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 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 Genomic and demographic processes differentially influence genetic variation across the X chromosome

2021 ◽  
Author(s):  
Daniel J. Cotter ◽  
Timothy H. Webster ◽  
Melissa A. Wilson
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Linkage Disequilibrium ◽  
X Chromosome ◽  
Global Scale ◽  
Careful Consideration ◽  
Human Populations ◽  
Evolutionary Forces ◽  
Ideal System ◽  
Demographic Patterns

AbstractMutation, recombination, selection, and demography affect genetic variation across the genome. Increased mutation and recombination both lead to increases in genetic diversity in a region-specific manner, while complex demographic patterns shape patterns of diversity on a more global scale. The X chromosome is particularly interesting because it contains several distinct regions that are subject to different combinations and strengths of these processes, notably the pseudoautosomal regions (PARs) and the X-transposed region (XTR). The X chromosome thus can serve as a unique model for studying how genetic and demographic forces act in different contexts to shape patterns of observed variation. Here we investigate diversity, divergence, and linkage disequilibrium in each region of the X chromosome using genomic data from 26 human populations. We find that both diversity and substitution rate are consistently elevated in PAR1 and the XTR compared to the rest of the X chromosome. In contrast, linkage disequilibrium is lowest in PAR1 and highest on the non-recombining X chromosome, with the XTR falling in between, suggesting that the XTR (usually included in the non-recombining X) may need to be considered separately in future studies. We also observed strong population-specific effects on genetic diversity; not only does genetic variation differ on the X and autosomes among populations, but the effects of linked selection on the X relative to autosomes have been shaped by population-specific history. The substantial variation in patterns of variation across these regions provides insight into the unique evolutionary history contained within the X chromosome.Significance StatementDemography and selection affect the X chromosome differently from non-sex chromosomes. However, the X chromosome can be subdivided into multiple distinct regions that facilitate even more fine-scaled assessment of these processes. Here we study regions of the human X chromosome in 26 populations to find evidence that recombination may be mutagenic in humans and that the X-transposed region may undergo recombination. Further we observe that the effects of selection and demography act differently on the X chromosome relative to the autosomes across human populations. Together, our results highlight profound regional differences across the X chromosome, simultaneously making it an ideal system for exploring the action of evolutionary forces as well as necessitating its careful consideration and treatment in genomic analyses.

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.

Genetic Diversity and Population Genetic Structure in the Rare Chittering Grass Wattle, Acacia anomala Court

1988 ◽  
Vol 36 (3) ◽  
pp. 273 ◽  
Author(s):  
DJ Coates
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Structure ◽  
Population Genetic Structure ◽  
Population Genetic ◽  
Genetic System ◽  
Small Population ◽  
Vegetative Multiplication ◽  
The Mean ◽  
Allozyme Loci

There are 10 known populations of Acacia anomala occurring in two small disjunct groups some 30 km apart. The Chittering populations reproduce sexually whereas the Kalamunda populations appear to reproduce almost exclusively by vegetative multiplication. The level and distribution of genetic variation were studied at 15 allozyme loci. Two loci were monomorphic in all populations. In the Chittering populations the mean number of alleles per locus was 2.0 and the expected panmictic heterozygosity (genetic diversity) 0.209. In the Kalamunda populations the mean number of alleles per locus was 1.15 and the expected panmictic heterozygosity 0.079, although the observed heterozygosity of 0.150 was only marginally less than the Chittering populations (0.177). These data support the contention that the Chittering populations are primarily outcrossing whereas the Kalamunda populations are clonal, with each population consisting of individuals with identical and, in three of the four populations, heterozygous, multilocus genotypes. The level of genetic diversity within the Chittering populations is high for plants in general even though most populations are relatively smsll and isolated. It is proposed that either the length of time these populations have been reduced in size and isolated is insufficient for genetic diversity to be reduced or the genetic system of this species is adapted to small population conditions. Strategies for the adequate conservation of the genetic resources of Acacia anomala are discussed.

