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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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Xie N, Chen LN, Dong YR, Yang HQ. Mixed mating system and variable mating patterns in tropical woody bamboos. BMC PLANT BIOLOGY 2019; 19:418. [PMID: 31604418 PMCID: PMC6787975 DOI: 10.1186/s12870-019-2024-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 09/10/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND So far, little is known in detail about mating systems of woody bamboos. Paternity analysis of offspring improved our understanding of these systems, and contributed to their germplasm conservation and genetic improvement. RESULTS In this study, a paternity analysis of offspring from two consecutive mass or sporadically flowering events of Dendrocalamus membranaceus and D. sinicus were conducted to determine their mating system and pollen dispersal using the program COLONY based on simple sequence repeat (SSR) markers. Two sporadically flowering populations of D. sinicus (C1, C2) obtained relatively high paternity assignments rates (69.0-71.4%). Meanwhile, among three populations of D. membranaceus, the sporadically flowering population A also had much higher paternity assignments rates (56.4%) than mass flowering populations B1(28.6%) and B2 (42.5%). Both D. membranaceus and D. sinicus had mixed mating systems while their mating patterns were variable depending on pollination conditions. The maximum pollen dispersal distances were 90 m and 4378 m for D. membranaceus and D. sinicus populations, respectively, and the mating distances of these two species focused on ranges of ca. 0-50 m and 0-1500 m, respectively. CONCLUSIONS These results revealed for the first time variable mating patterns in woody bamboos. This suggests half-sib seeds from the same bamboo clump may have different male parents and it is crucial to clarify genetic origin in woody bamboos' breeding programs. The results also indicate the importance of pollinators in the mating systems of tropical woody bamboos.
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Affiliation(s)
- Ning Xie
- Research Institute of Resources Insects, Chinese Academy of Forestry, Bailongsi, Panlong District, Kunming, 650233 China
- Lushan Botanical Garden, Jiangxi Province and Chinese Academy of Sciences, Guling, Lushan District, Jiujiang, 332900 China
| | - Ling-Na Chen
- Research Institute of Resources Insects, Chinese Academy of Forestry, Bailongsi, Panlong District, Kunming, 650233 China
| | - Yu-Ran Dong
- Research Institute of Resources Insects, Chinese Academy of Forestry, Bailongsi, Panlong District, Kunming, 650233 China
| | - Han-Qi Yang
- Research Institute of Resources Insects, Chinese Academy of Forestry, Bailongsi, Panlong District, Kunming, 650233 China
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Wang Y, Yuan X, Li Y, Zhang J. The complete chloroplast genome sequence of Dendrocalamus sinicus. Mitochondrial DNA B Resour 2019; 4:2988-2989. [PMID: 33365823 PMCID: PMC7706990 DOI: 10.1080/23802359.2019.1664947] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Dendrocalamus sinicus is the world’s largest bamboo species. In this study, the complete chloroplast genome (cpDNA) sequence of D. sinicus was determined from Illumina HiSeq pair-end sequencing data. The cpDNA is 139,441 bp in length, contains a large single-copy region (LSC) of 82,777 bp and a small single-copy region (SSC) of 12,803 bp, which were separated by a pair of inverted repeat (IR) regions of 21,296 bp. The genome contains 136 genes, including 89 protein-coding genes, 8 ribosomal RNA genes, and 40 transfer RNA genes. The overall GC content of the whole genome is 38.9%, and the corresponding values of the LSC, SSC, and IR regions are 37%, 33.2%, and 44.2%, respectively. Further, phylogenomic analysis showed that D. sinicus clustered together with D. latiflorus.
