COR), which is a phytotoxin and produced by the pathogen Pseudomonas syringae, is a functional and structural analogue of jasmonic acid (JA). RESULTS In this study, we found COR, as a new plant growth regulator, could effectively reduce plant height and ear height of both hybrids (ZD958 and XY335) and inbred (B73) maize by inhibiting internode growth during elongation, thus improve maize lodging resistance. To study gene expression changes in internode after COR treatment, we collected spatio-temporal transcriptome of inbred B73 internode under normal condition and COR treatment, including the three different regions of internode (fixed, meristem and elongation regions) at three different developmental stages. The gene expression levels of the three regions at normal condition were described and then compared with that upon COR treatment. In total, 8605 COR-responsive genes (COR-RGs) were found, consist of 802 genes specifically expressed in internode. For these COR-RGs, 614, 870, 2123 of which showed expression changes in only fixed, meristem and elongation region, respectively. Both the number and function were significantly changed for COR-RGs identified in different regions, indicating genes with different functions were regulated at the three regions. Besides, we found more than 80% genes of gibberellin and jasmonic acid were changed under COR treatment. CONCLUSIONS These data provide a gene expression profiling in different regions of internode development and molecular mechanism of COR affecting internode elongation. A putative schematic of the internode response to COR treatment is proposed which shows the basic process of COR affecting internode elongation. This research provides a useful resource for studying maize internode development and improves our understanding of the COR regulation mechanism based on plant height.
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Affiliation(s)
- Zhaobin Ren
- State Key Laboratory of Plant Physiology and Biochemistry, Engineering Research Center of Plant Growth Regulator, Ministry of Education &College of Agronomy and Biotechnology, China Agricultural University, No.2 Yuanmingyuan West Road, Haidian, Beijing, 100193, China
| | - Xing Wang
- State Key Laboratory of Plant Physiology and Biochemistry, Engineering Research Center of Plant Growth Regulator, Ministry of Education &College of Agronomy and Biotechnology, China Agricultural University, No.2 Yuanmingyuan West Road, Haidian, Beijing, 100193, China
| | - Qun Tao
- State Key Laboratory of Plant Physiology and Biochemistry, Engineering Research Center of Plant Growth Regulator, Ministry of Education &College of Agronomy and Biotechnology, China Agricultural University, No.2 Yuanmingyuan West Road, Haidian, Beijing, 100193, China
| | - Qing Guo
- State Key Laboratory of Plant Physiology and Biochemistry, Engineering Research Center of Plant Growth Regulator, Ministry of Education &College of Agronomy and Biotechnology, China Agricultural University, No.2 Yuanmingyuan West Road, Haidian, Beijing, 100193, China
| | - Yuyi Zhou
- State Key Laboratory of Plant Physiology and Biochemistry, Engineering Research Center of Plant Growth Regulator, Ministry of Education &College of Agronomy and Biotechnology, China Agricultural University, No.2 Yuanmingyuan West Road, Haidian, Beijing, 100193, China
| | - Fei Yi
- State Key Laboratory of Plant Physiology and Biochemistry, Engineering Research Center of Plant Growth Regulator, Ministry of Education &College of Agronomy and Biotechnology, China Agricultural University, No.2 Yuanmingyuan West Road, Haidian, Beijing, 100193, China.
| | - Guanmin Huang
- State Key Laboratory of Plant Physiology and Biochemistry, Engineering Research Center of Plant Growth Regulator, Ministry of Education &College of Agronomy and Biotechnology, China Agricultural University, No.2 Yuanmingyuan West Road, Haidian, Beijing, 100193, China
| | - Yanxia Li
- State Key Laboratory of Plant Physiology and Biochemistry, Engineering Research Center of Plant Growth Regulator, Ministry of Education &College of Agronomy and Biotechnology, China Agricultural University, No.2 Yuanmingyuan West Road, Haidian, Beijing, 100193, China
| | - Mingcai Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, Engineering Research Center of Plant Growth Regulator, Ministry of Education &College of Agronomy and Biotechnology, China Agricultural University, No.2 Yuanmingyuan West Road, Haidian, Beijing, 100193, China
| | - Zhaohu Li
- State Key Laboratory of Plant Physiology and Biochemistry, Engineering Research Center of Plant Growth Regulator, Ministry of Education &College of Agronomy and Biotechnology, China Agricultural University, No.2 Yuanmingyuan West Road, Haidian, Beijing, 100193, China
| | - Liusheng Duan
- State Key Laboratory of Plant Physiology and Biochemistry, Engineering Research Center of Plant Growth Regulator, Ministry of Education &College of Agronomy and Biotechnology, China Agricultural University, No.2 Yuanmingyuan West Road, Haidian, Beijing, 100193, China.
- College of Plant Science and Technology, Beijing University of Agriculture, No.7 Beinong Road, Changping, Beijing, 102206, China.
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Chen M, Ju Y, Ahmad Z, Yin Z, Ding Y, Que F, Yan J, Chu J, Wei Q. Multi-analysis of sheath senescence provides new insights into bamboo shoot development at the fast growth stage. TREE PHYSIOLOGY 2021; 41:491-507. [PMID: 33079187 DOI: 10.1093/treephys/tpaa140] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 10/05/2020] [Accepted: 10/05/2020] [Indexed: 05/16/2023]
Abstract
Sheath senescence is an important part of bamboo shoot development during the fast growth stage. However, no information has been reported about this distinctive process until now. Using multiple approaches, we found that sheath senescence is a complex process that occurs sequentially with chloroplast corruption, chlorophyll degradation and water loss. Reactive oxygen species (ROS), salicylic acid and abscisic acid also accumulate in the senescing sheath. Transcriptome analysis showed that NAC and WRKY transcription factors, such as NAC2 and WRKY75, as well as their possible downstream target genes, such as those involved in ROS production, proteolysis and nutrition recycling, constitute the gene network of the bamboo sheath senescence process. Furthermore, the initiation of sheath senescence might be triggered by hexokinase genes, such as HXK6, which is localized to the mitochondrion and could promote leaf senescence when overexpressed in Arabidopsis. Sheath senescence occurs after the growth decrease of the internodes, which provides assimilates. The slowing of internode growth possibly results in sugar accumulation, such as glucose, in the sheath, which finally upregulates hexokinase genes and initiates sheath senescence. These findings reveal that sheath senescence is a multilevel regulation process and has a close link to the corresponding internode growth, which provides new insights into the shoot development of bamboo during the fast growth stage.
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Affiliation(s)
- Ming Chen
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
- College of Biology and Environment, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Ye Ju
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
- College of Biology and Environment, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Zishan Ahmad
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
- College of Biology and Environment, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Zengfang Yin
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
- College of Biology and Environment, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Yulong Ding
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Feng Que
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Jijun Yan
- National Centre for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jinfang Chu
- National Centre for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qiang Wei
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
- College of Biology and Environment, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
- Jiangxi Provincial Key Laboratory for Bamboo Germplasm Resources and Utilization, Jiangxi Agriculture University, Nanchang, Jiangxi 330045, China
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28
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Liu M, He W, Zhang A, Zhang L, Sun D, Gao Y, Ni P, Ma X, Cui Z, Ruan Y. Genetic analysis of maize shank length by QTL mapping in three recombinant inbred line populations. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 303:110767. [PMID: 33487352 DOI: 10.1016/j.plantsci.2020.110767] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 11/12/2020] [Accepted: 11/17/2020] [Indexed: 06/12/2023]
Abstract
In maize, the shank is a unique tissue linking the stem to the ear. Shank length (SL) mainly affects the transport of photosynthetic products to the ear and the dehydration of kernels via regulated husk morphology. The limited studies on SL revealed it is a highly heritable quantitative trait controlled by significant additive and additive-dominance effects. However, the genetic basis of SL remains unclear. In this study, we analyzed three maize recombinant inbred line (RIL) populations to elucidate the molecular mechanism underlying the SL. The data indicated the SL varied among the three RIL populations and was highly heritable. Additionally, the SL was positively correlated with the husk length (HL), husk number (HN), ear length (EL), and ear weight (EW) in the BY815/K22 (BYK) and CI7/K22 (CIK) RIL populations, but was negatively correlated with the husk width (HW) in the BYK RIL population. Moreover, 10 quantitative trait loci (QTL) for SL were identified in the three RIL populations, five of which were large-effect QTL. The percentage of the total phenotypic variation explained by the QTL for SL was 13.67 %, 20.45 %, and 30.81 % in the BY815/DE3 (BYD), BYK, and CIK RIL populations, respectively. Further analyses uncovered some genetic overlap between SL and EL, SL and ear row number (ERN), SL and cob weight (CW), and SL and HN. Unlike the large-effect QTL qSL BYK-2-2, which spanned the centromere, the other four large-effect QTL were delimited to a single peak bin via bin map. Furthermore, 2, 5, 6, and 12 genes associated with SL were identified for qSL BYK-2-1, qSL CIK-2-1, qSL CIK-9-1, and qSL CIK-9-2, respectively. Five of the candidate genes for SL may contribute to the hormone metabolism and sphingolipid biosynthesis regulating cell elongation, division, differentiation, and expansion. These results may be relevant for future studies on the genetic basis of SL and for the molecular breeding of maize based on marker-assisted selection to develop new varieties with an ideal SL.
