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Sareen A, Sharma V, Gupta RC. Assessment of genetic diversity and population structure in wild Ziziphus species from northwest India using SSR marker technique. J Genet Eng Biotechnol 2023; 21:4. [PMID: 36637660 PMCID: PMC9839936 DOI: 10.1186/s43141-022-00458-6] [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: 09/19/2022] [Accepted: 12/28/2022] [Indexed: 01/14/2023]
Abstract
BACKGROUND Ziziphus species particularly Ziziphus mauritiana and Ziziphus nummularia constitute an important part of genetic resources in India. They contribute economically as a fruit crop with lots of morphological and pomological variability. In current study, 48 accessions belonging to two wild Ziziphus species, i.e., Z. mauritiana and Z. nummularia, were characterized using SSR markers. In addition, external features were also examined using stereomicroscope. RESULTS Present investigation was done to explore the genetic structure of North Indian jujube. In total, 23 SSR markers detected 57 SSR alleles with an average of 2.47 alleles. Highest number of alleles (4) were detected by three primers, namely BFU1178, BFU479, and ZCMS14, while lowest number of alleles (2) were detected by fifteen primers. Highest Polymorphism Information Content (PIC) was 0.500 and shown by two primers, namely BFU528 and BFU1248, while lowest PIC (0.041) was observed in primers BFU286 with mean value of 0.443. Similarly, highest value of marker index (MI) was detected by primer BFU1178 i.e. 1.969, and lowest value of marker index was observed in primer BFU286 i.e. 0.021. Dendrogram generated using SSR markers data and principal component analysis showed two major groups of the analyzed germplasm with intermixing. STRUCTURE analysis also clustered all the accessions into two groups. We did not found correlation between geographic and genetic distances. CONCLUSIONS The preliminary results suggest that there is high level of gene pool mixing in these species which can be attributed to their cross-pollination habit. However, more such studies with large numbers of samples are required in future to gain concrete insights of the genetic structure in these species.
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Affiliation(s)
- Amit Sareen
- grid.412580.a0000 0001 2151 1270Department of Botany, Punjabi University Patiala, Patiala, Punjab India
| | - Vikas Sharma
- Department of Agriculture, Sant Baba Bhag Singh University Khiala, Jalandhar, 144030 India
| | - Raghbir Chand Gupta
- grid.412580.a0000 0001 2151 1270Department of Botany, Punjabi University Patiala, Patiala, Punjab India
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Mahima K, Sunil Kumar KN, Rakhesh KV, Rajeswaran PS, Sharma A, Sathishkumar R. Advancements and future prospective of DNA barcodes in the herbal drug industry. Front Pharmacol 2022; 13:947512. [PMID: 36339543 PMCID: PMC9635000 DOI: 10.3389/fphar.2022.947512] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 10/10/2022] [Indexed: 08/04/2023] Open
Abstract
Ethnopharmacological relevance: The past couple of decades have witnessed the global resurgence of medicinal plants in the field of herbal-based health care. Increased consumption of medicinal plants and their derivative products is the major cause of the adulteration issues in herbal industries. As a result, the quality of herbal products is affected by spurious and unauthorized raw materials. Recent development in molecular plant identification using DNA barcodes has become a robust methodology to identify and authenticate the adulterants in herbal samples. Hence, rapid and accurate identification of medicinal plants is the key to success for the herbal industry. Aim of the study: This paper provides a comprehensive review of the application of DNA barcoding and advanced technologies that have emerged over the past 10 years related to medicinal plant identification and authentication and the future prospects of this technology. Materials and methods: Information on DNA barcodes was compiled from scientific databases (Google Scholar, Web of Science, SciFinder and PubMed). Additional information was obtained from books, Ph.D. thesis and MSc. Dissertations. Results: Working out an appropriate DNA barcode for plants is challenging; the single locus-based DNA barcodes (rbcL, ITS, ITS2, matK, rpoB, rpoC, trnH-psbA) to multi-locus DNA barcodes have become the successful species-level identification among herbal plants. Additionally, multi-loci have become efficient in the authentication of herbal products. Emerging advances in DNA barcoding and related technologies such as next-generation sequencing, high-resolution melting curve analysis, meta barcodes and mini barcodes have paved the way for successful herbal plant/samples identification. Conclusion: DNA barcoding needs to be employed together with other techniques to check and rationally and effectively quality control the herbal drugs. It is suggested that DNA barcoding techniques combined with metabolomics, transcriptomics, and proteomics could authenticate the herbal products. The invention of simple, cost-effective and improved DNA barcoding techniques to identify herbal drugs and their associated products of medicinal value in a fool-proof manner will be the future thrust of Pharmacopoeial monograph development for herbal drugs.