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)

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.

scholarly journals Genetic polymorphism and natural selection of circumsporozoite protein in Myanmar Plasmodium vivax

2020 ◽  
Vol 19 (1) ◽  
Author(s):  
Tuấn Cường Võ ◽  
Hương Giang Lê ◽  
Jung-Mi Kang ◽  
Mya Moe ◽  
Haung Naw ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Natural Selection ◽  
Plasmodium Vivax ◽  
Surface Protein ◽  
Genetic Profile ◽  
Repeat Region ◽  
Polymorphic Pattern ◽  
High Level ◽  
Global Population ◽  
Selection Of

Abstract Background Circumsporozoite surface protein (CSP) of malaria parasites has been recognized as one of the leading vaccine candidates. Clinical trials of vaccines for vivax malaria incorporating Plasmodium vivax CSP (PvCSP) have demonstrated their effectiveness in preventing malaria, at least in part. However, genetic diversity of pvcsp in the natural population remains a major concern. Methods A total of 171 blood samples collected from patients infected with Plasmodium vivax in Myanmar were analysed in this study. The pvcsp was amplified by polymerase chain reaction, followed by cloning and sequencing. Polymorphic characteristics and natural selection of pvcsp population in Myanmar were analysed using DNASTAR, MEGA6 and DnaSP programs. The polymorphic pattern and natural selection of publicly accessible global pvcsp sequences were also comparatively analysed. Results Myanmar pvcsp sequences were divided into two subtypes VK210 and VK247 comprising 143 and 28 sequences, respectively. The VK210 subtypes showed higher levels of genetic diversity and polymorphism than the VK247 subtypes. The N-terminal non-repeat region of pvcsp displayed limited genetic variations in the global population. Different patterns of octapeptide insertion (ANKKAEDA in VK210 and ANKKAGDA in VK247) and tetrapeptide repeat motif (GGNA) were identified in the C-terminal region of global pvcsp population. Meanwhile, the central repeat region (CRR) of Myanmar and global pvcsp, both in VK210 and VK247 variants, was highly polymorphic. The high level of genetic diversity in the CRR has been attributed to the different numbers, types and combinations of peptide repeat motifs (PRMs). Interestingly, 27 and 5 novel PRMs were found in Myanmar VK210 and VK247 variants, respectively. Conclusion Comparative analysis of the global pvcsp population suggests a complex genetic profile of pvcsp in the global population. These results widen understanding of the genetic make-up of pvcsp in the global P. vivax population and provide valuable information for the development of a vaccine based on PvCSP.

scholarly journals Forest decline has not reduced genetic diversity of naturally regenerated Norway spruce from the Beskids, Poland

2015 ◽  
Vol 64 (1-6) ◽  
pp. 270-278 ◽  
Author(s):  
Elżbieta Chomicz-Zegar ◽  
J. A. Nowakowska ◽  
A. Tereba
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Norway Spruce ◽  
Forest Decline ◽  
Gene Diversity ◽  
Young Generation ◽  
Primeval Forest ◽  
Initial Stage ◽  
Spruce Stands ◽  
High Level

AbstractNorway spruce forests decline in the Beskids raises concerns about reduction of genetic variation in a next generation of forest. We aim to determine whether the genetic diversity in declining spruce stands was successfully transmitted to its self-seeded progeny. Using three nuclear microsatellite markers, we carried out the genetic assessment of naturally regenerated progeny and compered them with their maternal stands at an initial stage of decline. We investigated three spruce stands from the Śląski and Żywiecki Beskid and one primeval forest from the Tatras, as a reference. We noticed a high level of gene diversity, allelic richness and an effective number of alleles in progeny of all stands, without differences between declining stands from the Beskids and the primeval forest. The gene diversity was similar in maternal trees and their offspring. Higher gene diversity and generally higher number of alleles were noticed in young generation of stands. Genetic identity between generations was high in analyzed seed stands and the highest in the primeval forest. The results we presented indicate no significant effect of drastic reduction in the population size due to the forest decline on the level of genetic variation in self-seeded progeny of Norway spruce from the Beskids.

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