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Affiliation(s)
- Meiling Liu
- College of Biological Science and Technology, Liaoning Province Research Center of Plant Genetic Engineering Technology, Shenyang Key Laboratory of Maize Genomic Selection Breeding, Shenyang Agricultural University, Shenyang, 110866, China
| | - Wenshu He
- College of Biological Science and Technology, Liaoning Province Research Center of Plant Genetic Engineering Technology, Shenyang Key Laboratory of Maize Genomic Selection Breeding, Shenyang Agricultural University, Shenyang, 110866, China; Department of Plant Production and Forestry Science, University of Lleida-Agrotecnio Center, Av. Alcalde Rovira Roure, Lleida, 25198, Spain
| | - Ao Zhang
- College of Biological Science and Technology, Liaoning Province Research Center of Plant Genetic Engineering Technology, Shenyang Key Laboratory of Maize Genomic Selection Breeding, Shenyang Agricultural University, Shenyang, 110866, China
| | - Lijun Zhang
- College of Biological Science and Technology, Liaoning Province Research Center of Plant Genetic Engineering Technology, Shenyang Key Laboratory of Maize Genomic Selection Breeding, Shenyang Agricultural University, Shenyang, 110866, China
| | - Daqiu Sun
- College of Biological Science and Technology, Liaoning Province Research Center of Plant Genetic Engineering Technology, Shenyang Key Laboratory of Maize Genomic Selection Breeding, Shenyang Agricultural University, Shenyang, 110866, China
| | - Yuan Gao
- College of Biological Science and Technology, Liaoning Province Research Center of Plant Genetic Engineering Technology, Shenyang Key Laboratory of Maize Genomic Selection Breeding, Shenyang Agricultural University, Shenyang, 110866, China
| | - Pengzun Ni
- College of Biological Science and Technology, Liaoning Province Research Center of Plant Genetic Engineering Technology, Shenyang Key Laboratory of Maize Genomic Selection Breeding, Shenyang Agricultural University, Shenyang, 110866, China
| | - Xinglin Ma
- Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Zhenhai Cui
- College of Biological Science and Technology, Liaoning Province Research Center of Plant Genetic Engineering Technology, Shenyang Key Laboratory of Maize Genomic Selection Breeding, Shenyang Agricultural University, Shenyang, 110866, China.
| | - Yanye Ruan
- College of Biological Science and Technology, Liaoning Province Research Center of Plant Genetic Engineering Technology, Shenyang Key Laboratory of Maize Genomic Selection Breeding, Shenyang Agricultural University, Shenyang, 110866, China.
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29
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Wang X, Yan X, Li S, Jing Y, Gu L, Zou S, Zhang J, Liu B. Genome-wide identification, evolution and expression analysis of the aspartic protease gene family during rapid growth of moso bamboo (Phyllostachys edulis) shoots. BMC Genomics 2021; 22:45. [PMID: 33423665 PMCID: PMC7798191 DOI: 10.1186/s12864-020-07290-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 11/28/2020] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND Aspartic proteases (APs) are a class of aspartic peptidases belonging to nine proteolytic enzyme families whose members are widely distributed in biological organisms. APs play essential functions during plant development and environmental adaptation. However, there are few reports about APs in fast-growing moso bamboo. RESULT In this study, we identified a total of 129 AP proteins (PhAPs) encoded by the moso bamboo genome. Phylogenetic and gene structure analyses showed that these 129 PhAPs could be divided into three categories (categories A, B and C). The PhAP gene family in moso bamboo may have undergone gene expansion, especially the members of categories A and B, although homologs of some members in category C have been lost. The chromosomal location of PhAPs suggested that segmental and tandem duplication events were critical for PhAP gene expansion. Promoter analysis revealed that PhAPs in moso bamboo may be involved in plant development and responses to environmental stress. Furthermore, PhAPs showed tissue-specific expression patterns and may play important roles in rapid growth, including programmed cell death, cell division and elongation, by integrating environmental signals such as light and gibberellin signals. CONCLUSION Comprehensive analysis of the AP gene family in moso bamboo suggests that PhAPs have experienced gene expansion that is distinct from that in rice and may play an important role in moso bamboo organ development and rapid growth. Our results provide a direction and lay a foundation for further analysis of plant AP genes to clarify their function during rapid growth.
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Affiliation(s)
- Xiaqin Wang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Fujian Colleges and Universities Engineering Research Institute of Conservation & Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Zhejiang, 311300, Hangzhou, China
| | - Xinyang Yan
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Fujian Colleges and Universities Engineering Research Institute of Conservation & Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Shubin Li
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yun Jing
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Lianfeng Gu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Shuangquan Zou
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Fujian Colleges and Universities Engineering Research Institute of Conservation & Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jin Zhang
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Zhejiang, 311300, Hangzhou, China.
| | - Bobin Liu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. .,Fujian Colleges and Universities Engineering Research Institute of Conservation & Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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30
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Tao GY, Ramakrishnan M, Vinod KK, Yrjälä K, Satheesh V, Cho J, Fu Y, Zhou M. Multi-omics analysis of cellular pathways involved in different rapid growth stages of moso bamboo. TREE PHYSIOLOGY 2020; 40:1487-1508. [PMID: 32705116 DOI: 10.1093/treephys/tpaa090] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 04/29/2020] [Accepted: 07/09/2020] [Indexed: 06/11/2023]
Abstract
Moso bamboo (Phyllostachys edulis (Carriere) J. Houzeau) is a rapidly growing grass of industrial and ecological importance. However, the molecular mechanisms of its remarkable growth are not well understood. In this study, we investigated the early-stage growth of moso bamboo shoots and defined three different growth stages based on histological and biochemical analyses, namely, starting of cell division (SD), rapid division (RD) and rapid elongation (RE). Further analyses on potentially relevant cellular pathways in these growth stages using multi-omics approaches such as transcriptomics and proteomics revealed the involvement of multiple cellular pathways, including DNA replication, repair and ribosome biogenesis. A total of 8045 differentially expressed genes (DEGs) and 1053 differentially expressed proteins (DEPs) were identified in our analyses. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses of detected DEGs identified several key biological pathways such as phytohormone metabolism, signal transduction, cell wall development and carbohydrate metabolism. The comparative analysis of proteins displayed that a total of 213 DEPs corresponded with DEGs and 3 significant expression profiles that could be promoting the fast growth of bamboo internodes. Moreover, protein-protein interaction network prediction analysis is suggestive of the involvement of five major proteins of signal transduction, DNA synthesis and RNA transcription, and may act as key elements responsible for the rapid shoot growth. Our work exploits multi-omics and bioinformatic approaches to unfurl the complexity of molecular networks involved in the rapid growth of moso bamboo and opens up questions related to the interactions between the functions played by individual molecular pathway.
