scholarly journals Genetic Diversity and Structure of Common Carp (Cyprinus carpio L.) in the Centre of Carpathian Basin: Implications for Conservation

Genes ◽  
2020 ◽  
Vol 11 (11) ◽  
pp. 1268
Author(s):  
Bianka Tóth ◽  
Rasoul Khosravi ◽  
Mohammad Reza Ashrafzadeh ◽  
Zoltán Bagi ◽  
Milán Fehér ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Differentiation ◽  
Common Carp ◽  
Assignment Test ◽  
Original Strain ◽  
Genetic Purity ◽  
Animal Genetic Resources ◽  
Genetic Diversity And Structure ◽  
Low Levels ◽  
Few Data

Hungary is one of the largest common carp-production countries in Europe and now, there is a large number of local breeds and strains in the country. For proper maintenance of the animal genetic resources, information on their genetic diversity and structure is essential. At present, few data are available on the genetic purity and variability of the Hungarian common carp. In this study, we genetically analyzed 13 strains in Hungary and, in addition, the Amur wild carp, using 12 microsatellite markers. A total of 117 unique alleles were detected in 630 individuals. Low levels of genetic differentiation (Fst and Cavalli–Sforza and Edwards distance) were estimated among strains. The AMOVA showed the low but significant level of genetic differentiation among strains (3.79%). Bayesian clustering analysis using STRUCTURE classified the strains into 14 different clusters. The assignment test showed that 93.64% of the individuals could be assigned correctly into their original strain. Overall, our findings can be contributed to complementing scientific knowledge for conservation and management of threatened strains of common carp.

Genetic Diversity and Population Structure of Kerala Rice Landraces Using Genotyping-By-Sequencing

2021 ◽  
Author(s):  
Maya Peringottillam ◽  
Smitha Kunhiraman Vasumathy ◽  
Hari Krishna Kumar ◽  
Manickavelu Alagu
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genotyping By Sequencing ◽  
Snp Markers ◽  
Genetic Purity ◽  
Next Generation Sequencing Technology ◽  
Distance Analysis ◽  
Rice Landraces ◽  
Genetic Diversity And Structure ◽  
Rice Landrace

Abstract Researchers stand at the vanguard of advancement and application of next-generation sequencing technology for creating opportunities to guide more realistic and applicable strategies for the sustainable management of genetically diverse rice resources. This study is a pioneering effort where GBS-SNP markers were employed to assess the tremendous genetic diversity and structure of rice landrace collections from northern Kerala. Kerala holds an immense diversity of rice landraces that encountered selection pressures of environmental heterogeneity, biotic and abiotic stresses, however competent rather provide good yields, whereby drawing the attention of the rice breeding sector. The population structure and diversity analyses separated the accessions into three distinct subpopulations with a huge amount of genetic variation within subpopulations. Nei’s genetic distance analysis confirmed the existence of strong genetic differentiation among rice landrace populations. The values of FST and Nm established the farmers’ effort to preserve the genetic purity of rice landraces despite the extensive seed exchange programs across the states of India. Moreover, this low level of gene flow among subpopulations could provide the opportunity for well-adapted combinations of genes to be established by natural selection. The clustering pattern based on SNP markers furnished sufficient knowledge in identifying rice genotypes that eliminates the likelihood of duplication among indigenous cultivars. Similar clustering patterns of genotypes revealed shared genetic characters among them. Collectively these analyses can be used to completely understand the population of rice landraces in Kerala while contributing insights toward the evolution and selective pressures underlying these unique landraces.

scholarly journals Microsatellite analysis of genetic diversity and structure of Bruguiera gymnorrhiza and Kandelia obovate

2018 ◽  
Vol 52 ◽  
pp. 00027 ◽  
Author(s):  
Mohammad Basyuni ◽  
Shigeyuki Baba ◽  
Hirosuke Oku
Keyword(s):  
Genetic Diversity ◽  
Allelic Diversity ◽  
Geographic Range ◽  
Microsatellite Analysis ◽  
Bruguiera Gymnorrhiza ◽  
Low Genetic Diversity ◽  
Genetic Diversity And Structure ◽  
Low Levels ◽  
High Level ◽  
F Statistics

