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

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.

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Provenance Trials of the Mexican Spruces in Nursery Conditions: Three Species Endangered by Climatic Variation

Environmental Sciences Proceedings ◽

10.3390/iecf2020-08080 ◽

2020 ◽

Vol 3 (1) ◽

pp. 12

Author(s):

José Marcos Torres-Valverde ◽

José Ciro Hernández-Díaz ◽

Artemio Carrillo-Parra ◽

Eduardo Mendoza-Maya ◽

Christian Wehenkel

Keyword(s):

Cluster Analysis ◽

Genetic Differentiation ◽

Local Adaptation ◽

Quantitative Traits ◽

Climatic Factors ◽

Climatic Variation ◽

Climatic Variables ◽

Provenance Trials ◽

Survival And Growth ◽

Picea Species

The three Mexican spruces’ distributions are fragmented, which could lead to phenological, morphological and genetic differentiation, partially caused by local adaptation. In this study, we examined the effect that climatic variables had on the survival and growth of 5641 Picea seedlings, coming from eight seed provenances of three species and produced in identical nursery conditions. The respective responses of each species and provenance can be considered as a proxy of the genetic differentiation and adaptation of each population. A cluster analysis revealed: (i) significant differences in genetic quantitative traits among the three Picea species and (ii) significant correlations between genetic quantitative traits and climatic factors.

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Genetic Structure and Eco-Geographical Differentiation of Lancea tibetica in the Qinghai-Tibetan Plateau

Genes ◽

10.3390/genes10020097 ◽

2019 ◽

Vol 10 (2) ◽

pp. 97 ◽

Cited By ~ 2

Author(s):

Xiaofeng Chi ◽

Faqi Zhang ◽

Qingbo Gao ◽

Rui Xing ◽

Shilong Chen

Keyword(s):

Genetic Diversity ◽

Cluster Analysis ◽

Gene Flow ◽

Tibetan Plateau ◽

Environmental Changes ◽

Restricted Gene Flow ◽

Principal Coordinates Analysis ◽

Principal Coordinates ◽

Genetic Diversity And Structure ◽

Tanggula Mountains

The uplift of the Qinghai-Tibetan Plateau (QTP) had a profound impact on the plant speciation rate and genetic diversity. High genetic diversity ensures that species can survive and adapt in the face of geographical and environmental changes. The Tanggula Mountains, located in the central of the QTP, have unique geographical significance. The aim of this study was to investigate the effect of the Tanggula Mountains as a geographical barrier on plant genetic diversity and structure by using Lancea tibetica. A total of 456 individuals from 31 populations were analyzed using eight pairs of microsatellite makers. The total number of alleles was 55 and the number per locus ranged from 3 to 11 with an average of 6.875. The polymorphism information content (PIC) values ranged from 0.2693 to 0.7761 with an average of 0.4378 indicating that the eight microsatellite makers were efficient for distinguishing genotypes. Furthermore, the observed heterozygosity (Ho), the expected heterozygosity (He), and the Shannon information index (I) were 0.5277, 0.4949, and 0.9394, respectively, which indicated a high level of genetic diversity. We detected high genetic differentiation among all sampling sites and restricted gene flow among populations. Bayesian-based cluster analysis (STRUCTURE), principal coordinates analysis (PCoA), and Neighbor-Joining (NJ) cluster analysis based on microsatellite markers grouped the populations into two clusters: the southern branch and the northern branch. The analysis also detected genetic barriers and restricted gene flow between the two groups separated by the Tanggula Mountains. This study indicates that the geographical isolation of the Tanggula Mountains restricted the genetic connection and the distinct niches on the two sides of the mountains increased the intraspecific divergence of the plants.

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Genetic Diversity in Nephelium

HortScience ◽

10.21273/hortsci.30.4.795f ◽

1995 ◽

Vol 30 (4) ◽

pp. 795F-795

Author(s):

K.M. Aradhva ◽

F. Zee ◽

R.M. Manshardt

Keyword(s):

Genetic Diversity ◽

Cluster Analysis ◽

Genetic Differentiation ◽

Genetic Divergence ◽

Taxonomic Revision ◽

Isozyme Polymorphism ◽

High Level

Fifty-six accessions involving five taxa of Nephelium (N. Iappaceum varieties lappaceum and pallens, N. hypoleucum, N. ramboutan-ake, and N. cuspidatum) were fingerprinted and evaluated for genetic diversity using isozyme polymorphism. All five taxa were polymorphic for most of the enzymes encoded by 10 putative loci. Number of alleles per locus ranged from three for Pgi-1 to nine for Pgi-2 with a total of 57 alleles. Thirty-eight accessions out of 56 possessed unique isozyme genotypes, indicating a high level of diversity in the collection. On average, 80% of the loci were polymorphic and the expected and observed heterozygosities were 0.374 and 0.373, respectively. The cluster analysis of the isozyme data revealed five distinct clusters representing the five taxa included in the study. Genetic differentiation within N. Iappaceum var. Iappaceum was evident from the cluster analysis. Isozyme data indicated that N. ramboutan-ake is the closest relative of N. Iappaceum var. Iappaceum, followed by N. hypoleucum, N. Iappaceum var. pallens, and N. cuspidatum. Interestingly, the varieties of N. Iappaceum exhibited genetic divergence far beyond that of the congenerics, N. hypoleucum and N. ramboutan-ake and may require a taxonomic revision.