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Affiliation(s)
- Gui-Yun Tao
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, Zhejiang, China
- Zhejiang Provincial Collaborative Innovation Centre for Bamboo Resources and High-efficiency Utilization, Zhejiang A&F University, Lin'an, Hangzhou 311300, Zhejiang, China
- The State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Xiangshan, Haidian District, Beijing, China
- Research Institute of Forestry, Chinese Academy of Forestry, Xiangshan, Haidian District, Beijing, China
| | - Muthusamy Ramakrishnan
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, Zhejiang, China
| | | | - Kim Yrjälä
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, Zhejiang, China
- Department of Forest Sciences, University of Helsinki, Helsinki P.O. Box 27 00014, Finland
| | - Viswanathan Satheesh
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Jungnam Cho
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
- CAS-JIC Centre of Excellence for Plant and Microbial Science, Chinese Academy of Sciences, Shanghai 200032, China
| | - Ying Fu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, Zhejiang, China
- Zhejiang Provincial Collaborative Innovation Centre for Bamboo Resources and High-efficiency Utilization, Zhejiang A&F University, Lin'an, Hangzhou 311300, Zhejiang, China
| | - Mingbing Zhou
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, Zhejiang, China
- Zhejiang Provincial Collaborative Innovation Centre for Bamboo Resources and High-efficiency Utilization, Zhejiang A&F University, Lin'an, Hangzhou 311300, Zhejiang, China
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31
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Effects of ecological factors on growth of Arundinaria spanostachya shoots in Liziping National Nature Reserve, China. Glob Ecol Conserv 2020. [DOI: 10.1016/j.gecco.2020.e01121] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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32
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Guo X, Chen H, Liu Y, Chen W, Ying Y, Han J, Gui R, Zhang H. The acid invertase gene family is involved in internode elongation in Phyllostachys heterocycla cv. pubescens. TREE PHYSIOLOGY 2020; 40:1217-1231. [PMID: 32333784 DOI: 10.1093/treephys/tpaa053] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 02/17/2020] [Accepted: 04/20/2020] [Indexed: 06/11/2023]
Abstract
Acid invertases (INVs) play a pivotal role in both vegetative and reproductive growth of plants. However, their possible functions in fast-growing plants such as bamboo are largely unknown. Here, we report the molecular characterization of acid INVs in Phyllostachys heterocycla cv. pubescens, a fast-growing bamboo species commercially grown worldwide. Nine acid INVs (PhINVs), including seven cell wall INVs (PhCWINV1, PhCWINV2, PhCWINV3, PhCWINV4, PhCWINV5, PhCWINV6 and PhCWINV7) and two vacuolar INVs (PhVINV11 and PhVINV12) were isolated. Bioinformatic analyses demonstrated that they all share high amino acid identity with other INVs from different plant species and contain the motifs typically conserved in acid INV. Enzyme activity assays revealed a significantly higher INV activity in the fast-growing tissues, such as the elongating internodes of stems. Detailed quantitative reverse-transcription PCR analyses showed various expression patterns of PhINVs at different developmental stages of the elongating stems. With the exception of PhCWINV6, all PhINVs were ubiquitously expressed in a developmental-specific manner. Further studies in Arabidopsis exhibited that constitutive expression of PhCWINV1, PhCWINV4 or PhCWINV7 increased the biomass production of transgenic plants, as indicated by augmented plant heights and shoot dry weights than the wild-type plants. All these results suggest that acid INVs play a crucial role in the internode elongation of P. heterocycla cv. pubescens and would provide valuable information for the dissection of their exact biological functions in the fast growth of bamboo.
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Affiliation(s)
- Xiaoqin Guo
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, 666 Wusu Street, Hangzhou 311300, China
| | - Hongjun Chen
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, 666 Wusu Street, Hangzhou 311300, China
| | - Yue Liu
- College of Life Sciences, Qingdao University, 308 Ningxia Road, Qingdao 266071, China
| | - Wei Chen
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, 666 Wusu Street, Hangzhou 311300, China
| | - Yeqing Ying
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, 666 Wusu Street, Hangzhou 311300, China
| | - Junjie Han
- Yantai Academy of Agricultural Sciences, 26 West Gangcheng Street, Yantai 265500, China
| | - Renyi Gui
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, 666 Wusu Street, Hangzhou 311300, China
| | - Hongxia Zhang
- College of Agriculture, Ludong University, 186 Hongqizhong Road, Yantai 264025, China
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong (Ludong University), 186 Hongqizhong Road, Yantai 264025, China
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Ramakrishnan M, Yrjälä K, Vinod KK, Sharma A, Cho J, Satheesh V, Zhou M. Genetics and genomics of moso bamboo (Phyllostachys edulis): Current status, future challenges, and biotechnological opportunities toward a sustainable bamboo industry. Food Energy Secur 2020. [DOI: 10.1002/fes3.229] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Affiliation(s)
| | - Kim Yrjälä
- State Key Laboratory of Subtropical Silviculture Zhejiang A&F University Hangzhou China
- Department of Forest Sciences University of Helsinki Helsinki Finland
| | | | - Anket Sharma
- State Key Laboratory of Subtropical Silviculture Zhejiang A&F University Hangzhou China
| | - Jungnam Cho
- National Key Laboratory of Plant Molecular Genetics CAS Center for Excellence in Molecular Plant Sciences Shanghai Institute of Plant Physiology and Ecology Chinese Academy of Sciences Shanghai China
- CAS‐JIC Centre of Excellence for Plant and Microbial Science (CEPAMS) Chinese Academy of Sciences Shanghai China
| | - Viswanathan Satheesh
- National Key Laboratory of Plant Molecular Genetics CAS Center for Excellence in Molecular Plant Sciences Shanghai Institute of Plant Physiology and Ecology Chinese Academy of Sciences Shanghai China
- Shanghai Center for Plant Stress Biology CAS Center for Excellence in Molecular Plant Sciences Chinese Academy of Sciences Shanghai China
| | - Mingbing Zhou
- State Key Laboratory of Subtropical Silviculture Zhejiang A&F University Hangzhou China
- Zhejiang Provincial Collaborative Innovation Centre for Bamboo Resources and High‐efficiency Utilization Zhejiang A&F University Hangzhou China
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34
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Zhang Z, Yang X, Cheng L, Guo Z, Wang H, Wu W, Shin K, Zhu J, Zheng X, Bian J, Li Y, Gu L, Zhu Q, Wang ZY, Wang W. Physiological and transcriptomic analyses of brassinosteroid function in moso bamboo (Phyllostachys edulis) seedlings. PLANTA 2020; 252:27. [PMID: 32712728 DOI: 10.1007/s00425-020-03432-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 07/17/2020] [Indexed: 06/11/2023]
Abstract
This study demonstrates that brassinosteroid is essential for seedling and shoot growth in moso bamboo. The shoot of moso bamboo is known to grow extremely fast. The roles of phytohormones in such fast growth of bamboo shoot remain unclear. Here we reported that endogenous brassinosteroid (BR) is a major factor promoting bamboo shoot internode elongation. Reducing endogenous brassinosteroid level by its biosynthesis inhibitor propiconazole stunted shoot growth in seedling stage, whereas exogenous BR application promoted scale leaf elongation and the inclination of lamina joint of leaves and scale leaves. Genome-wide transcriptome analysis identified hundreds of genes whose expression levels are altered by BR and propiconazole in shoots and roots of bamboo seedling. The data show that BR regulates cell wall-related genes, hydrogen peroxide catabolic genes, and auxin-related genes. Our study demonstrates an essential role of BR in fast growth bamboo shoots and identifies a large number of BR-responsive genes in bamboo seedlings.
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Affiliation(s)
- Zhe Zhang
- Basic Forestry and Proteomics Research Center, Forestry College, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xuelian Yang
- Basic Forestry and Proteomics Research Center, Forestry College, Fujian Agriculture and Forestry University, Fuzhou, China
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - Ling Cheng
- Basic Forestry and Proteomics Research Center, Forestry College, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zejun Guo
- Basic Forestry and Proteomics Research Center, Forestry College, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Huiyuan Wang
- Basic Forestry and Proteomics Research Center, Forestry College, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Weihuang Wu
- Basic Forestry and Proteomics Research Center, Forestry College, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Kihye Shin
- Basic Forestry and Proteomics Research Center, Forestry College, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jinyao Zhu
- Basic Forestry and Proteomics Research Center, Forestry College, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiaoli Zheng
- Basic Forestry and Proteomics Research Center, Forestry College, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jianghu Bian
- Basic Forestry and Proteomics Research Center, Forestry College, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yangchen Li
- Basic Forestry and Proteomics Research Center, Forestry College, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Lianfeng Gu
- Basic Forestry and Proteomics Research Center, Forestry College, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qiang Zhu
- Basic Forestry and Proteomics Research Center, Forestry College, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhi-Yong Wang
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - Wenfei Wang
- Basic Forestry and Proteomics Research Center, Forestry College, Fujian Agriculture and Forestry University, Fuzhou, China.
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China.
