scholarly journals Genetic Analysis of Inonotus Obliquus Strains by RAPD

2007 ◽  
Vol 26 (3) ◽  
pp. 201-205
Author(s):  
Yan-Qiu Chen ◽  
Xiao-Fan Guo ◽  
Chang-Tian Li ◽  
Yu Li
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Genetic Analysis ◽  
Genetic Distances ◽  
Dna Fingerprints ◽  
Inonotus Obliquus ◽  
Medicinal Fungus ◽  
Different Strains ◽  
Rapd Fragment ◽  
Intraspecific Difference

Genetic Analysis ofInonotus ObliquusStrains by RAPDRAPD profiling of eightInonotus obliquusstrains isolated from sclerotia collected from different areas of China was conducted to determine the genetic variability within this important medicinal fungus and to better define relationships between the genotype and geographical origins of isolation. Twelve 10-mer primers generated a total of 167 stable and reproducible DNA fragments, of which 101 (60.5%) were polymorphic. DNA fingerprints revealed genetic diversity among the strains tested, but there was the little intraspecific difference between the fingerprints of individual strains. A phenogram constructed based on UPGMA analysis of genetic distances calculated from RAPD fragment data identified three distinct groupings: (1) BCX01 and BCX02, (2) JL01, JL02, JL03, JL04 and JL05, (3) HLJ01. Our data confirm that the genetic variability among different strains may be a useful ancillary tool for identifyingl. obliquussclerotia of different geographical origins.

scholarly journals Genetic variability in the peach palm genebank with RAPD markers

2010 ◽  
Vol 10 (3) ◽  
pp. 211-217 ◽  
Author(s):  
Michelly de Cristo Araújo ◽  
Doriane Picanço Rodrigues ◽  
Spartaco Astolfi Filho ◽  
Charles Roland Clement
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Genetic Variability ◽  
Genetic Analysis ◽  
Rapd Markers ◽  
Genetic Distances ◽  
Peach Palm ◽  
Fruit Species ◽  
High Gene ◽  
Average Gene

Peach palm is a native Amazonian fruit species with broad genetic diversity in its wild and domesticated populations. This study completed the molecular characterization and genetic analysis of the accessions in the Peach Palm genebank, Brazil, using RAPD markers. Eight primers generated 132 markers, of which 128 were polymorphic. Average heterozigosity was 0.35, with 95.5% polymorphism. The genetic variability within the landraces (H S) was 0.32, while genetic divergence (G ST) was 0.09 among the four well-represented landraces. The average gene flow was 5.0, with high gene flow between the Solimões and Pampa Hermosa (Nm=10.07), and between the Putumayo and Solimões (Nm=10.73) landraces, all western landraces. The dendrograms of the Nei's and Rogers' genetic distances of the well-represented landraces presented similar groupings to previous analyses, with the Solimões, Putumayo and Pampa Hermosa landraces grouped together in western Amazonia, and distant from the Pará landrace in central and eastern Amazonia.

scholarly journals Genetic analysis of silver-fir populations in the Beskids

2011 ◽  
Vol 72 (2) ◽  
pp. 115-119 ◽  
Author(s):  
Leon Mejnartowicz
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Analysis ◽  
Abies Alba ◽  
Genetic Distances ◽  
Silver Fir ◽  
Geographical Distance ◽  
Polymorphic Loci ◽  
Expected Heterozygosity ◽  
Rare Alleles

Twenty-eight isozymic loci were studied in the Beskid Mts., in four populations of common silver-fir (<em>Abies alba</em>): one in Beskid Makowski (BM) and three populations in Beskid Sądecki (BS). Their genetic variation and diversity were analyzed, and Nei's genetic distances between the populations were calculated. The results show that the geographical distance between the BM population and the three BS populations is reflected in genetic distances. The BM population is clearly distinct from the others. It has the lowest genetic diversity (<em>I</em> = <em>0.42</em>), percentage of polymorphic loci <em>(%PoL </em>= <em>64.29</em>) and number of rare alleles (<em>NoRa </em>= <em>5</em>). Besides, the BM population has the highest observed heterozygosity (<em>Ho </em>= <em>0.291</em>), which exceeds the expected heterozygosity (<em>He </em>= <em>0.254</em>), estimated on the basis of the Hardy-Weinberg Principle. On the contrary, BS populations are in the state of equilibrium, which is manifested, in similar values of <em>He </em>= <em>0.262 </em>and <em>Ho </em>= <em>0.264</em>.