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Affiliation(s)
- Yi Wang
- Laboratory of Forest Plant Cultivation and Utilization, Yunnan Academy of Forestry, Kunming, Yunnan, People's Republic of China
| | - Xiaolong Yuan
- Laboratory of Forest Plant Cultivation and Utilization, Yunnan Academy of Forestry, Kunming, Yunnan, People's Republic of China
| | - Yunqing Li
- Laboratory of Forest Plant Cultivation and Utilization, Yunnan Academy of Forestry, Kunming, Yunnan, People's Republic of China
| | - Jinfeng Zhang
- Laboratory of Forest Plant Cultivation and Utilization, Yunnan Academy of Forestry, Kunming, Yunnan, People's Republic of China
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Meena RK, Bhandhari MS, Barhwal S, Ginwal HS. Genetic diversity and structure of Dendrocalamus hamiltonii natural metapopulation: a commercially important bamboo species of northeast Himalayas. 3 Biotech 2019; 9:60. [PMID: 30729084 DOI: 10.1007/s13205-019-1591-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 01/21/2019] [Indexed: 12/20/2022] Open
Abstract
Dendrocalamus hamiltonii is a commercially important bamboo species of India, experiencing population depletion due to heavy extraction from natural forests. Nuclear simple sequence repeats (nSSRs) were used to study the genetic diversity and population genetic structure of 19 natural stands of D. hamiltonii distributed across the northeast Himalayas. A total of 68 nSSR primer pairs of D. latiflorus and Bambusa arundinacea have been tested in D. hamiltonii for their transferability, out of which 17 primers showing positive and polymorphic amplification were used for genotyping. A total of 130 alleles were generated in 535 individuals of all the populations using selected primer pairs. The marker analysis indicated that D. hamiltonii populations have maintained a low level of genetic diversity (h = 0.175, I = 0.291) in northeastern region of India. Despite a large proportion of the genetic variation (83.47%) confined within the populations, a moderate level of genetic differentiation (F ST = 0.165) was observed among the populations. The clustering pattern obtained in UPGMA and STRUCTURE analysis revealed that most of the populations were clustered in accordance with their geographical distribution. Two populations (DH03 and DH13) exhibiting significant genetic admixture were identified and recommended for in situ conservation. In addition, six highly diverse populations were also suggested for conservation in different geographical area under study. The study has revealed useful nSSR markers for D. hamiltonii, which were lacking earlier and the information generated herein is of paramount importance in devising programs for species conservation and genetic improvement.
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Yang JB, Dong YR, Wong KM, Gu ZJ, Yang HQ, Li DZ. Genetic structure and differentiation in Dendrocalamus sinicus (Poaceae: Bambusoideae) populations provide insight into evolutionary history and speciation of woody bamboos. Sci Rep 2018; 8:16933. [PMID: 30446690 PMCID: PMC6240087 DOI: 10.1038/s41598-018-35269-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 11/02/2018] [Indexed: 12/14/2022] Open
Abstract
Evolutionary processes, speciation in woody bamboos are presently little understood. Here we used Dendrocalamus sinicus Chia & J.L. Sun as a model species to investigate dispersal or vicariance speciation in woody bamboos. Variation in three chloroplast DNA (cpDNA) fragments and eight simple sequence repeat markers (SSR) among 232 individuals sampled from 18 populations across the known geographic range of D. sinicus was surveyed. D. sinicus populations exhibited a high level of genetic differentiation which divided them into two groups that are consistent with different culm types. Eleven haplotypes and two lineages (Straight-culm and Sinuous-culm lineages) were identified from phylogenetic analyses, and a strong phylogeographic structure across the distribution range was found. The demographic and spatial expansion times of the Straight-culm lineage were calculated as 11.3 Kya and 20.8 Kya, respectively. The populations of D. sinicus had experienced dispersal and long-term isolation, although this trace was diluted by contemporary gene flow revealed by SSR data. Our results provide an phylogeographic insight to better understand the speciation processes of woody bamboos.
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Affiliation(s)
- Jun Bo Yang
- Research Institute of Resources Insects, Chinese Academy of Forestry, Kunming, Yunnan, 650233, China.,Germplasm Bank of Wild Species, Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650204, China
| | - Yu Ran Dong
- Research Institute of Resources Insects, Chinese Academy of Forestry, Kunming, Yunnan, 650233, China
| | - Khoon Meng Wong
- Singapore Botanic Gardens, 1 Cluny Road, Singapore, 259569, Republic of Singapore
| | - Zhi Jia Gu
- Research Institute of Resources Insects, Chinese Academy of Forestry, Kunming, Yunnan, 650233, China.,Germplasm Bank of Wild Species, Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650204, China
| | - Han Qi Yang
- Research Institute of Resources Insects, Chinese Academy of Forestry, Kunming, Yunnan, 650233, China.
| | - De Zhu Li
- Germplasm Bank of Wild Species, Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650204, China.