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Guo Z, Zhang Z, Yang X, Yin K, Chen Y, Zhang Z, Shin K, Zhu Q, Wang ZY, Wang W. PSBR1, encoding a mitochondrial protein, is regulated by brassinosteroid in moso bamboo (Phyllostachys edulis). PLANT MOLECULAR BIOLOGY 2020; 103:63-74. [PMID: 32040757 DOI: 10.1007/s11103-020-00975-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 01/31/2020] [Indexed: 06/10/2023]
Abstract
PSBR1 is a moso bamboo gene negatively regulated by brassinosteroid, which encodes a mitochondrial localized protein. Overexpression of PSBR1 leads to growth inhibition in various growth progresses in Arabidopsis. The young shoot of moso bamboo (Phyllostachys edulis) is known as one of the fastest growing plant organs. The roles of phytohormones in the fast-growth of bamboo shoot are not fully understood. Brassinosteroids (BRs) are a group of growth-promoting steroid hormones that play important roles in cell elongation and division. While BR related genes are highly enriched in fast-growing internodes in moso bamboo, the functions of BR in the fast-growth process is not understood at the molecular level. Here, we identified a poaceae specific gene, PSBR1 (Poaceae specific and BR responsive gene 1) from the moso bamboo genome. PSBR1 was highly expressed in the stem and leaves of bamboo seedling, and the elongating nodes of fast-growing bamboo shoot. PSBR1's expression is increased by BR biosynthesis inhibitor propiconazole but decreased by BR treatment. PSBR1 encodes a novel protein that is localized to the mitochondria in tobacco and bamboo protoplast. The Arabidopsis transgenic plants overexpressing PSBR1 show growth inhibition in both vegetative and reproductive stages. This study suggests that PSBR1 is a BR regulated mitochondrial protein in bamboo, which inhibits plant growth when overexpressed in Arabidopsis.
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Affiliation(s)
- Zejun Guo
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Agriculture and Forestry University, 15 Shangxiadian Road, Fuzhou, 350002, Fujian, China
| | - Zhe Zhang
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Agriculture and Forestry University, 15 Shangxiadian Road, Fuzhou, 350002, Fujian, China
| | - Xuelian Yang
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Agriculture and Forestry University, 15 Shangxiadian Road, Fuzhou, 350002, Fujian, China
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - Kuixing Yin
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Agriculture and Forestry University, 15 Shangxiadian Road, Fuzhou, 350002, Fujian, China
| | - Yitao Chen
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Agriculture and Forestry University, 15 Shangxiadian Road, Fuzhou, 350002, Fujian, China
| | - Zhenzhen Zhang
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Agriculture and Forestry University, 15 Shangxiadian Road, Fuzhou, 350002, Fujian, China
| | - Kihye Shin
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Agriculture and Forestry University, 15 Shangxiadian Road, Fuzhou, 350002, Fujian, China
| | - Qiang Zhu
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Agriculture and Forestry University, 15 Shangxiadian Road, Fuzhou, 350002, Fujian, China
| | - Zhi-Yong Wang
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - Wenfei Wang
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Agriculture and Forestry University, 15 Shangxiadian Road, Fuzhou, 350002, Fujian, China.
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36
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Wang S, Chen TH, Liu EU, Liu CP. Accessing the nursing behaviour of Moso bamboo (Phyllostachys edilus) on carbohydrates dynamics and photosystems. Sci Rep 2020; 10:1015. [PMID: 31974388 PMCID: PMC6978378 DOI: 10.1038/s41598-020-57643-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 12/30/2019] [Indexed: 11/28/2022] Open
Abstract
Nursing behaviour, also known as breastfeeding behaviour, is the feeding of juvenile individuals with nutrients or proteins from matures especially in mammals. As a hypothetical phenomenon in bamboo forests, mature bamboos have transferred photoassimilates to young bamboos for recovering and rebuilding their photosystems especially in winter. This process is accompanied by changes in the ability of photosystems and the mass fraction of non-structural carbohydrates (NSCs), structural carbohydrates (SCs), and lignin. We analysed carbohydrates and chlorophyll fluorescence to compare the physiological traits in mature (age 2, 3, 4) and immature (age 1) Moso bamboos (Phyllostachys edilus) during a year using the Portable Chlorophyll Fluorometer (PCF) and the Liquid Chromatographic (LC) method. The results showed that the mass fraction of total soluble carbohydrates (TSCs) and starch in the bottom of bamboo at age 1 was higher than other parts and ages in spring, whereas the mass fraction of TSCs, starch, and sucrose at age 3 was higher than other parts and ages in winter. The Fv/Fm, an indicator to reveal photosystems were functional or not, at age 1 dramatically dropped when the cold current attacked first time in October, and then quickly recovered in November. Our findings indicate that mature bamboos very possibly provide carbohydrates to immature bamboos and help them rebuild their photosystems when a bamboo forest resists cold stress.
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Affiliation(s)
- Shitephen Wang
- Kyoto University, Graduate School of Agriculture, Kyoto, 606-0096, Japan
| | - Tsai-Huei Chen
- Taiwan Forest Research Institute, Silviculture Division, Taipei, 10066, Taiwan
| | - En-U Liu
- Taiwan Forest Research Institute, Forestry Economics Division, Taipei, 10066, Taiwan
| | - Chiung-Pin Liu
- National Chung Hsing University, Department of Forestry, Taichung, 40227, Taiwan.
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Qiu L, Chen R, Fan Y, Huang X, Luo H, Xiong F, Liu J, Zhang R, Lei J, Zhou H, Wu J, Li Y. Integrated mRNA and small RNA sequencing reveals microRNA regulatory network associated with internode elongation in sugarcane (Saccharum officinarum L.). BMC Genomics 2019; 20:817. [PMID: 31699032 PMCID: PMC6836457 DOI: 10.1186/s12864-019-6201-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 10/18/2019] [Indexed: 12/31/2022] Open
Abstract
Background Internode elongation is one of the most important traits in sugarcane because of its relation to crop productivity. Understanding the microRNA (miRNA) and mRNA expression profiles related to sugarcane internode elongation would help develop molecular improvement strategies but they are not yet well-investigated. To identify genes and miRNAs involved in internode elongation, the cDNA and small RNA libraries from the pre-elongation stage (EI), early elongation stage (EII) and rapid elongation stage (EIII) were sequenced and their expression were studied. Results Based on the sequencing results, 499,495,518 reads and 80,745 unigenes were identified from stem internodes of sugarcane. The comparisons of EI vs. EII, EI vs. EIII, and EII vs. EIII identified 493, 5035 and 3041 differentially expressed genes, respectively. Further analysis revealed that the differentially expressed genes were enriched in the GO terms oxidoreductase activity and tetrapyrrole binding. KEGG pathway annotation showed significant enrichment in “zeatin biosynthesis”, “nitrogen metabolism” and “plant hormone signal transduction”, which might be participating in internode elongation. miRNA identification showed 241 known miRNAs and 245 novel candidate miRNAs. By pairwise comparison, 11, 42 and 26 differentially expressed miRNAs were identified from EI and EII, EI and EIII, and EII and EIII comparisons, respectively. The target prediction revealed that the genes involved in “zeatin biosynthesis”, “nitrogen metabolism” and “plant hormone signal transduction” pathways are targets of the miRNAs. We found that the known miRNAs miR2592-y, miR1520-x, miR390-x, miR5658-x, miR6169-x and miR8154-x were likely regulators of genes with internode elongation in sugarcane. Conclusions The results of this study provided a global view of mRNA and miRNA regulation during sugarcane internode elongation. A genetic network of miRNA-mRNA was identified with miRNA-mediated gene expression as a mechanism in sugarcane internode elongation. Such evidence will be valuable for further investigations of the molecular regulatory mechanisms underpinning sugarcane growth and development.
