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Li JW, Li H, Liu ZW, Wang YX, Chen Y, Yang N, Hu ZH, Li T, Zhuang J. Molecular markers in tea plant (Camellia sinensis): Applications to evolution, genetic identification, and molecular breeding. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 198:107704. [PMID: 37086694 DOI: 10.1016/j.plaphy.2023.107704] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 04/03/2023] [Accepted: 04/13/2023] [Indexed: 05/03/2023]
Abstract
Tea plants have a long cultivation history in the world, and the beverage (tea) made from its leaves is well known in the world. Due to the characteristics of self-incompatibility, long-term natural and artificial hybridization, tea plants have a very complex genetic background, which make the classification of tea plants unclear. Molecular marker, one type of genetic markers, has the advantages of stable inheritance, large amount of information, and high reliability. The development of molecular marker has facilitated the understanding of complex tea germplasm resources. So far, molecular markers had played important roles in the study of the origin and evolution, the preservation and identification of tea germplasms, and the excellent cultivars breeding of tea plants. However, the information is scattered, making it difficult to understand the advance of molecular markers in tea plants. In this paper, we summarized the development process and types of molecular markers in tea plants. In addition, the application advance of these molecular markers in tea plants was reviewed. Perspectives of molecular markers in tea plants were also systematically provided and discussed. The elaboration of molecular markers in this paper should help us to renew understanding of its application in tea plants.
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Affiliation(s)
- Jing-Wen Li
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Hui Li
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Zhi-Wei Liu
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Yong-Xin Wang
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Yi Chen
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Ni Yang
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Zhi-Hang Hu
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Tong Li
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, China
| | - Jing Zhuang
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, China.
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Zhang ZB, Xiong T, Chen JH, Ye F, Cao JJ, Chen YR, Zhao ZW, Luo T. Understanding the Origin and Evolution of Tea (Camellia sinensis [L.]): Genomic Advances in Tea. J Mol Evol 2023; 91:156-168. [PMID: 36859501 DOI: 10.1007/s00239-023-10099-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 02/07/2023] [Indexed: 03/03/2023]
Abstract
Tea, which is processed by the tender shoots or leaves of tea plant (Camellia sinensis), is one of the most popular nonalcoholic beverages in the world and has numerous health benefits for humans. Along with new progress in biotechnologies, the refined chromosome-scale reference tea genomes have been achieved, which facilitates great promise for the understanding of fundamental genomic architecture and evolution of the tea plants. Here, we summarize recent achievements in genome sequencing in tea plants and review the new progress in origin and evolution of tea plants by population sequencing analysis. Understanding the genomic characterization of tea plants is import to improve tea quality and accelerate breeding in tea plants.
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Affiliation(s)
- Zai-Bao Zhang
- College of Life Science, Xinyang Normal University, Xinyang, 464000, China.
| | - Tao Xiong
- College of Life Science, Xinyang Normal University, Xinyang, 464000, China
| | - Jia-Hui Chen
- College of International Education, Xinyang Normal University, Xinyang, 464000, China
| | - Fan Ye
- College of International Education, Xinyang Normal University, Xinyang, 464000, China
| | - Jia-Jia Cao
- College of International Education, Xinyang Normal University, Xinyang, 464000, China
| | - Yu-Rui Chen
- College of International Education, Xinyang Normal University, Xinyang, 464000, China
| | - Zi-Wei Zhao
- College of Life Science, Xinyang Normal University, Xinyang, 464000, China
| | - Tian Luo
- College of Life Science, Xinyang Normal University, Xinyang, 464000, China
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Bajpai R, Chaturvedi R. In vitro production of doubled haploid plants in Camellia spp. and assessment of homozygosity using microsatellite markers. J Biotechnol 2023; 361:89-98. [PMID: 36470314 DOI: 10.1016/j.jbiotec.2022.11.019] [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: 03/30/2022] [Revised: 11/25/2022] [Accepted: 11/30/2022] [Indexed: 12/07/2022]
Abstract
In this report, in vitro doubled haploid (DH) plants were established in two tea (Camellia spp) cultivars, TV21 (Assam Type) and TV19 (Cambod Type). Androgenic globular stage haploid embryos, obtained via callusing from microspores at an early-to-late uninucleate stage in anther cultures, were diploidized by colchicine treatments at varying concentrations and durations under dark incubation at 25 ± 2 °C temperature. Thereafter, treated embryos were transferred to development medium, Murashige and Skoog (MS) medium supplemented with 6-benzylaminopurine (BAP; 1 μM) + gibberellic acid (GA3; 0.3 μM) + L-glutamine (80 mg l-1) + L-serine (20 mg l-1) and incubated in diffused light. Ploidy of germinating embryos was evaluated by flow-cytometry and cytological squash preparation. High chromosome doubling, 76.89% and 67.34%, was obtained in embryos of TV21 and TV19, respectively, at 0.2% colchicine treatment for 24 h. The DH plants were further multiplied via axillary-bud proliferation on multiplication medium, MS + glucose (30 g l-1) + BAP (5 μM) + GA3 (0.5 μM) + IBA (0.5 μM) + L- glutamine (80 mg l-1) + L-serine (20 mg l-1). Rooting of shoots was achieved on ⅓ MS basal medium within 50 days of inoculation when shoots were pre-treated with IBA (175 μM) for ten days. The rooted plants were acclimatized in field. Homozygosity in diploidized plants was validated by SSR marker.
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Affiliation(s)
- Ruchira Bajpai
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Rakhi Chaturvedi
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India.
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Phenotypic diversity of rosemary (Salvia rosmarinus Schleid.) accessions for qualitative characters. Heliyon 2022; 8:e11895. [DOI: 10.1016/j.heliyon.2022.e11895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 05/12/2022] [Accepted: 11/17/2022] [Indexed: 11/30/2022] Open
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Muoki CR, Maritim TK, Oluoch WA, Kamunya SM, Bore JK. Combating Climate Change in the Kenyan Tea Industry. FRONTIERS IN PLANT SCIENCE 2020; 11:339. [PMID: 32269583 PMCID: PMC7109314 DOI: 10.3389/fpls.2020.00339] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 03/06/2020] [Indexed: 05/23/2023]
Abstract
Climate change triggered by global warming poses a major threat to agricultural systems globally. This phenomenon is characterized by emergence of pests and diseases, extreme weather events, such as prolonged drought, high intensity rains, hailstones and frosts, which are becoming more frequent ultimately impacting negatively to agricultural production including rain-fed tea cultivation. Kenya is predominantly an agricultural based economy, with the tea sector generating about 26% of the total export earnings and about 4% gross domestic product (GDP). In the recent years, however, the country has witnessed unstable trends in tea production associated with climate driven stresses. Toward mitigation and adaptation of climate change, multiple approaches for impact assessment, intensity prediction and adaptation have been advanced in the Kenyan tea sub-sector. Further, pressure on tea breeders to release improved climate-compatible cultivars for the rapidly deteriorating environment has resulted in the adoption of a multi-targeted approach seeking to understand the complex molecular regulatory networks associated with biotic and abiotic stresses adaptation and tolerance in tea. Genetic modeling, a powerful tool that assists in breeding process, has also been adopted for selection of tea cultivars for optimal performance under varying climatic conditions. A range of physiological and biochemical responses known to counteract the effects of environmental stresses in most plants that include lowering the rates of cellular growth and net photosynthesis, stomatal closure, and the accumulation of organic solutes such as sugar alcohols, or osmolytes have been used to support breeding programs through screening of new tea cultivars suitable for changing environment. This review describes simulation models combined with high resolution climate change scenarios required to quantify the relative importance of climate change on tea production. In addition, both biodiversity and ecosystem based approaches are described as a part of an overall adaptation strategy to mitigate adverse effects of climate change on tea in Kenya and gaps highlighted for urgent investigations.