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Affiliation(s)
- Karthikeyan Mahima
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, Tamil Nadu, India
- Department of Pharmacognosy, Siddha Central Research Institute, Chennai, Tamil Nadu, India
| | | | | | | | - Ashutosh Sharma
- Tecnologico de Monterrey, Centre of Bioengineering, Santiago de Queretaro, Queretaro, Mexico
| | - Ramalingam Sathishkumar
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, Tamil Nadu, India
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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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Li W, Shi C, Li K, Zhang QJ, Tong Y, Zhang Y, Wang J, Clark L, Gao LZ. Draft genome of the herbaceous bamboo Raddia distichophylla. G3-GENES GENOMES GENETICS 2021; 11:6066164. [PMID: 33585868 PMCID: PMC8022951 DOI: 10.1093/g3journal/jkaa049] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 11/01/2020] [Indexed: 11/19/2022]
Abstract
Bamboos are important nontimber forest plants widely distributed in the tropical and subtropical regions of Asia, Africa, America, and Pacific islands. They comprise the Bambusoideae in the grass family (Poaceae), including approximately 1700 described species in 127 genera. In spite of the widespread uses of bamboo for food, construction, and bioenergy, the gene repertoire of bamboo still remains largely unexplored. Raddia distichophylla (Schrad. ex Nees) Chase, belonging to the tribe Olyreae (Bambusoideae, Poaceae), is a diploid herbaceous bamboo with only slightly lignified stems. In this study, we report a draft genome assembly of the ∼589 Mb whole-genome sequence of R. distichophylla with a contig N50 length of 86.36 Kb. Repeat sequences account for ∼49.08% of the genome assembly, of which LTR retrotransposons occupy ∼35.99% of the whole genome. A total of 30,763 protein-coding genes were annotated in the R. distichophylla genome with an average transcript size of 2887 bp. Access to this herbaceous bamboo genome sequence will provide novel insights into biochemistry, molecular marker-assisted breeding programs, and germplasm conservation for bamboo species worldwide.
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Affiliation(s)
- Wei Li
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou 510642, China
| | - Cong Shi
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China
| | - Kui Li
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China
| | - Qun-Jie Zhang
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou 510642, China
| | - Yan Tong
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China
| | - Yun Zhang
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China
| | - Jun Wang
- Institution of Sustainable Development, Southwest China Forestry University, Kunming 650224, China
| | - Lynn Clark
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA 50011-1020, USA
| | - Li-Zhi Gao
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou 510642, China.,Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China
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Unnikrishnan R, Dev SA, Jayaraj R. Pitfalls and promises of raw drug identification techniques in the ayurvedic industry: an overview. 3 Biotech 2020; 10:497. [PMID: 33150123 DOI: 10.1007/s13205-020-02482-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 10/13/2020] [Indexed: 11/26/2022] Open
Abstract
India, with a rich heritage of floral diversity, is well-known for its medicinal plant wealth and is the largest producer of medicinal herbs in the world. Ethnobiological Survey of Ministry of Environment and Forests (MOEF) could identify 8000 plant species utilized in various systems of medicine with approximately 25,000 effective herbal formulations. The extensive consumption to meet demand-supply ratio exerts a heavy strain on the existing resources. This subsequently led to the adulteration and substitution of medicinal plants with look-alike species. The consumer's faith on herbal medicine is in the phase of decline due to the extremities in adulteration/substitution and ensuing consequences. It is imperative to bring forth universally acceptable standard tools to authenticate raw drugs before being processed further into formulations. A vast array of techniques such as physical, chemical (analytical), biochemical, anatomical, organoleptic, and recently emerged DNA based molecular methods are widely used for plant species authentication. In recent years, DNA barcoding has made remarkable progress in the field of medicinal plants research. DNA metabarcoding is the latest development for qualitative evaluation of the herbal formulations, whereas for quantitative analysis, combination of pharmacognostic, pharmacovigilance and analytical methods are inevitable for authentication. This review addresses the overall strengths and shortcomings of the existing as well as recently emerged techniques in authenticating ayurvedic raw drugs.
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Affiliation(s)
- Remya Unnikrishnan
- Forest Genetics and Biotechnology Division, Kerala Forest Research Institute, Peechi, Thrissur, Kerala India
- Cochin University of Science & Technology, Kochi, Kerala India
| | - Suma Arun Dev
- Forest Genetics and Biotechnology Division, Kerala Forest Research Institute, Peechi, Thrissur, Kerala India
| | - R Jayaraj
- Forest Ecology and Biodiversity Division, Kerala Forest Research Institute, Peechi, Thrissur, Kerala India
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Kapoor M, Mawal P, Sharma V, Gupta RC. Analysis of genetic diversity and population structure in Asparagus species using SSR markers. J Genet Eng Biotechnol 2020; 18:50. [PMID: 32926220 PMCID: PMC7490301 DOI: 10.1186/s43141-020-00065-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 09/02/2020] [Indexed: 11/10/2022]
Abstract
BACKGROUND Various Asparagus species constitute the significant vegetable and medicinal genetic resource throughout the world. Asparagus species serve as important commodity of food and pharmaceutical industries in India. A diverse collection of Asparagus species from different localities of Northwest India was investigated for its genetic diversity using simple sequence repeat (SSR) markers. RESULTS Polymorphic SSR markers revealed high genetic diversity. Primer SSR-15 amplified maximum of 8 fragments while 3 primers, namely, SSR-43, SSR-63, and AGA1 amplified minimum of 3 fragments. Collectively, 122 alleles were amplified in a range between 3 and 8 with an average of 5 alleles per marker. The size of the amplified alleles ranged between 90 and 680 base pairs. Polymorphism information content (PIC) value varied from a highest value of 0.499 in primer AGA1 to a lowest value of 0.231 in primer SSR-63 with a mean value of 0.376 showing considerable SSR polymorphism. Dendrogram developed on the basis of Jaccard's similarity coefficient and neighbor-joining tree segregated all the studied Asparagus species into two discrete groups. Structure analysis based on Bayesian clustering allocated different accessions to two independent clusters and exhibited low level of individual admixture. CONCLUSIONS The genetic diversity analysis showed a conservative genetic background for maximum species of asparagus. Only Accessions of Asparagus adscendens were split into two diverse clusters suggesting a wide genetic base of this species as compared to other species. Overall genetic diversity was high, and this germplasm of Asparagus can be used in future improvement programs. The findings of current research on Asparagus germplasm can make a momentous contribution to initiatives of interbreeding, conservation, and improvement of Asparagus in future.
