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Lin Y, Xiang Y, Wei S, Zhang Q, Liu Y, Zhang Z, Tang S. Genetic diversity and population structure of an insect-pollinated and bird-dispersed dioecious tree Magnolia kwangsiensis in a fragmented karst forest landscape. Ecol Evol 2024; 14:e70094. [PMID: 39091326 PMCID: PMC11291554 DOI: 10.1002/ece3.70094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 06/24/2024] [Accepted: 07/10/2024] [Indexed: 08/04/2024] Open
Abstract
This study combined population genetics and parentage analysis to obtain foundational data for the conservation of Magnolia kwangsiensis. M. kwangsiensis is a Class I tree species that occurs in two disjunct regions in a biodiversity hotspot in southwest China. We assessed the genetic diversity and structure of this species across its distribution range to support its conservation management. Genetic diversity and population structure of 529 individuals sampled from 14 populations were investigated using seven nuclear simple sequence repeat (nSSR) markers and three chloroplast DNA (cpDNA) fragments. Parentage analysis was used to evaluate the pollen and seed dispersal distances. The nSSR marker analysis revealed a high genetic diversity in M. kwangsiensis, with an average observed (Ho) and expected heterozygosities (He) of 0.726 and 0.687, respectively. The mean and maximum pollen and seed dispersal distances were 66.4 and 95.7 m and 535.4 and 553.8 m, respectively. Our data revealed two distinct genetic groups, consistent with the disjunct geographical distribution of the M. kwangsiensis populations. Both pollen and seed dispersal movements help maintain genetic connectivity among M. kwangsiensis populations, contributing to high levels of genetic diversity. Both genetically differentiated groups corresponding to the two disjunct regions should be recognized as separate conservation units.
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Affiliation(s)
- Yanfang Lin
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of EducationGuangxi Normal UniversityGuilinChina
- Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River BasinGuangxi Normal UniversityGuilinChina
- Wuzhou No. 18 Middle SchoolWuzhouChina
| | - Yingying Xiang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of EducationGuangxi Normal UniversityGuilinChina
- Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River BasinGuangxi Normal UniversityGuilinChina
| | - Sujian Wei
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of EducationGuangxi Normal UniversityGuilinChina
- Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River BasinGuangxi Normal UniversityGuilinChina
| | - Qiwei Zhang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of EducationGuangxi Normal UniversityGuilinChina
- Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River BasinGuangxi Normal UniversityGuilinChina
| | - Yanhua Liu
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of EducationGuangxi Normal UniversityGuilinChina
- Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River BasinGuangxi Normal UniversityGuilinChina
| | - Zhiyong Zhang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of EducationGuangxi Normal UniversityGuilinChina
- Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River BasinGuangxi Normal UniversityGuilinChina
| | - Shaoqing Tang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of EducationGuangxi Normal UniversityGuilinChina
- Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River BasinGuangxi Normal UniversityGuilinChina
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Cai L, Liu D, Yang F, Zhang R, Yun Q, Dao Z, Ma Y, Sun W. The chromosome-scale genome of Magnolia sinica (Magnoliaceae) provides insights into the conservation of plant species with extremely small populations (PSESP). Gigascience 2024; 13:giad110. [PMID: 38206588 PMCID: PMC10999834 DOI: 10.1093/gigascience/giad110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 07/28/2023] [Accepted: 12/04/2023] [Indexed: 01/12/2024] Open
Abstract
Magnolia sinica (Magnoliaceae) is a highly threatened tree endemic to southeast Yunnan, China. In this study, we generated for the first time a high-quality chromosome-scale genome sequence from M. sinica, by combining Illumina and ONT data with Hi-C scaffolding methods. The final assembled genome size of M. sinica was 1.84 Gb, with a contig N50 of ca. 45 Mb and scaffold N50 of 92 Mb. Identified repeats constituted approximately 57% of the genome, and 43,473 protein-coding genes were predicted. Phylogenetic analysis shows that the magnolias form a sister clade with the eudicots and the order Ceratophyllales, while the monocots are sister to the other core angiosperms. In our study, a total of 21 individuals from the 5 remnant populations of M. sinica, as well as 22 specimens belonging to 8 related Magnoliaceae species, were resequenced. The results showed that M. sinica had higher genetic diversity (θw = 0.01126 and θπ = 0.01158) than other related species in the Magnoliaceae. However, population structure analysis suggested that the genetic differentiation among the 5 M. sinica populations was very low. Analyses of the demographic history of the species using different models consistently revealed that 2 bottleneck events occurred. The contemporary effective population size of M. sinica was estimated to be 10.9. The different patterns of genetic loads (inbreeding and numbers of deleterious mutations) suggested constructive strategies for the conservation of these 5 different populations of M. sinica. Overall, this high-quality genome will be a valuable genomic resource for conservation of M. sinica.
