scholarly journals Analysis of genetic diversity among Iranian populations of Ficus carica L. (Moraceae)

2019 ◽  
Vol 5 (3) ◽  
pp. 131-138
Author(s):  
M.R. Zolfaghari ◽  
F. Salimpour ◽  
F. Sharifnia ◽  
S.J. Marandi
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Structure Analysis ◽  
Natural Populations ◽  
Ficus Carica ◽  
Molecular Technique ◽  
Limited Gene Flow ◽  
Genetic Clustering ◽  
Clustering Patterns ◽  
Nei's Genetic Distance

Ficus carica L. is a species of Moraceae family that has been cultivated in different parts of the world from ancient time. Its fruit is eaten by human and has several medicinal properties. This species widely grows and cultivated in various parts of Iran. For this, in the current study, we investigated infraspecific genetic variation and population structure of F. carica in the country. 14 natural populations of F. carica were collected and their genomic DNA were extracted and tested with RAPD molecular technique. Parameters of population’s genetic diversity varied among the studied populations. In addition, AMOVA test revealed significant variations among the populations.  The studied populations clustered separately in UPGMA tree of RAPD data, moreover PCA and MDS plots produced similar results. STRUCTURE analysis revealed the best number of k = 9. Based on Nei’s genetic distance, we had nine distinct groups. Genetic clustering patterns according to UPGMA trees of RAPD data and Nei’s genetic distance were more similar with the results of STRUCTURE analysis. The small amount of Nm) the product of the effective size of individual populations (N) and the rate of migration among them (m) (value showed limited gene flow among the studied populations, therefore it seems that high genetic variations among these populations may be related less or few amount of gene exchange among populations.

Genetic Diversity and Genetic Structure Analysis of the Natural Populations of Lilium brownii from Guangdong, China

2009 ◽  
Vol 47 (7-8) ◽  
pp. 503-510 ◽  
Author(s):  
Yong-fang Huang ◽  
Mao-xun Yang ◽  
Hao Zhang ◽  
Xue-ying Zhuang ◽  
Xue-hui Wu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Structure Analysis ◽  
Natural Populations

Genetic structure and proposed conservation strategy for natural populations of Calycanthus chinensis Cheng et S.Y. Chang (Calycanthaceae)

2008 ◽  
Vol 88 (1) ◽  
pp. 179-186 ◽  
Author(s):  
Chu-Chuan Fan ◽  
Nicola Pecchioni ◽  
Long-Qing Chen
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Genetic Differentiation ◽  
Genetic Distance ◽  
Gene Diversity ◽  
Genetic Relationships ◽  
Natural Populations ◽  
Population Level ◽  
Conservation Strategy ◽  
Information Index

Calycanthus chinensis Cheng et S.Y. Chang, a tertiary relic species in China, is a shade-loving and deciduous bush withan elegant shape and beautiful flower of high ornamental value. It was widely planted in gardens and miniature scapes in China.The objective of this study was to characterize the genetic variation and structure in the three extant populations of the species, in order to provide useful information for a future conservation strategy. Twenty-two of 120 RAPD primers were selected and a total of 257 stable and clear DNA fragments were scored. Calycanthus chinensis showed a lower level of genetic diversity. At the population level, the percentage of polymorphic loci, Nei's gene diversity and Shannon’s information index were 40.9%, 0.1641 and 0.2386, respectively; while at the species level, the corresponding values were 59.1%, 0.2097 and 0.3123, respectively. The estimates of genetic differentiation based on Shannon’s information index (0.2360), Nei’s gene diversity (0.2175) and AMOVA (24.94%) were very similar, and significantly higher than the average genetic differentiation reported in outcrossed spermatophyte. So it suggested high genetic differentiation emerged among populations of C. chinensis. Genetic relationships among populations were assessed by Nei’s standard genetic distance, which suggested that the Tiantai population was genetically distinct from the other two populations. Moreover, the genetic distance was significantly correlated with geographical distance among populations (r = 0.997, t > t0.05). The gene flow (Nm) was 0.8994, indicating that gene exchange among populations was restricted. A conservation strategy was proposed based on the low gene flow and habitat deterioration, which are contributing to the endangered status of this species. Key words: Genetic diversity, endangered plant, population genetics, RAPD