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Affiliation(s)
- Manish Kapoor
- Department of Botany, Punjabi University Patiala, Patiala, Punjab, 147002, India.
| | - Pooja Mawal
- Department of Botany, Punjabi University Patiala, Patiala, Punjab, 147002, India
| | - Vikas Sharma
- Department of Botany, Sant Baba Bhag Singh University, Khiala, Jalandhar, Punjab, 144030, India
| | - Raghbir Chand Gupta
- Department of Botany, Punjabi University Patiala, Patiala, Punjab, 147002, India
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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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8
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Estimation of genetic diversity and population structure in Tinospora cordifolia using SSR markers. 3 Biotech 2020; 10:310. [PMID: 32582507 DOI: 10.1007/s13205-020-02300-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Accepted: 06/11/2020] [Indexed: 12/13/2022] Open
Abstract
Thirty polymorphic SSRs, derived from RNA sequencing of Tinospora cordifolia (willd.), were utilized for genetic diversity and population structure evaluation among 96 accessions collected from ten different geographical regions of India. A total of 7611 SSRs were identified from 268149 transcripts. Of all SSR loci, 69.07% of them were tri-nucleotide repeat motifs, followed by di-nucleotide repeat motifs (12.82%). A total of 230 alleles were generated by 30 SSRs with an average of 7.67 alleles per locus with comparatively higher polymorphic information content (average 0.68). The expected (He) and observed (Ho) heterozygosity means were 0.71 and 0.12, respectively. All the loci showed significant deviation from Hardy-Weinberg Equilibrium (HWE). The neighbor joining clustering based on jaccard's coefficient grouped all the 96 accessions into three major cluster which was also in congruence with model-based structure plot. The result of molecular variance (AMOVA) revealed higher genetic variance within populations than among populations. The result reflects an existence of high level of genetic diversity in the collected accessions of T. cordifolia. The accessions Tc131, Tc31, Tc129, Tc38, Tc16, Tc59, Tc60, Tc17, Tc106 and Tc130 was found to be potential and diverse in nature and the SSRs TCSSR-18, TCSSR-37, TCTSSR-59, TCTSSR-92, TCTSSR-123 and TCTSSR-126 as potential markers. These accessions and newly developed SSR markers provide valuable resource and could be strategically utilized for further genetic improvement of T. cordifolia.
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Lopes JML, de Carvalho HH, Zorzatto C, Azevedo ALS, Machado MA, Salimena FRG, Grazul RM, Gitzendanner MA, Soltis DE, Soltis PS, Viccini LF. Genetic relationships and polyploid origins in the Lippia alba complex. AMERICAN JOURNAL OF BOTANY 2020; 107:466-476. [PMID: 32115694 DOI: 10.1002/ajb2.1443] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Accepted: 12/04/2019] [Indexed: 06/10/2023]
Abstract
PREMISE Plant genomes vary in size and complexity due in part to polyploidization. Latitudinal analyses of polyploidy are biased toward floras of temperate regions, with much less research done in the tropics. Lippia alba has been described as a tropical polyploid complex with diploid, triploid, tetraploid, and hexaploid accessions. However, no data regarding relationships among the ploidal levels and their origins have been reported. Our goals are to clarify the relationships among accessions of Lippia alba and the origins of each ploidal level. METHODS We investigated 98 samples representing all five geographical regions of Brazil and all ploidal levels using microsatellite (SSR) allelic variation and DNA sequences of ITS and trnL-F. Nine morphological structures were analyzed from 33 herbarium samples, and the chemical compounds of 78 accessions were analyzed by GC-MS. RESULTS Genetic distance analysis, the alignment block pattern, as well as RAxML and Bayesian trees showed that accessions grouped by ploidal level. The triploids form a well-defined group that originated from a single group of diploids. The tetraploids and hexaploid grouped together in SSR and trnL-F analyses. The recovered groups agree with chemical data and morphology. CONCLUSIONS The accessions grouped by ploidal level. Only one origin of triploids from a single group of diploids was observed. The tetraploid origin is uncertain; however, it appears to have contributed to the origin of the hexaploid. This framework reveals linkages among the ploidal levels, providing new insights into the evolution of a polyploid complex of tropical plants.
