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Geographic and longitudinal variations of anatomical characteristics and mechanical properties in three bamboo species naturally grown in Lombok Island, Indonesia. Sci Rep 2023; 13:2265. [PMID: 36755112 PMCID: PMC9908941 DOI: 10.1038/s41598-023-29288-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 02/01/2023] [Indexed: 02/10/2023] Open
Abstract
The anatomical characteristics (fiber length and fiber area) and mechanical properties (modulus of elasticity, modulus of rupture, compressive strength, tensile Young's modulus, and tensile strength) of Bambusa vulgaris, Bambusa maculata, and Gigantochloa atter, naturally growing at four different sites in Lombok Island, Indonesia, were examined for evaluating geographic and longitudinal variations by mixed-effects modeling to effectively utilize bamboo culm resources for structural materials. We found geographic and longitudinal variations of bamboo culm properties in these three species. Based on the results, we concluded that, for utilization of bamboo culm as a structural material, variation of individual culm rather than site, and longitudinal variations should be considered for Bambusa species and G. atter, respectively.
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Liu Y, Wu M, Xu X, Zhu X, Dai Z, Gou G. Genetic diversity and phylogeography of the endemic species Chimonobambusa utilis growing in southwest China: Chloroplast DNA sequence and microsatellite marker analyses. FRONTIERS IN PLANT SCIENCE 2022; 13:943225. [PMID: 36407620 PMCID: PMC9671600 DOI: 10.3389/fpls.2022.943225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 10/06/2022] [Indexed: 06/16/2023]
Abstract
Chimonobambusa utilis (Keng) Keng F is an endemic species distributed only in the Daluoshan Mountains, southwest China. Ch. utilis is popular due to its unique flavor and deliciousness and plays an important role in the industrial revolution in many counties in China. A total of 20 natural populations were sampled from the entire distribution range of Ch. utilis. In the present study, we used five EST-SSR molecular markers, three chloroplast DNA (trnH-psbA, atpF-atpH, and psbK-psbI), and one ITS molecular marker to elucidate the genetic diversity and phylogeography analyses of these Ch. utilis populations. The results exhibited that Ch. utilis populations showed lower genetic diversity than other angiosperms (HT = 0.752, HS = 0.364, and FST = 0.05021 for EST-SSR; HT = 0.956, Hs = 0.507, and FST = 0.70121 for cpDNA; HT = 0.868, Hs = 0.495, and FST = 0.70121 for nrDNA). A total of 40 alleles were detected for five polymorphic loci. We detected 20 polymorphic sites and 11 haplotypes within 1,398 bp of cpDNA and 59 polymorphic sites and 32 haplotypes within the 589 bp of the ITS sequence. Based on the haplotype distribution, we infer that there were at least two glacial refuges of Ch. utilis populations during the Quaternary Ice Age. The genetic and geographic distance were correlated (p < 0.05), indicating that narrow distribution might be the primary cause of the low genetic differentiation of Ch. utilis populations. Based on the genetic diversity of Ch. utilis populations, we recommend implementing effective genetic resource management and sustainable utilization.
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Affiliation(s)
- Yanjiang Liu
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang, China
- Bamboo Research Institute, Guizhou University, Guiyang, China
| | - Mingli Wu
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang, China
- Bamboo Research Institute, Guizhou University, Guiyang, China
| | - Xue Xu
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang, China
- Bamboo Research Institute, Guizhou University, Guiyang, China
| | - Xiao Zhu
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang, China
- Bamboo Research Institute, Guizhou University, Guiyang, China
| | - Zhaoxia Dai
- Bamboo Research Institute, Guizhou University, Guiyang, China
- College of Forestry, Guizhou University, Guiyang, China
| | - Guangqian Gou
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang, China
- Bamboo Research Institute, Guizhou University, Guiyang, China
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Traditional System Versus DNA Barcoding in Identification of Bamboo Species: A Systematic Review. Mol Biotechnol 2021; 63:651-675. [PMID: 34002354 DOI: 10.1007/s12033-021-00337-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 05/11/2021] [Indexed: 02/07/2023]
Abstract
Bamboo, a gramineous plant belonging to the family Poaceae, comprises of 1575 species from 116 genera across the globe. It has the ability to grow and evolve on degraded land and hence, can be utilized in the various applications as an alternative for plastic and wood. DNA barcoding, a long genomic sequence, identifies barcode region which shows species-specific nucleotide differences. This technology is considered as advanced molecular technique utilized for characterization and classification of the various species by applying distinctive molecular markers. Recent investigations revealed the potential application of various barcode regions such as matK, rbcL, rpoB, rpoC1, psbA-trnH, and ITS2, in identification of many bamboo species from different genus. In this review we comprehensively discussed the relevance of DNA barcoding as a tool in classification/identification of various bamboo species. We highlighted the methodology, how this advance technology overcomes the challenges associated with traditional methods along with prospects for future research.