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Affiliation(s)
- Lei Cai
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations/Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Detuan Liu
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations/Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Fengmao Yang
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations/Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Rengang Zhang
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations/Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Quanzheng Yun
- Department of Bioinformatics, Ori (Shandong) Gene Science and Technology Co., Ltd., Weifang, 261000, Shandong, China
| | - Zhiling Dao
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations/Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Yongpeng Ma
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations/Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Weibang Sun
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations/Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
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History cooling events contributed to the endangered status of Pseudotsuga brevifolia endemic to limestone habitats. Glob Ecol Conserv 2023. [DOI: 10.1016/j.gecco.2023.e02414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023] Open
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Effect of the landscape on functional and spatial connectivity in Magnolia cubensis (Magnoliaceae) in two mountain massifs of Cuba. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01395-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Yang L, Hisoriev H, Kurbonova P, Boboev M, Bobokalonov K, Feng Y, Li W. High genetic diversity and low differentiation of endangered Ferula tadshikorum Pimenov in Tajikistan. Glob Ecol Conserv 2021. [DOI: 10.1016/j.gecco.2021.e01627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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Yun SA, Kim SC. Genetic diversity and structure of Saussurea polylepis (Asteraceae) on continental islands of Korea: Implications for conservation strategies and management. PLoS One 2021; 16:e0249752. [PMID: 33831066 PMCID: PMC8031399 DOI: 10.1371/journal.pone.0249752] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 03/24/2021] [Indexed: 11/24/2022] Open
Abstract
Saussurea polylepis Nakai is an herbaceous perennial endemic to Korea and is highly restricted to several continental islands in the southwestern part of the Korean Peninsula. Given its very narrow geographical distribution, it is more vulnerable to anthropogenic activities and global climate changes than more widely distributed species. Despite the need for comprehensive genetic information for conservation and management, no such population genetic studies of S. polylepis have been conducted. In this study, genetic diversity and population structure were evaluated for 97 individuals from 5 populations (Gwanmaedo, Gageodo, Hongdo, Heusando, and Uido) using 19 polymorphic microsatellites. The populations were separated by a distance of 20–90 km. We found moderate levels of genetic diversity in S. polylepis (Ho = 0.42, He = 0.43). This may be due to long lifespans, outcrossing, and gene flow, despite its narrow range. High levels of gene flow (Nm = 1.76, mean Fst = 0.09), especially from wind-dispersed seeds, would contribute to low levels of genetic differentiation among populations. However, the small population size and reduced number of individuals in the reproductive phase of S. polylepis can be a major threat leading to inbreeding depression and genetic diversity loss. Bayesian cluster analysis revealed three significant structures at K = 3, consistent with DAPC and UPGMA. It is thought that sea level rise after the last glacial maximum may have acted as a geographical barrier, limiting the gene flow that would lead to distinct population structures. We proposed the Heuksando population, which is the largest island inhabited by S. polylepis, as a source population because of its large population size and high genetic diversity. Four management units (Gwanmaedo, Gageodo, Hongdo-Heuksando, and Uido) were suggested for conservation considering population size, genetic diversity, population structure, unique alleles, and geographical location (e.g., proximity).
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Affiliation(s)
- Seon A. Yun
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Gyeonggi-do, Korea
| | - Seung-Chul Kim
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Gyeonggi-do, Korea
- * E-mail: ,
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Senkoro AM, Talhinhas P, Simões F, Batista-Santos P, Shackleton CM, Voeks RA, Marques I, Ribeiro-Barros AI. The genetic legacy of fragmentation and overexploitation in the threatened medicinal African pepper-bark tree, Warburgia salutaris. Sci Rep 2020; 10:19725. [PMID: 33184322 PMCID: PMC7661512 DOI: 10.1038/s41598-020-76654-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 09/28/2020] [Indexed: 11/09/2022] Open
Abstract
The pepper-bark tree (Warburgia salutaris) is one of the most highly valued medicinal plant species worldwide. Native to southern Africa, this species has been extensively harvested for the bark, which is widely used in traditional health practices. Illegal harvesting coupled with habitat degradation has contributed to fragmentation of populations and a severe decline in its distribution. Even though the species is included in the IUCN Red List as Endangered, genetic data that would help conservation efforts and future re-introductions are absent. We therefore developed new molecular markers to understand patterns of genetic diversity, structure, and gene flow of W. salutaris in one of its most important areas of occurrence (Mozambique). In this study, we have shown that, despite fragmentation and overexploitation, this species maintains a relatively high level of genetic diversity supporting the existence of random mating. Two genetic groups were found corresponding to the northern and southern locations. Our study suggests that, if local extinctions occurred in Mozambique, the pepper-bark tree persisted in sufficient numbers to retain a large proportion of genetic diversity. Management plans should concentrate on maintaining this high level of genetic variability through both in and ex-situ conservation actions.
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Affiliation(s)
- Annae M Senkoro
- Department of Environmental Science, Rhodes University, Grahamstown, 6140, South Africa.,Departmento de Ciências Biológicas, Universidade Eduardo Mondlane CP 257, Maputo, Moçambique
| | - Pedro Talhinhas
- Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017, Lisbon, Portugal
| | - Fernanda Simões
- Instituto Nacional de Investigação Agrária E Veterinária, Av. da República, Quinta Marquês, Edificio Sede, 2780-157, Oeiras, Portugal
| | - Paula Batista-Santos
- Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017, Lisbon, Portugal
| | - Charlie M Shackleton
- Department of Environmental Science, Rhodes University, Grahamstown, 6140, South Africa
| | - Robert A Voeks
- Department of Geography and the Environment, California State University, 800 N State College Blvd, FullertonFullerton, CA, 92831, USA
| | - Isabel Marques
- Forest Research Centre (CEF), Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017, Lisbon, Portugal.
| | - Ana I Ribeiro-Barros
- Forest Research Centre (CEF), Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017, Lisbon, Portugal.
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Liu D, Zhang L, Wang J, Ma Y. Conservation Genomics of a Threatened Rhododendron: Contrasting Patterns of Population Structure Revealed From Neutral and Selected SNPs. Front Genet 2020; 11:757. [PMID: 33101354 PMCID: PMC7500208 DOI: 10.3389/fgene.2020.00757] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 06/25/2020] [Indexed: 12/13/2022] Open
Abstract
Though it is well-acknowledged that next generation sequencing (NGS) technologies can provide further insights into plant conservation management than traditional molecular markers, studies employing NGS to address conservation genomics and subsequent conservation strategies for threatened plants are still rare. Rhododendron is the largest genus of woody plants in China, and many species are threatened, however, to date there has been no conservation genetic research using NGS in this genus. In the present study, we investigated the conservation genetics of R. cyanocarpum, a threatened species endemic to the Cangshan Mountains in Yunnan, China, using a double digest restriction-site-associated DNA-sequencing (ddRAD-seq) approach. Due to the availability of sufficient SNPs, we were able to distinguish between neutral and putatively selected SNPs and were able to further investigate the genetic diversity, population structure, and differentiation in R. cyanocarpum, as well as make an estimation of its demographic history. A total of 6,584 SNPs were obtained, of which 5,729 were neutral (detected using Tajima’s D). In terms of the 5,729 neutral SNPs, R. cyanocarpum had a higher genetic diversity (π = 0.0702 ± 0.0017, He = 0.0675 ± 0.0016) than other plant species assessed using Rad-seq methods, while population differentiation (Fst from 0.0314 to 0.0452) was weak. Interestingly, contrasting patterns of population structure were revealed from all neutral and selected SNPs, with distinct genetic clusters forming for all SNPs and neutral SNPs, but no distinct subgroups for selected ones. Moreover, we were able to detect changes in effective population size (Ne) of R. cyanocarpum from 150,000 years ago, including a bottleneck event ca. 60,000 years ago, followed by recovery of Ne over a short period, and a subsequent gradual decline in Ne to date. Implications for conserving R. cyanocarpum based on these main results are then discussed.