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Affiliation(s)
- Juliana M L Lopes
- Department of Biology, Federal University of Juiz de Fora, Juiz de Fora, MG, 36036-241, Brazil
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | | | - Cristiane Zorzatto
- Department of Biology, Federal University of Juiz de Fora, Juiz de Fora, MG, 36036-241, Brazil
| | | | | | | | - Richard M Grazul
- Department of Chemistry, Federal University of Juiz de Fora, Juiz de Fora, MG, 36036-241, Brazil
| | | | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - Lyderson F Viccini
- Department of Biology, Federal University of Juiz de Fora, Juiz de Fora, MG, 36036-241, Brazil
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Bhandawat A, Singh G, Seth R, Singh P, Sharma RK. Genome-Wide Transcriptional Profiling to Elucidate Key Candidates Involved in Bud Burst and Rattling Growth in a Subtropical Bamboo ( Dendrocalamus hamiltonii). FRONTIERS IN PLANT SCIENCE 2017; 7:2038. [PMID: 28123391 PMCID: PMC5225089 DOI: 10.3389/fpls.2016.02038] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 12/20/2016] [Indexed: 05/29/2023]
Abstract
Bamboo, one of the fastest growing plants, can be a promising model system to understand growth. The study provides an insight into the complex interplay between environmental signaling and cellular machineries governing initiation and persistence of growth in a subtropical bamboo (Dendrocalamus hamiltonii). Phenological and spatio-temporal transcriptome analysis of rhizome and shoot during the major vegetative developmental transitions of D. hamiltonii was performed to dissect factors governing growth. Our work signifies the role of environmental cues, predominantly rainfall, decreasing day length, and high humidity for activating dormant bud to produce new shoot, possibly through complex molecular interactions among phosphatidylinositol, calcium signaling pathways, phytohormones, circadian rhythm, and humidity responses. We found the coordinated regulation of auxin, cytokinin, brassinosteroid signaling and cell cycle modulators; facilitating cell proliferation, cell expansion, and cell wall biogenesis supporting persistent growth of emerging shoot. Putative master regulators among these candidates were identified using predetermined Arabidopsis thaliana protein-protein interaction network. We got clues that the growth signaling begins far back in rhizome even before it emerges out as new shoot. Putative growth candidates identified in our study can serve in devising strategies to engineer bamboos and timber trees with enhanced growth and biomass potentials.
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Affiliation(s)
- Abhishek Bhandawat
- Molecular Genetics and Genomics Lab, Department of Biotechnology, CSIR-Institute of Himalayan Bioresource TechnologyPalampur, India
- Department of Biotechnology, Panjab UniversityChandigarh, India
| | - Gagandeep Singh
- Molecular Genetics and Genomics Lab, Department of Biotechnology, CSIR-Institute of Himalayan Bioresource TechnologyPalampur, India
| | - Romit Seth
- Molecular Genetics and Genomics Lab, Department of Biotechnology, CSIR-Institute of Himalayan Bioresource TechnologyPalampur, India
| | - Pradeep Singh
- Molecular Genetics and Genomics Lab, Department of Biotechnology, CSIR-Institute of Himalayan Bioresource TechnologyPalampur, India
| | - Ram K. Sharma
- Molecular Genetics and Genomics Lab, Department of Biotechnology, CSIR-Institute of Himalayan Bioresource TechnologyPalampur, India
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Nilkanta H, Amom T, Tikendra L, Rahaman H, Nongdam P. ISSR Marker Based Population Genetic Study of Melocanna baccifera (Roxb.) Kurz: A Commercially Important Bamboo of Manipur, North-East India. SCIENTIFICA 2017; 2017:3757238. [PMID: 28168084 PMCID: PMC5259607 DOI: 10.1155/2017/3757238] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2016] [Accepted: 12/04/2016] [Indexed: 06/06/2023]
Abstract
Melocanna baccifera (Roxb.) Kurz is an economically important bamboo of North-East India experiencing population depletion in its natural habitats. Genetic variation studies were conducted in 7 populations sampled from 5 districts of Manipur using ISSR molecular markers. The investigation was carried out as a primary step towards developing effective conservation strategies for the protection of bamboo germplasm. ISSR marker analysis showed significant level of genetic variation within the populations as revealed by moderately high average values of Nei's genetic diversity (H 0.1639), Shannon's diversity index (I 0.2563), percentage of polymorphic bands (PPB 59.18), total genetic variation (Ht 0.1961), and genetic diversity within population (Hs 0.1639). The study also divulged a high genetic variation at species level with Shannon's diversity index (I), Nei's genetic diversity (H), and percentage of polymorphic band (PPB%) recorded at 0.3218, 0.1939, and 88.37, respectively. Genetic differentiation among the populations (Gst) was merely 19.42% leaving 80.58% of genetic variation exhibited within the populations. The low genetic diversity between populations was consistent with AMOVA. The low genetic differentiation among populations coupled with existence of significantly high genetic diversity at species level indicated the urgent necessity of preserving and protecting all the existing natural bamboo populations in the region.
