scholarly journals Genetic Diversity of Two Evergreen Oaks [Quercus suber (L.) and Quercus ilex subsp. rotundifolia (Lam.)] in Portugal using AFLP Markers

2006 ◽  
Vol 55 (1-6) ◽  
pp. 105-118 ◽  
Author(s):  
A. C. Coelho ◽  
M. B. Lima ◽  
D. Neves ◽  
A. Cravador
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Numerical Taxonomy ◽  
Quercus Ilex ◽  
Quercus Suber ◽  
Cork Oak ◽  
Holm Oak ◽  
Genetic Profile ◽  
Polymorphic Markers ◽  
High Level

Abstract The genetic variability of cork oak (Quercus suber, L.) in Portugal was evaluated by AFLP using five primer combinations. Three hundred and thirteen trees from three geographically contrasting regions exhibited a high level of genetic variation. The genetic profile of each individual is composed of 291 loci, randomly positioned in the genome and consists of monomorphic and polymorphic fragments. Similarities and dissimilarities among the individuals were quantitatively evaluated by numerical taxonomy. The overall sample shows a proportion of AFLP polymorphic markers of 71%, denoting a high level of variability. Ninety percent of the polymorphic markers identified in cork oak genotypes are uniformly distributed throughout the cork oak populations of Algarve, Alentejo and Trás-os-Montes regions. The coefficients of genetic similarity vary from 0.61 to 0.88 implying that 60% of fragments found are common. A sample of 52 holm oak [Quercus ilex subsp. rotundifolia (Lam.)] trees from overlapping areas was also analysed by AFLP with the same five primer combinations. However the codification of markers together with those selected on cork oak profiles was feasible with only one primer combination due to an apparent much higher polymorphism. AFLP and numerical taxonomy analysis enabled to differentiate the taxa and showed that the level of similarity observed between the profiles of the individuals from holm oak species was lower than that observed in cork oak, implying that apparently the degree of polymorphism is higher in Q. ilex subsp. rotundifolia than that quantified in Q. suber. A Bayesian approach was used to assess Q. suber total genetic diversity (Ht = 0.2534, P < 0.001) of which 1.7% (Fst = 0.0172, P < 0.001) was assigned to differences among populations. Analysis of molecular variance (AMOVA) showed that most genetic variation is comprised within populations (96%) while 3.6% is among populations (Φst = 0.036, P < 0.001). Differences among populations within geographic regions account for 2.6% (Φsc = 0.026, P < 0.001) of the total variation and only 1.3% (Φct = 0.013, P = 0.007) is attributed to variation among regions denoting little differentiation of populations over a range of 700 km.

scholarly journals Genetic Diversity and Evolutionary Relationships of Chinese Pepper Based on nrDNA Markers

Forests ◽  
2020 ◽  
Vol 11 (5) ◽  
pp. 543
Author(s):  
Shijing Feng ◽  
Jinshuang Niu ◽  
Zhenshan Liu ◽  
Lu Tian ◽  
Xiangyuan Wang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic System ◽  
Haplotype Network ◽  
Evolutionary Relationships ◽  
Genetic Profile ◽  
Coding Region ◽  
Demographic Trends ◽  
Evolutionary Forces ◽  
High Level

Chinese pepper, referring to Zanthoxylum bungeanum Maxim. and Zanthoxylum armatum DC. species, is an important spice crop that has long attracted people’s interest due to its extensive application in Asian cuisine to improve taste. Numerous cultivars have been developed during the long history of domestication and cultivation. However, little to no information is available on the genetic diversity and evolutionary relationships of Chinese pepper cultivars and their historical diversification has not been clarified. Herein, we sequenced two nrDNA non-coding region markers, the external transcribed spacer (ETS) and the internal transcribed spacer 2 (ITS2), to assess genetic diversity and phylogenetic relationships among 39 cultivated and wild populations of Chinese pepper from eight provinces and to address the question of ancient demographic trends which were probably influenced by changing climate during evolutionary history. In total, 31 haplotypes were identified based on 101 polymorphism sites. Our results revealed relatively high level of genetic variation despite long-term cultivation of this crop. AMOVA revealed that genetic variation existed predominantly within provinces rather than among provinces. The genetic structure result based on haplotype network analysis largely reflected historical records, which suggested a Gansu origin for Chinese pepper and an ancient west-to-east spread of Chinese pepper circulating in China. We also provided evidence that changing Pleistocene climates had shaped the demographic trends of Chinese pepper. Taken together, our findings not only suggest that Chinese pepper is a dynamic genetic system that responds to evolutionary forces, but it also provides a fundamental genetic profile for the conservation and responsible exploitation of the extant germplasm of Chinese pepper and for improving the genetic basis for breeding the cultivars.