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Affiliation(s)
- Lihang Qiu
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/Sugarcane Research Center, Chinese Academy of Agricultural Sciences, East Daxue Road 172, Nanning, 530004, Guangxi, China.,Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, and Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning, Guangxi, China
| | - Rongfa Chen
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/Sugarcane Research Center, Chinese Academy of Agricultural Sciences, East Daxue Road 172, Nanning, 530004, Guangxi, China.,Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, and Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning, Guangxi, China
| | - Yegeng Fan
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/Sugarcane Research Center, Chinese Academy of Agricultural Sciences, East Daxue Road 172, Nanning, 530004, Guangxi, China.,Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, and Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning, Guangxi, China
| | - Xing Huang
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/Sugarcane Research Center, Chinese Academy of Agricultural Sciences, East Daxue Road 172, Nanning, 530004, Guangxi, China.,Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, and Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning, Guangxi, China
| | - Hanmin Luo
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/Sugarcane Research Center, Chinese Academy of Agricultural Sciences, East Daxue Road 172, Nanning, 530004, Guangxi, China.,Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, and Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning, Guangxi, China
| | - Faqian Xiong
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, and Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning, Guangxi, China
| | - Junxian Liu
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/Sugarcane Research Center, Chinese Academy of Agricultural Sciences, East Daxue Road 172, Nanning, 530004, Guangxi, China.,Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, and Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning, Guangxi, China
| | - Ronghua Zhang
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/Sugarcane Research Center, Chinese Academy of Agricultural Sciences, East Daxue Road 172, Nanning, 530004, Guangxi, China.,Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, and Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning, Guangxi, China
| | - Jingchao Lei
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/Sugarcane Research Center, Chinese Academy of Agricultural Sciences, East Daxue Road 172, Nanning, 530004, Guangxi, China.,Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, and Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning, Guangxi, China
| | - Huiwen Zhou
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/Sugarcane Research Center, Chinese Academy of Agricultural Sciences, East Daxue Road 172, Nanning, 530004, Guangxi, China.,Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, and Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning, Guangxi, China
| | - Jianming Wu
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/Sugarcane Research Center, Chinese Academy of Agricultural Sciences, East Daxue Road 172, Nanning, 530004, Guangxi, China. .,Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, and Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning, Guangxi, China.
| | - Yangrui Li
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/Sugarcane Research Center, Chinese Academy of Agricultural Sciences, East Daxue Road 172, Nanning, 530004, Guangxi, China. .,Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, and Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning, Guangxi, China.
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38
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Zhao J, Gao P, Li C, Lin X, Guo X, Liu S. PhePEBP family genes regulated by plant hormones and drought are associated with the activation of lateral buds and seedling growth in Phyllostachys edulis. TREE PHYSIOLOGY 2019; 39:1387-1404. [PMID: 31115464 DOI: 10.1093/treephys/tpz056] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 04/08/2019] [Accepted: 05/10/2019] [Indexed: 06/09/2023]
Abstract
Development of lateral buds on the underground rhizome in moso bamboo is essentially the early stage of the development of aboveground branching, which is regulated by Phosphatidyl-Ethanolamine Binding Protein (PEBP) family genes, but it is unknown whether the PEBP family genes are involved in the activation and development of lateral buds underground. By scanning the whole-genome sequence of moso bamboo, we identified 25 PhePEBP family genes and amplified their full-length open reading frames (ORFs). A sequence analysis revealed that they are composed of four exons and three introns, except for PheFT10, which contains six exons and five introns. PheFT10 underwent alternative splicing, resulting in at least four transcripts (PheFT10α, PheFT10β, PheFT10γ and PheFT10δ). Although PhePEBP genes are generally expressed at low levels and show dramatically organ-specific expressions, the transcription levels of most PhePEBP genes, including the transcripts of PheFT10, change with plant age. Together with the observation that the expression of PhePEBP family genes can be regulated by plant hormones and drought, our data suggest that PhePEBP family genes might be involved in the activation of lateral buds and seedling growth. Particularly, PheFT9, PheTFL2 and PheTFL8 may play vital roles during the activation of dormant buds based on the analysis of amino acid substitution and expression profile. These findings provide insights for in-depth exploration of the biological functions of the PhePEBP family genes in regulating the activation of dormant bud and the development of seedling in moso bamboo.
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Affiliation(s)
- Jianwen Zhao
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Peijun Gao
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Chunlong Li
- Section of Horticulture, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Xinchun Lin
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Xiaoqin Guo
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
- Zhejiang Provincial Collaborative Innovation Center for Bamboo Resources and High-Efficiency Utilization, Zhejiang A&F University, Lin'An, Zhejiang, China
| | - Shenkui Liu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
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39
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Yu X, Wang Y, Kohnen MV, Piao M, Tu M, Gao Y, Lin C, Zuo Z, Gu L. Large Scale Profiling of Protein Isoforms Using Label-Free Quantitative Proteomics Revealed the Regulation of Nonsense-Mediated Decay in Moso Bamboo ( Phyllostachys edulis). Cells 2019; 8:E744. [PMID: 31330982 PMCID: PMC6678154 DOI: 10.3390/cells8070744] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 07/12/2019] [Accepted: 07/16/2019] [Indexed: 12/13/2022] Open
Abstract
Moso bamboo is an important forest species with a variety of ecological, economic, and cultural values. However, the gene annotation information of moso bamboo is only based on the transcriptome sequencing, lacking the evidence of proteome. The lignification and fiber in moso bamboo leads to a difficulty in the extraction of protein using conventional methods, which seriously hinders research on the proteomics of moso bamboo. The purpose of this study is to establish efficient methods for extracting the total proteins from moso bamboo for following mass spectrometry-based quantitative proteome identification. Here, we have successfully established a set of efficient methods for extracting total proteins of moso bamboo followed by mass spectrometry-based label-free quantitative proteome identification, which further improved the protein annotation of moso bamboo genes. In this study, 10,376 predicted coding genes were confirmed by quantitative proteomics, accounting for 35.8% of all annotated protein-coding genes. Proteome analysis also revealed the protein-coding potential of 1015 predicted long noncoding RNA (lncRNA), accounting for 51.03% of annotated lncRNAs. Thus, mass spectrometry-based proteomics provides a reliable method for gene annotation. Especially, quantitative proteomics revealed the translation patterns of proteins in moso bamboo. In addition, the 3284 transcript isoforms from 2663 genes identified by Pacific BioSciences (PacBio) single-molecule real-time long-read isoform sequencing (Iso-Seq) was confirmed on the protein level by mass spectrometry. Furthermore, domain analysis of mass spectrometry-identified proteins encoded in the same genomic locus revealed variations in domain composition pointing towards a functional diversification of protein isoform. Finally, we found that part transcripts targeted by nonsense-mediated mRNA decay (NMD) could also be translated into proteins. In summary, proteomic analysis in this study improves the proteomics-assisted genome annotation of moso bamboo and is valuable to the large-scale research of functional genomics in moso bamboo. In summary, this study provided a theoretical basis and technical support for directional gene function analysis at the proteomics level in moso bamboo.
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Affiliation(s)
- Xiaolan Yu
- Basic Forestry and Proteomics Research Center, College of Life Science, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yongsheng Wang
- Basic Forestry and Proteomics Research Center, College of Life Science, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Markus V Kohnen
- Basic Forestry and Proteomics Research Center, College of Life Science, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Mingxin Piao
- Basic Forestry and Proteomics Research Center, College of Life Science, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, 5333 Xi'an Road, Changchun 130062, China
| | - Min Tu
- Basic Forestry and Proteomics Research Center, College of Life Science, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yubang Gao
- Basic Forestry and Proteomics Research Center, College of Life Science, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Chentao Lin
- Basic Forestry and Proteomics Research Center, College of Life Science, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Department of Molecular, Cell & Developmental Biology, University of California, Los Angeles, CA 90095, USA
| | - Zecheng Zuo
- Basic Forestry and Proteomics Research Center, College of Life Science, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, 5333 Xi'an Road, Changchun 130062, China.
| | - Lianfeng Gu
- Basic Forestry and Proteomics Research Center, College of forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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40
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Patil V, McDermott HI, McAllister T, Cummins M, Silva JC, Mollison E, Meikle R, Morris J, Hedley PE, Waugh R, Dockter C, Hansson M, McKim SM. APETALA2 control of barley internode elongation. Development 2019; 146:dev.170373. [PMID: 31076487 PMCID: PMC6589076 DOI: 10.1242/dev.170373] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 05/02/2019] [Indexed: 01/08/2023]
Abstract
Many plants dramatically elongate their stems during flowering, yet how this response is coordinated with the reproductive phase is unclear. We demonstrate that microRNA (miRNA) control of APETALA2 (AP2) is required for rapid, complete elongation of stem internodes in barley, especially of the final ‘peduncle’ internode directly underneath the inflorescence. Disrupted miR172 targeting of AP2 in the Zeo1.b barley mutant caused lower mitotic activity, delayed growth dynamics and premature lignification in the peduncle leading to fewer and shorter cells. Stage- and tissue-specific comparative transcriptomics between Zeo1.b and its parent cultivar showed reduced expression of proliferation-associated genes, ectopic expression of maturation-related genes and persistent, elevated expression of genes associated with jasmonate and stress responses. We further show that applying methyl jasmonate (MeJA) phenocopied the stem elongation of Zeo1.b, and that Zeo1.b itself was hypersensitive to inhibition by MeJA but less responsive to promotion by gibberellin. Taken together, we propose that miR172-mediated restriction of AP2 may modulate the jasmonate pathway to facilitate gibberellin-promoted stem growth during flowering. Summary: Regulation of reproductive stem elongation in barley by APETALA2 suggests a pivotal role for phase change repression of JA-associated responses to promote internode growth.