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Affiliation(s)
- Heikrujam Nilkanta
- Department of Biotechnology, Manipur University, Canchipur, Imphal, Manipur 795003, India
| | - Thoungamba Amom
- Department of Biotechnology, Manipur University, Canchipur, Imphal, Manipur 795003, India
| | - Leimapokpam Tikendra
- Department of Biotechnology, Manipur University, Canchipur, Imphal, Manipur 795003, India
| | - Hamidur Rahaman
- Department of Biotechnology, Manipur University, Canchipur, Imphal, Manipur 795003, India
| | - Potshangbam Nongdam
- Department of Biotechnology, Manipur University, Canchipur, Imphal, Manipur 795003, India
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Kaur K, Sharma V, Singh V, Wani MS, Gupta RC. Development of novel SSR markers for evaluation of genetic diversity and population structure in Tribulus terrestris L. (Zygophyllaceae). 3 Biotech 2016; 6:156. [PMID: 28330228 PMCID: PMC4951381 DOI: 10.1007/s13205-016-0469-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 07/04/2016] [Indexed: 01/12/2023] Open
Abstract
Tribulus terrestris L., commonly called puncture vine and gokhru, is an important member of Zygophyllaceae. The species is highly important in context to therapeutic uses and provides important active principles responsible for treatment of various diseases and also used as tonic. It is widely distributed in tropical regions of India and the world. However, status of its genetic diversity remained concealed due to lack of research work in this species. In present study, genetic diversity and structure of different populations of T. terrestris from north India was examined at molecular level using newly developed Simple Sequence Repeat (SSR) markers. In total, 20 primers produced 48 alleles in a size range of 100–500 bp with maximum (4) fragments amplified by TTMS-1, TTMS-25 and TTMS-33. Mean Polymorphism Information Content (PIC) and Marker Index (MI) were 0.368 and 1.01, respectively. Dendrogram showed three groups, one of which was purely containing accessions from Rajasthan while other two groups corresponded to Punjab and Haryana regions with intermixing of few other accessions. Analysis of molecular variance partitioned 76 % genetic variance within populations and 24 % among populations. Bayesian model based STRUCTURE analysis detected two genetic stocks for analyzed germplasm and also detected some admixed individuals. Different geographical populations of this species showed high level of genetic diversity. Results of present study can be useful in identifying diverse accessions and management of this plant resource. Moreover, the novel SSR markers developed can be utilized for various genetic analyses in this species in future.
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Affiliation(s)
- Kuljit Kaur
- Department of Botany, Punjabi University, Patiala, Punjab 147002 India
| | - Vikas Sharma
- Department of Botany, Punjabi University, Patiala, Punjab 147002 India
| | - Vijay Singh
- Department of Botany, Punjabi University, Patiala, Punjab 147002 India
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Mishra P, Kumar A, Nagireddy A, Mani DN, Shukla AK, Tiwari R, Sundaresan V. DNA barcoding: an efficient tool to overcome authentication challenges in the herbal market. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:8-21. [PMID: 26079154 DOI: 10.1111/pbi.12419] [Citation(s) in RCA: 141] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Revised: 04/28/2015] [Accepted: 05/16/2015] [Indexed: 05/21/2023]
Abstract
The past couple of decades have witnessed global resurgence of herbal-based health care. As a result, the trade of raw drugs has surged globally. Accurate and fast scientific identification of the plant(s) is the key to success for the herbal drug industry. The conventional approach is to engage an expert taxonomist, who uses a mix of traditional and modern techniques for precise plant identification. However, for bulk identification at industrial scale, the process is protracted and time-consuming. DNA barcoding, on the other hand, offers an alternative and feasible taxonomic tool box for rapid and robust species identification. For the success of DNA barcode, the barcode loci must have sufficient information to differentiate unambiguously between closely related plant species and discover new cryptic species. For herbal plant identification, matK, rbcL, trnH-psbA, ITS, trnL-F, 5S-rRNA and 18S-rRNA have been used as successful DNA barcodes. Emerging advances in DNA barcoding coupled with next-generation sequencing and high-resolution melting curve analysis have paved the way for successful species-level resolution recovered from finished herbal products. Further, development of multilocus strategy and its application has provided new vistas to the DNA barcode-based plant identification for herbal drug industry. For successful and acceptable identification of herbal ingredients and a holistic quality control of the drug, DNA barcoding needs to work harmoniously with other components of the systems biology approach. We suggest that for effectively resolving authentication challenges associated with the herbal market, DNA barcoding must be used in conjunction with metabolomics along with need-based transcriptomics and proteomics.
