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Zhao JX, Wang S, Liu J, Jiang XD, Wen J, Suo ZQ, Liu J, Zhong MC, Wang Q, Gu Z, Liu C, Deng Y, Hu JY, Li DZ. A comparative full-length transcriptomic resource provides insight into the perennial monocarpic mass flowering. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:1842-1855. [PMID: 37665679 DOI: 10.1111/tpj.16452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 08/21/2023] [Accepted: 08/23/2023] [Indexed: 09/06/2023]
Abstract
Perennial monocarpic mass flowering represents as a key developmental innovation in flowering time diversity in several biological and economical essential families, such as the woody bamboos and the shrubby Strobilanthes. However, molecular and genetic mechanisms underlying this important biodiversity remain poorly investigated. Here, we generated a full-length transcriptome resource incorporated into the BlueOmics database (http://blueomics.iflora.cn) for two Strobilanthes species, which feature contrasting flowering time behaviors. Using about 112 and 104 Gb Iso-seq reads together with ~185 and ~75 Gb strand-specific RNA seq data, we annotated 80 971 and 79 985 non-redundant full-length transcripts for the perennial polycarpic Strobilanthes tetrasperma and the perennial monocarpic Strobilanthes biocullata, respectively. In S. tetrasperma, we identified 8794 transcripts showing spatiotemporal expression in nine tissues. In leaves and shoot apical meristems at two developmental stages, 977 and 1121 transcripts were differentially accumulated in S. tetrasperma and S. biocullata, respectively. Interestingly, among the 33 transcription factors showing differential expression in S. tetrasperma but without differential expression in S. biocullata, three were involved potentially in the photoperiod and circadian-clock pathway of flowering time regulation (FAR1 RELATED SEQUENCE 12, FRS12; NUCLEAR FACTOR Y A1, NFYA1; PSEUDO-RESPONSE REGULATOR 5, PRR5), hence provides an important clue in deciphering the flowering diversity mechanisms. Our data serve as a key resource for further dissection of molecular and genetic mechanisms underpinning key biological innovations, here, the perennial monocarpic mass flowering.
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Affiliation(s)
- Jiu-Xia Zhao
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shu Wang
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Jiazhi Liu
- University of Chinese Academy of Sciences, Beijing, 100049, China
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Yunnan Key Laboratory of Crop Wild Relatives Omics, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223, China
| | - Xiao-Dong Jiang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Jing Wen
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhi-Quan Suo
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Jie Liu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Mi-Cai Zhong
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Qin Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Zhirong Gu
- Administration of National Nature Reserve of Badagongshan, Sangzhi, 427000, Hunan, China
| | - Changning Liu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Yunnan Key Laboratory of Crop Wild Relatives Omics, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223, China
| | - Yunfei Deng
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Jin-Yong Hu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
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Sun H, Wang J, Li H, Li T, Gao Z. Advancements and challenges in bamboo breeding for sustainable development. TREE PHYSIOLOGY 2023; 43:1705-1717. [PMID: 37471643 DOI: 10.1093/treephys/tpad086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 06/14/2023] [Accepted: 06/27/2023] [Indexed: 07/22/2023]
Abstract
Bamboo is a highly renewable biomass resource with outstanding ecological, economic and social benefits. However, its lengthy vegetative growth stage and uncertain flowering period have hindered the application of traditional breeding methods. In recent years, significant progress has been made in bamboo breeding. While technical advances in bamboo breeding have been impressive, it is essential to also consider the broader implications we can learn from bamboo's extraordinary features for sustainable development. This review provides an overview of the current status of bamboo breeding technology, including a detailed history of bamboo breeding divided into four eras, a comprehensive map of bamboo germplasm gardens worldwide, with a focus on China, and a summary of available transgenic technologies for gene function verification and genetic improvement. As the demand for bamboo as a sustainable and renewable resource increases continuously, breeding objectives should be focused on enhancing yield, wood properties and adaptability to diverse environmental conditions. In particular, priority should be given to improving fiber length, internode length and wall thickness, as well as regulating lignin and cellulose content for papermaking, substitute for plastic and other applications. Furthermore, we highlight the challenges and opportunities for future research and development in bamboo breeding, including the application of omics technologies, artificial intelligence and the development of new breeding methods. Finally, by integrating the technical advances in bamboo breeding with a discussion of its broader implications for sustainable development, this review provides a comprehensive framework for the development of bamboo industry.