Genetic diversity analysis of the Greek lentil (Lens culinaris) landrace ‘Eglouvis’ using morphological and molecular markers

2018 ◽  
Vol 16 (5) ◽  
pp. 469-477 ◽  
Author(s):  
Georgios F. Tsanakas ◽  
Photini V. Mylona ◽  
Katerina Koura ◽  
Anthoula Gleridou ◽  
Alexios N. Polidoros
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Genetic Variability ◽  
Morphological Analysis ◽  
Phenotypic Variability ◽  
Market Price ◽  
Genetic Distances ◽  
Reaction Products ◽  
Principal Coordinates Analysis ◽  
Principal Coordinates

AbstractThe Greek lentil landrace ‘Eglouvis’ is cultivated continuously at the Lefkada island for more than 400 years. It has great taste, high nutritional value and high market price. In the present study, we used morphological and molecular markers to estimate genetic diversity within the landrace. Morphological analysis was based on characteristics of the seed. Molecular analysis was performed using simple sequence repeat (SSR) molecular markers in a high-resolution melting (HRM) approach. ‘Samos’ and ‘Demetra’, two of the most widely cultivated commercial lentil varieties in Greece, were used for comparisons. Morphological analysis was performed with 584 seeds randomly selected from a lot. Analysis of seed dimensions and colour distributed the samples in different categories and highlighted the phenotypic variability in ‘Eglouvis’ lentil seeds. Genetic variability was estimated from 91 individual DNA samples with 11 SSR markers using HRM analysis. Genotyping was based upon the shape of the melting curves and the difference plots; all polymerase chain reaction products were also run on agarose gels. Genetic distances of individuals and principal coordinates analysis suggested that ‘Eglouvis’ landrace has a unique genetic background that significantly differs from ‘Samos’ and ‘Demetra’ and no overlapping could be detected. Genetic variability within the ‘Eglouvis’ landrace can be considered in targeted breeding programs as a significant phytogenetic resource of lentils in Greece.

Microsatellite analysis of genetic variability in Waler horses from Australia

2013 ◽  
Vol 61 (5) ◽  
pp. 357 ◽  
Author(s):  
Anas M. Khanshour ◽  
Rytis Juras ◽  
E. Gus Cothran
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Bayesian Method ◽  
Genetic Relationships ◽  
Similarity Measures ◽  
Genetic Distances ◽  
Microsatellite Analysis ◽  
Population Subdivision ◽  
Factorial Correspondence Analysis ◽  
Horse Breed

The Waler horse breed is an integral part of Australian history. The purposes of this study were to analyse the genetic variability in Waler horses from Australia and to investigate genetic relationships with other horse breeds. We examined the genetic diversity of 70 Waler horses sampled from seven breeding stations in Australia. Also we analysed the relationships of these horses with 11 other horse breeds. Analysis of the genetic structure was carried out using 15 microsatellite loci, genetic distances, AMOVA, factorial correspondence analysis and a Bayesian method. We found that the genetic diversity in the Waler was greater than the domestic horse mean and exceeded that of all endangered horse breeds. Our findings also revealed moderate population subdivision rather than inbreeding. All genetic similarity measures indicated that the Thoroughbred might be a key ancestor to the Waler. This study indicates that there is no immediate concern for loss of variation in Waler horses. Also, there clearly has been a strong input from the Thoroughbred into the Waler horse breed. However, the genetic evidence suggests that this input was not just direct but also came through other types of horses with a Thoroughbred cross background.

scholarly journals Genetic Diversity and Variability in Endangered Pantesco and Two Other Sicilian Donkey Breeds Assessed by Microsatellite Markers

2012 ◽  
Vol 2012 ◽  
pp. 1-6 ◽  
Author(s):  
Salvatore Bordonaro ◽  
Anna Maria Guastella ◽  
Andrea Criscione ◽  
Antonio Zuccaro ◽  
Donata Marletta
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variability ◽  
Genetic Information ◽  
Gene Diversity ◽  
Genetic Distances ◽  
Conservation Strategies ◽  
Population Structure Analysis ◽  
The Mean ◽  
Differentiation Index