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Affiliation(s)
- Chalo Richard Muoki
- Crop Improvement and Management Programme, Kenya Agricultural and Livestock Research Organization, Tea Research Institute, Kericho, Kenya
| | - Tony Kipkoech Maritim
- Crop Improvement and Management Programme, Kenya Agricultural and Livestock Research Organization, Tea Research Institute, Kericho, Kenya
| | - Wyclife Agumba Oluoch
- Sustainable Ecosystem Management and Conservation Programme, Kenya Agricultural and Livestock Research Organization, Tea Research Institute, Kericho, Kenya
| | - Samson Machohi Kamunya
- Crop Improvement and Management Programme, Kenya Agricultural and Livestock Research Organization, Tea Research Institute, Kericho, Kenya
| | - John Kipkoech Bore
- Sustainable Ecosystem Management and Conservation Programme, Kenya Agricultural and Livestock Research Organization, Tea Research Institute, Kericho, Kenya
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Dubey H, Rawal HC, Rohilla M, Lama U, Kumar PM, Bandyopadhyay T, Gogoi M, Singh NK, Mondal TK. TeaMiD: a comprehensive database of simple sequence repeat markers of tea. Database (Oxford) 2020; 2020:baaa013. [PMID: 32159215 PMCID: PMC7065459 DOI: 10.1093/database/baaa013] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 01/05/2020] [Accepted: 01/25/2020] [Indexed: 12/05/2022]
Abstract
Tea is a highly cross-pollinated, woody, perennial tree. High heterozygosity combined with a long gestational period makes conventional breeding a cumbersome process. Therefore, marker-assisted breeding is a better alternative approach when compared with conventional breeding. Considering the large genome size of tea (~3 Gb), information about simple sequence repeat (SSR) is scanty. Thus, we have taken advantage of the recently published tea genomes to identify large numbers of SSR markers in the tea. Besides the genomic sequences, we identified SSRs from the other publicly available sequences such as RNA-seq, GSS, ESTs and organelle genomes (chloroplasts and mitochondrial) and also searched published literature to catalog validated set of tea SSR markers. The complete exercise yielded a total of 935 547 SSRs. Out of the total, 82 SSRs were selected for validation among a diverse set of tea genotypes. Six primers (each with four to six alleles, an average of five alleles per locus) out of the total 27 polymorphic primers were used for a diversity analysis in 36 tea genotypes with mean polymorphic information content of 0.61-0.76. Finally, using all the information generated in this study, we have developed a user-friendly database (TeaMiD; http://indianteagenome.in:8080/teamid/) that hosts SSR from all the six resources including three nuclear genomes of tea and transcriptome sequences of 17 Camellia wild species. Database URL: http://indianteagenome.in:8080/teamid/.
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Affiliation(s)
- Himanshu Dubey
- Indian Council Agricultural Research-National Institute for Plant Biotechnology, Lal Bahadur Sashtri Centre, Indian Agricultural Research Institute, Pusa, New Delhi 110012, India
| | - Hukam C Rawal
- Indian Council Agricultural Research-National Institute for Plant Biotechnology, Lal Bahadur Sashtri Centre, Indian Agricultural Research Institute, Pusa, New Delhi 110012, India
| | - Megha Rohilla
- Indian Council Agricultural Research-National Institute for Plant Biotechnology, Lal Bahadur Sashtri Centre, Indian Agricultural Research Institute, Pusa, New Delhi 110012, India
| | - Urvashi Lama
- Darjeeling Tea Research and Development Centre, Tea Board, Ministry of Commerce, B.T.M. Sarani (Brabourne Road), Kolkata, West Bengal 700001, India
| | - P Mohan Kumar
- Darjeeling Tea Research and Development Centre, Tea Board, Ministry of Commerce, B.T.M. Sarani (Brabourne Road), Kolkata, West Bengal 700001, India
| | - Tanoy Bandyopadhyay
- Department of Biotechnology, Tocklai Experimental Station, Tea Research Association, Jorhat, Assam, India
| | - Madhurjya Gogoi
- Department of Biotechnology, Tocklai Experimental Station, Tea Research Association, Jorhat, Assam, India
| | - Nagendra Kumar Singh
- Indian Council Agricultural Research-National Institute for Plant Biotechnology, Lal Bahadur Sashtri Centre, Indian Agricultural Research Institute, Pusa, New Delhi 110012, India
| | - Tapan Kumar Mondal
- Indian Council Agricultural Research-National Institute for Plant Biotechnology, Lal Bahadur Sashtri Centre, Indian Agricultural Research Institute, Pusa, New Delhi 110012, India
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Xia EH, Tong W, Wu Q, Wei S, Zhao J, Zhang ZZ, Wei CL, Wan XC. Tea plant genomics: achievements, challenges and perspectives. HORTICULTURE RESEARCH 2020; 7:7. [PMID: 31908810 PMCID: PMC6938499 DOI: 10.1038/s41438-019-0225-4] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 10/17/2019] [Accepted: 11/03/2019] [Indexed: 05/18/2023]
Abstract
Tea is among the world's most widely consumed non-alcoholic beverages and possesses enormous economic, health, and cultural values. It is produced from the cured leaves of tea plants, which are important evergreen crops globally cultivated in over 50 countries. Along with recent innovations and advances in biotechnologies, great progress in tea plant genomics and genetics has been achieved, which has facilitated our understanding of the molecular mechanisms of tea quality and the evolution of the tea plant genome. In this review, we briefly summarize the achievements of the past two decades, which primarily include diverse genome and transcriptome sequencing projects, gene discovery and regulation studies, investigation of the epigenetics and noncoding RNAs, origin and domestication, phylogenetics and germplasm utilization of tea plant as well as newly developed tools/platforms. We also present perspectives and possible challenges for future functional genomic studies that will contribute to the acceleration of breeding programs in tea plants.
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Affiliation(s)
- En-Hua Xia
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036 China
| | - Wei Tong
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036 China
| | - Qiong Wu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036 China
| | - Shu Wei
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036 China
| | - Jian Zhao
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036 China
| | - Zheng-Zhu Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036 China
| | - Chao-Ling Wei
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036 China
| | - Xiao-Chun Wan
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036 China
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Narrow gene pool can threaten the survival of Calamus nagbettai R. R. Fernald & Dey: a highly, endemic dioecious rattan species in the Western Ghats of India. J Genet 2019. [DOI: 10.1007/s12041-019-1147-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Sharma S, Kaushik S, Raina SN. Estimation of nuclear DNA content and its variation among Indian Tea accessions by flow cytometry. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2019; 25:339-346. [PMID: 30956418 PMCID: PMC6419702 DOI: 10.1007/s12298-018-0587-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Revised: 07/14/2018] [Accepted: 07/24/2018] [Indexed: 05/29/2023]
Abstract
Nuclear DNA content and genome size variation among 36 Indian tea accessions were analyzed by flow cytometry. Initial standardization of protocols for isolation of nuclei, DNA staining and selection of an internal standard for tea accessions which have significantly high amount of phenolic secondary metabolites in their cytosol was carried out. Results obtained revealed that 2C DNA content of Indian tea is 7.46 pg which corresponds to 1C genome size of 3673 Mb. Inter accession variation in 2C DNA content was also observed among 35 diploid taxa ranging from 7.23 to 7.73 pg which was significant at 1% probability level. The 2C DNA content of triploid (UPASI 3) was observed to be 11.47 pg which is concurrent with the expected value. Results obtained showed that Assam and Cambod type tea accession have higher 2C DNA content of 7.73 pg whereas Assam Cambod hybrids and Assam China hybrids have reduction in DNA content with 2C amounts, 7.23 and 7.32 pg DNA respectively. The present study suggests that the species involved in origin of Indian tea must have differed in their genome sizes owing to significant inter accession variation in nuclear DNA content.