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Affiliation(s)
- Detuan Liu
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Lu Zhang
- Flower Research Institute, Yunnan Academy of Agriculture Sciences, Kunming, China
| | - Jihua Wang
- Flower Research Institute, Yunnan Academy of Agriculture Sciences, Kunming, China
| | - Yongpeng Ma
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
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10
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Stathi E, Kougioumoutzis K, Abraham EM, Trigas P, Ganopoulos I, Avramidou EV, Tani E. Population genetic variability and distribution of the endangered Greek endemic Cicer graecum under climate change scenarios. AOB PLANTS 2020; 12:plaa007. [PMID: 32257090 PMCID: PMC7102496 DOI: 10.1093/aobpla/plaa007] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 02/10/2020] [Indexed: 06/11/2023]
Abstract
The Mediterranean hot spot includes numerous endemic and socio-economically important plant species seriously threatened by climate change and habitat loss. In this study, the genetic diversity of five populations of Cicer graecum, an endangered endemic species from northern Peloponnisos, Greece and a wild relative of the cultivated Cicer arietinum, was investigated using inter-simple sequence repeats (ISSRs) and amplified fragment length polymorphism (AFLP) markers in order to determine levels and structure of genetic variability. Nei's gene diversity by ISSR and AFLP markers indicated medium to high genetic diversity at the population level. Moreover, AMOVA results suggest that most of the variation exists within (93 % for AFLPs and 65 % for ISSRs), rather than among populations. Furthermore, Principal Component Analysis based on ISSRs positively correlated the genetic differentiation among the populations to the geographic distances, suggesting that the gene flow among distant populations is limited. The ecological adaptation of C. graecum populations was also investigated by correlation of their genetic diversity with certain environmental variables. Aridity arose as the dominant factor positively affecting the genetic diversity of C. graecum populations. We modelled the realized climatic niche of C. graecum in an ensemble forecasting scheme under three different global circulation models and two climate change scenarios. In all cases, a severe range contraction for C. graecum is projected, highlighting the high extinction risk that is probably going to face during the coming decades. These results could be a valuable tool towards the implementation of an integrated in situ and ex situ conservation scheme approach for activating management programmes for this endemic and threatened species.
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Affiliation(s)
- Efthalia Stathi
- Department of Crop Science, Laboratory of Plant Breeding and Biometry, Agricultural University of Athens, Iera Odos, Athens, Greece
| | - Konstantinos Kougioumoutzis
- Department of Crop Science, Laboratory of Systematic Botany, Agricultural University of Athens, Iera Odos, Athens, Greece
| | - Eleni M Abraham
- Laboratory of Range Science, School of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Panayiotis Trigas
- Department of Crop Science, Laboratory of Systematic Botany, Agricultural University of Athens, Iera Odos, Athens, Greece
| | - Ioannis Ganopoulos
- Institute of Plant Breeding and Genetic Resources, HAO-DEMETER, Thermi, Thessaloniki, Greece
| | - Evangelia V Avramidou
- Laboratory of Forest Genetics and Biotechnology, Institute of Mediterranean Forest Ecosystems, Athens, HAO “DEMETER”, Terma Alkmanos, Ilisia, Athens, Greece
| | - Eleni Tani
- Department of Crop Science, Laboratory of Plant Breeding and Biometry, Agricultural University of Athens, Iera Odos, Athens, Greece
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Jha SR, Naz R, Asif A, Okla MK, Soufan W, Al-Ghamdi AA, Ahmad A. Development of an In Vitro Propagation Protocol and a Sequence Characterized Amplified Region (SCAR) Marker of Viola serpens Wall. ex Ging. PLANTS 2020; 9:plants9020246. [PMID: 32074984 PMCID: PMC7076368 DOI: 10.3390/plants9020246] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 01/30/2020] [Accepted: 02/10/2020] [Indexed: 11/22/2022]
Abstract
An efficient protocol of plant regeneration through indirect organogenesis in Viola serpens was developed in the present study. Culture of leaf explants on MS (Murashige and Skoog) medium supplemented with 2.0 mg/L 6-benzyladenine and 0.13 mg/L 2,4-dichloro phenoxy acetic acid. Adventitious shoot formation was observed when calli were transferred on to MS medium containing 0.5 mg/L α-naphthalene acetic acid and 2.25 mg/L kinetin, which showed the maximum 86% shoot regeneration frequency. The highest root frequency (80.92%) with the 5.6 roots per explant and 1.87 cm root length was observed on MS medium supplemented with 2 mg/L indole-3-butyric acid. The plantlets were transferred to the mixture of sand, coffee husk and soil in the ratio of 1:2:1 in a pot, and placed under 80% shade net for one month. It was then transferred to 30% shade net for another one month, prior to transplantation in the field. These plantlets successfully acclimatized under field conditions. A Sequence Characterized Amplified Region (SCAR) marker was also developed using a 1135 bp amplicon that was obtained from RAPD (Random Amplification of Polymorphic DNA) analysis of six accessions of V. serpens. Testing of several market samples of V. serpens using the SCAR marker revealed successful identification of the genuine samples of V. serpens. This study, therefore, provides a proficient in vitro propagation protocol of V. serpens using leaf explants and a SCAR marker for the authentic identification of V. serpens. This study will be helpful for conservation of authentic V. serpens.
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Affiliation(s)
- Shipra Rani Jha
- Department of Botany, Jamia Hamdard, New Delhi 110062, India;
| | - Ruphi Naz
- Department of Botany, Aligarh Muslim University, Aligarh 202002, India; (R.N.); (A.A.)
| | - Ambreen Asif
- Department of Botany, Aligarh Muslim University, Aligarh 202002, India; (R.N.); (A.A.)
| | - Mohammad K. Okla
- Botany and Microbiology Department, College of Science, King Saud University, P.O. Box. 2460, Riyadh 11451, Saudi Arabia; (M.K.O.); (A.A.A.-G.)
| | - Walid Soufan
- Plant Production Department, Faculty of Food and Agricultural Sciences, King Saud University, P.O. Box 2460, Riyadh 11451, Saudi Arabia;
| | - Abdullah A. Al-Ghamdi
- Botany and Microbiology Department, College of Science, King Saud University, P.O. Box. 2460, Riyadh 11451, Saudi Arabia; (M.K.O.); (A.A.A.-G.)
| | - Altaf Ahmad
- Department of Botany, Aligarh Muslim University, Aligarh 202002, India; (R.N.); (A.A.)