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Oumer OA, Dagne K, Feyissa T, Tesfaye K, Durai J, Hyder MZ. Genetic diversity, population structure, and gene flow analysis of lowland bamboo [ Oxytenanthera abyssinica (A. Rich.) Munro] in Ethiopia. Ecol Evol 2020; 10:11217-11236. [PMID: 33144960 PMCID: PMC7593185 DOI: 10.1002/ece3.6762] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 08/19/2020] [Accepted: 08/20/2020] [Indexed: 12/12/2022] Open
Abstract
Bamboo, a member of subfamily Bambusoideae in the grass family (Poaceae), is one of the most important nontimber forest resources and a potential alternative to wood and wood products. Ethiopian lowland bamboo (Oxytenanthera abyssinica) is an economically and ecologically important species which accounts about 85% of total bamboo coverage in the country. This species is experiencing population decline due to a number of anthropogenic factors. As a foundation step, genetic diversity, population structure, and gene flow analysis of various O. abyssinica populations found in Ethiopia are studied using inter-simple sequence repeat markers. One hundred and thirty isolates of bamboo belonging to 13 geographically diverse populations were collected for DNA extraction and analysis. Heterozygosity, level of polymorphism, marker efficiency, Nei's gene diversity (H), and Shannon's information index (I) analysis, analysis of molecular variance (AMOVA), analysis for cluster, principal coordinates (PCoA), and admixture analyses were performed based on the markers banding pattern. The results indicated high genetic variation (84.48%) at species level. The H, I, observed and effective number of alleles at the species level were 0.2702, 0.4061, 1.8448, and 1.4744, respectively, suggesting a relatively high level of genetic diversity. However, genetic differentiation at the population level was relatively low. Using grouped populations, AMOVA revealed that most (61.05%) of the diversity was distributed within the populations with F ST = 0.38949, F SC = 0.10486, and F CT = 0.31797. Cluster analysis grouped the populations into markedly distinct clusters, suggesting confined propagation in distinct geographic regions. STRUCTURE analyses showed K = 2 for all populations and K = 11 excluding Gambella population. Using these markers, we found strong evidence that the genetic diversity of the lowland bamboo is associated with distinct geographic regions and that isolates of Gambella Region, with their unique genetic origin, are quite different from other bamboos found in the country.
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Affiliation(s)
- Oumer Abdie Oumer
- Department of Microbial, Cellular and Molecular BiologyAddis Ababa University (AAU)Addis AbabaEthiopia
- Department of BiologyAssosa University (ASU)AssosaEthiopia
| | - Kifle Dagne
- Department of Microbial, Cellular and Molecular BiologyAddis Ababa University (AAU)Addis AbabaEthiopia
| | - Tileye Feyissa
- Institute of Biotechnology (IoB)Addis Ababa University (AAU)Addis AbabaEthiopia
| | - Kassahun Tesfaye
- Institute of Biotechnology (IoB)Addis Ababa University (AAU)Addis AbabaEthiopia
- Ethiopian Biotechnology Institute (EBTi)Ministry of Science and Technology (MoST)Addis AbabaEthiopia
| | - Jayaraman Durai
- International Network for Bamboo and Rattan (INBAR) East Africa Regional Office (EARO)Addis AbabaEthiopia
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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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Amom T, Tikendra L, Apana N, Goutam M, Sonia P, Koijam AS, Potshangbam AM, Rahaman H, Nongdam P. Efficiency of RAPD, ISSR, iPBS, SCoT and phytochemical markers in the genetic relationship study of five native and economical important bamboos of North-East India. PHYTOCHEMISTRY 2020; 174:112330. [PMID: 32146386 DOI: 10.1016/j.phytochem.2020.112330] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 02/21/2020] [Accepted: 02/24/2020] [Indexed: 05/26/2023]
Abstract