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Affiliation(s)
- Vrushali Patil
- Division of Plant Sciences, School of Life Sciences, The University of Dundee at The James Hutton Institute, Invergowrie, Dundee DD2 5DA, Scotland
| | - Hannah I McDermott
- Division of Plant Sciences, School of Life Sciences, The University of Dundee at The James Hutton Institute, Invergowrie, Dundee DD2 5DA, Scotland
| | - Trisha McAllister
- Division of Plant Sciences, School of Life Sciences, The University of Dundee at The James Hutton Institute, Invergowrie, Dundee DD2 5DA, Scotland
| | - Michael Cummins
- Division of Plant Sciences, School of Life Sciences, The University of Dundee at The James Hutton Institute, Invergowrie, Dundee DD2 5DA, Scotland
| | - Joana C Silva
- Division of Plant Sciences, School of Life Sciences, The University of Dundee at The James Hutton Institute, Invergowrie, Dundee DD2 5DA, Scotland
| | - Ewan Mollison
- Division of Plant Sciences, School of Life Sciences, The University of Dundee at The James Hutton Institute, Invergowrie, Dundee DD2 5DA, Scotland
| | - Rowan Meikle
- Division of Plant Sciences, School of Life Sciences, The University of Dundee at The James Hutton Institute, Invergowrie, Dundee DD2 5DA, Scotland
| | - Jenny Morris
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, Scotland
| | - Pete E Hedley
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, Scotland
| | - Robbie Waugh
- Division of Plant Sciences, School of Life Sciences, The University of Dundee at The James Hutton Institute, Invergowrie, Dundee DD2 5DA, Scotland.,Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, Scotland
| | - Christoph Dockter
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Mats Hansson
- Department of Biology, Lund University, Sölvegatan 35B, 22362 Lund, Sweden
| | - Sarah M McKim
- Division of Plant Sciences, School of Life Sciences, The University of Dundee at The James Hutton Institute, Invergowrie, Dundee DD2 5DA, Scotland
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Wang X, Zhang R, Shi Z, Zhang Y, Sun X, Ji Y, Zhao Y, Wang J, Zhang Y, Xing J, Wang Y, Wang R, Song W, Zhao J. Multi-omics analysis of the development and fracture resistance for maize internode. Sci Rep 2019; 9:8183. [PMID: 31160669 PMCID: PMC6547879 DOI: 10.1038/s41598-019-44690-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 05/21/2019] [Indexed: 12/26/2022] Open
Abstract
The maize stalk is an important mechanical supporting tissue. The stalk fracture resistance is closely related to lodging resistance, and thus the yield. In this study, we showed that the basal zone (BZ) was more fragile than the middle zone (MZ) of the stalk internode before tasseling. In order to clarify the relationship between the different zones and fragile resistance between the internodes, we systematically analyzed the phenotypic, metabolomic and transcriptomic differences. The results indicated that the BZ zone had lower stalk strength, which corresponded to the results of less lignin, cellulose and hemicellulose than that of the MZ. The 27 highly enriched metabolites and 4430 highly expressed genes in the BZ mainly participated in pentose phosphate, and in ribosome and sterol synthesis pathways, respectively. In addition, the BZ had higher vascular bundles density but smaller size compared with the MZ. By contrast, the 28 highly enriched known metabolites and 4438 highly expressed genes in the MZ were mainly involved in lignin synthesis, and secondary metabolites synthesis, respectively, especially the phenylpropanoid synthesis. The results provide a deeper understanding of the relationship between development and fracture differences in stalk, and may facilitate the improvement of field management practice to reduce lodging.
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Affiliation(s)
- Xiaqing Wang
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Maize Research Center, Beijing Academy of Agriculture and Forestry Sciences, Shuguang Huayuan Middle Road, Haidian District, No. 9, Beijing, 100097, China
| | - Ruyang Zhang
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Maize Research Center, Beijing Academy of Agriculture and Forestry Sciences, Shuguang Huayuan Middle Road, Haidian District, No. 9, Beijing, 100097, China
| | - Zi Shi
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Maize Research Center, Beijing Academy of Agriculture and Forestry Sciences, Shuguang Huayuan Middle Road, Haidian District, No. 9, Beijing, 100097, China
| | - Ying Zhang
- Beijing Key Lab of Digital Plant, Beijing Research Center for Information Technology in Agriculture, Beijing Academy of Agriculture and Forestry Sciences, Shuguang Huayuan Middle Road, Haidian District, No. 11, Beijing, 100097, China
| | - Xuan Sun
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Maize Research Center, Beijing Academy of Agriculture and Forestry Sciences, Shuguang Huayuan Middle Road, Haidian District, No. 9, Beijing, 100097, China
| | - Yulong Ji
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Maize Research Center, Beijing Academy of Agriculture and Forestry Sciences, Shuguang Huayuan Middle Road, Haidian District, No. 9, Beijing, 100097, China
| | - Yanxin Zhao
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Maize Research Center, Beijing Academy of Agriculture and Forestry Sciences, Shuguang Huayuan Middle Road, Haidian District, No. 9, Beijing, 100097, China
| | - Jidong Wang
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Maize Research Center, Beijing Academy of Agriculture and Forestry Sciences, Shuguang Huayuan Middle Road, Haidian District, No. 9, Beijing, 100097, China
| | - Yunxia Zhang
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Maize Research Center, Beijing Academy of Agriculture and Forestry Sciences, Shuguang Huayuan Middle Road, Haidian District, No. 9, Beijing, 100097, China
| | - Jinfeng Xing
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Maize Research Center, Beijing Academy of Agriculture and Forestry Sciences, Shuguang Huayuan Middle Road, Haidian District, No. 9, Beijing, 100097, China
| | - Yuandong Wang
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Maize Research Center, Beijing Academy of Agriculture and Forestry Sciences, Shuguang Huayuan Middle Road, Haidian District, No. 9, Beijing, 100097, China
| | - Ronghuan Wang
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Maize Research Center, Beijing Academy of Agriculture and Forestry Sciences, Shuguang Huayuan Middle Road, Haidian District, No. 9, Beijing, 100097, China
| | - Wei Song
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Maize Research Center, Beijing Academy of Agriculture and Forestry Sciences, Shuguang Huayuan Middle Road, Haidian District, No. 9, Beijing, 100097, China.
| | - Jiuran Zhao
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Maize Research Center, Beijing Academy of Agriculture and Forestry Sciences, Shuguang Huayuan Middle Road, Haidian District, No. 9, Beijing, 100097, China.
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Wang T, Li Q, Lou S, Yang Y, Peng L, Lin Z, Hu Q, Ma L. GSK3/shaggy-like kinase 1 ubiquitously regulates cell growth from Arabidopsis to Moso bamboo (Phyllostachys edulis). PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 283:290-300. [PMID: 31128699 DOI: 10.1016/j.plantsci.2019.03.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Revised: 03/17/2019] [Accepted: 03/18/2019] [Indexed: 06/09/2023]
Abstract
Moso bamboo (Phyllostachys edulis) is one of the fastest growing species with a maximum growth rate of 1 m/day. However, the regulator genes for this explosive growth phenomenon have not been functionally studied. Here, we found that Moso bamboo GSK3/shaggy-like kinase 1 (PeGSK1) acts as a negative regulator of cell growth. Over-expression of PeGSK1 in Arabidopsis showed significant growth arrest phenotypes, including dwarfism, small leaves, reduced cell length, and disturbed cell elongation of petiole. Furthermore, Overexpression of PeGSK1 fully inhibited the longer hypocotyl phenotype of Arabidopsis atgsk1 mutants. In addition, PeGSK1-overexpressing lines were resistant to exogenous BR treatment and PeGSK1 interacted with the brassinosteroid signal transduction key regulator BZR1. The BZR1-dependent cell growth genes were down-regulated in PeGSK1-overexpressing lines. These results indicated that PeGSK1 is functionally similar to AtGSK1 and inhibited cell growth via the brassinosteroid signaling pathway. Importantly, PeGSK1 also interacted with PeBZR1, and the expression pattern of PeGSK1 was negatively correlated with the internode elongation of bamboo, indicating that PeGSK1 is involved in the cell growth of bamboo. In summary, our results provide insight into the role of brassinosteroids in the rapid-growth of bamboo culms and identifying target genes for the genetic manipulation of plant height.