- Correspondence:
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Yang S, Xue S, Kang W, Qian Z, Yi Z. Genetic diversity and population structure of Miscanthus lutarioriparius, an endemic plant of China. PLoS One 2019; 14:e0211471. [PMID: 30707722 PMCID: PMC6358086 DOI: 10.1371/journal.pone.0211471] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2018] [Accepted: 01/15/2019] [Indexed: 11/19/2022] Open
Abstract
Miscanthus lutarioriparius is a native perennial Miscanthus species of China, which is currently used as raw material of papermaking and bioenergy crop. It also has been considered as a promising eco-bioindustrial plant, which can offer raw material and gene for the biomass industry. However, lack of germplasm resources and genetic diversity information of M. lutarioriparius have become the bottleneck that prevents the stable and further development of the biomass industry. In the present study, genetic diversity of 153 M. lutarioriparius individuals nine populations was studied using 27 Start Codon Targeted (SCoT) markers. High polymorphic bands (97.67%), polymorphic information content (0.26) and allele number (1.88) showed SCoT as a reliable marker system for genetic analysis in M. lutarioriparius. At the species, the percentage of polymorphic loci [PPL] was 97.2%, Nei's gene diversity [H] was 0.36, Shannon index [I] was 0.54 and Expected Heterozygosity [He] was 0.56. Genetic variation within populations (84.91%) was higher than among populations (15.09%) based on analysis of molecular variance (AMOVA). Moderate level of genetic differentiation was found in M. lutarioriparius populations (Fst = 0.15), which is further confirmed by STRUCTURE, principal coordinates analysis (PCoA) and an unweighted pair group method with arithmetic mean (UPGMA) analysis that could reveal a clear separation between groups of the north and south of Yangtze River. The gene flow of the populations within the respective south and north of Yangtze River area was higher, but lower between the areas. There was no obvious correlation between genetic distance and geographic distance. The breeding systems, geographical isolation and fragmented habitat of M. lutarioriparius may be due to the high level of genetic diversity, moderate genetic differentiation, and the population, structure. The study further suggests some measure for conservation of genetic resources and provides the genetic basis for improving the efficiency of breeding based on the results of diversity analysis.
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Affiliation(s)
- Sai Yang
- College of Bioscience & Biotechnology, Hunan Agricultural University, Changsha, Hunan, China
- Orient Science & Technology College of Hunan Agricultural University, Changsha, Hunan, China
| | - Shuai Xue
- College of Bioscience & Biotechnology, Hunan Agricultural University, Changsha, Hunan, China
| | - Weiwei Kang
- College of Bioscience & Biotechnology, Hunan Agricultural University, Changsha, Hunan, China
| | - Zhuxi Qian
- Orient Science & Technology College of Hunan Agricultural University, Changsha, Hunan, China
| | - Zili Yi
- College of Bioscience & Biotechnology, Hunan Agricultural University, Changsha, Hunan, China
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13
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Veltjen E, Asselman P, Hernández Rodríguez M, Palmarola Bejerano A, Testé Lozano E, González Torres LR, Goetghebeur P, Larridon I, Samain MS. Genetic patterns in Neotropical Magnolias (Magnoliaceae) using de novo developed microsatellite markers. Heredity (Edinb) 2018; 122:485-500. [PMID: 30368529 PMCID: PMC6460770 DOI: 10.1038/s41437-018-0151-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 09/01/2018] [Accepted: 09/05/2018] [Indexed: 12/24/2022] Open
Abstract
Conserving tree populations safeguards forests since they represent key elements of the ecosystem. The genetic characteristics underlying the evolutionary success of the tree growth form: high genetic diversity, extensive gene flow and strong species integrity, contribute to their survival in terms of adaptability. However, different biological and landscape contexts challenge these characteristics. This study employs 63 de novo developed microsatellite or SSR (Single Sequence Repeat) markers in different datasets of nine Neotropical Magnolia species. The genetic patterns of these protogynous, insect-pollinated tree species occurring in fragmented, highly-disturbed landscapes were investigated. Datasets containing a total of 340 individuals were tested for their genetic structure and degree of inbreeding. Analyses for genetic structure depicted structuring between species, i.e. strong species integrity. Within the species, all but one population pair were considered moderate to highly differentiated, i.e. no indication of extensive gene flow between populations. No overall correlation was observed between genetic and geographic distance of the pairwise species’ populations. In contrast to the pronounced genetic structure, there was no evidence of inbreeding within the populations, suggesting mechanisms favouring cross pollination and/or selection for more genetically diverse, heterozygous offspring. In conclusion, the data illustrate that the Neotropical Magnolias in the context of a fragmented landscape still have ample gene flow within populations, yet little gene flow between populations.
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Affiliation(s)
- Emily Veltjen
- Research Group Spermatophytes, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, Gent, 9000, Belgium.