Microsatellite loci were used for estimating genetic diversity and structure for three populations of B. gymnorrhiza and K. obovata (Rhizophoracea) in Okinawa, Japan. Thirty propagules of individual samples representing the population of both species were genotyped at five microsatellites. The level of observed heterozygosity (HO) was observed for several population, overall loci, ranged 0.422-0.800 with an average 0.627 for B. gymnorrhiza and 0.477-0.822 with an average 0.665 for K. obovata, indicating both species had relatively low genetic diversity. Both species showed low levels of allelic diversity, 3-5 and 3-5 alleles per locus, respectively. Gene diversitywas also maintained within populations (HS: 0.741 and 0.954). Additionally, an analysis of molecular variance (AMOVA) based on the immeasurable alleles model (F-statistics), for B. gymnorrhiza and K. obovata found that most of the variation resided within individuals in the total populations, i.e. 79.78 % and 69.90 % respectively, and among individuals within populations, i.e.14.30 % and 27.95 % respectively. There was little variation between populations, i.e. 5.92 % and 2.15 % for B. gymnorrhiza and K. obovata, respectively. The high-level genetic differentiation within individuals and populations both species may be due to the geographic range of the species, mating system, and environmental factors.

scholarly journals Genetic Diversity and Structure of Pinus densiflora Siebold & Zucc. Populations in Republic of Korea Based on Microsatellite Markers

Forests ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 750
Author(s):  
Ji-Young Ahn ◽  
Jei-Wan Lee ◽  
Kyung-Nak Hong
Keyword(s):  
Genetic Diversity ◽  
Genetic Differentiation ◽  
Microsatellite Markers ◽  
Environmental Changes ◽  
Pinus Densiflora ◽  
Republic Of Korea ◽  
Conifer Species ◽  
Principal Coordinates ◽  
Genetic Diversity And Structure ◽  
The Republic

Pinus densiflora Siebold & Zucc. is a widely distributed conifer species in the Republic of Korea with economic and ecologic importance. However, P. densiflora is negatively influenced by various factors, such as forest fires, clearing of large numbers of trees infected with Pinus disease, and dieback. We aimed to use microsatellite markers to estimate the genetic diversity, differentiation, and structure of P. densiflora populations in the Republic of Korea. A total of 1844 samples from 60 populations were evaluated using 11 polymorphic microsatellite markers. The observed heterozygosity and expected heterozygosity were 0.652 and 0.673, respectively. The mean genetic differentiation among the populations was 0.013. Moreover, P. densiflora showed high genetic diversity and low genetic differentiation compared with conifer species, including Pinus species with similar life histories. Principal coordinates analysis and Bayesian clustering showed that P. densiflora has a weak geographical structure. The P. densiflora population at Mt. Halla, Jeju Island, showed the lowest genetic diversity and significant genetic differentiation compared with other mainland populations due to genetic drift and restricted gene flow. These findings can be useful for designing new conservation, management, and breeding strategies for P. densiflora populations in response to future environmental changes.

scholarly journals Ocean Currents Drove Genetic Structure of Seven Dominant Mangrove Species Along the Coastlines of Southern China

2021 ◽  
Vol 12 ◽  
Author(s):  
Qifang Geng ◽  
Zhongsheng Wang ◽  
Jianmin Tao ◽  
Megumi K. Kimura ◽  
Hong Liu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Genetic Differentiation ◽  
South China ◽  
Population Genetic ◽  
Ocean Currents ◽  
Mangrove Species ◽  
Contemporary Gene Flow ◽  
Low Levels ◽  
Oceanic Currents