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Genetic differentiation of Norway spruce (Picea abies (L.) Karst.) trees with diferent crown types from the mountain Golija

Genetika ◽

10.2298/gensr1503849g ◽

2015 ◽

Vol 47 (3) ◽

pp. 849-861 ◽

Cited By ~ 1

Author(s):

Vladislava Galovic ◽

Mirjana Sijacic-Nikolic ◽

Robert Safhauzer ◽

Dijana Cortan ◽

Sasa Orlovic

Keyword(s):

Genetic Diversity ◽

Cluster Analysis ◽

Picea Abies ◽

Genetic Differentiation ◽

Norway Spruce ◽

Plant Species ◽

Genetic Characterization ◽

Similarity Matrix ◽

Primer Sets

The knowledge of genetic diversity degree of given species is of great importance for the successful process of breeding and genetic conservation. The aim of conducted research was to determine the genetic differentiation of Norway spruce (Picea abies (L.) Karst) genotypes with very specific narrow pyramidal and normal crown type, which grows at different altitude of the mountain Golija. For assessment of genetic similarities or differences between studied genotypes co-dominant microsatellite system had been used. This system has proven to be reliable and efficient in the genetic characterization of plant species. In total 22 primer sets have been tested, while 16 (73%) of them resulted in the successful yield of the amplified product. The analysis show that studied individuals had in total 130 alleles, in average 8.125 polymorphic alleles per each locus. The lowest polymorphism was detected in the locus EATC1D10, EATC1F03B and EATC2G09, while the highest level of polymorphism was detected in EATC2G08. Based on microsatellite date and similarity matrix, cluster analysis dendrogram indicates existence of the vertical differentiation of studied genotypes, which is consistent with results of previous Norway spruce studies.

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

Forests ◽

10.3390/f12060750 ◽

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.

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

Genes ◽

10.3390/genes11111268 ◽

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.

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Fine-scale genetic structure of the overwintering Chilo suppressalis in the typical bivoltine areas of northern China

PLoS ONE ◽

10.1371/journal.pone.0243999 ◽

2020 ◽

Vol 15 (12) ◽

pp. e0243999

Author(s):

Ke-Xin Zhu ◽

Shan Jiang ◽

Lei Han ◽

Ming-Ming Wang ◽

Xing-Ya Wang

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Genetic Differentiation ◽

Isolation By Distance ◽

Genetic Relationships ◽

Management Strategies ◽

Geographic Distance ◽

Northern China ◽

Economic Losses ◽

Chilo Suppressalis

The rice stem borer (RSB), Chilo suppressalis (Lepidoptera: Pyralidae), is an important agricultural pest that has caused serious economic losses in the major rice-producing areas of China. To effectively control this pest, we investigated the genetic diversity, genetic differentiation and genetic structure of 16 overwintering populations in the typical bivoltine areas of northern China based on 12 nuclear microsatellite loci. Moderate levels of genetic diversity and genetic differentiation among the studied populations were detected. Neighbour-joining dendrograms, Bayesian clustering and principal coordinate analysis (PCoA) consistently divided these populations into three genetic clades: western, eastern and northern/central. Isolation by distance (IBD) and spatial autocorrelation analyses demonstrated no correlation between genetic distance and geographic distance. Bottleneck analysis illustrated that RSB populations had not undergone severe bottleneck effects in these regions. Accordingly, our results provide new insights into the genetic relationships of overwintering RSB populations and thus contribute to developing effective management strategies for this pest.

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High genetic diversity and strong genetic structure of Strongyllodes variegatus populations in oilseed rape production areas of China

10.21203/rs.3.rs-19659/v3 ◽

2020 ◽

Author(s):

HaiXia Zhan ◽

ZhongPing Hao ◽

Rui Tang ◽

LiNi Zhu ◽

JingJiang Zhou ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Oilseed Rape ◽

Demographic History ◽

Insect Pest ◽

Distribution Analysis ◽

Geographical Distance ◽

Geographical Regions ◽

Genetic Diversity And Structure ◽

Production Areas

Abstract Background: Strongyllodes variegatus (Fairmaire) is a major insect pest of oilseed rape in China. Despite its economic importance, the contribution of its population genetics in the development of any suitable protection control strategy for the management of oilseed rape crops is poorly studied. It is a much urgent need to prevent its spread to the rest of the world. Results: Using the sequences of mitochondrial DNA cytochrome c oxidase subunit I (COI) and cytochrome b (Cytb) as genetic markers, we analyzed the population genetic diversity and structure of 437 individuals collected from 15 S. variegates populations located in different oilseed rape production areas in China. In addition, we estimated the demographic history using neutrality test and mismatch distribution analysis. The high level of genetic diversity was detected among the COI and Cytb sequences of S. variegates. The population structure analyses strongly suggested three distinct genetic and geographical regions in China with limited gene flow. The Mantel test showed that the genetic distance was greatly influenced by the geographical distance. The demographic analyses showed that S. variegates had experienced population fluctuation during the Pleistocene Epoch, which was likely to be related to the climatic changes.Conclusion: Overall, these results demonstrate that the strong genetic structure of S. variegates populations in China, which is attributed by the isolation through the geographical distance among populations, their weak flight capacity and subsequent adaptation to the regional ecological conditions.

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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 ◽

10.1163/15685403-00003398 ◽

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.

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

Journal of Tropical Ecology ◽

10.1017/s0266467417000268 ◽

2017 ◽

Vol 33 (4) ◽

pp. 285-294 ◽

Cited By ~ 1

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.

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