10 primers each of random amplified polymorphic DNA (RAPD), inter-simple sequence repeats (ISSR), inter primer binding site (iPBS) and start codon targeted (SCoT) were used to analyze genetic polymorphism and relationship between 50 genotypes of 5 economical important native bamboos (Bambusa cacharensis, B. mizorameana, Dendrocalamus manipureanus, D. hamiltonii and D. sikkimensis) of North-East India. The 40 different primers generated 111, 115, 116 and 138 polymorphic bands for RAPD, ISSR, iPBS and SCoT markers respectively. The comparative analysis of 4 marker systems based on polymorphic information content (PIC), effective multiplex ratio (EMR) and marker index (MI) values showed SCoT to be more informative with higher discriminating power than the other three markers. The correlation value (r) as determined by the Mantel test ranged from 0.60 (SCoT and RAPD) to 0.83 (iPBS and ISSR) indicating a high positive correlation between the markers. The close correspondence between the genetic matrices of RAPD, ISSR, iPBS and SCoT markers revealed the effectiveness of each marker system in determining the genetic relationship between bamboos. UPGMA (Unweighted Pair Group Arithmetic Mean Method) dendrograms generated from DNA marker analysis demonstrated species-specific clustering of different bamboo genotypes. Except for RAPD, the dendrograms of ISSR, iPBS and SCoT markers also showed a close association of bamboo genotypes based on geographical origin. Principal coordinate analysis (PCoA) revealed the distribution of different bamboo genotypes in accordance with the cluster analysis. The cluster grouping based on phytochemical study not only discriminated the different bamboo species but also illustrated a location-specific grouping of the genotypes. The bamboo clustering pattern derived from phytochemical analysis matched closely with the dendrograms generated by the DNA markers. The present investigation established the possibility of using a combined molecular and phytochemical marker approach to determine the genetic relationship between 5 native bamboos of North-East India with high precision.
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Affiliation(s)
- Thoungamba Amom
- Department of Biotechnology, Manipur University, Canchipur, Imphal, 795003, Manipur, India
| | - Leimapokpam Tikendra
- Department of Biotechnology, Manipur University, Canchipur, Imphal, 795003, Manipur, India
| | - Nandeibam Apana
- Department of Biotechnology, Manipur University, Canchipur, Imphal, 795003, Manipur, India
| | - Moirangthem Goutam
- Department of Biotechnology, Manipur University, Canchipur, Imphal, 795003, Manipur, India
| | - Paonam Sonia
- Department of Biotechnology, Manipur University, Canchipur, Imphal, 795003, Manipur, India
| | - Arunkumar Singh Koijam
- Department of Biotechnology, Manipur University, Canchipur, Imphal, 795003, Manipur, India
| | | | - Hamidur Rahaman
- Department of Biotechnology, Manipur University, Canchipur, Imphal, 795003, Manipur, India
| | - Potshangbam Nongdam
- Department of Biotechnology, Manipur University, Canchipur, Imphal, 795003, Manipur, India.
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Cai K, Zhu L, Zhang K, Li L, Zhao Z, Zeng W, Lin X. Development and Characterization of EST-SSR Markers From RNA-Seq Data in Phyllostachys violascens. FRONTIERS IN PLANT SCIENCE 2019; 10:50. [PMID: 30774640 PMCID: PMC6367221 DOI: 10.3389/fpls.2019.00050] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 01/15/2019] [Indexed: 05/02/2023]
Abstract
Bamboo are woody grass species containing important economic and ecological values. Lei bamboo (Phyllostachys violascens) is a kind of shoot-producing bamboo species with the highest economic yield per unit area. However, identifying different varieties of Lei bamboo based on morphological characteristics is difficult. Microsatellites play an important role in plant identification and genetic diversity analysis and are superior to other molecular markers. In this study, we identified 18,356 expressed sequence tag-simple sequence repeat (EST-SSR) loci in Lei bamboo transcriptome data. A total of 11,264 primer pairs were successfully designed from unigenes of all EST-SSR loci, and 96 primer pairs were randomly selected and synthesized. A total of 54 primer pairs were used for classifying 16 Lei bamboo varieties and 10 different Phyllostachys species. The number of polymorphism alleles among the 54 primer pairs ranged from 3 to 12 for P. violascens varieties and 3 to 20 for Phyllostachys. The phylogenetic tree based on polymorphism alleles successfully distinguished 16 P. violascens varieties and 10 Phyllostachys species. Our study provides abundant EST-SSR resources that are useful for genetic diversity analysis and molecular verification of bamboo and suggests that SSR markers developed from Lei bamboo are more efficient and reliable than ISSR, SRAP or AFLP markers.