Mangrove forest ecosystems, which provide important ecological services for marine environments and human activities, are being destroyed worldwide at an alarming rate. The objective of our study was to use molecular data and analytical techniques to separate the effects of historical and contemporary processes on the distribution of mangroves and patterns of population genetic differentiation. Seven mangrove species (Acanthus ilicifolius, Aegiceras corniculatum, Avicennia marina, Bruguiera gymnorrhiza, Kandelia obovata, Lumnitzera racemosa, and Rhizophora stylosa), which are predominant along the coastlines of South China, were genotyped at nuclear (nSSR) and chloroplast (cpSSR) microsatellite markers. We estimated historical and contemporary gene flow, the genetic diversity and population structure of seven mangrove species in China. All of these seven species exhibited few haplotypes, low levels of genetic diversity (HE = 0.160–0.361, with the exception of K. obovata) and high levels of inbreeding (FIS = 0.104–0.637), which may be due to their marginal geographical distribution, human-driven and natural stressors on habitat loss and fragmentation. The distribution patterns of haplotypes and population genetic structures of seven mangrove species in China suggest historical connectivity between populations over a large geographic area. In contrast, significant genetic differentiation [FST = 0.165–0.629 (nSSR); GST = 0.173–0.923 (cpSSR)] indicates that populations of mangroves are isolated from one another with low levels of contemporary gene flow among populations. Our results suggest that populations of mangroves were historically more widely inter-connected and have recently been isolated, likely through a combination of ocean currents and human activities. In addition, genetic admixture in Beibu Gulf populations and populations surrounding Hainan Island and southern mainland China were attributed to asymmetric gene flow along prevailing oceanic currents in China in historical times. Even ocean currents promote genetic exchanges among mangrove populations, which are still unable to offset the effects of natural and anthropogenic fragmentation. The recent isolation and lack of gene flow among populations of mangroves may affect their long-term survival along the coastlines of South China. Our study enhances the understanding of oceanic currents contributing to population connectivity, and the effects of anthropogenic and natural habitat fragmentation on mangroves, thereby informing future conservation efforts and seascape genetics toward mangroves.

Genetic diversity and differentiation in the swimming crab, Portunus trituberculatus (Miers, 1876) (Decapoda, Brachyura) along the coast of China based on fluorescent AFLP markers: implications for conservation and genetic improvement

Crustaceana ◽  
2015 ◽  
Vol 88 (1) ◽  
pp. 1-17
Author(s):  
Xiaoying Li ◽  
Zhiguo Dong ◽  
Hongbo Su ◽  
Qingqi Zhang ◽  
Huan Gao ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Differentiation ◽  
Genetic Improvement ◽  
The Other ◽  
Aflp Markers ◽  
Ex Situ ◽  
Portunus Trituberculatus ◽  
Swimming Crab ◽  
Species Introduction ◽  
Genetic Diversity And Structure

Using fluorescent AFLP-markers, the genetic diversity and structure of six geographical populations of the swimming crab,Portunus trituberculatus(Miers, 1876), from the coast of China were analysed to assess their genetic resource state. Eight primer combinations generated 925 loci among 85 individuals, and revealed a high polymorphism within these populations that varied from 57.41% (Zhoushan population) to 76.86% (Dalian population). According to the combination of percentage of polymorphic loci (PPL) and Shannon’s information index (I), the populations from Zhangzhou, Dongying and Dalian showed more genetic variation than the Lianyungang, Zhanjiang and Zhoushan populations. The gene flow () and across all populations overall were 1.935 and 0.205, respectively, showing moderate genetic differentiation. Differentiation was highest in the Zhoushan and Zhanjiang populations, and the geographical distribution and UPGMA cluster tree were not fully accordant. Neutrality test results revealed that the Zhangzhou population faced a smaller selective pressure than the other five populations (). In general, a high genetic diversity among theP. trituberculatuspopulations was observed along the coast of China, especially in the Zhangzhou, Dongying, Dalian and Lianyungang populations, while a pronounced level () of genetic differentiation has occurred between the Zhoushan population and the other populations. Therefore, these findings have the following implications for conservation and genetic improvement: (1) high diversity levels and good genetic resources, especially in the Zhangzhou population, which could lay the foundations for breeding research and genetic improvement; (2) the importance of preventing species escape and gene pool contamination in ex-situ conservation and species introduction programs in the Zhoushan population.

Genetic diversity and structure of the treeManilkara zapotain a naturally fragmented tropical forest

2017 ◽  
Vol 33 (4) ◽  
pp. 285-294 ◽  
Author(s):  
Daniela A. Martínez-Natarén ◽  
Víctor Parra-Tabla ◽  
Miguel A. Munguía-Rosas
Keyword(s):  
Genetic Diversity ◽  
Genetic Differentiation ◽  
Tropical Forest ◽  
Isolation By Distance ◽  
Allelic Diversity ◽  
Long Distance ◽  
Population Genetic Differentiation ◽  
Continuous Forest ◽  
Genetic Diversity And Structure ◽  
Degree Of Isolation

