Using Random Amplified Polymorphic DNA to Assess Genetic Diversity and Structure of NaturalCalophyllum brasiliense(Clusiaceae) Populations in Riparian Forests

The objective of this study was to assess the genetic variability in two natural populations ofCalophyllum brasilienselocated along two different rivers in the state of Minas Gerais, Brazil, using RAPD molecular markers. Eighty-two polymorphic fragments were amplified using 27 primers. The values obtained for Shannon index (I) were 0.513 and 0.530 for the populations located on the margins of the Rio Grande and Rio das Mortes, respectively, demonstrating the high genetic diversity in the studied populations. Nei’s genetic diversity (He) was 0.341 for the Rio Grande population and 0.357 for the Rio das Mortes population. These results were not significantly different between populations and suggest a large proportion of heterozygote individuals within both populations. AMOVA showed that 70.42% of the genetic variability is found within populations and 29.58% is found among populations (ФST=0.2958). The analysis of kinship coefficients detected the existence of family structures in both populations. Average kinship coefficients between neighboring individuals were 0.053 (P<0.001) in Rio das Mortes and 0.040 (P<0.001) in Rio Grande. This could be due to restricted pollen and seed dispersal and the history of anthropogenic disturbance in the area. These factors are likely to contribute to the relatedness observed among these genotypes.

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Population genetics of the freshwater fish Prochilodus magdalenae (Characiformes: Prochilodontidae), using species-specific microsatellite loci

PeerJ ◽

10.7717/peerj.10327 ◽

2020 ◽

Vol 8 ◽

pp. e10327

Author(s):

Ricardo M. Landínez-García ◽

Juan Carlos Narváez ◽

Edna J. Márquez

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Freshwater Fish ◽

Microsatellite Loci ◽

Natural Populations ◽

Genetic Stock ◽

High Genetic Diversity ◽

Genetic Diversity And Structure ◽

Genetic Stocks ◽

Species Specific

Prochilodus magdalenae is a freshwater fish endemic to the Colombian Magdalena-Cauca and Caribbean hydrographic basins. The genetic structure patterns of populations of different members of Prochilodus and the historic restocking of its depleted natural populations suggest that P. magdalenae exhibits genetic stocks that coexist and co-migrate throughout the rivers Magdalena, Cauca, Cesar, Sinú and Atrato. To test this hypothesis and explore the levels of genetic diversity and population demography of 725 samples of P. magdalenae from the studied rivers, we developed a set of 11 species-specific microsatellite loci using next-generation sequencing, bioinformatics, and experimental tests of the levels of diversity of the microsatellite loci. The results evidenced that P. magdalenae exhibits high genetic diversity, significant inbreeding coefficient ranging from 0.162 to 0.202, and signs of erosion of the genetic pool. Additionally, the population genetic structure constitutes a mixture of genetic stocks heterogeneously distributed along the studied rivers, and moreover, a highly divergent genetic stock was detected in Chucurí, Puerto Berrío and Palagua that may result from restocking practices. This study provides molecular tools and a wide framework regarding the genetic diversity and structure of P. magdalenae, which is crucial to complement its baseline information, diagnosis and monitoring of populations, and to support the implementation of adequate regulation, management, and conservation policies.

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Conservation of Billbergia zebrina genetic resources: AFLP polymorphism of in vitro regenerated genotypes

Plant Genetic Resources ◽

10.1017/s1479262111000918 ◽

2011 ◽

Vol 10 (1) ◽

pp. 20-23 ◽

Cited By ~ 1

Author(s):

Lirio L. Dal Vesco ◽

Valdir M. Stefenon ◽

Leocir J. Welter ◽

Neusa Steiner ◽

Miguel P. Guerra

Keyword(s):