| | - Pieter Asselman
- Research Group Spermatophytes, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, Gent, 9000, Belgium.,Botanic Garden Meise, Nieuwelaan 38, Meise, 1860, Belgium
| | - Majela Hernández Rodríguez
- Departamento de Biología Vegetal, Facultad de Biología, Universidad de La Habana, C/ 25 e/ I y J, Vedado, La Habana, Cuba
| | - Alejandro Palmarola Bejerano
- Grupo de Ecología y Conservación, Jardín Botánico Nacional, Universidad de La Habana, Carretera "El Rocio" km 3 ½, Boyeros, La Habana, Cuba
| | - Ernesto Testé Lozano
- Departamento de Biología Vegetal, Facultad de Biología, Universidad de La Habana, C/ 25 e/ I y J, Vedado, La Habana, Cuba
| | | | - Paul Goetghebeur
- Research Group Spermatophytes, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, Gent, 9000, Belgium
| | - Isabel Larridon
- Research Group Spermatophytes, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, Gent, 9000, Belgium.,Royal Botanic Gardens, Kew, Surrey, Richmond, TW9 3AE, UK
| | - Marie-Stéphanie Samain
- Research Group Spermatophytes, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, Gent, 9000, Belgium.,Red de Diversidad Biológica del Occidente Mexicano, Instituto de Ecología, A.C., Avenida Lázaro Cárdenas 253, Pátzcuaro, Michoacán, 61600, Mexico
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14
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Genetic survey on a reed-bed in Central Italy showing early die-back symptoms. Biologia (Bratisl) 2018. [DOI: 10.2478/s11756-018-0096-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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15
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von Kohn C, Conrad K, Kramer M, Pooler M. Genetic diversity of Magnolia ashei characterized by SSR markers. CONSERV GENET 2018. [DOI: 10.1007/s10592-018-1065-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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16
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De Novo Transcriptome Assembly and Population Genetic Analyses for an Endangered Chinese Endemic Acer miaotaiense (Aceraceae). Genes (Basel) 2018; 9:genes9080378. [PMID: 30060522 PMCID: PMC6115825 DOI: 10.3390/genes9080378] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 07/23/2018] [Accepted: 07/24/2018] [Indexed: 12/17/2022] Open
Abstract
Acer miaotaiense (P. C. Tsoong) is a rare and highly endangered plant in China. Because of the lack of genomic information and the limited number of available molecular markers, there are insufficient tools to determine the genetic diversity of this species. Here, 93,305 unigenes were obtained by multiple assembled contigs with a transcriptome sequencing program. Furthermore, 12,819 expressed sequence tag-derived simple sequence repeat (EST-SSR) markers were generated, 300 were randomly selected and synthesized, 19 primer pairs were identified as highly polymorphic (average number of alleles (Na) = 8, expected heterozygosity (He) = 0.635, polymorphism information content (PIC) = 0.604) and were further used for population genetic analysis. All 261 samples were grouped into two genetic clusters by UPGMA, a principal component analyses and a STRUCTURE analyses. A moderate level of genetic differentiation (genetic differentiation index (Fst) = 0.059–0.116, gene flow = 1.904–3.993) among the populations and the major genetic variance (81.01%) within populations were revealed by the AMOVA. Based on the results, scientific conservation strategies should be established using in situ and ex situ conservation strategies. The study provides useful genetic information for the protection of precious wild resources and for further research on the origin and evolution of this endangered plant and its related species.
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17
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Mohammad N, Dahayat A, Yadav M, Shirin F, Ansari SA. Genetic diversity and population structure of Litsea glutinosa (Lour.) in Central India. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2018; 24:655-663. [PMID: 30042620 PMCID: PMC6041236 DOI: 10.1007/s12298-018-0556-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 03/27/2018] [Accepted: 05/21/2018] [Indexed: 06/08/2023]
Abstract
Litsea glutinosa (Lour.), one of the most dwindling forest species in central India, is represented by highly fragmented populations that have been drastically reduced for the last 40 years, promulgating government ban on its extraction. For the first time with the help of ISSR markers, we investigated genetic variation and population structure of L. glutinosa in central Indian states. A total of 84 genotypes from 10 populations covering the entire potential pockets of the species in central India were collected. The percentage of polymorphic loci ranged from 44.79% (Rewa) to 94.79% (Marvahi) with a mean value of 70.10%. The sampled populations harbored high level of genetic diversity (mean h = 0.294 and I = 0.424) that was partitioned more within populations (73%) than between populations (27%). Bayesian structure analysis revealed the existence of four admixed genetic pools in L. glutinosa. The unsustainable extraction rather than genetic factor seems to be responsible for population fragmentation and dwindling status of this species. The dioecious nature of the species advocates an in-situ conservation to be the most suited approach for which Chhindwara, Jagdalpur, Balaghat and Jabalpur populations are appropriate.
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Affiliation(s)
- Naseer Mohammad
- Tropical Forest Research Institute, Mandla Road, Jabalpur, Madhya Pradesh 482 021 India
| | - Ankur Dahayat
- Tropical Forest Research Institute, Mandla Road, Jabalpur, Madhya Pradesh 482 021 India
| | - Manorama Yadav
- Tropical Forest Research Institute, Mandla Road, Jabalpur, Madhya Pradesh 482 021 India
| | - Fatima Shirin
- Tropical Forest Research Institute, Mandla Road, Jabalpur, Madhya Pradesh 482 021 India
| | - S. A. Ansari
- Institute of Forest Productivity, Lalgutwa, Ranchi, Jharkhand 835 303 India
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18
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Peng YQ, Fan LL, Mao FY, Zhao YS, Xu R, Yin YJ, Chen X, Wan DG, Zhang XH. Genetic diversity and population structure of a protected species: Polygala tenuifolia Willd. C R Biol 2018; 341:152-159. [PMID: 29477283 DOI: 10.1016/j.crvi.2018.01.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 12/30/2017] [Accepted: 01/25/2018] [Indexed: 11/15/2022]
Abstract
Polygala tenuifolia Willd. is an important protected species used in traditional Chinese medicine. In the present study, amplified fragment length polymorphism (AFLP) markers were employed to characterize the genetic diversity in wild and cultivated P. tenuifolia populations. Twelve primer combinations of AFLP produced 310 unambiguous and repetitious bands. Among these bands, 261 (84.2%) were polymorphic. The genetic diversity was high at the species level: percentage of polymorphic loci (PPL)=84.2%, Nei's gene diversity (h)=0.3296 and Shannon's information index (I)=0.4822. Between the two populations, the genetic differentiation of 0.1250 was low and the gene flow was relatively high, at 3.4989. The wild population (PPL=81.9%, h=0.3154, I=0.4635) showed a higher genetic diversity level than the cultivated population (PPL=63.9%, h=0.2507, I=0.3688). The results suggest that the major factors threatening the persistence of P. tenuifolia resources are ecological and human factors rather than genetic. These results will assist with the design of conservation and management programs, such as in natural habitat conservation, setting the excavation time interval for resource regeneration and the substitution of cultivated for wild plants.