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Affiliation(s)
- Huayu Sun
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, No. 8 Futong East Road, Chaoyang District, Beijing 100102, China
- Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Centre for Bamboo and Rattan, No. 8 Futong East Road, Chaoyang District, Beijing 100102, China
| | - Jiangfei Wang
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, No. 8 Futong East Road, Chaoyang District, Beijing 100102, China
- Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Centre for Bamboo and Rattan, No. 8 Futong East Road, Chaoyang District, Beijing 100102, China
| | - Hui Li
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, No. 8 Futong East Road, Chaoyang District, Beijing 100102, China
- Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Centre for Bamboo and Rattan, No. 8 Futong East Road, Chaoyang District, Beijing 100102, China
| | - Tiankuo Li
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, No. 8 Futong East Road, Chaoyang District, Beijing 100102, China
- Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Centre for Bamboo and Rattan, No. 8 Futong East Road, Chaoyang District, Beijing 100102, China
| | - Zhimin Gao
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, No. 8 Futong East Road, Chaoyang District, Beijing 100102, China
- Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Centre for Bamboo and Rattan, No. 8 Futong East Road, Chaoyang District, Beijing 100102, China
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Yang D, Yang J, Wan J, Xu Y, Li L, Rong J, Chen L, He T, Zheng Y. Genome-Wide Identification of MIKCc-Type MADS-Box Family Gene and Floral Organ Transcriptome Characterization in Ma Bamboo ( Dendrocalamus latiflorus Munro). Genes (Basel) 2022; 14:genes14010078. [PMID: 36672819 PMCID: PMC9859424 DOI: 10.3390/genes14010078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 12/21/2022] [Accepted: 12/23/2022] [Indexed: 12/28/2022] Open
Abstract
Most bamboos die after flowering, and the molecular mechanisms responsible for flowering is poorly understood. The MIKCc-type MADS-box family gene is involved in the flowering process. To explore the mechanism of the MIKCc-type MADS-box gene and phytohormone regulation in the flowering of Dendrocalamus latiflorus Munro (D. latiflorus), characterized by extremely rapid growth and widely cultivated woody bamboo, we initially did a genome-wide analysis of the MIKCc-type MADS-box gene in D. latiflorus. In the meantime, transcriptome analysis was performed using the floral organs. A total of 170 MIKCc-Type MADS-Box genes were identified and divided into 15 categories. The cis-acting element analysis in promoters regions revealed that MIKC-type MADS-box family genes were associated with hormones, including auxin, abscisic acid (ABA), gibberellin (GA) and jasmonic acid (JA), which was found at 79, 476, 96, 486 sites and cover 61, 103, 73, 128 genes. Genome synteny analysis showed subgenome AA and BB were better than CC and obtained 49, 40, 39 synteny genes compared with Oryza sativa (O. sativa). In transcriptome analysis of floral organs, the enriched pathway from DEGs included circadian, vernalization and gibberellin pathways associated with the flowering process. We found that the jasmonic acid synthesis gene is highly expressed in the pistil, which may be the cause of Ma bamboo pollen abortion. The expression profile showed that most MIKC-type MADS-box genes exhibited high expression in flower organs. The consequences of this study will provide insight into the irregular flowering and low pollen counts of Ma bamboo.
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Affiliation(s)
- Deming Yang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jing Yang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jiayi Wan
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yanping Xu
- College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Lei Li
- College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jundong Rong
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Lingyan Chen
- College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Tianyou He
- College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yushan Zheng
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Correspondence:
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Mustafa AA, Derise MR, Yong WTL, Rodrigues KF. A Concise Review of Dendrocalamus asper and Related Bamboos: Germplasm Conservation, Propagation and Molecular Biology. PLANTS 2021; 10:plants10091897. [PMID: 34579429 PMCID: PMC8468032 DOI: 10.3390/plants10091897] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 07/26/2021] [Accepted: 07/26/2021] [Indexed: 11/16/2022]
Abstract
Bamboos represent an emerging forest resource of economic significance and provide an avenue for sustainable development of forest resources. The development of the commercial bamboo industry is founded upon efficient molecular and technical approaches for the selection and rapid multiplication of elite germplasm for its subsequent propagation via commercial agro-forestry business enterprises. This review will delve into the micropropagation of Dendrocalamus asper, one of the most widely cultivated commercial varieties of bamboo, and will encompass the selection of germplasm, establishment of explants in vitro and micropropagation techniques. The currently available information pertaining to molecular biology, DNA barcoding and breeding, has been included, and potential areas for future research in the area of genetic engineering and gene regulation have been highlighted. This information will be of relevance to both commercial breeders and molecular biologists who have an interest in establishing bamboo as a crop of the future.