Genetic Diversity ◽

Genetic Resources ◽

Gene Diversity ◽

Plant Genetic Resources ◽

Natural Populations ◽

Shannon Index ◽

Aflp Markers ◽

High Genetic Diversity ◽

Index Of Diversity

Biotechnological techniques comprise useful tools for the conservation of endangered plant genetic resources. In the present work, polymorphism and usefulness of amplified fragment length polymorphism (AFLP) markers in assessing the genetic diversity in populations of Billbergia zebrina were investigated in nodular cultures and adult plants of the species. AFLP markers revealed moderate-to-high genetic diversity based on the estimations of Nei's gene diversity (mean He = 0.28), Shannon index of diversity (mean HS = 0.48) and the number of polymorphic fragments (mean of 56.17 polymorphic fragments over six primer pairs). In comparison to published studies of population genetics performed in other bromeliad species, the present study suggests that natural populations of B. zebrina likely maintain high levels of genetic diversity, an important feature towards conservation of plant genetic resources. The results obtained reveal that AFLP markers comprise a powerful tool in order to assess the levels of genetic diversity in natural populations of this endangered species. Integrating AFLP markers with in vitro propagation techniques is understood as an adequate strategy for conservation programmes of this species.

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Genetic diversity and structure among natural populations of Mytilaria laosensis (Hamamelidaceae) revealed by microsatellite markers

Silvae Genetica ◽

10.2478/sg-2018-0013 ◽

2018 ◽

Vol 67 (1) ◽

pp. 93-98 ◽

Cited By ~ 1

Author(s):

Niu Yu ◽

Jie Yuan ◽

Guangtian Yin ◽

Jinchang Yang ◽

Rongsheng Li ◽

...

Keyword(s):

Genetic Diversity ◽

Geographic Distance ◽

Natural Populations ◽

Magnetic Bead ◽

Mantel Test ◽

High Genetic Diversity ◽

Information Index ◽

Genetic Diversity And Structure ◽

High Level ◽

Mytilaria Laosensis

Abstract Mytilaria laosensis is a fast-growing tropical broadleaf tree that is extensively used for wood production and has significant ecological benefits. To investigate the genetic diversity and population structure of M. laosensis, eight major natural populations in China were analyzed by using simple sequence repeat (SSR) markers. A total of 88 microsatellite-containing fragments were obtained by the method of magnetic bead enrichment, among which 26 pairs of SSR primers were screened out and used to generate a total of 190 alleles among 152 individuals. The average of observed number of alleles, Shannon’s information index and polymorphism information content per locus were 18.3, 1.1577 and 0.7759, respectively, implying a high level of genetic diversity in M. laosensis populations. The variation within populations accounted for 81.74 % of total variation based on analysis of molecular variance. Cluster analysis divided the eight populations into four groups, among which five populations from the southern parts of Guangxi province were classified as one major group. Mantel test showed that there was highly significant correlation between Euclidean genetic distance and geographic distance, suggesting that geographic isolation contribute to the high genetic diversity of M. laosensis. Together, these could provide support for the feasibility of exploration and utilization of M. laosensis in subtropical areas of East Asia including Jiangxi, Hunan and Fujian province of China.

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CONTRASTING LEVELS OF GENETIC DIVERSITY AMONG POPULATIONS OF THE ENDANGERED TROPICAL PALM EUTERPE EDULIS MARTIUS

CERNE ◽

10.1590/01047760201723012237 ◽

2017 ◽

Vol 23 (1) ◽

pp. 31-42 ◽

Cited By ~ 3

Author(s):

Enéas Ricardo Konzen ◽

Maisa Pimentel Martins

Keyword(s):