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Affiliation(s)
- Kai Cai
- Sino-Australia Plant Cell Wall Research Centre, State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin’an, China
- Zhejiang Provincial Collaborative Innovation Center for Bamboo Resources and High-Efficiency Utilization, Zhejiang A & F University, Lin’an, China
| | - Longfei Zhu
- Sino-Australia Plant Cell Wall Research Centre, State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin’an, China
- Department of Genome Biology, Adam Mickiewicz University, Poznań, Poland
| | - Keke Zhang
- Sino-Australia Plant Cell Wall Research Centre, State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin’an, China
| | - Ling Li
- Sino-Australia Plant Cell Wall Research Centre, State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin’an, China
| | - Zhongyu Zhao
- Sino-Australia Plant Cell Wall Research Centre, State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin’an, China
| | - Wei Zeng
- Sino-Australia Plant Cell Wall Research Centre, State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin’an, China
| | - Xinchun Lin
- Sino-Australia Plant Cell Wall Research Centre, State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin’an, China
- Zhejiang Provincial Collaborative Innovation Center for Bamboo Resources and High-Efficiency Utilization, Zhejiang A & F University, Lin’an, China
- *Correspondence: Xinchun Lin,
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Basumatary A, Middha SK, Usha T, Bhattacharya S, Brahma BK, Goyal AK. Morphological phylogeny among 15 accessions of bamboos growing in Kokrajhar district of the Bodoland Territorial Area Districts, Assam. JOURNAL OF FORESTRY RESEARCH 2018; 29:1379-1386. [DOI: 10.1007/s11676-017-0535-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
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Nimbalkar SD, Jade SS, Kauthale VK, Agale S, Bahulikar RA. Genetic diversity in the candidate trees of Madhuca indica J. F. Gmel. (Mahua) revealed by inter-simple sequence repeats (ISSRs). 3 Biotech 2018; 8:143. [PMID: 29484282 PMCID: PMC5818362 DOI: 10.1007/s13205-018-1168-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 02/10/2018] [Indexed: 11/28/2022] Open
Abstract
Madhuca indica provides livelihood to several tribal people in India, where the flowers are used for extraction of sweet juices having multiple applications. Certain trees have more value as judged by the tribal people mainly based on yield and quality performance of the trees, and these trees were selected for the genetic diversity analyses. Genetic diversity of 48 candidate Mahua trees from Etapalli, Dadagaon, and Jawhar, Maharashtra, India, was assessed using ISSR markers. Fourteen ISSR primers revealed a total of 132 polymorphic bands giving overall 92% polymorphism. Genetic diversity, in terms of expected number of alleles (Ne), the observed number of alleles (Na), Nei's genetic diversity (H), and Shannon's information index (I) was 1.921, 1.333, 0.211, and 0.337, respectively, and suggested lower genetic diversity. Region wise analysis revealed higher genetic diversity for site Etapalli (H = 0.206) and lowest at Dhadgaon (H = 0.140). Etapalli area possesses higher forest cover than Dhadgaon and Jawhar. Additionally, in Dhadgaon and Jawhar M. indica trees are restricted to field bunds; both reasons might contribute to lower genetic diversity in these regions. The dendrogram and the principal coordinate analyses showed no region-specific clustering. The clustering patterns were supported by AMOVA where higher genetic variance was observed within trees and lower variance among regions. Long-distance dispersal and/or higher human interference might be responsible for low diversity and higher genetic variance within the candidate trees.
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Affiliation(s)
- S. D. Nimbalkar
- BAIF Development Research Foundation, Central Research Station, Urulikanchan, Tq. Haveli, Dist., Pune, Maharashtra 412 202 India
| | - S. S. Jade
- BAIF Development Research Foundation, Central Research Station, Urulikanchan, Tq. Haveli, Dist., Pune, Maharashtra 412 202 India
| | - V. K. Kauthale
- BAIF Development Research Foundation, Central Research Station, Urulikanchan, Tq. Haveli, Dist., Pune, Maharashtra 412 202 India
| | - S. Agale
- BAIF Development Research Foundation, Central Research Station, Urulikanchan, Tq. Haveli, Dist., Pune, Maharashtra 412 202 India
| | - R. A. Bahulikar
- BAIF Development Research Foundation, Central Research Station, Urulikanchan, Tq. Haveli, Dist., Pune, Maharashtra 412 202 India
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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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Liu H, Guo X, Wu J, Chen GB, Ying Y. Development of universal genetic markers based on single-copy orthologous (COSII) genes in Poaceae. PLANT CELL REPORTS 2013; 32:379-388. [PMID: 23233129 DOI: 10.1007/s00299-012-1371-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Revised: 10/15/2012] [Accepted: 11/18/2012] [Indexed: 06/01/2023]
Abstract
KEY MESSAGE : We develop a set of universal genetic markers based on single-copy orthologous (COSII) genes in Poaceae. Being evolutionary conserved, single-copy orthologous (COSII) genes are particularly useful in comparative mapping and phylogenetic investigation among species. In this study, we identified 2,684 COSII genes based on five sequenced Poaceae genomes including rice, maize, sorghum, foxtail millet, and brachypodium, and then developed 1,072 COSII markers whose transferability and polymorphism among five bamboo species were further evaluated with 46 pairs of randomly selected primers. 91.3 % of the 46 primers obtained clear amplification in at least one bamboo species, and 65.2 % of them produced polymorphism in more than one species. We also used 42 of them to construct the phylogeny for the five bamboo species, and it might reflect more precise evolutionary relationship than the one based on the vegetative morphology. The results indicated a promising prospect of applying these markers to the investigation of genetic diversity and the classification of Poaceae. To ease and facilitate access of the information of common interest to readers, a web-based database of the COSII markers is provided ( http://www.sicau.edu.cn/web/yms/PCOSWeb/PCOS.html ).