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Chen LN, Cui YZ, Wong KM, Li DZ, Yang HQ. Breeding system and pollination of two closely related bamboo species. AOB PLANTS 2017; 9:plx021. [PMID: 28685014 PMCID: PMC5493747 DOI: 10.1093/aobpla/plx021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Revised: 05/21/2017] [Accepted: 05/27/2017] [Indexed: 05/28/2023]
Abstract
An understanding of the breeding systems and pollination of agriculturally important plants is critical to germplasm improvement. Breeding system characteristics greatly influence the amount and spatial distribution of genetic variation within and amongst populations and influence the rarity and extinction vulnerability of plant species. Many woody bamboos have a long vegetative period (20-150 years) followed by gregarious monocarpy. Relatively, little is known about their pollination and breeding systems. We studied these characteristics in wild Dendrocalamus membranaceus populations and cultivated Dendrocalamus sinicus populations distributed in the Yunnan Province of China. Floral morphology, flower visitors and breeding system were studied from 2013 to 2015. Both bamboos were protogynous, but flowering periods of florets overlapped providing opportunities for self-pollination amongst florets, especially in D. membranaceus. There was no agamospermy in either species. Seed set of D. sinicus was low (0.42 ± 0.42 %) under natural pollination but higher (8.89 ± 2.55 %) after artificial xenogamy. Seed set of D. membranaceus was higher (7.49 ± 0.82 %) in mass flowering populations and 2.14 ± 0.25 % in sporadically flowering populations. The Asian honeybee Apis cerana could provide cross-pollination of D. membranaceus and D. sinicus, and flower visitation peaked at 1000-1200 h. Pollination limitation due to lack of pollinators or pollen was detected in the cultivated populations of D. sinicus and sporadically flowering populations of D. membranaceus. Pollination limitation was not obvious within mass flowering populations. Hand pollination could significantly increase seed set of these two bamboo species. Dendrocalamus membranaceus and D. sinicus were self-compatible and have a mixed-mating system with outcrossing being pre-dominant. Their seed production was limited by the quantity of pollen and pollinator activity. Honeybees were observed as effective pollinators.
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Affiliation(s)
- Ling-Na Chen
- Research Institute of Insect Resources, Chinese Academy of Forestry, Bailongsi, Panlong District, Kunming 650233, China
| | - Yong-Zhong Cui
- Research Institute of Insect Resources, Chinese Academy of Forestry, Bailongsi, Panlong District, Kunming 650233, China
| | - Khoon-Meng Wong
- Singapore Botanic Gardens, 1 Cluny Road, Singapore 259569, Singapore
| | - De-Zhu Li
- Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, No. 132, Lanhei Road, Panlong District, Kunming 650201, China
| | - Han-Qi Yang
- Research Institute of Insect Resources, Chinese Academy of Forestry, Bailongsi, Panlong District, Kunming 650233, China
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Cui K, Wang H, Liao S, Tang Q, Li L, Cui Y, He Y. Transcriptome Sequencing and Analysis for Culm Elongation of the World's Largest Bamboo (Dendrocalamus sinicus). PLoS One 2016; 11:e0157362. [PMID: 27304219 PMCID: PMC4909198 DOI: 10.1371/journal.pone.0157362] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2015] [Accepted: 05/27/2016] [Indexed: 12/29/2022] Open
Abstract
Dendrocalamus sinicus is the world’s largest bamboo species with strong woody culms, and known for its fast-growing culms. As an economic bamboo species, it was popularized for multi-functional applications including furniture, construction, and industrial paper pulp. To comprehensively elucidate the molecular processes involved in its culm elongation, Illumina paired-end sequencing was conducted. About 65.08 million high-quality reads were produced, and assembled into 81,744 unigenes with an average length of 723 bp. A total of 64,338 (79%) unigenes were annotated for their functions, of which, 56,587 were annotated in the NCBI non-redundant protein database and 35,262 were annotated in the Swiss-Prot database. Also, 42,508 and 21,009 annotated unigenes were allocated to gene ontology (GO) categories and clusters of orthologous groups (COG), respectively. By searching against the Kyoto Encyclopedia of Genes and Genomes Pathway database (KEGG), 33,920 unigenes were assigned to 128 KEGG pathways. Meanwhile, 8,553 simple sequence repeats (SSRs) and 81,534 single-nucleotide polymorphism (SNPs) were identified, respectively. Additionally, 388 transcripts encoding lignin biosynthesis were detected, among which, 27 transcripts encoding Shikimate O-hydroxycinnamoyltransferase (HCT) specifically expressed in D. sinicus when compared to other bamboo species and rice. The phylogenetic relationship between D. sinicus and other plants was analyzed, suggesting functional diversity of HCT unigenes in D. sinicus. We conjectured that HCT might lead to the high lignin content and giant culm. Given that the leaves are not yet formed and culm is covered with sheaths during culm elongation, the existence of photosynthesis of bamboo culm is usually neglected. Surprisedly, 109 transcripts encoding photosynthesis were identified, including photosystem I and II, cytochrome b6/f complex, photosynthetic electron transport and F-type ATPase, and 24 transcripts were characterized as antenna proteins that regarded as the main tool for capturing light of plants, implying stem photosynthesis plays a key role during culm elongation due to the unavailability of its leaf. By real-time quantitative PCR, the expression level of 6 unigenes was detected. The results showed the expression level of all genes accorded with the transcriptome data, which confirm the reliability of the transcriptome data. As we know, this is the first study underline the D. sinicus transcriptome, which will deepen the understanding of the molecular mechanisms of culm development. The results may help variety improvement and resource utilization of bamboos.