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Hou D, Li L, Ma T, Pei J, Zhao Z, Lu M, Wu A, Lin X. The SOC1-like gene BoMADS50 is associated with the flowering of Bambusa oldhamii. HORTICULTURE RESEARCH 2021; 8:133. [PMID: 34059654 PMCID: PMC8166863 DOI: 10.1038/s41438-021-00557-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 03/16/2021] [Accepted: 03/26/2021] [Indexed: 05/27/2023]
Abstract
Bamboo is known for its edible shoots and beautiful texture and has considerable economic and ornamental value. Unique among traditional flowering plants, many bamboo plants undergo extensive synchronized flowering followed by large-scale death, seriously affecting the productivity and application of bamboo forests. To date, the molecular mechanism of bamboo flowering characteristics has remained unknown. In this study, a SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1)-like gene, BoMADS50, was identified from Bambusa oldhamii. BoMADS50 was highly expressed in mature leaves and the floral primordium formation period during B. oldhamii flowering and overexpression of BoMADS50 caused early flowering in transgenic rice. Moreover, BoMADS50 could interact with APETALA1/FRUITFULL (AP1/FUL)-like proteins (BoMADS14-1/2, BoMADS15-1/2) in vivo, and the expression of BoMADS50 was significantly promoted by BoMADS14-1, further indicating a synergistic effect between BoMADS50 and BoAP1/FUL-like proteins in regulating B. oldhamii flowering. We also identified four additional transcripts of BoMADS50 (BoMADS50-1/2/3/4) with different nucleotide variations. Although the protein-CDS were polymorphic, they had flowering activation functions similar to those of BoMADS50. Yeast one-hybrid and transient expression assays subsequently showed that both BoMADS50 and BoMADS50-1 bind to the promoter fragment of itself and the SHORT VEGETATIVE PHASE (SVP)-like gene BoSVP, but only BoMADS50-1 can positively induce their transcription. Therefore, nucleotide variations likely endow BoMADS50-1 with strong regulatory activity. Thus, BoMADS50 and BoMADS50-1/2/3/4 are probably important positive flowering regulators in B. oldhamii. Moreover, the functional conservatism and specificity of BoMADS50 and BoMADS50-1 might be related to the synchronized and sporadic flowering characteristics of B. oldhamii.
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Affiliation(s)
- Dan Hou
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin'an, 311300, Hangzhou, China
| | - Ling Li
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin'an, 311300, Hangzhou, China
| | - Tengfei Ma
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin'an, 311300, Hangzhou, China
| | - Jialong Pei
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin'an, 311300, Hangzhou, China
| | - Zhongyu Zhao
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin'an, 311300, Hangzhou, China
| | - Mengzhu Lu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin'an, 311300, Hangzhou, China
| | - Aimin Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, 510642, Guangzhou, China.
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, 510642, Guangzhou, China.
| | - Xinchun Lin
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin'an, 311300, Hangzhou, China.
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Ramakrishnan M, Yrjälä K, Satheesh V, Zhou MB. Bamboo Transposon Research: Current Status and Perspectives. Methods Mol Biol 2021; 2250:257-270. [PMID: 33900611 DOI: 10.1007/978-1-0716-1134-0_24] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Bamboo, a fast-growing non-timber forest plant with many uses, is a valuable species for green development. However, bamboo flowering is very infrequent, extending, in general, for up to 120 years. Ecologically, bamboo species are generally better adapted to various environments than other grasses. Therefore, the species deserves a special status in what could be called Ecological Bioeconomy. An understanding of the genetic processes of bamboo can help us sustainably develop and manage bamboo forests. Transposable elements (TEs), jumping genes or transposons, are major genetic elements in plant genomes. The rapid development of the bamboo reference genome, at the chromosome level, reveals that TEs occupy over 63.24% of the genome. This is higher than found in rice, Brachypodium, and sorghum. The bamboo genome contains diverse families of TEs, which play a significant role in bamboo's biological processes including growth and development. TEs provide important clues for understanding the evolution of the bamboo genome. In this chapter, we briefly describe the current status of research on TEs in the bamboo genome, their regulation, and transposition mechanisms. Perspectives for future research are also provided.