Genetic Diversity ◽

Genetic Variability ◽

Natural Populations ◽

Tropical Species ◽

Isozyme Markers ◽

Euterpe Edulis ◽

Dense Forest ◽

Genetic Diversity And Structure ◽

Euterpe Edulis Martius ◽

Structure Patterns

ABSTRACT Euterpe edulis is a tropical species that produces the heart of palm, an edible product of high economic importance. However, its natural populations have been severely threatened by unrestricted exploitation, along with the destruction of its natural biome, the Atlantic Rainforest in Brazil. In this work, we examined the genetic diversity status of five natural populations using isozyme markers. Despite their limitations and replacement by DNA-based markers, isozymes are codominant markers that reveal accurate estimates of genetic diversity and structure patterns, as do microsatellites. Six informative isozyme markers were used to analyze the genetic variability of populations located in different areas of the Atlantic Forest (Ombrophilous Dense Forest and Seasonal Forest), and with different degrees of perturbation. Mean genetic diversity for all populations (Ho = 0.172, for 13 loci) was considered low for a tropical species, even for the markers used. Populations from Ombrophilous Dense Forest at the very South limit of distribution of the heart of palm presented the lowest genetic variability (Ho = 0.141), which is clearly observed from the allele frequencies, and might implicate in less adaptive potential in a scenario of climate change. On the contrary, the Seasonal Forest population presented the highest diversity (Ho = 0.237). It comprises one of the largest remaining reservoirs of heart of palm and maybe of its genetic variability. The contrasting levels of genetic diversity encountered in this study rehash the constant need of monitoring and conserving the current genetic diversity of E. edulis populations, as well as exploring strategies for its breeding.

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Genetic diversity and fragmentation of Aspidosperma quebracho-blanco (Apocynaceae) natural habitats, conservation issues in Chaco forest and savanna biomes

Darwiniana nueva serie ◽

10.14522/darwiniana.2021.91.932 ◽

2021 ◽

Vol 9 (1) ◽

pp. 115-129

Author(s):

Thomáz S. Guerreiro Botelho ◽

Gecele Matos Paggi ◽

Maria Ana Farinaccio

Keyword(s):

Genetic Diversity ◽

Polymorphic Information Content ◽

Natural Habitat ◽

Mantel Test ◽

Shannon Index ◽

Conservation Strategies ◽

Conservation Units ◽

Natural Habitats ◽

High Genetic Diversity ◽

Genetic Diversity And Structure

The present study analyses the first data on genetic diversity of A. quebracho-blanco with the fragmentation of its natural habitat, supporting conservation strategies such as the definition of priority areas for conservation. DNA was extracted from 25 individuals of five populations of A. quebracho-blanco from Argentina, Paraguay, and Brazil. Six ISSR primers were used to characterize the genetic diversity and structure of this species. The genotypes were grouped according to a distance matrix, considering the genetic diversity indices of Nei (He), Shannon (H’), polymorphic information content (PIC), and heterozygosis (H). The populations showed an average genetic diversity that ranged from 0.09 to 0.15 for the Shannon index and from 0.19 to 0.31 for the Nei index; the Mantel test was not significant (r2 = 0.25, P = 0.106). The results obteined for the sampled populations reveal that conservation units are indispensable for conserving the species genetic resources. In addition, it would be essential to construct a germplasm bank for the Cordoba (Argentina) population, which is a population with high genetic diversity in a region of lower fragmentation compared to other regions evaluated, to ensure the conservation of A. quebracho-blanco.

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Detection of genetic diversity in tea (Camellia sinensis) using RAPD markers

Genome ◽

10.1139/g95-025 ◽

1995 ◽

Vol 38 (2) ◽

pp. 201-210 ◽

Cited By ~ 89

Author(s):

F. N. Wachira ◽

R. Waugh ◽

W. Powell ◽

C. A. Hackett

Keyword(s):