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Affiliation(s)
- Suman Sharma
- Department of Botany, Ramjas College, University of Delhi, New Delhi, Delhi 110007 India
| | - Sandeep Kaushik
- Department of Environmental Science, Indira Gandhi National Tribal University, Lalpur, Amarkantak, Madhya Pradesh 484887 India
| | - Soom Nath Raina
- Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh 201303 India
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Next generation crop improvement program: Progress and prospect in tea ( Camellia sinensis (L.) O. Kuntze). ACTA ACUST UNITED AC 2018. [DOI: 10.1016/j.aasci.2018.02.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Tony M, Samson K, Charles M, Paul M, Richard M, Mark W, Stomeo F, Sarah S, Martina K, Francis W. Transcriptome-based identification of water-deficit stress responsive genes in the tea plant,Camellia sinensis. ACTA ACUST UNITED AC 2016. [DOI: 10.5010/jpb.2016.43.3.302] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Maritim Tony
- Tea Breeding and Genetics Improvement, Kenya Agriculture and Livestock Research Organization-Tea Research Institute, P. O Box 820-20200, Kericho, Kenya
| | - Kamunya Samson
- Tea Breeding and Genetics Improvement, Kenya Agriculture and Livestock Research Organization-Tea Research Institute, P. O Box 820-20200, Kericho, Kenya
| | - Mwendia Charles
- Department of Biochemistry and Molecular Biology, Egerton University, P.O Box 536, Njoro-Nakuru, Kenya
| | - Mireji Paul
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, 60 College St., New Haven, CT 06510, USA
| | - Muoki Richard
- Tea Breeding and Genetics Improvement, Kenya Agriculture and Livestock Research Organization-Tea Research Institute, P. O Box 820-20200, Kericho, Kenya
| | - Wamalwa Mark
- International Livestock Research Institute- Bioscience East and Central Africa, P.O Box 30709, Nairobi, Kenya
| | - Francesca Stomeo
- International Livestock Research Institute- Bioscience East and Central Africa, P.O Box 30709, Nairobi, Kenya
| | - Schaack Sarah
- International Livestock Research Institute- Bioscience East and Central Africa, P.O Box 30709, Nairobi, Kenya
| | - Kyalo Martina
- International Livestock Research Institute- Bioscience East and Central Africa, P.O Box 30709, Nairobi, Kenya
| | - Wachira Francis
- Association for Strengthening Agricultural Research in Eastern and Central Africa, P.O Box 765, Entebbe, Uganda
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Wambulwa MC, Meegahakumbura MK, Kamunya S, Muchugi A, Möller M, Liu J, Xu JC, Ranjitkar S, Li DZ, Gao LM. Insights into the Genetic Relationships and Breeding Patterns of the African Tea Germplasm Based on nSSR Markers and cpDNA Sequences. FRONTIERS IN PLANT SCIENCE 2016; 7:1244. [PMID: 27625655 PMCID: PMC5004484 DOI: 10.3389/fpls.2016.01244] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Accepted: 08/05/2016] [Indexed: 05/19/2023]
Abstract
Africa is one of the key centers of global tea production. Understanding the genetic diversity and relationships of cultivars of African tea is important for future targeted breeding efforts for new crop cultivars, specialty tea processing, and to guide germplasm conservation efforts. Despite the economic importance of tea in Africa, no research work has been done so far on its genetic diversity at a continental scale. Twenty-three nSSRs and three plastid DNA regions were used to investigate the genetic diversity, relationships, and breeding patterns of tea accessions collected from eight countries of Africa. A total of 280 African tea accessions generated 297 alleles with a mean of 12.91 alleles per locus and a genetic diversity (H S) estimate of 0.652. A STRUCTURE analysis suggested two main genetic groups of African tea accessions which corresponded well with the two tea types Camellia sinensis var. sinensis and C. sinensis var. assamica, respectively, as well as an admixed "mosaic" group whose individuals were defined as hybrids of F2 and BC generation with a high proportion of C. sinensis var. assamica being maternal parents. Accessions known to be C. sinensis var. assamica further separated into two groups representing the two major tea breeding centers corresponding to southern Africa (Tea Research Foundation of Central Africa, TRFCA), and East Africa (Tea Research Foundation of Kenya, TRFK). Tea accessions were shared among countries. African tea has relatively lower genetic diversity. C. sinensis var. assamica is the main tea type under cultivation and contributes more in tea breeding improvements in Africa. International germplasm exchange and movement among countries within Africa was confirmed. The clustering into two main breeding centers, TRFCA, and TRFK, suggested that some traits of C. sinensis var. assamica and their associated genes possibly underwent selection during geographic differentiation or local breeding preferences. This study represents the first step toward effective utilization of differently inherited molecular markers for exploring the breeding status of African tea. The findings here will be important for planning the exploration, utilization, and conservation of tea germplasm for future breeding efforts in Africa.