Evaluation of the genetic diversity and population structure of five indigenous and one introduced Chinese goose breeds using microsatellite markers

2012 ◽  
Vol 92 (4) ◽  
pp. 417-423 ◽  
Author(s):  
Jinjun Li ◽  
Qingyuan Yuan ◽  
Junda Shen ◽  
Zhengrong Tao ◽  
Guoqing Li ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Differentiation ◽  
Genetic Distance ◽  
Microsatellite Markers ◽  
Genetic Relationships ◽  
Evolutionary Relationships ◽  
Distance Estimate ◽  
Cluster Analyses ◽  
Nei's Genetic Distance

Li, J., Yuan, Q., Shen, J., Tao, Z., Li, G., Tian, Y., Wang, D., Chen, L. and Lu, L. 2012. Evaluation of the genetic diversity and population structure of five indigenous and one introduced Chinese goose breeds using microsatellite markers. Can. J. Anim. Sci. 92: 417–423. The aim of this study was to determine the genetic diversity and evolutionary relationships among five indigenous Chinese goose breeds and one introduced goose breed using 29 microsatellite markers. A total of 334 distinct alleles were observed across the six breeds, and 45 of the 334 alleles (13.5%) were unique to only one breed. The indigenous geese showed higher diversity in terms of the observed number of alleles per locus (4.48–5.90) and observed heterozygosity (0.46–0.53) compared with the introduced breed (3.97 and 0.29, respectively). The pairwise genetic differentiation (FST) between the six goose breeds ranged from 0.04 between Panshi Grey goose (PS) and Yongkang Grey goose to 0.47 between PS and Landes goose; similarly, Nei's genetic distance varied between 0.25 and 0.75. However, the FST between the indigenous Chinese goose breeds was very small. In addition, genetic distance estimate, phylogenic, and cluster analyses of the genetic relationships and population structure revealed that some indigenous goose breeds had hybridized more frequently, resulting in a loss of genetic distinctiveness.

scholarly journals Genetic Diversity and Population Structure Analysis of Triticum aestivum L. Landrace Panel from Afghanistan

Genes ◽  
2021 ◽  
Vol 12 (3) ◽  
pp. 340
Author(s):  
Muhammad Massub Tehseen ◽  
Deniz Istipliler ◽  
Zakaria Kehel ◽  
Carolina P. Sansaloni ◽  
Marta da Silva Lopes ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Distance ◽  
Bread Wheat ◽  
Structure Analysis ◽  
Geographic Origin ◽  
Climatic Conditions ◽  
Population Structure Analysis ◽  
North Eastern ◽  
Wheat Landraces