The genetic variability of Pantesco and other two Sicilian autochthonous donkey breeds (Ragusano and Grigio Siciliano) was assessed using a set of 14 microsatellites. The main goals were to describe the current differentiation among the breeds and to provide genetic information useful to safeguard the Pantesco breed as well as to manage Ragusano and Grigio Siciliano. In the whole sample, that included 108 donkeys representative of the three populations, a total of 85 alleles were detected. The mean number of alleles was lower in Pantesco (3.7), than in Grigio Siciliano and Ragusano (4.4 and 5.9, resp.). The three breeds showed a quite low level of gene diversity (He) ranging from 0.471 in Pantesco to 0.589 in Grigio. The overall genetic differentiation index (Fst) was quite high; more than 10% of the diversity was found among breeds. Reynolds’ () genetic distances, correspondence, and population structure analysis reproduced the same picture, revealing that, (a) Pantesco breed is the most differentiated in the context of the Sicilian indigenous breeds, (b) within Ragusano breed, two well-defined subgroups were observed. This information is worth of further investigation in order to provide suitable data for conservation strategies.

scholarly journals Genetic variability of dairy cattle breeds in Lithuania

Biologija ◽  
2021 ◽  
Vol 67 (3) ◽  
Author(s):  
Romualdas Lapickis ◽  
Loreta Griciuvienė ◽  
Asta Aleksandravičienė ◽  
Indrė Lipatova ◽  
Algimantas Paulauskas
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Dairy Cattle ◽  
Genetic Material ◽  
Genetic Distances ◽  
Principal Coordinates Analysis ◽  
Black And White ◽  
Cattle Breeds ◽  
Principal Coordinates ◽  
High Degree

Large numbers of different scientific studies are conducted to preserve the breeds and improve the existing ones by introducing the variability of the plate genes, which best shows the phenotypic characteristics that can improve the health of dairy cattle and the quality of their production. The main purpose of this study was to perform an analysis of genetic variability of Lithuanian cattle breeds. Three subpopulation groups were studied: Lithuanian Black and White (95 individuals), Lithuanian Red (49), and Lithuanian White and Red (48). Bovine genetic material was genotyped using a total of 11 fluorescent microsatellite primers to estimate genetic variability. All loci presented a high degree of polymorphism and a total of 292 different alleles (Na) were detected. Thirty-two private alleles were detected in all evaluated subpopulations. After completing pairwise population assignment, which is based on the distribution of allelic frequencies, three populations showed the tendency to group into three separate clusters. However, the performed Principal Coordinates Analysis (PCoA), which is based on genetic distances, showed no anticipated clear grouping. Bayesian structure analysis revealed three genetic clusters. Analysis of FST (0.001–0.027) and Nei genetic distance (0.029–0.084) revealed that the genetic diversity of inter subpopulation in cattle groups was estimated to be lower than the genetic diversity of intra subpopulation.

scholarly journals Post-Genotyping Optimization of Dataset Formation Could Affect Genetic Diversity Parameters: An Example of Analyses with Alpine Goat Breeds

2020 ◽  
Author(s):  
Neža Pogorevc ◽  
Mojca Simčič ◽  
Negar Khayatzadeh ◽  
Johann Soelkner ◽  
Beate Berger ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Genetic Distances ◽  
Phylogenetic Study ◽  
European Alps ◽  
Global Context ◽  
Outlier Test ◽  
Snp Data ◽  
Genome Wide ◽  
A Genome

Abstract BackgroundLocal breeds retained unique genetic variability important for adaptive potential especially in light of challenges related to climate change. One objective was to perform, for the first time, a genome-wide diversity characterization using Illumina GoatSNP50 BeadChip of autochthonous Drežnica goat breed from Slovenia, five and one local breeds from neighboring Austria and Italy, respectively. For optimal conservation and breeding programs of endangered local breeds, it is important to detect past admixture events and strive for preservation of purebred representatives of each breed with low or without admixture. In the second objective, we hence investigated the effect of inclusion or exclusion of outliers from datasets on genetic diversity and population structure parameters.ResultsDistinct genetic origin of the Drežnica goat was demonstrated having closest nodes to Austrian and Italian breeds. A phylogenetic study of these breeds with other goat breeds having SNP data available in the DRYAD repository positioned them in the alpine, European and global context. Swiss breeds clustered with cosmopolitan alpine breeds and were closer to French and Spanish breeds. On the other hand, the Drežnica goat, Austrian and Italian breeds were closer to Turkish breeds. Datasets where outliers were excluded affected estimates of genetic diversity parameters within the breed and increased the pairwise genetic distances between most of the breeds. Alpine breeds, including Drežnica, Austrian and Italian goats analyzed here, still exhibit relatively high levels of genetic variability, homogeneous genetic structure and strong geographical partitioning.ConclusionsGenetic diversity analyses revealed that the Slovenian Drežnica goat has a distinct genetic identity and is closely related to the neighboring Austrian and Italian alpine breeds. These results expand our knowledge on phylogeny of goat breeds from easternmost part of the European Alps. The here employed outlier test and datasets optimization approaches provided an objective and statistically powerful tool for removal of admixed outliers. Importance of this test in selecting the representatives of each breed is warranted to obtain more objective diversity parameters and phylogenetic analysis. Such parameters are often the basis of the breeding and management programs and therefore important for preserving genetic variability and uniqueness of local rare breeds.

scholarly journals Diversidade genética em acessos do banco de germoplasma de camu-camu (Myrciaria dúbia [H.B.K.] McVaugh) do INPA usando marcadores microssatélites (EST-SSR).