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Affiliation(s)
- Kai Cui
- Research Institute of Resources Insects, Chinese Academy of Forestry, Kunming, 650224, People’s Republic of China
| | - Haiying Wang
- Research Institute of Resources Insects, Chinese Academy of Forestry, Kunming, 650224, People’s Republic of China
| | - Shengxi Liao
- Research Institute of Resources Insects, Chinese Academy of Forestry, Kunming, 650224, People’s Republic of China
- * E-mail:
| | - Qi Tang
- Hunan Co-Innovation Center for Utilization of Botanical Functional Ingredients, Hunan Agricultral University, Changsha, 410128, People’s Republic of China
| | - Li Li
- Research Institute of Resources Insects, Chinese Academy of Forestry, Kunming, 650224, People’s Republic of China
| | - Yongzhong Cui
- Research Institute of Resources Insects, Chinese Academy of Forestry, Kunming, 650224, People’s Republic of China
| | - Yuan He
- Research Institute of Resources Insects, Chinese Academy of Forestry, Kunming, 650224, People’s Republic of China
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Yeasmin L, Ali MN, Gantait S, Chakraborty S. Bamboo: an overview on its genetic diversity and characterization. 3 Biotech 2015; 5:1-11. [PMID: 28324361 PMCID: PMC4327751 DOI: 10.1007/s13205-014-0201-5] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Accepted: 02/11/2014] [Indexed: 11/30/2022] Open
Abstract
Genetic diversity represents the heritable variation both within and among populations of organisms, and in the context of this paper, among bamboo species. Bamboo is an economically important member of the grass family Poaceae, under the subfamily Bambusoideae. India has the second largest bamboo reserve in Asia after China. It is commonly known as "poor man's timber", keeping in mind the variety of its end use from cradle to coffin. There is a wide genetic diversity of bamboo around the globe and this pool of genetic variation serves as the base for selection as well as for plant improvement. Thus, the identification, characterization and documentation of genetic diversity of bamboo are essential for this purpose. During recent years, multiple endeavors have been undertaken for characterization of bamboo species with the aid of molecular markers for sustainable utilization of genetic diversity, its conservation and future studies. Genetic diversity assessments among the identified bamboo species, carried out based on the DNA fingerprinting profiles, either independently or in combination with morphological traits by several researchers, are documented in the present review. This review will pave the way to prepare the database of prevalent bamboo species based on their molecular characterization.
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Affiliation(s)
- Lucina Yeasmin
- Department of Agricultural Biotechnology, Faculty Centre for Integrated Rural Development and Management, School of Agriculture and Rural Development, Ramakrishna Mission Vivekananda University, Ramakrishna Mission Ashrama, Narendrapur, Kolkata, 700103, India
| | - Md Nasim Ali
- Department of Agricultural Biotechnology, Faculty Centre for Integrated Rural Development and Management, School of Agriculture and Rural Development, Ramakrishna Mission Vivekananda University, Ramakrishna Mission Ashrama, Narendrapur, Kolkata, 700103, India.
| | - Saikat Gantait
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
- Department of Biotechnology, Instrumentation and Environmental Science, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, WB, 741252, India
| | - Somsubhra Chakraborty
- Department of Agricultural Biotechnology, Faculty Centre for Integrated Rural Development and Management, School of Agriculture and Rural Development, Ramakrishna Mission Vivekananda University, Ramakrishna Mission Ashrama, Narendrapur, Kolkata, 700103, India
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