Genetic Diversity ◽

Genetic Variability ◽

Southeast Asia ◽

Camellia Sinensis ◽

Rapd Markers ◽

Rapd Analysis ◽

Random Amplified Polymorphic Dna ◽

Systematic Assessment ◽

Tree Crop ◽

Taxonomic Relationships

Camellia sinensis is a beverage tree crop native to Southeast Asia and introductions have been made into several nonindigenous countries. No systematic assessment of genetic variability in tea has been done anywhere. In this study, random amplified polymorphic DNA (RAPD) analysis was used to estimate genetic diversity and taxonomic relationships in 38 clones belonging to the three tea varieties, assamica, sinensis, and assamica ssp. lasiocalyx. Extensive genetic variability was detected between species, which was partitioned into between and within population components. Seventy percent of the variation was detected within populations. Analyses based on band sharing separated the three populations in a manner consistent with both the present taxonomy of tea and with the known pedigrees of some clones. RAPD analysis also discriminated all of the 38 commercial clones, even those which cannot be distinguished on the basis of morphological and phenotypic traits.Key words: genetic diversity, RAPDs, Camellia sinensis.

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Genetic variability in the natural populations of Lasioderma serricorne (F.) (Coleoptera: Anobiidae), detected by RAPD markers and by esterase isozymes

Bulletin of Entomological Research ◽

10.1017/s0007485315000723 ◽

2015 ◽

Vol 106 (1) ◽

pp. 47-53 ◽

Cited By ~ 4

Author(s):

T. Coelho-Bortolo ◽

C.A. Mangolin ◽

A.S. Lapenta

Keyword(s):

Genetic Variability ◽

Random Amplified Polymorphic Dna ◽

Natural Populations ◽

Electrophoretic Analysis ◽

Effective Control ◽

Lasioderma Serricorne ◽

Control Programs ◽

Dried Fruit ◽

High Level ◽

High Degree

AbstractLasioderma serricorne (F.) is a small cosmopolitan beetle regarded as a destructive pest of several stored products such as grains, flour, spices, dried fruit and tobacco. Chemical insecticides are one of the measures used against the pest. However, intensive insecticide use has resulted in the appearance of resistant insect populations. Therefore, for the elaboration of more effective control programs, it is necessary to know the biological aspects of L. serricorne. Among these aspects, the genetic variability knowledge is very important and may help in the development of new control methods. The objective of this study was to evaluate the genetic variability of 11 natural populations of L. serricorne collected respectively in three and four towns in the states of Paraná and São Paulo, Brazil, using 20 primers random amplified polymorphic DNA (RAPD) and polymorphisms of esterases. These primers produced 352 polymorphic bands. Electrophoretic analysis of esterases allowed the identification of four polymorphic loci (Est-2, Est-4, Est-5 and Est-6) and 18 alleles. Results show that populations are genetically differentiated and there is a high level of genetic variability within populations. The high degree of genetic differentiation is not directly correlated to geographical distance. Thus, our data indicate that movement of infested commodities may contribute to the dissemination of L. serricorne, facilitating gene flow.

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Genetic diversity and structure of Dorstenia elata (Moraceae) in an Atlantic Forest remnant

Rodriguésia ◽

10.1590/2175-7860202172081 ◽

2021 ◽

Vol 72 ◽

Author(s):

Liliana Aparecida Ribeiro Martins ◽

Rodrigo Monte Lorenzoni ◽

Ronald Martins Pereira Júnior ◽

Fábio Demolinari de Miranda ◽

Milene Miranda Praça Fontes ◽

...

Keyword(s):

Genetic Diversity ◽

Atlantic Forest ◽

Shannon Index ◽

The Road ◽

Expected Heterozygosity ◽

Forest Remnant ◽

Genetic Diversity And Structure ◽

Native Populations ◽

The Matrix ◽

Issr Primers

Abstract Plant species that show gregarious spatial distribution and endemism to the Atlantic Forest, such as Dorstenia elata, are particularly sensitive to the effects of genetic diversity loss. In the present study, we aimed to quantify the genetic diversity in native populations of this species in an Atlantic Forest remnant. The sample included three aggregates of individuals, and molecular characterization was performed with twelve ISSR primers. Intrapopulation analyses were based on the calculation of the Shannon index; total expected heterozygosity and the matrix of distances between pairs of individuals were also calculated. The obtained grouping dendrogram evinced the formation of two groups. Interpopulation investigations were based on the analysis of molecular variance and the estimate of historical gene flow. The results demonstrate that one group comprised the genotypes from two subpopulations, and the other contained exclusively the genotypes of a third subpopulation. The greatest genetic variability was observed within rather than among populations, indicating that the geographical distance and the road that divides the studied populations are not causing loss of genetic diversity.