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Affiliation(s)
- Moses C. Wambulwa
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
- Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
- College of Life Science, University of Chinese Academy of SciencesKunming, China
- Genetic Resources Unit, World Agroforestry CentreNairobi, Kenya
- Tea Research Institute, Kenya Agricultural and Livestock Research OrganizationKericho, Kenya
| | - Muditha K. Meegahakumbura
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
- Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
- College of Life Science, University of Chinese Academy of SciencesKunming, China
- Genetic and Plant Breeding Division, Coconut Research InstituteLunuwila, Sri Lanka
| | - Samson Kamunya
- Tea Research Institute, Kenya Agricultural and Livestock Research OrganizationKericho, Kenya
| | - Alice Muchugi
- Genetic Resources Unit, World Agroforestry CentreNairobi, Kenya
| | - Michael Möller
- Department of Science, Royal Botanic Garden EdinburghEdinburgh, UK
| | - Jie Liu
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
| | - Jian-Chu Xu
- Genetic Resources Unit, World Agroforestry CentreNairobi, Kenya
- Centre for Mountain Ecosystems, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
| | - Sailesh Ranjitkar
- Centre for Mountain Ecosystems, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
| | - De-Zhu Li
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
- Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
- College of Life Science, University of Chinese Academy of SciencesKunming, China
| | - Lian-Ming Gao
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
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Wang RJ, Gao XF, Kong XR, Yang J. An efficient identification strategy of clonal tea cultivars using long-core motif SSR markers. SPRINGERPLUS 2016; 5:1152. [PMID: 27504250 PMCID: PMC4958088 DOI: 10.1186/s40064-016-2835-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 07/14/2016] [Indexed: 02/02/2023]
Abstract
Microsatellites, or simple sequence repeats (SSRs), especially those with long-core motifs (tri-, tetra-, penta-, and hexa-nucleotide) represent an excellent tool for DNA fingerprinting. SSRs with long-core motifs are preferred since neighbor alleles are more easily separated and identified from each other, which render the interpretation of electropherograms and the true alleles more reliable. In the present work, with the purpose of characterizing a set of core SSR markers with long-core motifs for well fingerprinting clonal cultivars of tea (Camellia sinensis), we analyzed 66 elite clonal tea cultivars in China with 33 initially-chosen long-core motif SSR markers covering all the 15 linkage groups of tea plant genome. A set of 6 SSR markers were conclusively selected as core SSR markers after further selection. The polymorphic information content (PIC) of the core SSR markers was >0.5, with ≤5 alleles in each marker containing 10 or fewer genotypes. Phylogenetic analysis revealed that the core SSR markers were not strongly correlated with the trait 'cultivar processing-property'. The combined probability of identity (PID) between two random cultivars for the whole set of 6 SSR markers was estimated to be 2.22 × 10(-5), which was quite low, confirmed the usefulness of the proposed SSR markers for fingerprinting analyses in Camellia sinensis. Moreover, for the sake of quickly discriminating the clonal tea cultivars, a cultivar identification diagram (CID) was subsequently established using these core markers, which fully reflected the identification process and provided the immediate information about which SSR markers were needed to identify a cultivar chosen among the tested ones. The results suggested that long-core motif SSR markers used in the investigation contributed to the accurate and efficient identification of the clonal tea cultivars and enabled the protection of intellectual property.
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Affiliation(s)
- Rang Jian Wang
- Institute of Tea, Fu Jian Academy of Agricultural Sciences, 1 Hu Tou Yang Road, She Kou, Fu An, 355015 Fu Jian China ; Fu Jian Branch, National Center for Tea Improvement, 1 Hu Tou Yang Road, She Kou, Fu An, 355015 Fu Jian China
| | - Xiang Feng Gao
- Institute of Tea, Fu Jian Academy of Agricultural Sciences, 1 Hu Tou Yang Road, She Kou, Fu An, 355015 Fu Jian China ; Fu Jian Branch, National Center for Tea Improvement, 1 Hu Tou Yang Road, She Kou, Fu An, 355015 Fu Jian China
| | - Xiang Rui Kong
- Institute of Tea, Fu Jian Academy of Agricultural Sciences, 1 Hu Tou Yang Road, She Kou, Fu An, 355015 Fu Jian China ; Fu Jian Branch, National Center for Tea Improvement, 1 Hu Tou Yang Road, She Kou, Fu An, 355015 Fu Jian China
| | - Jun Yang
- Institute of Tea, Fu Jian Academy of Agricultural Sciences, 1 Hu Tou Yang Road, She Kou, Fu An, 355015 Fu Jian China ; Fu Jian Branch, National Center for Tea Improvement, 1 Hu Tou Yang Road, She Kou, Fu An, 355015 Fu Jian China
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Fang W, Meinhardt LW, Tan H, Zhou L, Mischke S, Wang X, Zhang D. Identification of the varietal origin of processed loose-leaf tea based on analysis of a single leaf by SNP nanofluidic array. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.cj.2016.02.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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15
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Mukhopadhyay M, Mondal TK, Chand PK. Biotechnological advances in tea (Camellia sinensis [L.] O. Kuntze): a review. PLANT CELL REPORTS 2016; 35:255-87. [PMID: 26563347 DOI: 10.1007/s00299-015-1884-8] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 10/10/2015] [Accepted: 10/13/2015] [Indexed: 05/28/2023]
Abstract
This article presents a comprehensive review on the success and limitations of biotechnological approaches aimed at genetic improvement of tea with a purpose to explore possibilities to address challenging areas. Tea is a woody perennial tree with a life span of more than 100 years. Conventional breeding of tea is slow and limited primarily to selection which leads to narrowing down of its genetic base. Harnessing the benefits of wild relatives has been negligible due to low cross-compatibility, genetic drag and undesirable alleles for low yield. Additionally, being a recalcitrant species, in vitro propagation of tea is constrained too. Nevertheless, maneuvering with tissue/cell culture techniques, a considerable success has been achieved in the area of micropropagation, somatic embryogenesis as well as genetic transformation. Besides, use of molecular markers, "expressomics" (transcriptomics, proteomics, metabolomics), map-based cloning towards construction of physical maps, generation of expressed sequenced tags (ESTs) have facilitated the identification of QTLs and discovery of genes associated with abiotic or biotic stress tolerance and agronomic traits. Furthermore, the complete genome (or at least gene space) sequence of tea is expected to be accessible in the near future which will strengthen combinational approaches for improvement of tea. This review presents a comprehensive account of the success and limitations of the biotechnological tools and techniques hitherto applied to tea and its wild relatives. Expectedly, this will form a basis for making further advances aimed at genetic improvement of tea in particular and of economically important woody perennials in general.
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Affiliation(s)
- Mainaak Mukhopadhyay
- Department of Botany, University of Kalyani, Kalyani, 741235, Nadia, West Bengal, India.
| | - Tapan K Mondal
- Division of Genomic Resources, National Bureau of Plant Genetic Resources, Pusa, New Delhi, 110012, India.
| | - Pradeep K Chand
- Plant Cell and Tissue Culture Facility, Post-Graduate Department of Botany, Utkal University, Vani Vihar, Bhubaneswar, 751004, Odisha, 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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Katoh Y, Katoh M, Omori M. Identification of Teas Cultivated in Eastern, Southeastern and Southern Asia Based on Nucleotide Sequence Comparison of Ribulose 1,5-bisphosphate Carboxylase Large-subunit of Chloroplast DNA and 18S Ribosomal RNA of Nuclear DNA. FOOD SCIENCE AND TECHNOLOGY RESEARCH 2015. [DOI: 10.3136/fstr.21.381] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
| | | | - Masashi Omori
- Department of Food Science, Otsuma Women's University
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Fraser K, Lane GA, Otter DE, Hemar Y, Quek SY, Harrison SJ, Rasmussen S. Analysis of metabolic markers of tea origin by UHPLC and high resolution mass spectrometry. Food Res Int 2013. [DOI: 10.1016/j.foodres.2012.10.015] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Ling Y, Zhang XQ, Ma X, Chen SY, Chen TT, Liu W. Analysis of genetic diversity among wild bermudagrass germplasm from southwest China using SSR markers. GENETICS AND MOLECULAR RESEARCH 2012; 11:4598-608. [PMID: 23096923 DOI: 10.4238/2012.october.17.5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Fifty-five wild accessions of bermudagrass (Cynodon dactylon) were collected from southwest China (Sichuan, Chongqing, Yunnan, Guizhou, and Tibet), and their genetic diversity was analyzed using simple sequence repeat markers. A total of 267 polymorphic bands were detected with 18 primer combinations. The genetic similarity among the accessions ranged from 0.688 to 0.894 with an average of 0.797. All 55 wild accessions were clustered into 7 eco-geographic groups. Our data showed that the dendrogram was almost in accordance with geographic distribution, and accessions from the same collection sites tended to be clustered into the same group. A genetic differentiation analysis revealed that the percentage of genetic variance was 70.07 and 29.93% within and among groups, respectively. Finally, we discuss the implications of these results for C. dactylon in southwest China.