scholarly journals The use of cotyledon proteins to assess the genetic diversity in sweet holm oak

2009 ◽  
Vol 55 (No. 11) ◽  
pp. 526-531 ◽  
Author(s):  
A. Martín M ◽  
R. Navarro-Cerrillo ◽  
P. Ortega ◽  
B. Alvarez J
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Quercus Ilex ◽  
Storage Proteins ◽  
Allelic Variation ◽  
Seed Proteins ◽  
Wide Distribution ◽  
Holm Oak ◽  
Additional Tool ◽  
The Mediterranean Basin

Sweet holm oak (<I>Quercus ilex</I> ssp. <I>ballota</I> Desf. Samp.) is an important broad-leaved tree spread in the Mediterranean basin. In Spain, few studies on the genetic variability of this species have been displayed. Storage seed proteins are a useful tool in the evaluation of the genetic variability of many species. The objective of this study was to analyze the usefulness of cotyledon proteins as markers of the genetic diversity in sweet holm oak. The evaluated populations were highly polymorphic for the glutelins, being detected up to 32 polymorphic bands with a wide distribution among all them. Considering all evaluated populations, about 35.8% of the total allelic variation was distributed among populations. This method of analysis of cotyledon storage proteins (glutelins) could be considered an additional tool for the evaluation of genetic diversity in this species.

Genetic diversity in Elymus caninus as revealed by isozyme, RAPD, and microsatellite markers

Genome ◽  
1999 ◽  
Vol 42 (3) ◽  
pp. 420-431 ◽  
Author(s):  
Gen-Lou Sun ◽  
Oscar Díaz ◽  
Björn Salomon ◽  
Roland von Bothmer
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Microsatellite Markers ◽  
Correlation Coefficients ◽  
Geographic Isolation ◽  
Elymus Caninus ◽  
Distance Matrices ◽  
High Level ◽  
Mantel’S Test ◽  
Similarity Matrices

Genetic diversity of 33 Elymus caninus accessions was investigated using isozyme, RAPD, and microsatellite markers. The three assays differed in the amount of polymorphism detected. Microsatellites detected the highest polymorphism. Six microsatellite primer pairs generated a total of 74 polymorphic bands (alleles), with an average of 15.7 bands per primer pair. Three genetic similarity matrices were estimated based on band presence or absence. Genetic diversity trees (dendrograms) were derived from each marker technique, and compared using Mantel's test. The correlation coefficients were 0.204, 0.267, and 0.164 between isozyme and RAPD distance matrices, RAPD and microsatellite distance matrices, and between isozyme and microsatellite distance matrices, respectively. The three methodologies gave differing views of the amount of variation present but all showed a high level of genetic variation in E. caninus. The following points may be drawn from this study whether based on RAPD, microsatellite, or isozyme data: (i) The Icelandic populations are consistently revealed by the three dendrograms. The congruence of the discrimination of this accession group by RAPD, microsatellite, and isozyme markers suggests that geographic isolation strongly influenced the evolution of the populations; (ii) The degree of genetic variation within accessions was notably great; and (iii) The DNA-based markers will be the more useful ones in detecting genetic diversity in closely related accessions. In addition, a dendrogram, which took into account all fragments produced by isozymes, RAPDs, and microsatellites, reflected better the relationships than did dendrograms based on only one type of marker.Key words: Elymus caninus, genetic diversity, isozymes, RAPDs, microsatellites.

scholarly journals Effect of geographical discontinuity on genetic variation in Quercus ilex L. (holm oak). Evidence from enzyme polymorphism

Heredity ◽  
1995 ◽  
Vol 74 (6) ◽  
pp. 590-606 ◽  
Author(s):  
H Michaud ◽  
L Toumi ◽  
R Lumaret ◽  
T X Li ◽  
F Romane ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Quercus Ilex ◽  
Enzyme Polymorphism ◽  
Holm Oak