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Affiliation(s)
- Taotao Wang
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Qinzhen Li
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Shuaitong Lou
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yong Yang
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Lingfang Peng
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zezhong Lin
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Qin Hu
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Liuyin Ma
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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Biswal AK, McConnell EW, Werth EG, Lo SF, Yu SM, Hicks LM, Jones AM. The Nucleotide-Dependent Interactome of Rice Heterotrimeric G-Protein α -Subunit. Proteomics 2019; 19:e1800385. [PMID: 30866160 DOI: 10.1002/pmic.201800385] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 02/12/2019] [Indexed: 11/09/2022]
Abstract
The rice heterotrimeric G-protein complex, a guanine-nucleotide-dependent on-off switch, mediates vital cellular processes and responses to biotic and abiotic stress. Exchange of bound GDP (resting state) for GTP (active state) is spontaneous in plants including rice and thus there is no need for promoting guanine nucleotide exchange in vivo as a mechanism for regulating the active state of signaling as it is well known for animal G signaling. As such, a master regulator controlling the G-protein activation state is unknown in plants. Therefore, an ab initio approach is taken to discover candidate regulators. The rice Gα subunit (RGA1) is used as bait to screen for nucleotide-dependent protein partners. A total of 264 proteins are identified by tandem mass spectrometry of which 32 were specific to the GDP-bound inactive state and 22 specific to the transition state. Approximately, 10% are validated as previously identified G-protein interactors.
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Affiliation(s)
- Akshaya Kumar Biswal
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Evan Wesley McConnell
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Emily Grace Werth
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Shuen-Fang Lo
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, Taiwan, China
| | - Su-May Yu
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, Taiwan, China
| | - Leslie M Hicks
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Alan M Jones
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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McKim SM. How plants grow up. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2019; 61:257-277. [PMID: 30697935 DOI: 10.1111/jipb.12786] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 01/21/2019] [Indexed: 05/27/2023]
Abstract
A plant's lateral structures, such as leaves, branches and flowers, literally hinge on the shoot axis, making its integrity and growth fundamental to plant form. In all plants, subapical proliferation within the shoot tip displaces cells downward to extrude the cylindrical stem. Following the transition to flowering, many plants show extensive axial elongation associated with increased subapical proliferation and expansion. However, the cereal grasses also elongate their stems, called culms, due to activity within detached intercalary meristems which displaces cells upward, elevating the grain-bearing inflorescence. Variation in culm length within species is especially relevant to cereal crops, as demonstrated by the high-yielding semi-dwarfed cereals of the Green Revolution. Although previously understudied, recent renewed interest the regulation of subapical and intercalary growth suggests that control of cell division planes, boundary formation and temporal dynamics of differentiation, are likely critical mechanisms coordinating axial growth and development in plants.
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Affiliation(s)
- Sarah M McKim
- Division of Plant Sciences, University of Dundee at The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
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45
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Chen L, Zheng X, Guo X, Cui Y, Yang H. The roles of Aux/IAA gene family in development of Dendrocalamus sinicus (Poaceae: Bambusoideae) inferred by comprehensive analysis and expression profiling. Mol Biol Rep 2019; 46:1625-1634. [PMID: 30690658 DOI: 10.1007/s11033-019-04611-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 01/17/2019] [Indexed: 11/30/2022]
Abstract
Auxin is an important hormone in many plant developmental processes. In this study, the auxin/indole acetic acid (Aux/IAA) gene family was comprehensively identified using Dendrocalamus sinicus transcriptome data. A total of 26 Aux/IAA genes (DsIAA1-DsIAA26) were mined using four conserved Aux/IAA family motifs (PF02309). They encoded hydrophilic proteins, including one or two nuclear localisation signals. The D. sinicus Aux/IAA proteins were classified into two groups, including seven sister-gene pairs based on their phylogenetic relationships. A phylogenetic tree generated by aligning 108 predicted protein sequences of 26 DsIAAs, 43 PhIAAs (Phyllostachys heterocycla), 29 AtIAAs (Arabidopsis), 31 OsIAAs (Oryza sativa) and 22 PtIAAs (Populus) revealed nine major groups. Among them, four groups, including 96 IAA proteins of all five species, suggested that the genes originated before divergence of monocots and dicots. The expression profiling in different tissues showed that most of the DsIAAs preferentially expressed in leaves and shoots, suggesting their important roles in the development of leaves and shoots in D. sinicus. Continuously high expression of DsIAA3, DsIAA4, DsIAA15, and DsIAA20 may be important for regulating shoot development in D. sinicus. These results provide useful information for further research into the function of Aux/IAA genes in woody sympodial bamboos.
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Affiliation(s)
- Lingna Chen
- Research Institute of Resources Insects, Chinese Academy of Forestry, Bailongsi, Kunming, 650233, Panlong, China
| | - Xianggan Zheng
- Research Institute of Resources Insects, Chinese Academy of Forestry, Bailongsi, Kunming, 650233, Panlong, China
| | - Xiaojuan Guo
- Research Institute of Resources Insects, Chinese Academy of Forestry, Bailongsi, Kunming, 650233, Panlong, China
| | - Yongzhong Cui
- Research Institute of Resources Insects, Chinese Academy of Forestry, Bailongsi, Kunming, 650233, Panlong, China
| | - Hanqi Yang
- Research Institute of Resources Insects, Chinese Academy of Forestry, Bailongsi, Kunming, 650233, Panlong, China.
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Zhang H, Wang H, Zhu Q, Gao Y, Wang H, Zhao L, Wang Y, Xi F, Wang W, Yang Y, Lin C, Gu L. Transcriptome characterization of moso bamboo (Phyllostachys edulis) seedlings in response to exogenous gibberellin applications. BMC PLANT BIOLOGY 2018; 18:125. [PMID: 29925317 PMCID: PMC6011363 DOI: 10.1186/s12870-018-1336-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Accepted: 05/31/2018] [Indexed: 05/23/2023]
Abstract
BACKGROUND Moso bamboo (Phyllostachys edulis) is a well-known bamboo species of high economic value in the textile industry due to its rapid growth. Phytohormones, which are master regulators of growth and development, serve as important endogenous signals. However, the mechanisms through which phytohormones regulate growth in moso bamboo remain unknown to date. RESULTS Here, we reported that exogenous gibberellins (GA) applications resulted in a significantly increased internode length and lignin condensation. Transcriptome sequencing revealed that photosynthesis-related genes were enriched in the GA-repressed gene class, which was consistent with the decrease in leaf chlorophyll concentrations and the lower rate of photosynthesis following GA treatment. Exogenous GA applications on seedlings are relatively easy to perform, thus we used 4-week-old whole seedlings of bamboo for GA- treatment followed by high throughput sequencing. In this study, we identified 932 cis-nature antisense transcripts (cis-NATs), and 22,196 alternative splicing (AS) events in total. Among them, 42 cis-nature antisense transcripts (cis-NATs) and 442 AS events were differentially expressed upon exposure to exogenous GA3, suggesting that post-transcriptional regulation might be also involved in the GA3 response. Targets of differential expression of cis-NATs included genes involved in hormone receptor, photosynthesis and cell wall biogenesis. For example, LAC4 and its corresponding cis-NATs were GA3-induced, and may be involved in the accumulation of lignin, thus affecting cell wall composition. CONCLUSIONS This study provides novel insights illustrating how GA alters post-transcriptional regulation and will shed light on the underlying mechanism of growth modulated by GA in moso bamboo.