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Affiliation(s)
- Hailan Liu
- Institute of Maize Research, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.
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Singh SR, Singh R, Kalia S, Dalal S, Dhawan AK, Kalia RK. Limitations, progress and prospects of application of biotechnological tools in improvement of bamboo-a plant with extraordinary qualities. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2013; 19:21-41. [PMID: 24381435 PMCID: PMC3550689 DOI: 10.1007/s12298-012-0147-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Bamboos (family Poaceae) are the most beautiful and useful plants on the Earth, mainly found in the tropical and sub-tropical regions of the world. Bamboos are fast growing and early maturing, but lack of proper management of bamboo resources is leading to rapid reduction of the existing bamboosetum. Bamboo propagation through seeds is limited due to long flowering cycle of upto 120 years, seed sterility and short seed viability. Infrequent and unpredictable flowering events coupled with peculiar monocarpic behaviour i.e. flowering once before culm death, and extensive genome polyploidization are additional challenges for this woody group. Similarly, vegetative propagation by cuttings, offsets and rhizomes are also inadequate to cope up with the demand of planting stock due to large propagule size, limited availability, seasonal dependence, low multiplication rate and rooting percentage. Therefore, attempts have been made to propagate bamboos through in vitro techniques. In vitro flowering has also been achieved successfully in some bamboo species. Classification systems proposed to date need further support, as taxonomic delineation at lower levels is still lacking sufficient resolution. Tremendous advancement in molecular markers holds the promise to address the needs of bamboo taxonomy (systematics and identification) and diversity studies. Successful application of molecular marker techniques has been achieved in several bamboo species although, more studies are required to understand the population structure and genetic diversity of bamboos in a better way. In addition, some efforts have also been made to clone important genes from bamboos and also for genetic transformation using Agrobacterium and particle bombardment methods. An overview of the recent developments made in improvement of bamboos through in vitro propagation, molecular marker technologies, cloning, and transformation and transgenics has been presented. The future potential of improvement of bamboos using modern biotechnological tools has also been discussed.
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Affiliation(s)
- Sharbati R. Singh
- />Centre for Plant Biotechnology, CCS HAU New Campus, Hisar 125004, Haryana India
- />Department of Biotechnology, Kurukshetra University, Kurukshetra, 136119 India
| | - Rohtas Singh
- />Centre for Plant Biotechnology, CCS HAU New Campus, Hisar 125004, Haryana India
| | - Sanjay Kalia
- />Department of Biotechnology, Block 2, 8th Floor, CGO Complex, Lodhi Road, New Delhi, 110003 India
| | - Sunita Dalal
- />Department of Biotechnology, Kurukshetra University, Kurukshetra, 136119 India
| | - A. K. Dhawan
- />Centre for Plant Biotechnology, CCS HAU New Campus, Hisar 125004, Haryana India
- />National Institute of Food Technology Entrepreneurship and Management (NIFTEM), Kundli 131028, Haryana India
| | - Rajwant K. Kalia
- />Centre for Plant Biotechnology, CCS HAU New Campus, Hisar 125004, Haryana India
- />Central Arid Zone Research Institute (CAZRI), Jodhpur, 342003 Rajasthan India
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PICcalc: an online program to calculate polymorphic information content for molecular genetic studies. Biochem Genet 2012; 50:670-2. [PMID: 22573137 DOI: 10.1007/s10528-012-9509-1] [Citation(s) in RCA: 114] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Accepted: 02/03/2012] [Indexed: 10/28/2022]
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