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Affiliation(s)
- Y Ling
- College of Veterinary Medicine, Sichuan Agricultural University, Ya'an, Sichuan, P.R. China
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20
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Bai D, Brandle J, Reeleder R. Genetic diversity in North American ginseng (Panax quinquefolius L.) grown in Ontario detected by RAPD analysis. Genome 2012; 40:111-5. [PMID: 18464811 DOI: 10.1139/g97-015] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Genetic diversity within North American ginseng (Panax quinquefolius L.) grown in Ontario was investigated at the DNA level using the randomly amplified polymorphic DNA (RAPD) method via the polymerase chain reaction (PCR). A total of 420 random decamers were initially screened against DNA from four ginseng plants and 78.8% of them generated RAPD fragments. Thirty-six of the decamers that generated highly repeatable polymorphic RAPD markers were selected for further RAPD analysis of the ginseng population. With these primers, 352 discernible DNA fragments were produced from DNA of 48 ginseng plants, corresponding to an average of 9.8 fragments per primer, of which over 45% were polymorphic. The similarity coefficients among the DNA of ginseng plants analyzed were low, ranging from 0.149 to 0.605 with a mean of 0.412, indicating that a high degree of genetic diversity exists in the ginseng population. Lower levels of genetic diversity were detected among 3-year-old ginseng plants selected on the basis of greater plant height than among the plants randomly selected from the same subpopulation or over the whole population, suggesting that genetic factors at least partly contribute to morphological variation within the ginseng population and that visual selection can be effective in identifying the genetic differences. The significance of a high degree of genetic variation in the ginseng population on its potential for improvement by breeding is also discussed.
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Assessment of worldwide genetic diversity of Siberian wild rye (Elymus sibiricus L.) germplasm based on gliadin analysis. Molecules 2012; 17:4424-34. [PMID: 22499189 PMCID: PMC6268020 DOI: 10.3390/molecules17044424] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2012] [Revised: 03/09/2012] [Accepted: 03/26/2012] [Indexed: 11/16/2022] Open
Abstract
E. sibiricus L., the type species of the genus Elymus, is a perennial, self-pollinating and allotetraploid grass indigenous to Northern Asia, which in some countries can be cultivated as an important forage grass. In the present study, eighty-six Elymus sibiricus accessions, mostly from different parts of Asia, were assayed by gliadin markers based on Acid Polyacrylamide Gel Electrophoresis to differentiate and explore their genetic relationships. The genetic similarity matrix was calculated by 47 polymorphic bands, which ranged from 0.108 to 0.952 with an average of 0.373. The total Shannon diversity index (H(o)) and the Simpson index (H(e)) was 0.460 and 0.302, respectively. Cluster analysis showed a clear demarcation between accessions from Qinghai-Tibetan Plateau, China and the others as separate groups. The clustering pattern was probably dependent on geographic origin and ecological adaptability of the accessions. The population structure analysis based on Shannon indices showed that the proportion of variance within and among the five geographic regions of the Northern Hemisphere was 55.9 and 44.1%, respectively, or 63.4 and 36.6% within and among six Chinese provinces. This distinct geographical divergence was perhaps depended on ecogeographical conditions such as climate difference and mountain distribution. The results of gladin analysis in this study are useful for the collection and preservation of E. sibiricus germplasm resources.
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El-Hadidy A, Abd El-Ghani M, Amer W, Hassan R. Morphological and Molecular Differentiation between Egyptian Species of Pancratium L. (Amaryllidaceae). ACTA BIOLOGICA CRACOVIENSIA SERIES BOTANICA 2012; 54. [DOI: 10.2478/v10182-012-0005-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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Moubasher H, Abd El-Ghani MM, Kamel W, Mansi M, El-Bous M. Taxonomic considerations among and within some Egyptian taxa of Capparis and related genera (Capparaceae) as revealed by RAPD fingerprinting. COLLECTANEA BOTANICA 2011. [DOI: 10.3989/collectbot.2011.v30.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
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24
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Sarwat M, Nabi G, Das S, Srivastava PS. Molecular markers in medicinal plant biotechnology: past and present. Crit Rev Biotechnol 2011; 32:74-92. [DOI: 10.3109/07388551.2011.551872] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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25
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Katoh M, Omori M, Katoh Y. Identification of Japanese Green Tea Cultivars Using DNA Fragment Polymorphisms. J JPN SOC FOOD SCI 2011. [DOI: 10.3136/nskkk.58.421] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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AFLP-based genetic diversity assessment of commercially important tea germplasm in India. Biochem Genet 2010; 48:549-64. [PMID: 20390337 DOI: 10.1007/s10528-010-9338-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2009] [Accepted: 11/19/2009] [Indexed: 10/19/2022]
Abstract
India has a large repository of important tea accessions and, therefore, plays a major role in improving production and quality of tea across the world. Using seven AFLP primer combinations, we analyzed 123 commercially important tea accessions representing major populations in India. The overall genetic similarity recorded was 51%. No significant differences were recorded in average genetic similarity among tea populations cultivated in various geographic regions (northwest 0.60, northeast and south both 0.59). UPGMA cluster analysis grouped the tea accessions according to geographic locations, with a bias toward China or Assam/Cambod types. Cluster analysis results were congruent with principal component analysis. Further, analysis of molecular variance detected a high level of genetic variation (85%) within and limited genetic variation (15%) among the populations, suggesting their origin from a similar genetic pool.
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Katoh M, Katoh Y, Kinoshit T, Yamaguchi Y, Omori M. Identification of Tea Cultivar by Amolified DNA Fragment Length Polymorphism (AFLP) using Black Teas as Sample. J JPN SOC FOOD SCI 2010. [DOI: 10.3136/nskkk.57.389] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Sharma RK, Bhardwaj P, Negi R, Mohapatra T, Ahuja PS. Identification, characterization and utilization of unigene derived microsatellite markers in tea (Camellia sinensis L.). BMC PLANT BIOLOGY 2009; 9:53. [PMID: 19426565 PMCID: PMC2693106 DOI: 10.1186/1471-2229-9-53] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2008] [Accepted: 05/11/2009] [Indexed: 05/02/2023]
Abstract
BACKGROUND Despite great advances in genomic technology observed in several crop species, the availability of molecular tools such as microsatellite markers has been limited in tea (Camellia sinensis L.). The development of microsatellite markers will have a major impact on genetic analysis, gene mapping and marker assisted breeding. Unigene derived microsatellite (UGMS) markers identified from publicly available sequence database have the advantage of assaying variation in the expressed component of the genome with unique identity and position. Therefore, they can serve as efficient and cost effective alternative markers in such species. RESULTS Considering the multiple advantages of UGMS markers, 1,223 unigenes were predicted from 2,181 expressed sequence tags (ESTs) of tea (Camellia sinensis L.). A total of 109 (8.9%) unigenes containing 120 SSRs were identified. SSR abundance was one in every 3.55 kb of EST sequences. The microsatellites mainly comprised of di (50.8%), tri (30.8%), tetra (6.6%), penta (7.5%) and few hexa (4.1%) nucleotide repeats. Among the dinucleotide repeats, (GA)n.(TC)n were most abundant (83.6%). Ninety six primer pairs could be designed form 83.5% of SSR containing unigenes. Of these, 61 (63.5%) primer pairs were experimentally validated and used to investigate the genetic diversity among the 34 accessions of different Camellia spp. Fifty one primer pairs (83.6%) were successfully cross transferred to the related species at various levels. Functional annotation of the unigenes containing SSRs was done through gene ontology (GO) characterization. Thirty six (60%) of them revealed significant sequence similarity with the known/putative proteins of Arabidopsis thaliana. Polymorphism information content (PIC) ranged from 0.018 to 0.972 with a mean value of 0.497. The average heterozygosity expected (HE) and observed (Ho) obtained was 0.654 and 0.413 respectively, thereby suggesting highly heterogeneous nature of tea. Further, test for IAM and SMM models for the UGMS loci showed excess heterozygosity and did not show any bottleneck operating in the tea population. CONCLUSION UGMS markers identified and characterized in this study provided insight about the abundance and distribution of SSR in the expressed genome of C. sinensis. The identification and validation of 61 new UGMS markers will not only help in intra and inter specific genetic diversity assessment but also be enriching limited microsatellite markers resource in tea. Further, the use of these markers would reduce the cost and facilitate the gene mapping and marker-aided selection in tea. Since, 36 of these UGMS markers correspond to the Arabidopsis protein sequence data with known functions will offer the opportunity to investigate the consequences of SSR polymorphism on gene functions.