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Affiliation(s)
- Priyanka Mishra
- Department of Biology & Systematics, CSIR - Central Institute of Medicinal and Aromatic Plants, Research Centre, Bangalore, Karnataka, India
| | - Amit Kumar
- Department of Biology & Systematics, CSIR - Central Institute of Medicinal and Aromatic Plants, Research Centre, Bangalore, Karnataka, India
| | - Akshitha Nagireddy
- Department of Biology & Systematics, CSIR - Central Institute of Medicinal and Aromatic Plants, Research Centre, Bangalore, Karnataka, India
| | - Daya N Mani
- Herbal Medicinal Products Department, CSIR - Central Institute of Medicinal and Aromatic Plants, Lucknow, Uttar Pradesh, India
| | - Ashutosh K Shukla
- Biotechnology Division, CSIR - Central Institute of Medicinal and Aromatic Plants, Lucknow, Uttar Pradesh, India
| | - Rakesh Tiwari
- Publication Division, CSIR - Central Institute of Medicinal and Aromatic Plants, Lucknow, Uttar Pradesh, India
| | - Velusamy Sundaresan
- Department of Biology & Systematics, CSIR - Central Institute of Medicinal and Aromatic Plants, Research Centre, Bangalore, Karnataka, 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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Identification, cross-taxon transferability and application of full-length cDNA SSR markers in Phyllostachys pubescens. SPRINGERPLUS 2014; 3:486. [PMID: 25221740 PMCID: PMC4161718 DOI: 10.1186/2193-1801-3-486] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Accepted: 08/11/2014] [Indexed: 01/17/2023]
Abstract
Current databases of Phyllostachys pubescens full-length cDNAs (FL-cDNAs) provide a rich source of sequences for the development of potential FL-cDNA simple sequence repeat (SSR) markers. We screened 10,608 P. pubescens cDNAs, discovering 1614 SSRs in 1382 SSR-containing FL-cDNAs. The SSRs were more abundant within transposable elements (TEs) than expressed sequence tags (ESTs) and genome survey sequences (GSSs), and specific dinucleotide repeats tended to associate with particular TE families: (TA)n with En/Spm and (CT)n with Mutator. A selected panel of 100 FL-cDNAs containing type I SSRs yielded 68 functional SSR markers with an average polymorphism information content (PIC) value of 0.12, among which 22 loci contained polymorphisms. These markers became less transferrable (83.1% → 69.9% → 49.3%) but more polymorphic (79.4% → 92.3% → 92.8%) with increasing phylogenetic distance (intra-genus → intra-subtribe → intra-family). Transferability and polymorphism also depended on the location of the marker, with those located in the coding region being more transferrable (69.1%) and less polymorphic (89.4%) than those in the 5'-UTR (63.4% transferable, 90.7% polymorphic) and the 3'-UTR (61.8% transferable, 91.4% polymorphic). As proof of principle, we were able to use our FL-cDNA SSR markers to identify the parental stocks in interspecific hybrids of bamboo within and beyond P. pubescens, and estimate the outcrossing rate for P. pubescens. Our research should facilitate molecular breeding in bamboo species where original genetic markers are scarce.
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16
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Development and crosstransferability of functionally relevant microsatellite markers in Dendrocalamus latiflorus and related bamboo species. J Genet 2014. [DOI: 10.1007/s12041-014-0377-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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17
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Zhu S, Liu T, Tang Q, Fu L, Tang S. Evaluation of bamboo genetic diversity using morphological and SRAP analyses. RUSS J GENET+ 2014. [DOI: 10.1134/s1022795414030132] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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18
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Zhao H, Peng Z, Fei B, Li L, Hu T, Gao Z, Jiang Z. BambooGDB: a bamboo genome database with functional annotation and an analysis platform. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2014; 2014:bau006. [PMID: 24602877 PMCID: PMC3944406 DOI: 10.1093/database/bau006] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Bamboo, as one of the most important non-timber forest products and fastest-growing plants in the world, represents the only major lineage of grasses that is native to forests. Recent success on the first high-quality draft genome sequence of moso bamboo (Phyllostachys edulis) provides new insights on bamboo genetics and evolution. To further extend our understanding on bamboo genome and facilitate future studies on the basis of previous achievements, here we have developed BambooGDB, a bamboo genome database with functional annotation and analysis platform. The de novo sequencing data, together with the full-length complementary DNA and RNA-seq data of moso bamboo composed the main contents of this database. Based on these sequence data, a comprehensively functional annotation for bamboo genome was made. Besides, an analytical platform composed of comparative genomic analysis, protein–protein interactions network, pathway analysis and visualization of genomic data was also constructed. As discovery tools to understand and identify biological mechanisms of bamboo, the platform can be used as a systematic framework for helping and designing experiments for further validation. Moreover, diverse and powerful search tools and a convenient browser were incorporated to facilitate the navigation of these data. As far as we know, this is the first genome database for bamboo. Through integrating high-throughput sequencing data, a full functional annotation and several analysis modules, BambooGDB aims to provide worldwide researchers with a central genomic resource and an extensible analysis platform for bamboo genome. BambooGDB is freely available at http://www.bamboogdb.org/. Database URL: http://www.bamboogdb.org