2010 ◽  
Vol 12 (1) ◽  
pp. 51 ◽  
Author(s):  
Salvador Rojas ◽  
Yuyama K. Clement Ch. ◽  
Eduardo Ossamu Nagao
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Germplasm Conservation ◽  
Great Difficulty ◽  
Genetic Distances ◽  
Great Distance ◽  
Lack Of Information ◽  
Myrciaria Dubia ◽  
High Level ◽  
Diversity Studies

<p>O conhecimento da diversidade genética das espécies amazônicas é de grande importância para a domesticação e melhoramento das culturas. Uma das grandes dificuldades em espécies não domesticadas como o camu-camu é a falta de informação sobre a sua variabilidade genética. Devido ao potencial econômico do camu-camu por sua alta produção de vitamina C, foi realizado o presente trabalho, o qual tem como objetivo estimar a variabilidade genética de 139 acessos de camu-camu oriundos de 17 populações de diferentes rios da Amazônia brasileira, conservados no banco de germoplasma (BAG) de camu-camu do Instituto Nacional de Pesquisa da Amazônia INPA na cidade de Manaus, utilizando marcadores EST-SSR. Oito loci de EST-SSR detectaram um total de 102 alelos com uma média de 12,87 alelos por loco. Os resultados mostram altos níveis de diversidade para todos os locicom uma média de heterozigosidade esperada (H<sub>e</sub>) de 0,797 e heterozigosidade total (H<sub>t</sub>) de 0,502. As populações apresentaram altos valores de endogamia, o que sugere déficit de heterozigotos como observado pelos baixos valores de Heterozigosidade observada (H<sub>0</sub>), provavelmente devido ao isolamento das populações e as distâncias entre elas, o que limita o fluxo gênico favorecendo a endogamia. O valor de diferenciação genética (F<sub>ST</sub>) foi alto 0,21 indicando uma alta variabilidade entre as populações. As medidas baseadas nas freqüências alélicas, amostraram uma maior variabilidade dentro das populações (80,3%) que entre as populações (19,7%). Através das distâncias genéticas entre as populações foi encontrada uma grande variação entre os acessos provenientes de populações de Rondônia (Jarú) e os provenientes de Amazonas (Pirarucu e Tarumã) e Roraima (Urubu). No ordenamento pelo método UPGMA, observou-se a formação de dois grupos principais e cinco sub-grupos os quais estão relacionados geograficamente. Os resultados revelaram a utilidade dos marcadores EST-SSR nos estudos de diversidade genética entre acessos do camu-camu. Estes resultados serão úteis no planejamento de novas coletas e conservação do BAG, no analise de variabilidade de populações, assim como no direcionamento de cruzamentos através da escolha de genótipos geneticamente divergentes, o que contribuirá às atividades de melhoramento de camu-camu nos paises amazônicos.</p><p> </p><p><strong>Genetic diversity of the INPA germoplasm bank of camu-camu (Myrciaria dubia [H.B.K.] McVaugh) using microsatellites markers (EST-SSR).</strong><strong></strong></p><p>The knowledge of genetic diversity in Amazonian species is of great importance for domestication and breeding purposes. A great difficulty with non-domesticated species such as “camu-camu” is the lack of information about their genetic variability. Due to the economic potential of camu-camu, a fruit with a high level of vitamin C production, the aim of this study was to estimate the genetic diversity using the molecular markers EST-SSR, to study the genetic variability of 139 accessions from 17 “camu-camu” materiales from different rivers in the Brazilian's Amazon region, preserved at the INPA (Instituto Nacional de Pesquisas da Amazônia Brasilera) Active Germoplasm Bank (BAG) of “camu-camu” in Manaus. Eight of the EST-SSR polimorfic loci used had 102 alleles detected with an average of 12.87 alleles per locus. The results show high levels of diversity for all loci with an average expected heterocygocity (H<sub>e</sub>) of 0.797 and a total heterocygocity (H<sub>t</sub>) value of 0.502. Populations had high inbreeding values, suggesting a heterocigotes deficiency as observed by the heterocigocity (H<sub>0</sub>), perhaps as result of the great distance and isolation among populations, which limits gene flow and favors inbreeding. A high genetic differentiation value (F<sub>ST</sub>) of 0.21, indicates high variability among populations. Measures based on the alleles frequency, showed a larger variability within populations (80.3%) than among populations (19.7%). Genetic distances between populations showed high differences within accessions coming from Rondonia (Jaru) and those from Amazonas (and Pirarucu Tarumã) and Roraima (Urubu). The dendogram made by the UPGMA method, showed two major groups and five subgroups related geographically. Results proved EST-SSR marker's utility in genetic diversity studies among BAG of camu-camu. These results will be useful in planning new collections, germplasm conservation and population variability analysis, as well as directional crossover using divergent genotypes; which will contribute to camu-camu breeding in Amazonian countries. </p>