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Affiliation(s)
- Ram Kumar Sharma
- Biotechnology Division, Institute of Himalayan Bioresource Technology, IHBT, (CSIR), Post Box 6, Palampur, Himachal Pradesh, 176061, India
| | - Pankaj Bhardwaj
- Biotechnology Division, Institute of Himalayan Bioresource Technology, IHBT, (CSIR), Post Box 6, Palampur, Himachal Pradesh, 176061, India
| | - Rinu Negi
- Biotechnology Division, Institute of Himalayan Bioresource Technology, IHBT, (CSIR), Post Box 6, Palampur, Himachal Pradesh, 176061, India
| | - Trilochan Mohapatra
- National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute (IARI), New Delhi, 110012, India
| | - Paramvir Singh Ahuja
- Biotechnology Division, Institute of Himalayan Bioresource Technology, IHBT, (CSIR), Post Box 6, Palampur, Himachal Pradesh, 176061, India
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Fung KF, Carr HP, Poon BHT, Wong MH. A comparison of aluminum levels in tea products from Hong Kong markets and in varieties of tea plants from Hong Kong and India. CHEMOSPHERE 2009; 75:955-62. [PMID: 19230955 DOI: 10.1016/j.chemosphere.2009.01.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2008] [Revised: 11/09/2008] [Accepted: 01/02/2009] [Indexed: 05/21/2023]
Abstract
This study project aimed to investigate the concentrations of aluminum (Al) in tea products available in Hong Kong markets. Tea samples consisting of 47 different tea bags and 28 samples of tea leaves were analysed for concentrations of Al. All tea samples released Al (0.70-5.93 mg L(-1)) during a standard infusion period. In comparison to the Joint FAO/WHO Provisional Tolerable Weekly Intake guideline of 7 mg Al kg(-1) body weight, it was concluded that tea made with these tea leaves will not impose adverse human health impacts. The relative effects of age, soil available Al, and genetic differences on the levels of Al accumulated by tea bushes were investigated. It was found that there was no definite trend between the amount of Al accumulated and the age of tea bushes. The soil available Al influenced the levels of Al in Camellia sinensis to a certain extent, but it was evident that the ability of different varieties of C. sinensis to accumulate Al was variable. C. sinensis accumulated Al in all stages of growth. Young seedlings had lower contents of Al while the mobility of Al within the tea bushes was high. In a manner typical of hyperaccumulators, Al was not retained in the roots, but was consistently transported to the shoots. Aluminum in the tea bush was distributed between the different parts in the following order: mature leaves>roots>branches>young leaves.
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Affiliation(s)
- K F Fung
- Croucher Institute for Environmental Sciences, Department of Biology, Hong Kong Baptist University, Kowloon Tong, Hong Kong, PR China
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Karthigeyan S, Rajkumar S, Sharma RK, Gulati A, Sud RK, Ahuja PS. High Level of Genetic Diversity Among the Selected Accessions of Tea (Camellia sinensis) from Abandoned Tea Gardens in Western Himalaya. Biochem Genet 2008; 46:810-9. [DOI: 10.1007/s10528-008-9195-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2007] [Accepted: 05/28/2008] [Indexed: 10/21/2022]
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Abstract
RAPD profiles were used to identify the extent of diversity among 54 accessions of mung bean that included both improved and local land races. Out of the 40 primers screened, seven primers generated 174 amplification products with an average of 24.85 bands per primer. The RAPD profiles were analysed for Jaccard's similarity coefficients that was found to be in the range from 0 to 0.48, indicating the presence of wide range of genetic diversity at molecular level. Cluster analysis was carried out based on distances (1-similarity coefficient) using neighbour-joining method in Free Tree package. The dendrogram resolved all the accessions into two major clusters, I (with 11 accessions) and II (with 43 accessions). However, the cluster was further divided into four subclusters (II A with six, II B with nine, II C with 15 and II D with 13 accessions). The distribution of the accessions in different clusters and subclusters appears to be related to their performance in field conditions for 10 morphological traits that were scored. This study indicated that the RAPD profiles provide an easy and simple technique for preliminary genetic diversity assessment of mung bean accessions that may reflect morphological trait differences among them.
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Affiliation(s)
- G Roopa Lavanya
- Department of Genetics and Plant Breeding, Allahabad Agricultural Institute Deemed University, Allahabad 211 007, India.
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[Genetic diversity of wild Cynodon dactylon germplasm detected by SRAP markers]. YI CHUAN = HEREDITAS 2008; 30:94-100. [PMID: 18244909 DOI: 10.3724/sp.j.1005.2008.00094] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Sequence-related amplified polymorphism (SRAP) molecular markers were used to detect the genetic diversity of 32 wild accessions of Cynodon dactylon collected from Sichuan, Chongqing, Guizhou and Tibet, China. The following results were obtained. (1) Fourteen primer pairs produced 132 polymorphic bands, averaged 9.4 bands per primer pair. The percentage of polymorphic bands in average was 79.8%. The Nei's genetic similarity coefficient of the tested accessions ranged from 0.591 to 0.957, and the average Nei's coefficient was 0.759. These results suggested that there was rich genetic diversity among the wild resources of Cynodon dactylon tested. (2) Thirty two wild accessions were clustered into four groups. Moreover, the accessions from the same origin frequently clustered into one group. The findings implied that a correlation among the wild resources, geographical and ecological environment. (3) Genetic differentiation between and within six eco-geographical groups of C. dactylon was estimated by Shannon's diversity index, which showed that 65.56% genetic variance existed within group, and 34.44% genetic variance was among groups. (4) Based on Nei's unbiased measures of genetic identity, UPGMA cluster analysis measures of six eco-geographical groups of Cynodon dactylon, indicated that there was a correlation between genetic differentiation and eco-geographical habits among the groups.