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Affiliation(s)
- Hansheng Zhao
- State Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, International Center for Bamboo and Rattan, Beijing 100102, China, State key laboratory of tree genetics and breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China and Key Laboratory of Tree Breeding and Cultivation, State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
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Peng Z, Zhang C, Zhang Y, Hu T, Mu S, Li X, Gao J. Transcriptome sequencing and analysis of the fast growing shoots of moso bamboo (Phyllostachys edulis). PLoS One 2013; 8:e78944. [PMID: 24244391 PMCID: PMC3820679 DOI: 10.1371/journal.pone.0078944] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 09/17/2013] [Indexed: 01/23/2023] Open
Abstract
Background The moso bamboo, a large woody bamboo with the highest ecological, economic, and cultural value of all bamboos, has one of the highest growth speeds in the world. Genetic research into moso bamboo has been scarce, partly because of the lack of previous genomic resources. In the present study, for the first time, we performed de novo transcriptome sequencing and mapped to the moso bamboo genomic resources (reference genome and genes) to produce a comprehensive dataset for the fast growing shoots of moso bamboo. Results The fast growing shoots mixed with six different heights and culms after leaf expansion of moso bamboo transcriptome were sequenced using the Illumina HiSeq™ 2000 sequencing platform, respectively. More than 80 million reads including 65,045,670 and 68,431,884 clean reads were produced in the two libraries. More than 81% of the reads were matched to the reference genome, and nearly 50% of the reads were matched to the reference genes. The genes with log 2 ratio > 2 or < −2 (P<0.001) were characterized as the most differentially expressed genes. 6,076 up-regulated and 4,613 down-regulated genes were classified into functional categories. Candidate genes which mainly involved transcript factors, plant hormones, cell cycle regulation, cell wall metabolism and cell morphogenesis genes were further analyzed and they may form a network that regulates the fast growth of moso bamboo shoots. Conclusion Firstly, our data provides the most comprehensive transcriptomic resource for moso bamboo to date. Candidate genes have been identified and they are potentially involved in the growth and development of moso bamboo. The results give a better insight into the mechanisms of moso bamboo shoots rapid growth and provide gene resources for improving plant growth.
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Affiliation(s)
- Zhenhua Peng
- International Center for Bamboo and Rattan, Key Laboratory of Bamboo and Rattan Science and Technology, State Forestry Administration, Beijing, People's Republic of China
| | - Chunling Zhang
- International Center for Bamboo and Rattan, Key Laboratory of Bamboo and Rattan Science and Technology, State Forestry Administration, Beijing, People's Republic of China
| | - Ying Zhang
- International Center for Bamboo and Rattan, Key Laboratory of Bamboo and Rattan Science and Technology, State Forestry Administration, Beijing, People's Republic of China
| | - Tao Hu
- International Center for Bamboo and Rattan, Key Laboratory of Bamboo and Rattan Science and Technology, State Forestry Administration, Beijing, People's Republic of China
| | - Shaohua Mu
- International Center for Bamboo and Rattan, Key Laboratory of Bamboo and Rattan Science and Technology, State Forestry Administration, Beijing, People's Republic of China
| | - Xueping Li
- International Center for Bamboo and Rattan, Key Laboratory of Bamboo and Rattan Science and Technology, State Forestry Administration, Beijing, People's Republic of China
| | - Jian Gao
- International Center for Bamboo and Rattan, Key Laboratory of Bamboo and Rattan Science and Technology, State Forestry Administration, Beijing, People's Republic of China
- * E-mail:
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20
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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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21
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Peng Z, Lu Y, Li L, Zhao Q, Feng Q, Gao Z, Lu H, Hu T, Yao N, Liu K, Li Y, Fan D, Guo Y, Li W, Lu Y, Weng Q, Zhou C, Zhang L, Huang T, Zhao Y, Zhu C, Liu X, Yang X, Wang T, Miao K, Zhuang C, Cao X, Tang W, Liu G, Liu Y, Chen J, Liu Z, Yuan L, Liu Z, Huang X, Lu T, Fei B, Ning Z, Han B, Jiang Z. The draft genome of the fast-growing non-timber forest species moso bamboo (Phyllostachys heterocycla). Nat Genet 2013; 45:456-61, 461e1-2. [PMID: 23435089 DOI: 10.1038/ng.2569] [Citation(s) in RCA: 282] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Accepted: 02/01/2013] [Indexed: 11/09/2022]
Abstract
Bamboo represents the only major lineage of grasses that is native to forests and is one of the most important non-timber forest products in the world. However, no species in the Bambusoideae subfamily has been sequenced. Here, we report a high-quality draft genome sequence of moso bamboo (P. heterocycla var. pubescens). The 2.05-Gb assembly covers 95% of the genomic region. Gene prediction modeling identified 31,987 genes, most of which are supported by cDNA and deep RNA sequencing data. Analyses of clustered gene families and gene collinearity show that bamboo underwent whole-genome duplication 7-12 million years ago. Identification of gene families that are key in cell wall biosynthesis suggests that the whole-genome duplication event generated more gene duplicates involved in bamboo shoot development. RNA sequencing analysis of bamboo flowering tissues suggests a potential connection between drought-responsive and flowering genes.