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Affiliation(s)
- Yan Qun Peng
- Ningxia Medical University Pharmacy College, 750004 Yinchuan, Ningxia, China; Ningxia Research Center of Modern Hui Medicine Engineering and Technology, 750004 Yinchuan, Ningxia, China.
| | - Ling Ling Fan
- Ningxia Medical University Pharmacy College, 750004 Yinchuan, Ningxia, China; Ningxia Research Center of Modern Hui Medicine Engineering and Technology, 750004 Yinchuan, Ningxia, China.
| | - Fu Ying Mao
- Ningxia Medical University Pharmacy College, 750004 Yinchuan, Ningxia, China; Ningxia Research Center of Modern Hui Medicine Engineering and Technology, 750004 Yinchuan, Ningxia, China.
| | - Yun Sheng Zhao
- Ningxia Medical University Pharmacy College, 750004 Yinchuan, Ningxia, China; Ningxia Research Center of Modern Hui Medicine Engineering and Technology, 750004 Yinchuan, Ningxia, China; Ministry of Education Key Laboratory of Modern Hui Chinese Medicine, 750004 Yinchuan, Ningxia, China.
| | - Rui Xu
- Ningxia Medical University Pharmacy College, 750004 Yinchuan, Ningxia, China; Ningxia Research Center of Modern Hui Medicine Engineering and Technology, 750004 Yinchuan, Ningxia, China.
| | - Yu Jie Yin
- Ningxia Medical University Pharmacy College, 750004 Yinchuan, Ningxia, China; Ningxia Research Center of Modern Hui Medicine Engineering and Technology, 750004 Yinchuan, Ningxia, China.
| | - Xin Chen
- School of Pharmacy, Chengdu University of TCM, 611137 Chengdu, Sichuan, China.
| | - De Guang Wan
- School of Pharmacy, Chengdu University of TCM, 611137 Chengdu, Sichuan, China.
| | - Xin Hui Zhang
- Ningxia Medical University Pharmacy College, 750004 Yinchuan, Ningxia, China; Ningxia Research Center of Modern Hui Medicine Engineering and Technology, 750004 Yinchuan, Ningxia, China.
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19
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Zhang X, Shen S, Wu F, Wang Y. Inferring Genetic Variation and Demographic History of Michelia yunnanensis Franch. (Magnoliaceae) from Chloroplast DNA Sequences and Microsatellite Markers. FRONTIERS IN PLANT SCIENCE 2017; 8:583. [PMID: 28484472 PMCID: PMC5399939 DOI: 10.3389/fpls.2017.00583] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 03/31/2017] [Indexed: 06/07/2023]
Abstract
Michelia yunnanensis Franch., is a traditional ornamental, aromatic, and medicinal shrub that endemic to Yunnan Province in southwest China. Although the species has a large distribution pattern and is abundant in Yunnan Province, the populations are dramatically declining because of overexploitation and habitat destruction. Studies on the genetic variation and demography of endemic species are necessary to develop effective conservation and management strategies. To generate such knowledge, we used 3 pairs of universal cpDNA markers and 10 pairs of microsatellite markers to assess the genetic diversity, genetic structure, and demographic history of 7 M. yunnanensis populations. We calculated a total of 88 alleles for 10 polymorphic loci and 10 haplotypes for a combined 2,089 bp of cpDNA. M. yunnanensis populations showed high genetic diversity (Ho = 0.551 for nuclear markers and Hd = 0.471 for cpDNA markers) and low genetic differentiation (FST = 0.058). Geographical structure was not found among M. yunnanensis populations. Genetic distance and geographic distance were not correlated (P > 0.05), which indicated that geographic isolation is not the primary cause of the low genetic differentiation of M. yunnanensis. Additionally, M. yunnanensis populations contracted ~20,000-30,000 years ago, and no recent expansion occurred in current populations. Results indicated that the high genetic diversity of the species and within its populations holds promise for effective genetic resource management and sustainable utilization. Thus, we suggest that the conservation and management of M. yunnanensis should address exotic overexploitation and habitat destruction.
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Affiliation(s)
- Xue Zhang
- School of Life Sciences, Yunnan UniversityYunnan, China
| | - Shikang Shen
- School of Life Sciences, Yunnan UniversityYunnan, China
| | - Fuqin Wu
- Yunnan Research and Monitoring Center of Nature Reserve, Yunnan Institute for Forest Inventory and PlanningKunming, China
| | - Yuehua Wang
- School of Life Sciences, Yunnan UniversityYunnan, China
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20
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Chen C, Lu RS, Zhu SS, Tamaki I, Qiu YX. Population structure and historical demography of Dipteronia dyeriana (Sapindaceae), an extremely narrow palaeoendemic plant from China: implications for conservation in a biodiversity hot spot. Heredity (Edinb) 2017; 119:95-106. [PMID: 28379211 DOI: 10.1038/hdy.2017.19] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 02/02/2017] [Accepted: 02/03/2017] [Indexed: 11/09/2022] Open
Abstract
Inferring past demography is a central question in evolutionary and conservation biology. It is, however, sometimes challenging to disentangle their roles of contemporary versus historical processes in shaping the current patterns of genetic variation in endangered species. In this study, we used both chloroplast microsatellite (cpSSR) loci and nuclear microsatellite (nSSR) loci to assess the levels of genetic differentiation, genetic effective population size, contemporary/historical levels of gene flow and demographic history for five populations sampled across the range of Dipteronia dyeriana, an endangered palaeoendemism from Southwestern China. We found that D. dyeriana had a mixed pattern of moderate genetic diversity and high inbreeding. Bayesian clustering divided D. dyeriana populations into two nSSR genetic clusters. Coalescent-based approximate Bayesian computation analyses suggest the western and eastern groups of D. dyeriana likely persisted in a long-term refuge in Southern China since the beginning of the last glacial period, whereas increasingly colder and arid climates at the onset of the last glacial maximum might have fostered the fragmentation of D. dyeriana within refugia. Following their divergence, the western group kept relatively stable effective population size, whereas the eastern group had experienced 500-fold population expansion during the Holocene. Although clear loss of genetic diversity by human activities was not suggested, recent habitat fragmentation has led to a reduction of population connectivity and increased genetic differentiation by ongoing genetic drift in isolated populations, possibly owing to decreased population size in recent dozen years. Finally, we discussed the implications of these results on conservation policies.