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Genetic Diversity and Structure of Latvian Tilia cordata Populations

Proceedings of the Latvian Academy of Sciences. Section B. Natural, Exact, and Applied Sciences. ◽

10.2478/prolas-2021-0039 ◽

2021 ◽

Vol 75 (4) ◽

pp. 261-267

Author(s):

Dainis Edgars Ruņģis ◽

Baiba Krivmane

Keyword(s):

Genetic Diversity ◽

Microsatellite Markers ◽

Vegetative Reproduction ◽

Growth Conditions ◽

Climatic Conditions ◽

Tilia Cordata ◽

High Genetic Diversity ◽

Genetic Diversity And Structure ◽

Broadleaf Tree ◽

Broadleaf Species

Abstract Changing climatic conditions are transforming the ecological and silvicultural roles of broadleaf tree species in northern Europe. Small-leaved lime (Tilia cordata Mill.) is distributed throughout most of Europe, and is a common broadleaf species in Latvia. This species can tolerate a broad range of environmental and ecological conditions, including temperature, water availability, and soil types. The aim of this study was to assess the genetic diversity and differentiation of Latvian T. cordata populations using nuclear microsatellite markers developed for Tilia platyphyllos. After testing of 15 microsatellite markers, Latvian T. cordata samples were genotyped at 14 micro-satellite loci. Latvian T. cordata populations had high genetic diversity, and were not overly isolated from each other, with moderate gene flow between populations. No highly differentiated populations were identified. Vegetative reproduction was identified in most analysed populations, and almost one-third of analysed individuals are of clonal origin. T. cordata has high timber production potential under the current climatic and growth conditions in Latvia, and therefore this species has potential for use in forestry, as well as playing a significant role in maintaining biodiversity and other ecosystem services.

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There Is No Evidence of Geographical Patterning among Invasive Kentucky Bluegrass (Poa pratensis) Populations in the Northern Great Plains

Weed Science ◽

10.1614/ws-d-15-00169.1 ◽

2016 ◽

Vol 64 (3) ◽

pp. 409-420 ◽

Cited By ~ 2

Author(s):

Lauren A. Dennhardt ◽

Edward S. DeKeyser ◽

Sarah A. Tennefos ◽

Steven E. Travers

Keyword(s):

Genetic Diversity ◽

Great Plains ◽

Propagule Pressure ◽

Poa Pratensis ◽

Natural Populations ◽

Kentucky Bluegrass ◽

Grass Species ◽

Northern Great Plains ◽

Wild Populations ◽

High Genetic Diversity

The study of colonizing and of dominant grass species is essential for prairie conservation efforts. We sought to answer how naturalized Kentucky bluegrass in the northern Great Plains has become successful in the last 20 yr despite its long history in the northern Great Plains. We tested for evidence of geographical differentiation using flow cytometry and microsatellite markers to ascertain the population genetics of Kentucky bluegrass. Across all tested wild populations, high levels of genetic diversity were detected along with moderate levels of structure. Mantel tests of geographical patterns were not significant. Using clonal assignment, we found two major clones that made up the majority of the tested wild populations. When we compared the wild individuals to pedigree cultivars, we found virtually no genetic overlap across all tests, which did not support our hypothesis of developed cultivars contributing to high genetic diversity in natural populations. Furthermore, DNA content tests indicated a narrow range in ploidy in wild populations compared with lawn cultivars, further supporting a hypothesis of divergence between wild and pedigree cultivars. These results indicate the recent invasion of Kentucky bluegrass in the northern Great Plains is not because of adaptation or propagule pressure, but rather likely an environmental or land use shift.

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