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Affiliation(s)
- Muthusamy Ramakrishnan
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Kim Yrjälä
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang, China.,Department of Forest Sciences, University of Helsinki, Helsinki, Finland
| | - 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
| | - Ming-Bing Zhou
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang, China. .,Zhejiang Provincial Collaborative Innovation Centre for Bamboo Resources and High-Efficiency Utilization, Zhejiang A&F University, Hangzhou, Zhejiang, 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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Li Y, Zhang C, Yang K, Shi J, Ding Y, Gao Z. De novo sequencing of the transcriptome reveals regulators of the floral transition in Fargesia macclureana (Poaceae). BMC Genomics 2019; 20:1035. [PMID: 31888463 PMCID: PMC6937737 DOI: 10.1186/s12864-019-6418-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 12/19/2019] [Indexed: 12/25/2022] Open
Abstract
Background Fargesia macclureana (Poaceae) is a woody bamboo species found on the Qinghai–Tibet Plateau (QTP) approximately 2000 ~ 3800 m above sea level. It rarely blossoms in the QTP, but it flowered 20 days after growing in our lab, which is in a low-altitude area outside the QTP. To date, little is known regarding the molecular mechanism of bamboo flowering, and no studies of flowering have been conducted on wild bamboo plants growing in extreme environments. Here, we report the first de novo transcriptome sequence for F. macclureana to investigate the putative mechanisms underlying the flowering time control used by F. macclureana to adapt to its environment. Results Illumina deep sequencing of the F. macclureana transcriptome generated 140.94 Gb of data, assembled into 99,056 unigenes. A comprehensive analysis of the broadly, specifically and differentially expressed unigenes (BEUs, SEUs and DEUs) indicated that they were mostly involved in metabolism and signal transduction, as well as DNA repair and plant-pathogen interactions, which may be of adaptive importance. In addition, comparison analysis between non-flowering and flowering tissues revealed that expressions of FmFT and FmHd3a, two putative F. macclureana orthologs, were differently regulated in NF- vs F- leaves, and carbohydrate metabolism and signal transduction were two major KEGG pathways that DEUs were enriched in. Finally, we detected 9296 simple sequence repeats (SSRs) that may be useful for further molecular marker-assisted breeding. Conclusions F. macclureana may have evolved specific reproductive strategies for flowering-related pathways in response to photoperiodic cues to ensure long vegetation growing period. Our findings will provide new insights to future investigations into the mechanisms of flowering time control and adaptive evolution in plants growing at high altitudes.
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Affiliation(s)
- Ying Li
- State Forestry and Grassland Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Centre for Bamboo and Rattan, Beijing, 100102, China
| | - Chunxia Zhang
- Bamboo Research Institute, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Kebin Yang
- State Forestry and Grassland Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Centre for Bamboo and Rattan, Beijing, 100102, China
| | - Jingjing Shi
- State Forestry and Grassland Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Centre for Bamboo and Rattan, Beijing, 100102, China
| | - Yulong Ding
- Bamboo Research Institute, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Zhimin Gao
- State Forestry and Grassland Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Centre for Bamboo and Rattan, Beijing, 100102, China.
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Development and Deployment of High-Throughput Retrotransposon-Based Markers Reveal Genetic Diversity and Population Structure of Asian Bamboo. FORESTS 2019. [DOI: 10.3390/f11010031] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Bamboo, a non-timber grass species, known for exceptionally fast growth is a commercially viable crop. Long terminal repeat (LTR) retrotransposons, the main class I mobile genetic elements in plant genomes, are highly abundant (46%) in bamboo, contributing to genome diversity. They play significant roles in the regulation of gene expression, chromosome size and structure as well as in genome integrity. Due to their random insertion behavior, interspaces of retrotransposons can vary significantly among bamboo genotypes. Capitalizing this feature, inter-retrotransposon amplified polymorphism (IRAP) is a high-throughput marker system to study the genetic diversity of plant species. To date, there are no transposon based markers reported from the bamboo genome and particularly using IRAP markers on genetic diversity. Phyllostachys genus of Asian bamboo is the largest of the Bambusoideae subfamily, with great economic importance. We report structure-based analysis of bamboo genome for the LTR-retrotransposon superfamilies, Ty3-gypsy and Ty1-copia, which revealed a total of 98,850 retrotransposons with intact LTR sequences at both the ends. Grouped into 64,281 clusters/scaffold using CD-HIT-EST software, only 13 clusters of retroelements were found with more than 30 LTR sequences and with at least one copy having all intact protein domains such as gag and polyprotein. A total of 16 IRAP primers were synthesized, based on the high copy numbers of conserved LTR sequences. A study using these IRAP markers on genetic diversity and population structure of 58 Asian bamboo accessions belonging to the genus Phyllostachys revealed 3340 amplicons with an average of 98% polymorphism. The bamboo accessions were collected from nine different provinces of China, as well as from Italy and America. A three phased approach using hierarchical clustering, principal components and a model based population structure divided the bamboo accessions into four sub-populations, PhSP1, PhSP2, PhSP3 and PhSP4. All the three analyses produced significant sub-population wise consensus. Further, all the sub-populations revealed admixture of alleles. The analysis of molecular variance (AMOVA) among the sub-populations revealed high intra-population genetic variation (75%) than inter-population. The results suggest that Phyllostachys bamboos are not well evolutionarily diversified, although geographic speciation could have occurred at a limited level. This study highlights the usability of IRAP markers in determining the inter-species variability of Asian bamboos.