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Affiliation(s)
- C Chen
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and College of Life Sciences, Zhejiang University, Hangzhou, People's Republic of China.,College of Life Sciences, Nanjing Agricultural University, Nanjing, People's Republic of China
| | - R S Lu
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and College of Life Sciences, Zhejiang University, Hangzhou, People's Republic of China
| | - S S Zhu
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and College of Life Sciences, Zhejiang University, Hangzhou, People's Republic of China
| | - I Tamaki
- Gifu Academy of Forest Science and Culture, Mino, Japan
| | - Y X Qiu
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and College of Life Sciences, Zhejiang University, Hangzhou, People's Republic of China
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21
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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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22
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Dong W, Zhang X, Guansong Y, Yang L, Wang Y, Shen S. Biological characteristics and conservation genetics of the narrowly distributed rare plant Cinnamomum chago (Lauraceae). PLANT DIVERSITY 2016; 38:247-252. [PMID: 30159473 PMCID: PMC6112253 DOI: 10.1016/j.pld.2016.09.001] [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: 05/06/2016] [Revised: 08/31/2016] [Accepted: 09/02/2016] [Indexed: 06/08/2023]
Abstract
Cinnamomum chago (family Lauraceae) is an essential source of timber and oil. This plant is narrowly distributed in the western part of the Yunnan Province. In this study, the distribution, habitat, and biological characteristics of C. chago were examined through field investigation. The genetic diversity and the variation of the remnant populations were also studied using the inter-simple sequence repeat technique. Results showed that C. chago is mainly distributed in the upstream tributary mountains of Lancang River in Yunlong County of Yunnan Province. The species distribution exhibited a fragmented pattern with five isolated populations and high-frequency anthropogenic interference. A combination of morphological features (opposite leaves, pinnate leaf veins, absence of glandular fossa, large drupe, small punch, and pollen surface with triangular spike grain, with cushion bumps at the base) indicated that C. chago is a key phylogenetic taxon between the two sections of Asian Cinnamomum plants (Sect. Camphora (Trew) Meissn. and Sect. Cinnamomum). Analysis of the genetic diversity of C. chago indicated that it has a moderately high level of genetic diversity at the population and species levels (populations level: Ne = 1.629, H = 0.348, I = 0.504, and PPB = 83.3%; species level: Ne = 1.864, H = 0.460, I = 0.652, and PPB = 100%). Analysis of molecular variance revealed that 17% of the genetic variation was divided between the populations, whereas 83% was observed within the populations. Based on these results, we suggest the inclusion of C. chago in the Wild Plants with Extremely Small Populations in China. Moreover, the species should be given special attention and protection. Some strategies were proposed for the conservation of the C. chago populations.
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Affiliation(s)
| | | | | | | | - Yuehua Wang
- Corresponding author. School of Life Sciences, Yunnan University, No. 2 Green Lake North Road Kunming, Yunnan, 650091, People's Republic of China. Fax: +86 871 65031491.
| | - Shikang Shen
- Corresponding author. School of Life Sciences, Yunnan University, No. 2 Green Lake North Road Kunming, Yunnan, 650091, People's Republic of China. Fax: +86 871 65031491.
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23
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Li CY, Chiang TY, Chiang YC, Hsu HM, Ge XJ, Huang CC, Chen CT, Hung KH. Cross-Species, Amplifiable EST-SSR Markers for Amentotaxus Species Obtained by Next-Generation Sequencing. Molecules 2016; 21:67. [PMID: 26751439 PMCID: PMC6273106 DOI: 10.3390/molecules21010067] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 12/30/2015] [Accepted: 12/31/2015] [Indexed: 01/02/2023] Open
Abstract
Amentotaxus, a genus of Taxaceae, is an ancient lineage with six relic and endangered species. Four Amentotaxus species, namely A. argotaenia, A. formosana, A. yunnanensis, and A. poilanei, are considered a species complex because of their morphological similarities. Small populations of these species are allopatrically distributed in Asian forests. However, only a few codominant markers have been developed and applied to study population genetic structure of these endangered species. In this study, we developed and characterized polymorphic expressed sequence tag-simple sequence repeats (EST-SSRs) from the transcriptome of A. formosana. We identified 4955 putative EST-SSRs from 68,281 unigenes as potential molecular markers. Twenty-six EST-SSRs were selected for estimating polymorphism and transferability among Amentotaxus species, of which 23 EST-SSRs were polymorphic within Amentotaxus species. Among these, the number of alleles ranged from 1-4, the polymorphism information content ranged from 0.000-0.692, and the observed and expected heterozygosity were 0.000-1.000 and 0.080-0.740, respectively. Population genetic structure analyses confirmed that A. argotaenia and A. formosana were separate species and A. yunnanensis and A. poilanei were the same species. These novel EST-SSRs can facilitate further population genetic structure research of Amentotaxus species.
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Affiliation(s)
- Chiuan-Yu Li
- Taiwan Endemic Species Research Institute, Nantou 552, Taiwan.
- Graduate Institute of Bioresources, Pingtung University of Science and Technology, Pingtung 912, Taiwan.
| | - Tzen-Yuh Chiang
- Department of Life Sciences, National Cheng-Kung University, Tainan 701, Taiwan.
| | - Yu-Chung Chiang
- Department of Biological Sciences, National Sun Yat-sen University, Kaohsiung 804, Taiwan.
| | - Hsin-Mei Hsu
- Department of Forestry, Pingtung University of Science and Technology, Pingtung 912, Taiwan.
| | - Xue-Jun Ge
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.
| | | | - Chaur-Tzuhn Chen
- Department of Forestry, Pingtung University of Science and Technology, Pingtung 912, Taiwan.
| | - Kuo-Hsiang Hung
- Graduate Institute of Bioresources, Pingtung University of Science and Technology, Pingtung 912, Taiwan.