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Affiliation(s)
- Hangxiao Zhang
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Huihui Wang
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Qiang Zhu
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Yubang Gao
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Huiyuan Wang
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Liangzhen Zhao
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Yongsheng Wang
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Feihu Xi
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Wenfei Wang
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Yanqiu Yang
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Chentao Lin
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Department of Molecular, Cell & Developmental Biology, University of California, CA90095, Los Angeles, USA
| | - Lianfeng Gu
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
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Wang T, Liu L, Wang X, Liang L, Yue J, Li L. Comparative Analyses of Anatomical Structure, Phytohormone Levels, and Gene Expression Profiles Reveal Potential Dwarfing Mechanisms in Shengyin Bamboo ( Phyllostachys edulis f. tubaeformis). Int J Mol Sci 2018; 19:E1697. [PMID: 29875341 PMCID: PMC6032043 DOI: 10.3390/ijms19061697] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2018] [Revised: 06/03/2018] [Accepted: 06/04/2018] [Indexed: 01/01/2023] Open
Abstract
Moso bamboo (Phyllostachys edulis) is one of the most important bamboo species in China and the third most important plant species for timber production. However, the dwarf variant of moso bamboo, P. edulis f. tubaeformis (shengyin bamboo), which has shortened internodes, is not well studied. We used anatomical, hormonal, and transcriptomic approaches to study internode shortening and shoot growth in dwarf shengyin and wild moso bamboo. Phenotypic and anatomical observations showed that dwarfing in shengyin bamboo is due to reduced internode length, and the culm fibers in shengyin bamboo are significantly shorter and thicker than in wild moso bamboo. We measured the levels of endogenous hormones in the internodes and found that shengyin bamboo had lower levels of four hormones while two others were higher in wild moso bamboo. Comparative transcriptome analyses revealed a potential regulating mechanism for internode length involving genes for cell wall loosening-related enzymes and the cellulose and lignin biosynthesis pathways. Genes involved in hormone biosynthesis and signal transduction, especially those that showed significant differential expression in the internodes between shengyin and wild moso bamboo, may be important in determining the shortened internode phenotype. A hypothesis involving possible cross-talk between phytohormone signaling cues and cell wall expansion leading to dwarfism in shengyin bamboo is proposed. The results presented here provide a comprehensive exploration of the biological mechanisms that determine internode shortening in moso bamboo.
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Affiliation(s)
- Tao Wang
- State Key Laboratory of Forest Genetics and Tree Breeding, Key Laboratory of Silviculture of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China.
| | - Lei Liu
- State Key Laboratory of Forest Genetics and Tree Breeding, Key Laboratory of Silviculture of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China.
| | - Xiaojing Wang
- State Key Laboratory of Forest Genetics and Tree Breeding, Key Laboratory of Silviculture of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China.
| | - Lixiong Liang
- State Key Laboratory of Forest Genetics and Tree Breeding, Key Laboratory of Silviculture of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China.
| | - Jinjun Yue
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang 311400, China.
| | - Lubin Li
- State Key Laboratory of Forest Genetics and Tree Breeding, Key Laboratory of Silviculture of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China.
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48
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Proteomic analysis reveals that auxin homeostasis influences the eighth internode length heterosis in maize (Zea mays). Sci Rep 2018; 8:7159. [PMID: 29739966 PMCID: PMC5940786 DOI: 10.1038/s41598-018-23874-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 03/20/2018] [Indexed: 11/09/2022] Open
Abstract
Ear height is an important maize morphological trait that influences plant lodging resistance in the field, and is based on the number and length of internodes under the ear. To explore the effect of internodes on ear height, the internodes under the ear were analysed in four commercial hybrids (Jinsai6850, Zhengdan958, Xundan20, and Yuyu22) from different heterotic groups in China. The eighth internode, which is the third aboveground extended internode, exhibited high-parent or over high-parent heterosis and contributed considerably to ear height. Thus, the proteome of the eighth internode was examined. Sixty-six protein spots with >1.5-fold differences in accumulation (P < 0.05) among the four hybrids were identified by mass spectrometry and data analyses. Most of the differentially accumulated proteins exhibited additive accumulation patterns, but with epistatic effects on heterosis performance. Proteins involved in phenylpropanoid and benzoxazinoid metabolic pathways were observed to influence indole-3-acetic acid biosynthesis and polar auxin transport during internode development. Moreover, indole-3-acetic acid content was positively correlated with the eighth internode length, but negatively correlated with the extent of the heterosis of the eighth internode length.
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Wei Q, Jiao C, Ding Y, Gao S, Guo L, Chen M, Hu P, Xia S, Ren G, Fei Z. Cellular and molecular characterizations of a slow-growth variant provide insights into the fast growth of bamboo. TREE PHYSIOLOGY 2018; 38:641-654. [PMID: 29077967 DOI: 10.1093/treephys/tpx129] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Accepted: 09/24/2017] [Indexed: 05/16/2023]
Abstract
Few studies about bamboo naturally occurring mutants have been reported so far. Using an integrated anatomy, mathematics and genomics approach, we systematically characterized the cellular and molecular basis underlying the abnormal internode development of Pseudosasa japonica var. tsutsumiana, a stable variant with dwarf and swollen internodes that are caused by the compressed spiral growth and the swollen cells in the bottom part of the internode. P. japonica var. tsutsumiana is a slow-growth variant with disorderly cell division and cell growth during the fast growth stage. Comparative transcriptome analysis identified a number of genes related to cell growth that were significantly down-regulated in the variant, including those related to auxin, vesicle transport, cytoskeleton organization and cell wall modification, consistent with the thinner cell walls and lower contents of cellulose that were found in the variant, which together with the mechanic force composed by the extrusion pressure from the neighboring fast growth cells and the weight pressure above the growing cells might finally result in the radial and irregular growth of the variant cells. This study provides key candidate genes involved in the fast growth of bamboo from a 'mutant' perspective, and supports a plausible mechanism underlying the dwarf and swollen internodes of P. japonica var. tsutsumiana.
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Affiliation(s)
- Qiang Wei
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Chen Jiao
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
| | - Yulong Ding
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Shan Gao
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
- College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Lin Guo
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Ming Chen
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Pei Hu
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Sujuan Xia
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Guodong Ren
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Zhangjun Fei
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
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50
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Chang E, Deng N, Zhang J, Liu J, Chen L, Zhao X, Abbas M, Jiang Z, Shi S. Proteome-Level Analysis of Metabolism- and Stress-Related Proteins during Seed Dormancy and Germination in Gnetum parvifolium. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:3019-3029. [PMID: 29490456 DOI: 10.1021/acs.jafc.7b05001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Gnetum parvifolium is a rich source of materials for traditional medicines, food, and oil, but little is known about the mechanism underlying its seed dormancy and germination. In this study, we analyzed the proteome-level changes in its seeds during germination using isobaric tags for relative and absolute quantitation. In total, 1,040 differentially expressed proteins were identified, and cluster analysis revealed the distinct time points during which signal transduction and oxidation-reduction activity changed. Gene Ontology analysis showed that "carbohydrate metabolic process" and "response to oxidative stress" were the main enriched terms. Proteins associated with starch degradation and antioxidant enzymes were important for dormancy-release, while proteins associated with energy metabolism and protein synthesis were up-regulated during germination. Moreover, protein-interaction networks were mainly associated with heat-shock proteins. Furthermore, in accord with changes in the energy metabolism- and antioxidant-related proteins, indole-3-acetic acid, Peroxidase, and soluble sugar content increased, and the starch content decreased in almost all six stages of dormancy and germination analyzed (S1-S6). The activity of superoxide dismutase, abscisic acid, and malondialdehyde content increased in the dormancy stages (S1-S3) and then decreased in the germination stages (S4-S6). Our results provide new insights into G. parvifolium seed dormancy and germination at the proteome and physiological levels, with implications for improving seed propagation.
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Affiliation(s)
- Ermei Chang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry , Chinese Academy of Forestry , No. 1 Dongxiaofu, Xiangshan Road , Haidian, Beijing 100091 , China
| | - Nan Deng
- Institute of Ecology , Hunan Academy of Forestry , Changsha , Hunan 410004 , China
| | - Jin Zhang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry , Chinese Academy of Forestry , No. 1 Dongxiaofu, Xiangshan Road , Haidian, Beijing 100091 , China
| | - Jianfeng Liu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry , Chinese Academy of Forestry , No. 1 Dongxiaofu, Xiangshan Road , Haidian, Beijing 100091 , China
| | - Lanzhen Chen
- Institute of Apicultural Research , Chinese Academy of Agricultural Sciences , Beijing 100093 , China
- Risk Assessment Laboratory for Bee Products , Quality and Safety of Ministry of Agriculture , Beijing 100093 , China
| | - Xiulian Zhao
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry , Chinese Academy of Forestry , No. 1 Dongxiaofu, Xiangshan Road , Haidian, Beijing 100091 , China
| | - M Abbas
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry , Chinese Academy of Forestry , No. 1 Dongxiaofu, Xiangshan Road , Haidian, Beijing 100091 , China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology , Beijing Forestry University , Beijing 100083 , China
| | - Zeping Jiang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry , Chinese Academy of Forestry , No. 1 Dongxiaofu, Xiangshan Road , Haidian, Beijing 100091 , China
| | - Shengqing Shi
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry , Chinese Academy of Forestry , No. 1 Dongxiaofu, Xiangshan Road , Haidian, Beijing 100091 , China
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