Genetic variation within and among populations of Camelliajaponica (Theaceae) in Korea

1996 ◽  
Vol 26 (4) ◽  
pp. 537-542 ◽  
Author(s):  
Myong Gi Chung ◽  
Soon Suk Kang
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Pollen Dispersal ◽  
Island Populations ◽  
Generation Times ◽  
Genetic Diversity And Structure ◽  
Stump Sprouting ◽  
Ability To Regenerate ◽  
The Mean ◽  
High Level

The genetic diversity and structure of 17 Korean populations of Camelliajaponica L., a broad-leaved evergreen tree, was examined. Although most populations are restricted to several islands near the southern and southwestern coast of the Korean Peninsula, they maintain higher levels of genetic variation within populations than do long-lived, woody angiosperms. For example, 13 of 16 loci examined were polymorphic in at least one population, the mean number of alleles per locus was 2.63, and mean expected heterozygosity was 0.265. These values were comparable with those for continuously distributed, mainland populations of C. japonica in Japan. However, a considerably high level of heterozygote deficiency was observed in Korean populations of C. japonica (mean FIS = 0.202). About 13% of the total genetic variation was found among populations (GST = 0.129). Indirect estimates of the number of migrants per generation (1.69, calculated from FST; 2.14, calculated from the mean frequency of eight private alleles) indicate that gene flow among island populations is moderate. Factors contributing to the high levels of genetic diversity found in the entire species of C. japonica include long generation times, ability to regenerate by stump sprouting, predominant outcrossing induced by animal vectors, and occasional pollen dispersal by birds.

scholarly journals Genetic variation among Iranian alfalfa (Medicago sativa L.) populations based on RAPD markers

2011 ◽  
Vol 18 (2) ◽  
pp. 93-104 ◽  
Author(s):  
Fatemeh Mohammadzadeh ◽  
Hassan Monirifar ◽  
Jalal Saba ◽  
Mostafa Valizadeh ◽  
Ahmad Razban Haghighi ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Genetic Variation ◽  
Breeding Population ◽  
Genetic Distances ◽  
Analysis Of Molecular Variance ◽  
Molecular Variance ◽  
Geographical Patterns ◽  
Plant Taxon ◽  
High Level

Genetic diversity among and within 10 populations of Iranian alfalfa, from different areas of Azarbaijan, Iran was analyzed by screening DNA from seeds of individual plants and bulk samples. In individual study, 10 randomly amplified polymorphic DNA (RAPD) primers produced 156 polymorphic bands and a high level of genetic diversity was observed within populations. The averages of total and within population genetic diversity were 0.2349 and 0.1892, respectively. Results of analysis of molecular variance (AMOVA) showed the great genetic variation existed within populations (81.37%). These Results were in agreement with allogamous and polyploid nature of alfalfa. Cluster analysis was performed based on Nei’s genetic distances resulting in grouping into 3 clusters which could separate breeding population from other populations. Results of cluster analysis were in consistent with morphological and geographical patterns of populations. The results of bulk method were different from individual analysis. Our results showed that RAPD analysis is a suitable method to study genetic diversity and relationships among alfalfa populations.Keywords: Alfalfa; RAPD; Genetic diversity; Analysis of Molecular Variance; Cluster analysis.DOI: http://dx.doi.org/10.3329/bjpt.v18i2.9296Bangladesh J. Plant Taxon. 18: (2): 93-104, 2011 (December)

scholarly journals Diversity of Biscogniauxia mediterranea within Single Stromata on Cork Oak

2014 ◽  
Vol 2014 ◽  
pp. 1-5 ◽  
Author(s):  
Joana Henriques ◽  
Filomena Nóbrega ◽  
Edmundo Sousa ◽  
Arlindo Lima
Keyword(s):  
Polymerase Chain Reaction ◽  
Genetic Variation ◽  
Genetic Variability ◽  
Geographical Location ◽  
Cork Oak ◽  
Microsatellite Primers ◽  
Chain Reaction ◽  
Disease Symptoms ◽  
Polymerase Chain ◽  
High Level