Abstract:Forest fragmentation, habitat loss and isolation may have a strong effect on biodiversity in tropical forests. This can include modification of the genetic diversity and structure of plant populations. In this study, we assessed the genetic diversity and structure of the treeManilkara zapotain 15 naturally formed fragments of semi-evergreen tropical forest, as well as in an adjacent continuous forest for comparison. Forest fragments were scattered within a matrix of wetlands and were highly variable in terms of size and degree of isolation. The naturally fragmented populations ofM.zapotahad slightly less allelic diversity (Ar: 3.4) than those of the continuous forest (Ar: 3.6), when corrected for sample size. However, populations in the fragments and continuous forest had very similar heterozygosity levels (HE: 0.59 in both cases). Low levels of genetic differentiation were observed among populations (FST: 0.026) and genetic structure was not consistent with isolation by distance, indicating high levels of gene flow. Genetic diversity was not explained by fragment size or degree of isolation. The relatively high genetic diversity and low inter-population genetic differentiation observed inM. zapotamay be the result of long-distance pollen and seed dispersal, as well as the high proximity among patches.

Genetic diversity and structure of the threatened anti-cancerous plantNothapodytes nimmonianaas revealed by ISSR analysis

2011 ◽  
Vol 9 (4) ◽  
pp. 506-514 ◽  
Author(s):  
V. K. Abdul Kareem ◽  
P. E. Rajasekharan ◽  
S. Mini ◽  
T. Vasantha Kumar
Keyword(s):  
Genetic Diversity ◽  
Genetic Differentiation ◽  
Population Genetic ◽  
Gene Diversity ◽  
Species Level ◽  
Conservation Strategy ◽  
Group Method ◽  
Population Genetic Differentiation ◽  
Genetic Diversity And Structure ◽  
Western Ghats Of India

Inter simple sequence repeat markers were used to assess the genetic diversity and population genetic structure in 12 populations ofNothapodytes nimmonianafrom Western Ghats of India. A total of 16 selected primers produced 103 discernible bands, with 76 (73.7%) being polymorphic. The Nei's gene diversity (h) ranged from 0.1166 to 0.2124, with an average of 0.1518 at the population level and 0.2965 at the species level indicating high genetic diversity. The Shannon's index (I) was estimated to be 0.2189 within populations (range 0.1703–0.2947) and 0.4352 at the species level. The analysis of molecular variance showed that the genetic variation was found mainly within populations (73%), but variance among populations was only 27% and its value, ΦPT = 0.271,P < 0.001, implied that high genetic differentiation among populations. In addition, Nei's differentiation coefficient (GST) was found to be high (0.4882) and the gene flow (Nm) was low (0.5242), confirming the high population genetic differentiation. The unweighted pair-group method using arithmetic average clustering elicited similar results. Based on this, we propose conservation strategy for this plant species.

scholarly journals Seedling Selection Using Molecular Approach for Ex Situ Conservation of Critically Endangered Tree Species (Vatica bantamensis (Hassk.) Benth. & Hook. ex Miq.) in Java, Indonesia

2019 ◽  
Vol 12 ◽  
pp. 194008291984950 ◽  
Author(s):  
Yayan Wahyu C. Kusuma ◽  
Siti R. Ariati ◽  
Rosniati A. Risna ◽  
Chika Mitsuyuki ◽  
Yoshihisa Suyama ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Differentiation ◽  
Plant Species ◽  
Ex Situ Conservation ◽  
Critically Endangered ◽  
Ex Situ ◽  
Genetic Diversity And Structure ◽  
In The Wild ◽  
Genetic Clusters ◽  
Ex Situ Collection

Ex situ conservation is an important complementary strategy for in situ to conserve endangered plant species. However, the limited areas designated for ex situ conservation such as in botanic gardens have become a great challenge for conservation practitioners and scientists attempting to optimally conserve the genetic diversity of targeted plant species. Our study aimed to assess genetic diversity and structure of wild seedlings of Vatica bantamensis, an endemic and critically endangered dipterocarp from Java (Indonesia). We also estimated genetic differentiation between the wild seedlings and existing ex situ collection and evaluated the genetic diversity preserved in the ex situ collection. Our analysis, using 730 single-nucleotide polymorphisms loci, showed that wild seedlings exhibited higher genetic diversity than the ex situ collection (nucleotide diversity, µ = 0.26 and 0.16, respectively). Significant genetic differentiation was also detected ( FST = 0.32) between wild seedlings and ex situ collection. Furthermore, we found high kinship within the ex situ collection suggesting low genetic diversity since the founding collection. We also detected three distinct genetic clusters from all samples combined (analysis of molecular variance, ϕ = 0.48, p < .001), with two clusters present in the wild seedlings that were not represented in the ex situ collection. We recommend that supplementary collections from the two newly identified genetic clusters in the wild seedlings should be incorporated to increase genetic diversity in the ex situ collection. Furthermore, our study demonstrated that understanding the population genetics of targeted endangered species provides better results for ex situ conservation strategies.