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10
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Yang Z, Chen L, Kohnen MV, Xiong B, Zhen X, Liao J, Oka Y, Zhu Q, Gu L, Lin C, Liu B. Identification and Characterization of the PEBP Family Genes in Moso Bamboo (Phyllostachys heterocycla). Sci Rep 2019; 9:14998. [PMID: 31628413 PMCID: PMC6802209 DOI: 10.1038/s41598-019-51278-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 09/27/2019] [Indexed: 11/09/2022] Open
Abstract
Moso bamboo is one of the economically most important plants in China. Moso bamboo is a monocarpic perennial that exhibits poor and slow germination. Thus, the flowering often causes destruction of moso bamboo forestry. However, how control of flowering and seed germination are regulated in moso bamboo is largely unclear. In this study, we identified 5 members (PhFT1-5) of the phosphatidyl ethanolamine-binding proteins (PEBP) family from moso bamboo genome that regulate flowering, flower architecture and germination, and characterized the function of these PEBP family genes further in Arabidopsis. Phylogenetic analysis revealed that 3 (PhFT1, PhFT2 and PhFT3), 1 (PhFT4) and 1 (PhFT5) members belong to the TFL1-like clade, FT-like clade, and MFT-like clade, respectively. These PEBP family genes possess all structure necessary for PEBP gene function. The ectopic overexpression of PhFT4 and PhFT5 promotes flowering time in Arabidopsis, and that of PhFT1, PhFT2 and PhFT3 suppresses it. In addition, the overexpression of PhFT5 promotes seed germination rate. Interestingly, the overexpression of PhFT1 suppressed seed germination rate in Arabidopsis. The expression of PhFT1 and PhFT5 is significantly higher in seed than in tissues including leaf and shoot apical meristem, implying their function in seed germination. Taken together, our results suggested that the PEBP family genes play important roles as regulators of flowering and seed germination in moso bamboo and thereby are necessary for the sustainability of moso bamboo forest.
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Affiliation(s)
- Zhaohe Yang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Lei Chen
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Markus V Kohnen
- Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Bei Xiong
- Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Xi Zhen
- Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Jiakai Liao
- Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Yoshito Oka
- Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Qiang Zhu
- Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Lianfeng Gu
- Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Chentao Lin
- Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.
- Department of Molecular, Cell & Developmental Biology, University of California, Los Angeles, CA, 90095, USA.
| | - Bobin Liu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.
- Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.