Charcoal canker, caused by the fungus Biscogniauxia mediterranea, is one of the most frequent diseases of cork oak in Portugal. The pathogen has been considered a secondary invader that attacks only stressed hosts; however, in recent years, an increasing number of young trees exhibiting the disease symptoms have been recorded. A collection of monoascosporic cultures isolated from single stromata of B. mediterranea in cork oak from different locations was analyzed by means of microsatellite—Primed Polymerase Chain Reaction—using three microsatellite primers, in order to detect the genetic variation of the population thus discussing its plasticity and ability to adapt to different conditions. The results showed a high level of genetic variability among isolates obtained from the same stroma, being impossible to distinguish isolates from individual stromata neither from different geographical location.

Genetic diversity of arctic bramble (Rubus arcticus L. subsp. arcticus) as measured by amplified fragment length polymorphism

2003 ◽  
Vol 81 (8) ◽  
pp. 805-813 ◽  
Author(s):  
Hannele Lindqvist-Kreuze ◽  
Hilkka Koponen ◽  
Jari P.T Valkonen
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Fragment Length ◽  
Natural Habitat ◽  
Genotypic Variation ◽  
Natural Populations ◽  
Shannon Index ◽  
Length Polymorphisms ◽  
Amplified Fragment Length Polymorphisms ◽  
High Level

The levels of genotypic and genetic variation were estimated in six natural populations of arctic bramble (Rubus arcticus L. subsp. arcticus) in Finland. Using three primer combinations, a total of 117 amplified fragment length polymorphisms (AFLP) were found. The results were highly reproducible and allowed identification of 78 genets among the 122 plants of arctic bramble studied. Genotypic variation measured as Simpson index (D) was high in all populations, ranging from 0.72 to 0.94. Also, the level of genetic variation measured as Shannon index was relatively high in all populations, ranging from 0.19 to 0.32 (average 0.26). The high levels of genetic diversity indicate that sexual reproduction has played a significant role in these populations. The hierarchical analysis of molecular variance (AMOVA) partitioned 48% of the genetic variation among populations, suggesting a high level of population differentiation and a low level of interpopulation gene flow. Genetic diversity among ten currently grown cultivars of arctic bramble and hybrid arctic bramble (R. arcticus subsp. arcticus × R. arcticus subsp. stellatus) was large, and the subspecies were clearly distinguished from each other based on the AFLP marker data.Key words: AFLP, AMOVA, population, natural habitat, Rubus arcticus subsp. arcticus, Rubus arcticus subsp. stellatus.

Analysis of genetic diversity and spatial structure in Tunisian populations of Hordeum marinum ssp. marinum based on molecular markers

2019 ◽  
Vol 157 (5) ◽  
pp. 399-412 ◽  
Author(s):  
W. Saoudi ◽  
M. Badri ◽  
M. Gandour ◽  
A. Smaoui ◽  
C. Abdelly ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Random Amplified Polymorphic Dna ◽  
Geographic Origin ◽  
Conservation Strategies ◽  
Entire Collection ◽  
High Discrimination ◽  
High Level ◽  
Dna Primers ◽  
Altitudinal Difference

AbstractHordeum marinum commonly known as sea barley is a salinity-tolerant species of grass. In the current study, 150 lines from ten populations of H. marinum ssp. marinum collected from five Tunisian bioclimatic sites were screened for polymorphism with 13 selected random amplified polymorphic DNA primers. Results exhibited a high level of polymorphism (160 polymorphic bands with an average of 12.46 per primer) and a high level of genetic diversity in all the studied populations (on average UHe = 0.247 and I = 0.358). High discrimination capacity was found for the 13 primers and a combination of three allowed assignation of a unique profile for each of the 150 lines. The partition of genetic diversity with Analysis of Molecular Variance suggested that the majority of genetic variation (67%) was within populations. The components between-populations within ecoregions and between-ecoregions explained 21 and 12%, respectively, of the total genetic variance. There was no significant association of population differentiation (ФPT) with geographical distance or altitudinal difference. Results also showed that the 150 lines grouped into three clusters with no respect to geographic origin. A sub-set of 13 lines was identified, which captured the maximum genetic diversity of the entire collection. The genetic variation found in this collection of H. marinum is deemed to be useful in formulating conservation strategies for this species.

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