scholarly journals Genetic diversity and relatedness within and between species of the genus Oligoryzomys (Rodentia; Sigmodontinae)

2007 ◽  
Vol 67 (1) ◽  
pp. 153-160 ◽  
Author(s):  
A. Trott ◽  
SM. Callegari-Jacques ◽  
LFB. Oliveira ◽  
A. Langguth ◽  
MS. Mattevi
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Genetic Variation ◽  
Genetic Variability ◽  
Genetic Heterogeneity ◽  
Rain Forest ◽  
Rapd Analysis ◽  
Genetic Distances ◽  
Wide Area ◽  
Atlantic Rain Forest

A RAPD analysis on six species of the rodent genus Oligoryzomys trapped in a wide area (ranging from 01° N to 32° S) of Brazilian territory was performed in order to determine the levels of genetic variability within and between its populations and species. One-hundred and ninety-three animals were collected in 13 different sites (corresponding to 17 samples) located at Pampas, Atlantic Rain Forest, Cerrado, and Amazon domains. Oligoryzomys sp., O. nigripes (8 populations), O. flavescens (4 populations), O. moojeni, O. stramineus, and O. fornesi were the taxa analyzed. Of the 20 primers tested, 4 generated a total of 75 polymorphic products simultaneously amplified in 151 specimens. Various diversity estimators analyzed showed considerable differences between species and populations, indicating a great genetic variation occurring in the Oligoryzomys taxa investigated. A cluster analysis was made using Nei's standard genetic distances, however, it did not correlate the genetic heterogeneity of the species and populations with the geographical areas.

scholarly journals Molecular Genetic Variability of Spigelia marilandica and S. gentianoides

2015 ◽  
Vol 140 (2) ◽  
pp. 120-128
Author(s):  
Amanda J. Hershberger ◽  
Tracie M. Jenkins ◽  
Carol Robacker
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Variability ◽  
Gene Diversity ◽  
Molecular Genetic ◽  
Genetic Distances ◽  
Population Variation ◽  
Group Method ◽  
Polymorphism Analysis ◽  
Two Samples

Despite the ecologic and ornamental potential of southeastern U.S. native Spigelia, little is known about the intraspecific or the interpopulation genetic variation. The southeastern U.S. native Spigelia habitat is becoming more and more fragmented as a result of human activity, making it imperative to gain an understanding of natural genetic variation among and within species and populations for the purpose of obtaining variability for plant breeding and preserve the genetic variability in Spigelia. Therefore, the objective of this study was to use amplified fragment length polymorphism analysis to determine interspecific and intraspecific genetic variation and to evaluate gene flow. Thirteen populations of two species of native Spigelia, S. marilandica (SM), S. gentianoides var. gentianoides (SGG), and S. gentianoides var. alabamensis (SGA), were analyzed using four primer pairs that amplified a total of 269 bands. Based on analysis of molecular variance and estimates of Nei’s coefficients of gene diversity (percentage of polymorphic loci, average genetic diversity within populations, average genetic diversity within species, and proportion of species genetic diversity attributed to among population variation), the majority of variation found in Spigelia occurs within populations. Both among-species and among-population variation was low, likely the effect of common ancestry as well as relatively frequent introgression among individuals (and populations) of Spigelia. When all individuals were evaluated using Nei’s unbiased genetic distances and viewed as a unweighted pair group method with arithmetic mean phenogram, three main groups were shown, one with two samples of SGG from one population, one with 13 individuals from both SGG populations used in this study, and one with all of the SM, SGA, and remaining SGG individuals. Further evaluation using STRUCTURE software showed introgression between populations and species, although all allele clusters have not entirely introgressed into all populations. The significance of these results is discussed in relation to breeding in Spigelia.

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