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Affiliation(s)
- Zhenhua Peng
- Research Institute of Forestry, Chinese Academy of Forestry, Key Laboratory of Tree Breeding and Cultivation, State Forestry Administration, Beijing, 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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Yang HQ, An MY, Gu ZJ, Tian B. Genetic diversity and differentiation of Dendrocalamus membranaceus (Poaceae: Bambusoideae), a declining bamboo species in Yunnan, China, as based on Inter-Simple Sequence Repeat (ISSR) Analysis. Int J Mol Sci 2012; 13:4446-4457. [PMID: 22605989 PMCID: PMC3344225 DOI: 10.3390/ijms13044446] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2012] [Revised: 03/22/2012] [Accepted: 03/31/2012] [Indexed: 12/04/2022] Open
Abstract
Dendrocalamus membranaceus Munro is a woody bamboo with a high economic and ecological value that often occurs as natural stands, such as in the large-scale forested areas of China's Yunnan Province. Due to its overexploitation, the habitat of D. membranaceus in Yunnan has been dramatically reduced, and the quality of the stands has declined. As a preliminary analysis in considering the effective protection for these germplasm resources, we assessed the genetic diversity of 12 natural populations in Yunnan, using inter-simple sequence repeat (ISSR) markers. From 10 ISSR primers, we generated 155 bands, of which 153 were polymorphic (98.71%). Compared with other species in the genus, this species demonstrated a greater genetic diversity (S = 0.349) and lower genetic differentiation (G(ST) = 0.252). Our analysis of molecular variance revealed that the genetic differentiation among the populations is significant. A large proportion of the genetic variation (78.95%) resides among the individuals within populations, whereas only 21.05% are found among populations. Mantel tests indicated no significant correlation between genetic and geographic distances among the populations. Given the low sexual reproducibility and characteristics of monocarpic plants, we recommend implementing in situ conservation measures for all of the D. membranaceus populations in Yunnan and collecting sufficient samples for ex situ conservation. Furthermore, the conservation area should be extended to its main natural habitats, the Lancang-Mekong River Valley.
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Affiliation(s)
- Han-Qi Yang
- Research Institute of Resource Insects, Chinese Academy of Forestry, Kunming 650224, China; E-Mails: (H.-Q.Y.), (M.-Y.A.), (Z.-J.G.)
| | - Man-Yun An
- Research Institute of Resource Insects, Chinese Academy of Forestry, Kunming 650224, China; E-Mails: (H.-Q.Y.), (M.-Y.A.), (Z.-J.G.)
| | - Zhi-Jia Gu
- Research Institute of Resource Insects, Chinese Academy of Forestry, Kunming 650224, China; E-Mails: (H.-Q.Y.), (M.-Y.A.), (Z.-J.G.)
| | - Bo Tian
- Laboratory of Tropical Plant Resource Science, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, 88 Xuefu Road, Kunming 650223, China
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Genetic relationships among 22 taxa of bamboo revealed by ISSR and EST-based random primers. Biochem Genet 2010; 48:1015-25. [PMID: 20976539 DOI: 10.1007/s10528-010-9390-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2009] [Accepted: 10/04/2010] [Indexed: 10/18/2022]
Abstract
Genetic relationships among 22 taxa of bamboo were evaluated using 12 inter simple sequence repeats (ISSR) and four expressed sequence tag (EST)-based random primers, resulting in amplification of 220 loci. The grouping of species based on Jaccard's similarity matrix using UPGMA and principal coordinate analysis agreed with earlier published reports on molecular phylogenetic studies in bamboos with few deviations. In the dendrogram, however, species of one genus were placed in different clusters along with members of other genera. This calls for correct taxonomic delineation at the genus and species level using both vegetative and reproductive characters and correlation of molecular data with morphologically definable taxonomic groupings at the proper taxonomic level.
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ZHAO D, CHENG XZ, WANG LX, WANG SH, MA YL. Integration of Mungbean ( Vigna radiata) Genetic Linkage Map. ZUOWU XUEBAO 2010. [DOI: 10.3724/sp.j.1006.2010.00932] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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WANG LX, CHENG XZ, WANG SH, LIU CY, LIANG H. Transferability of SSR from Adzuki Bean to Mungbean. ZUOWU XUEBAO 2009. [DOI: 10.3724/sp.j.1006.2009.00816] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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WANG LX, CHENG XZ, WANG SH, LIU CY, LIANG H. Transferability of SSR Markers from Adzuki Bean into Mungbean. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/s1875-2780(08)60083-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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28
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Sharma V, Bhardwaj P, Kumar R, Sharma RK, Sood A, Ahuja PS. Identification and cross-species amplification of EST derived SSR markers in different bamboo species. CONSERV GENET 2008. [DOI: 10.1007/s10592-008-9630-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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