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24
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Mishra P, Kumar LD, Kumar A, Gokul S, Ravikumar K, Shukla AK, Sundaresan V. Population Dynamics and Conservation Implications of Decalepis arayalpathra (J. Joseph and V. Chandras.) Venter., a Steno Endemic Species of Western Ghats, India. Appl Biochem Biotechnol 2015; 176:1413-30. [DOI: 10.1007/s12010-015-1654-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Accepted: 04/27/2015] [Indexed: 10/23/2022]
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25
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Wu FQ, Shen SK, Zhang XJ, Wang YH, Sun WB. Genetic diversity and population structure of an extremely endangered species: the world's largest Rhododendron. AOB PLANTS 2014; 7:plu082. [PMID: 25477251 PMCID: PMC4294443 DOI: 10.1093/aobpla/plu082] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 11/18/2014] [Indexed: 05/29/2023]
Abstract
Comprehensive studies on the genetic diversity and structure of endangered species are urgently needed to promote effective conservation and management activities. The big tree rhododendron, Rhododendron protistum var. giganteum, is a highly endangered species with only two known endemic populations in a small area in the southern part of Yunnan Province in China. Unfortunately, limited information is available regarding the population genetics of this species. Therefore, we conducted amplified fragment length polymorphism (AFLP) analysis to characterize the genetic diversity and variation of this species within and between remaining populations. Twelve primer combinations of AFLP produced 447 unambiguous and repetitious bands. Among these bands, 298 (66.67 %) were polymorphic. We found high genetic diversity at the species level (percentage of polymorphic loci = 66.67 %, h = 0.240, I = 0.358) and low genetic differentiation (Gst = 0.110) between the two populations. Gene flow between populations (Nm) was relatively high at 4.065. Analysis of molecular variance results revealed that 22 % of the genetic variation was partitioned between populations and 78 % of the genetic variation was within populations. The presence of moderate to high genetic diversity and low genetic differentiation in the two populations can be explained by life history traits, pollen dispersal and high gene flow (Nm = 4.065). Bayesian structure and principal coordinate analysis revealed that 56 sampled trees were clustered into two groups. Our results suggest that some rare and endangered species are able to maintain high levels of genetic diversity even at small population sizes. These results will assist with the design of conservation and management programmes, such as in situ and ex situ conservation, seed collection for germplasm conservation and reintroduction.
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Affiliation(s)
- Fu Qin Wu
- Present address: School of Life Sciences, Yunnan University, Kunming No. 2, Green Lake North Road, Kunming, Yunnan 650091, The People's Republic of China
| | - Shi Kang Shen
- Present address: School of Life Sciences, Yunnan University, Kunming No. 2, Green Lake North Road, Kunming, Yunnan 650091, The People's Republic of China
| | - Xin Jun Zhang
- Present address: School of Life Sciences, Yunnan University, Kunming No. 2, Green Lake North Road, Kunming, Yunnan 650091, The People's Republic of China
| | - Yue Hua Wang
- Present address: School of Life Sciences, Yunnan University, Kunming No. 2, Green Lake North Road, Kunming, Yunnan 650091, The People's Republic of China
| | - Wei Bang Sun
- Kunming Botanical Garden, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, The People's Republic of China
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26
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Genetic diversity of endangered Manglietia patungensis assessed by inter simple sequence repeat and sequence-related amplified polymorphism markers. BIOCHEM SYST ECOL 2014. [DOI: 10.1016/j.bse.2014.08.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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27
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Highly differentiated populations of the narrow endemic and endangered species Primula cicutariifolia in China, revealed by ISSR and SSR. BIOCHEM SYST ECOL 2014. [DOI: 10.1016/j.bse.2013.12.025] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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28
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Qian X, Wang CX, Tian M. Genetic diversity and population differentiation of Calanthe tsoongiana, a rare and endemic orchid in China. Int J Mol Sci 2013; 14:20399-413. [PMID: 24129175 PMCID: PMC3821621 DOI: 10.3390/ijms141020399] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Revised: 09/24/2013] [Accepted: 09/25/2013] [Indexed: 11/16/2022] Open
Abstract
Calanthe tsoongiana is a rare terrestrial orchid endemic to China, and this species has experienced severe habitat loss and fragmentation. Inter-simple sequence repeat (ISSR) markers were employed to assess the genetic diversity and differentiation of six populations of C. tsoongiana. Based on 124 discernible fragments yielded by eleven selected primers, high genetic diversity was revealed at the species level; however, genetic diversity at the population level was relatively low. High-level genetic differentiation among populations was detected based on analysis of molecular variance (AMOVA), indicating potential limited gene flow. No significant relationship was observed between genetic and geographic distances among the sampled populations. These results suggested that restricted gene flow might be due to habitat fragmentation and reduced population size as a result of human activities. Based on the findings, several conservation strategies were proposed for the preservation of this threatened species.
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Affiliation(s)
- Xin Qian
- Research Institution of Subtropical Forestry, Chinese Academy of Forestry, 73, Daqiao Road, Fuyang 311400, Zhejiang, China.
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Liu J, Shi S, Chang E, Yang W, Jiang Z. Genetic diversity of the critically endangered Thuja sutchuenensis revealed by ISSR markers and the implications for conservation. Int J Mol Sci 2013; 14:14860-71. [PMID: 23863693 PMCID: PMC3742276 DOI: 10.3390/ijms140714860] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Revised: 07/02/2013] [Accepted: 07/02/2013] [Indexed: 11/16/2022] Open
Abstract
Thuja sutchuenensis Franch. is a critically endangered plant endemic to the North-East Chongqing, China. Genetic variation was studied to assess the distribution of genetic diversity within and among seven populations from the single remnant locations, using inter-simple sequence repeat (ISSR) markers. A total of 15 primers generated 310 well defined bands, with an average of 20.7 bands per primer. The seven populations revealed a relatively high level of genetic diversity in the species. The percentage of polymorphic bands, Nei’s gene diversity and Shannon’s information index at the population and species level were 76.1%, 0.155, 0.252 and 100%, 0.165, 0.295, respectively. A low level of genetic differentiation among populations (GST = 0.102), in line with the results of Analyses of Molecular Variance (AMOVA), and a high level of gene flow (Nm = 4.407) were observed. Both the Unweighted Pair Group Method with Arithmatic Mean (UPGMA) cluster analysis and Principal Coordinates Analysis (PCoA) supported the grouping of all seven populations into two groups. In addition, Mantel test revealed no significant correlation between genetic and geographical distances (r = 0.329, p = 0.100). The low genetic differentiation among populations implies that the conservation efforts should aim to preserve all the extant populations of this endangered species.
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Affiliation(s)
| | | | | | | | - Zeping Jiang
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +86-10-6288-9607; Fax: +86-10-6287-2015
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