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Zhang Y, Tang D, Lin X, Ding M, Tong Z. Genome-wide identification of MADS-box family genes in moso bamboo (Phyllostachys edulis) and a functional analysis of PeMADS5 in flowering. BMC PLANT BIOLOGY 2018; 18:176. [PMID: 30176795 PMCID: PMC6122543 DOI: 10.1186/s12870-018-1394-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 08/27/2018] [Indexed: 05/18/2023]
Abstract
BACKGROUND MADS-box genes encode a large family of transcription factors that play significant roles in plant growth and development. Bamboo is an important non-timber forest product worldwide, but previous studies on the moso bamboo (Phyllostachys edulis) MADS-box gene family were not accurate nor sufficiently detailed. RESULTS Here, a complete genome-wide identification and characterization of the MADS-box genes in moso bamboo was conducted. There was an unusual lack of type-I MADS-box genes in the bamboo genome database ( http://202.127.18.221/bamboo/index.php ), and some of the PeMADS sequences are fragmented and/or inaccurate. We performed several bioinformatics techniques to obtain more precise sequences using transcriptome assembly. In total, 42 MADS-box genes, including six new type-I MADS-box genes, were identified in bamboo, and their structures, phylogenetic relationships, predicted conserved motifs and promoter cis-elements were systematically investigated. An expression analysis of the bamboo MADS-box genes in floral organs and leaves revealed that several key members are involved in bamboo inflorescence development, like their orthologous genes in Oryza. The ectopic overexpression of one MADS-box gene, PeMADS5, in Arabidopsis triggered an earlier flowering time and the development of an aberrant flower phenotype, suggesting that PeMADS5 acts as a floral activator and is involved in bamboo flowering. CONCLUSION We produced the most comprehensive information on MADS-box genes in moso bamboo. Additionally, a critical PeMADS gene (PeMADS5) responsible for the transition from vegetative to reproductive growth was identified and shown to be related to bamboo floral development.
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Affiliation(s)
- Yuting Zhang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin’an, Zhejiang China
| | - Dingqin Tang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin’an, Zhejiang China
| | - Xinchun Lin
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin’an, Zhejiang China
| | - Mingquan Ding
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Agriculture and Food Science, Zhejiang A & F University, Lin’an, Zhejiang China
| | - Zaikang Tong
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin’an, Zhejiang China
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Dutta S, Biswas P, Chakraborty S, Mitra D, Pal A, Das M. Identification, characterization and gene expression analyses of important flowering genes related to photoperiodic pathway in bamboo. BMC Genomics 2018. [PMID: 29523071 PMCID: PMC5845326 DOI: 10.1186/s12864-018-4571-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Background Bamboo is an important member of the family Poaceae and has many inflorescence and flowering features rarely observed in other plant groups. It retains an unusual form of perennialism by having a long vegetative phase that can extend up to 120 years, followed by flowering and death of the plants. In contrast to a large number of studies conducted on the annual, reference plants Arabidopsis thaliana and rice, molecular studies to characterize flowering pathways in perennial bamboo are lacking. Since photoperiod plays a crucial role in flower induction in most plants, important genes involved in this pathway have been studied in the field grown Bambusa tulda, which flowers after 40-50 years. Results We identified several genes from B. tulda, including four related to the circadian clock [LATE ELONGATED HYPOCOTYL (LHY), TIMING OF CAB EXPRESSION1 (TOC1), ZEITLUPE (ZTL) and GIGANTEA (GI)], two circadian clock response integrators [CONSTANS A (COA), CONSTANS B (COB)] and four floral pathway integrators [FLOWERING LOCUS T1, 2, 3, 4 (FT1, 2, 3, 4)]. These genes were amplified from either gDNA and/or cDNA using degenerate as well as gene specific primers based on homologous sequences obtained from related monocot species. The sequence identity and phylogenetic comparisons revealed their close relationships to homologs identified in the temperate bamboo Phyllostachys edulis. While the four BtFT homologs were highly similar to each other, BtCOA possessed a full-length B-box domain that was truncated in BtCOB. Analysis of the spatial expression of these genes in selected flowering and non-flowering tissue stages indicated their possible involvement in flowering. The diurnal expression patterns of the clock genes were comparable to their homologs in rice, except for BtZTL. Among multiple BtCO and BtFT homologs, the diurnal pattern of only BtCOA and BtFT3, 4 were synchronized in the flower inductive tissue, but not in the non-flowering tissues. Conclusion This study elucidates the photoperiodic regulation of bamboo homologs of important flowering genes. The finding also identifies copy number expansion and gene expression divergence of CO and FT in bamboo. Further studies are required to understand their functional role in bamboo flowering. Electronic supplementary material The online version of this article (10.1186/s12864-018-4571-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Smritikana Dutta
- Department of Life Sciences, Presidency University, Kolkata, India
| | - Prasun Biswas
- Department of Life Sciences, Presidency University, Kolkata, India
| | | | - Devrani Mitra
- Department of Life Sciences, Presidency University, Kolkata, India
| | - Amita Pal
- Division of Plant Biology, Bose Institute, Kolkata, India
| | - Malay Das
- Department of Life Sciences, Presidency University, Kolkata, India.
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