scholarly journals Unraveling the genetic diversity and structure of Quercus liaotungensis population through analysis of microsatellite markers

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10922
Author(s):  
Bin Guo ◽  
Xiangchun Hao ◽  
Lijun Han ◽  
Yu Zhai ◽  
Shuai Zhou ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Genetic Differentiation ◽  
Climatic Factors ◽  
Northern China ◽  
Natural Hybridization ◽  
Geographical Distance ◽  
Physical Barrier ◽  
Quercus Liaotungensis ◽  
Genetic Diversity And Structure

Background Quercus liaotungensis Koidz. is an ecologically and economically important tree species widely distributed in Northern China. However, the effective assessment, utilization, and protection of Q. liaotungensis resources remain unexplored. Methods In total, 120 samples obtained from 12 Q. liaotungensis populations of Northern China were investigated for genetic diversity and structure using 19 simple sequence repeat (SSR) primer pairs. Results The total number of alleles detected was 293, the average number of effective allele (Ne) was 6.084, the genetic differentiation coefficient (Fst) was 0.033, and the mean observed heterozygosity (Ho) and expected heterozygosity (He) were 0.690 and 0.801, respectively. Moreover, analysis of molecular variance (AMOVA) showed a 5.5% genetic variation among 12 Q. liaotungensis populations, indicating that a high level of genetic diversity and a low degree of genetic differentiation among Q. liaotungensis populations. STRUCTURE and cluster analysis divided the 12 Q. liaotungensis populations into the following three subpopulations: Bashang Plateau subpopulation (SH), Liaodong Peninsula subpopulation (NC), and Loess Plateau subpopulation (other 10 populations). The cluster analysis based on 19 climatic factors was consistent with the genetic structure. A positive correlation was found between genetic distance and geographical distance (r = 0.638, p = 0.028) by the Mantel test, and two boundaries were found among the 12 Q. liaotungensis populations by the Barrier analysis, indicating that Q. liaotungensis populations existed isolated by geographical distance and physical barrier. Conclusion This study suggests that geographical isolation, physical barrier, climatic types, and natural hybridization promote the formation of genetic structures, which can contribute to future protection and genetic improvement of Q. liaotungensis.

scholarly journals Genetic diversity and structure of Oriental and European beech populations from Iran and Europe

2020 ◽  
Vol 69 (1) ◽  
pp. 55-62
Author(s):  
Mahboobeh Mohebi Bijarpasi ◽  
Markus Müller ◽  
Oliver Gailing
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Differentiation ◽  
Fagus Sylvatica ◽  
Expressed Sequence Tag ◽  
European Beech ◽  
Southeast Europe ◽  
Oriental Beech ◽  
Genetic Diversity And Structure ◽  
Iranian Populations

AbstractGenetic variation is a major component of plant development and adaptation, and recent studies have shown that genetic variation among plant species can have important ecological effects. Oriental beech (Fagus orientalis Lipsky) is a dominant tree species in the Hyrcanian forests, where it occupies approximately 18 % of the forested area. In this study, nine expressed sequence tag simple sequence repeat (EST-SSR) markers were used to determine the genetic diversity and structure of Iranian Oriental beech populations growing at different altitudes. We further compared the genetic structures of the Iranian populations to a F. orientalis and a Fagus sylvatica L. population from the hybrid zone of the two taxa in southeast Europe, and to a F. sylvatica population from central Europe. All populations showed a high genetic diversity, which was similar to other F. orientalis and F. sylvatica populations from Europe. The genetic differentiation among Iranian beech populations was very low. In contrast, distinct genetic differentiation was found between the Iranian populations and the analyzed European populations (F. orientalis and F. sylvatica). One EST-SSR was identified to differentiate (GST: 0.503) between F. orientalis and F. sylvatica with very pronounced allele frequency differences between taxa. Specifically, the Fagus sylvatica characteristic allele 189 was almost absent from all Iranian populations and present in low frequencies in F. orientalis populations from other regions. This study helps to extend the knowledge of genetic diversity and genetic structure of Iranian Oriental beech populations. It further gives insights into the genetic differentiation between F. orientalis populations from the center and the edge of the species’ distribution range as well as between Oriental and European beech.

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