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Singh D, Ahuja PS. 5S rDNA gene diversity in tea (Camellia sinensis (L.) O. Kuntze) and its use for variety identification. Genome 2006; 49:91-6. [PMID: 16462906 DOI: 10.1139/g05-065] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Variability in the organization of repeats of 5S rDNA is useful for phylogenetic studies in various crops. We found variable repeats of 5S rDNA gene in the genome of tea (Camellia sinensis (L.) O. Kuntze) during Southern hybridization. Variability in the repeats of 5S rDNA with specific restriction endonuleases (Sau3AI, BamHI, and ApoI) was analyzed in 28 different tea clones representing 3 types of tea. Our results clearly show that the 5S rDNA gene in tea could be used as a molecular marker to distinguish C. sinensis Chinary tea from the other important types of tea, namely Assamica and Cambod. Upon analysis with restriction endonucleases, the 5S rDNA gene in the tea genome was found to be heavily methylated.Key words: Camellia sinensis, 5S rDNA, DNA methylation, restriction endonucleases, molecular marker.
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Affiliation(s)
- Dharam Singh
- Institute of Himalayan Bioresource Technology, Palampur, India
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Saravanan M, Maria John KM, Raj Kumar R, Pius PK, Sasikumar R. Genetic diversity of UPASI tea clones (Camellia sinensis (L.) O. Kuntze) on the basis of total catechins and their fractions. PHYTOCHEMISTRY 2005; 66:561-5. [PMID: 15721948 DOI: 10.1016/j.phytochem.2004.06.024] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2004] [Revised: 06/07/2004] [Indexed: 05/23/2023]
Abstract
Tea leaf catechins and the ratio of dihydroxylated to trihydroxylated catechin fractions were analysed to identify the genetic diversity of 26 UPASI released tea clones. Principal component analysis (PCA) based on regression factor separated tea clones into five groups according to their jats (Jats are region based rays for e.g., Assam, China and Cambod origin) as well as their quality constituents (such as total polyphenols, total catechins, amino acids in the green leaves and liquor characteristics of black tea), particularly the catechins. Group 1 represented medium quality (quality of the final produce) clones, such as UPASI-10, UPASI-12 and UPASI-15 and drought tolerant clones like UPASI-1, UPASI-2, UPASI-9 and UPASI-10. Group 2 contained purely "China" cultivars while group 3 possessed high quality tea cultivars. "Assam" (group 5) teas had the lowest ratio of dihydroxylated to trihydroxylated catechin fractions (1:4) than the "Chinery" (group 2) teas (1:5). This biochemical differentiation indicated that there is a vast genetic diversity in UPASI released tea clones in terms of catechin fractions, even though the majority of them were selected from one tea estate located in the Nilgiris.
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Affiliation(s)
- M Saravanan
- Plant Physiology Division, UPASI Tea Research Foundation, Tea Research Institute, Nirar Dam BPO, Valparai 642 127, TN, India
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FREEMAN SUSAN, WEST JON, JAMES CELIA, LEA VINCE, MAYES SEAN. Isolation and characterization of highly polymorphic microsatellites in tea (Camellia sinensis). ACTA ACUST UNITED AC 2004. [DOI: 10.1111/j.1471-8286.2004.00682.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Ayana A, Bekele E. Geographical Patterns of Morphological Variation in Sorghum (Sorghum Bicolor (L.) Moench) Germplasm from Ethiopia and Eritrea: Qualitative Characters. Hereditas 2004. [DOI: 10.1111/j.1601-5223.1998.t01-1-00195.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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CARDOSO MA, PROVAN J, POWELL W, FERREIRA PCG, DE OLIVEIRA DE. High genetic differentiation among remnant populations of the endangeredCaesalpinia echinataLam. (Leguminosae–Caesalpinioideae). Mol Ecol 2003. [DOI: 10.1046/j.1365-294x.1998.00363.x] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- M. A. CARDOSO
- Departamento de Genética, Universidade Federal do Rio de Janeiro, CP: 68011, Rio de Janeiro 21944–970, Brasil, ,
- Jardim Botânico do Rio de Janeiro, Rua Pacheco Leão 915, Rio de Janeiro 22460–030, Brasil, ,
| | - J. PROVAN
- Cell and Molecular Genetics Department, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, Scotland, UK, ,
| | - W. POWELL
- Cell and Molecular Genetics Department, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, Scotland, UK, ,
| | - P. C. G. FERREIRA
- Departamento de Bioquímica Médica, Universidade Federal do Rio de Janeiro, CP: 68041, Rio de Janeiro 21491–590, Brasil
| | - D. E. DE OLIVEIRA
- Departamento de Genética, Universidade Federal do Rio de Janeiro, CP: 68011, Rio de Janeiro 21944–970, Brasil, ,
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40
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Kaundun SS, Matsumoto S. Heterologous nuclear and chloroplast microsatellite amplification and variation in tea, Camellia sinensis. Genome 2002; 45:1041-8. [PMID: 12502248 DOI: 10.1139/g02-070] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The advantage of the cross transferability of heterologous chloroplast and nuclear microsatellite primers was taken to detect polymorphism among 24 tea (Camellia sinensis (L.) O. Kuntze) genotypes, including both the assamica and the sinensis varieties. Primer information was obtained from the closely related Camellia japonica species for four nuclear microsatellites, and from Nicotiana tabaccum for seven universal chloroplast microsatellites. All of the nuclear microsatellite loci tested generated an expected DNA fragment in tea, revealing between three and five alleles per locus. Four out of the seven chloroplast microsatellites primers amplified positively, and of these only one was polymorphic with three alleles, which is in agreement with the conserved nature of chloroplast microsatellites at the intraspecific level. A factorial correspondence analysis carried out on all genotypes and nuclear microsatellite alleles separated the assamica and sinensis genotypes into two groups, thus demonstrating the value of these markers in establishing the genetic relationship between tea varieties. Genetic diversity measured with nuclear microsatellites was higher than that measured with other types of molecular markers, offering prospects for their use in fingerprinting, mapping, and population genetic studies, whereas polymorphisms detected at a cpSSR locus will allow the determination of plastid inheritance in the species.
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Affiliation(s)
- Shiv Shankhar Kaundun
- National Institute of Vegetable and Tea Science, 2769 Kanaya, Kanaya-cho, 428-8501 Shizuoka, Japan.
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41
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Persson K, Díaz O, von Bothmer R. Extent and patterns of RAPD variation in landraces and cultivars of rye (Secale cereale L.) from northern Europe. Hereditas 2002; 134:237-43. [PMID: 11833287 DOI: 10.1111/j.1601-5223.2001.00237.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Little is known about the extent and patterns of distribution of RAPD diversity in outcrossing species. This study is the first step in using RAPD markers to quantify the amount and distribution of genetic variation within and between accessions of 9 landraces and 3 cultivars of cultivated rye from Northern Europe. A high level of RAPD variation was detected, demonstrating the utility of RAPDs for genetic characterisation in rye. The results show that: (1) landraces and improved cultivars maintain roughly the same high levels of RAPD variation, (2) landraces from Norway, Germany and Finland showed the lowest level of variation, probably because of a small amount of seeds from the original samples, (3) most of the RAPD variation was found within rather than between the accessions, which is consistent with the pattern expected for a cross pollinated crop. Both the cluster and the principal coordinates analyses displayed the same pattern of genetic relationship among the accessions studied.
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Affiliation(s)
- K Persson
- Department of Crop Science, Swedish University of Agricultural Sciences, Alnarp, Sweden.
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42
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Ayana A, Bekele E, Bryngelsson T. Genetic variation in wild sorghum (Sorghum bicolor ssp. verticilliflorum (L.) Moench) germplasm from Ethiopia assessed by random amplified polymorphic DNA (RAPD). Hereditas 2001; 132:249-54. [PMID: 11075520 DOI: 10.1111/j.1601-5223.2000.t01-1-00249.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The extent and distribution of genetic variation in wild sorghum (Sorghum bicolor ssp. verticilliflorum (L.) Moench) collected from five different geographical regions in Ethiopia were analyzed using random amplified polymorphic DNA (RAPD) markers for 93 individuals representing 11 populations. Nine decamer primers generated a total of 83 polymorphic bands with 8-12 bands per primer and a mean of 9 bands across the 93 individuals. The amount of genetic variation among the populations (H = 0.37) and among the geographical region (H = 0.44) was low to moderate, despite the high degree of polymorphic bands per primer. Similarly, the mean genetic distance (0.08) among populations as well as among regions of origin (0.04) of the population was found to be low. The low genetic variation may be due to the reduced population size of the wild sorghum in Ethiopia because of habitat change. Partitioning of the genetic variation into between and within the population as well as between and within the regions of origin revealed that 75% and 88% of the variation was found within the populations and within the regions, respectively. Cluster analysis of genetic distance estimates further confirmed low level of differentiation of wild sorghum populations both on population and regional bases. The implications of the results for genetic conservation purposes are discussed.
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Affiliation(s)
- A Ayana
- Addis Ababa University, Faculty of Science, Department of Biology, Ethiopia
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43
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Hackett CA, Wachira FN, Paul S, Powell W, Waugh R. Construction of a genetic linkage map for Camellia sinensis (tea). Heredity (Edinb) 2000; 85 Pt 4:346-55. [PMID: 11122412 DOI: 10.1046/j.1365-2540.2000.00769.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Genetic maps are a vital tool in cultivar improvement programmes for woody perennial tree crops such as tea (Camellia sinensis). A population thought to be derived from two known, noninbred parents was scored for RAPD and AFLP markers, in order to develop a linkage map. However, a very high proportion of the markers exhibited unexpected segregation ratios in the light of their configurations in the parents, and an exploratory statistical analysis revealed patterns in the marker scores which can most easily be explained by the hypothesis of three male parents contributing pollen to this cross. We discuss the evidence for this and the subsequent analysis required to assemble the markers from the female parent into the first linkage map for tea. The map has 15 linkage groups of three or more markers, agreeing with the haploid chromosome number of tea. The statistical methods that revealed the subpopulations are easy to apply routinely, and may prove a useful diagnostic tool for the analysis of noninbred mapping populations.
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Affiliation(s)
- C A Hackett
- Biomathematics & Statistics Scotland, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, Scotland, UK.
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44
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Bessega C, Saidman BO, Vilardi JC. Isozyme and RAPD studies in Prosopis glandulosa and P. Velutina (Leguminosae, Mimosoideae). Genet Mol Biol 2000. [DOI: 10.1590/s1415-47572000000300024] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Allozyme and random amplified polymorphic DNA (RAPD) techniques have been compared for their usefulness for genetic and taxonomic studies in Prosopis glandulosa and P. velutina populations. Isozymes and RAPDs yielded similarly high estimates of genetic variability. Genetic structure and differentiation were analyzed through non-hierarchical Wright's F DT. For all populations considered, both markers produced low gene flow (Nm < 1) estimates. When only P. glandulosa populations were analyzed, isozyme data yielded higher gene flow estimates (Nm > 1), in agreement with that expected for conspecific populations. However, in RAPD data the expected reduction in F DT and the increase in Nm were not observed. Correlation between F DT and geographical distance matrices (Mantel test) for all populations was significant (P = 0.02) when based on isozymes, but not so (P = 0.33) when based on RAPDs. No significant associations among genetic and geographical or climatic variables were observed. Two isoenzyme systems (GOT and PRX) enabled us to distinguish between P. glandulosa and P. velutina, but no diagnostic band for recognition of populations or species studied here were detected by RAPD. However, RAPD markers showed higher values for genetic differentiation among conspecific populations of P. glandulosa and a lower coefficient of variation than those obtained from isozymes.
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45
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Gauer L, Cavalli-Molina S. Genetic variation in natural populations of maté (Ilex paraguariensis A. st.-hil., aquifoliaceae) using RAPD markers. Heredity (Edinb) 2000; 84 ( Pt 6):647-56. [PMID: 10886380 DOI: 10.1046/j.1365-2540.2000.00687.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This study characterized the genetic diversity of four populations of Ilex paraguariensis, a plant species native to South America, using random amplified polymorphic DNA (RAPD) markers. A total of 341 different RAPD bands were generated by the 15 primers analysed. High genetic variability was detected within each population, with an average diversity of 0.163. The within-population variation was large, probably as a result of the life history characteristics of I. paraguariensis. The average distance between individuals from each population was 0.392 and that between populations was 0.433, indicating a low between-population divergence. Most bands were common to all populations and the population-specific bands occurred at low frequencies. Partitioning of the genetic diversity indicated that 85% of the variation occurred within populations and only 15% between populations. Although most of the variability is within populations, clusterings of plants in each population were observed in the dendrogram.
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Affiliation(s)
- L Gauer
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
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46
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Colombo C, Second G, Charrier A. Diversity within American cassava germ plasm based on RAPD markers. Genet Mol Biol 2000. [DOI: 10.1590/s1415-47572000000100034] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
This work focuses on the genetic diversity of American cassava through RAPD molecular markers. The 126 genotypes studied were distributed on four geographical levels ranging from local to continental. Samples included ethnocultivars from the Santa Isabel community in the Brazilian Amazon, local cultivars collected in the State of São Paulo, native accessions from very diverse Brazilian regions, and representative accessions from the Centro Internacional de Agricultura Tropical (CIAT) core collection. Eighty-eight polymorphic bands were analyzed. Results revealed the weak genetic structure of the cassava analyzed. The pattern formed by the first two axes of the principal coordinates analysis (PCoA) revealed an overlapping of the São Paulo State genotype, the Brazilian group and the core collection accessions. The Santa Isabel ethnocultures formed a separate group. The weak genetic structure of cassava can be explained by the common practice of exchanging botanical material among small producers as well as by recombinations among genotypes. When the genotypes were analyzed using climatic data, the sample sites were found to be structured according to temperature and precipitation. RAPD markers proved very useful in the genetic diversity study, resulting in important implications for cassava germ plasm collections and genetic breeding.
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Affiliation(s)
| | | | - André Charrier
- Ecole Nationale Supérieure Agronomique de Montpellier, France
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47
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An assessment of genetic diversity among Camellia sinensis L. (cultivated tea) and its wild relatives based on randomly amplified polymorphic DNA and organelle-specific STS. Heredity (Edinb) 1997. [DOI: 10.1038/hdy.1997.99] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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48
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OWUOR PO, OBANDA M. The Effects of Some Agronomic and Processing Practices and Clones on the Relative Composition of the Theaflavins in Black Tea. ACTA ACUST UNITED AC 1997. [DOI: 10.3136/fsti9596t9798.3.344] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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49
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Paran I, Gidoni D, Jacobsohn R. Variation between and within broomrape (Orobanche) species revealed by RAPD markers. Heredity (Edinb) 1997. [DOI: 10.1038/hdy.1997.8] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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