Landraces are a potential source of genetic diversity and provide useful genetic resources to cope with the current and future challenges in crop breeding. Afghanistan is located close to the centre of origin of hexaploid wheat. Therefore, understanding the population structure and genetic diversity of Afghan wheat landraces is of enormous importance in breeding programmes for the development of high-yielding cultivars as well as broadening the genetic base of bread wheat. Here, a panel of 363 bread wheat landraces collected from seven north and north-eastern provinces of Afghanistan were evaluated for population structure and genetic diversity using single nucleotide polymorphic markers (SNPs). The genotyping-by-sequencing of studied landraces after quality control provided 4897 high-quality SNPs distributed across the genomes A (33.75%), B (38.73%), and D (27.50%). The population structure analysis was carried out by two methods using model-based STRUCTURE analysis and cluster-based discriminant analysis of principal components (DAPC). The analysis of molecular variance showed a higher proportion of variation within the sub-populations compared with the variation observed as a whole between sub-populations. STRUCTURE and DAPC analysis grouped the majority of the landraces from Badakhshan and Takhar together in one cluster and the landraces from Baghlan and Kunduz in a second cluster, which is in accordance with the micro-climatic conditions prevalent within the north-eastern agro-ecological zone. Genetic distance analysis was also studied to identify differences among the Afghan regions; the strongest correlation was observed for the Badakhshan and Takhar (0.003), whereas Samangan and Konarha (0.399) showed the highest genetic distance. The population structure and genetic diversity analysis highlighted the complex genetic variation present in the landraces which were highly correlated to the geographic origin and micro-climatic conditions within the agro-climatic zones of the landraces. The higher proportions of admixture could be attributed to historical unsupervised exchanges of seeds between the farmers of the central and north-eastern provinces of Afghanistan. The results of this study will provide useful information for genetic improvement in wheat and is essential for association mapping and genomic prediction studies to identify novel sources for resistance to abiotic and biotic stresses.

scholarly journals A MIXED MODEL OF MUTATION FOR ELECTROPHORETIC IDENTITY OF PROTEINS WITHIN AND BETWEEN POPULATIONS

Genetics ◽  
1976 ◽  
Vol 83 (2) ◽  
pp. 423-432
Author(s):  
Wen-Hsiung Li
Keyword(s):  
Genetic Distance ◽  
Mixed Model ◽  
Present Model ◽  
Natural Populations ◽  
The Other ◽  
Effective Number ◽  
Infinite Allele Model ◽  
Stepwise Mutation ◽  
Allele Model ◽  
Nei's Genetic Distance

ABSTRACT A model which is a mixture of the model of infinite alleles and the Ohta-Kimura model of stepwise mutation has been proposed for the study of eletcrophoretic variants in natural populations. Mutations which alter the mobility of a protein are divided into two classes: stepwise mutations and nonstepwise mutations. It is assumed that stepwise mutations follow the Ohta-Kimura model while nonstepwise mutations follow the infinite allele model. It is then shown that even if the proportion of nonstepwise mutations is only 5%, with the other 95% stepwise mutations, the effective number of alleles given by the present model is considerably larger than that given by the Ohta-Kimura model of stepwise mutation. The result has also been applied to study Nei's genetic distance.

scholarly journals Genetic Diversity in Finger Millet Landraces revealed by RAPD and SSR Markers

2020 ◽  
Vol 8 (1) ◽  
pp. 1-11
Author(s):  
Bal Krishna Joshi ◽  
Darbin Joshi ◽  
Surya Kanta Ghimire
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Ssr Markers ◽  
Finger Millet ◽  
Rapd Marker ◽  
Principal Component ◽  
Genetic Potential ◽  
Diversity Assessment ◽  
Ssr Primers ◽  
Nei's Genetic Distance

Genetic diversity assessment is the preliminary work for development of variety and conservation of diversity. Finger millet is a very important crop in Nepal however, its genetic potential has not been fully utilized. Genetic diversity was assessed in forty landraces of finger millet using 9 RAPD and 5 SSR markers. These landraces were collected from Kaski and Dhading districts. None of single primers of these RAPD and SSR could separate all 40 landraces. The average number of bands were 6.33 and 7.8 per RAPD and SSR primers respectively. Mean polymorphism information content was of 0.314 for RAPD and 0.37 for SSR. Primer OPA-4 produced the highest number of bands and the lowest numbers of bands were produced by OPA-16. Among the SSR primers, SSR-06 produced the highest number of polymorphic bands and UGEP-53 produced the lowest bands. RAPD based dendrogram has generated four clusters and SSR based dendrogram has generated two clusters. In both dendrogram and principal component analyses, Purbeli landrace was found unique locating separately in the cluster and scatter plot. Nei's genetic distance produced by RAPD and SSR primers was similar that is 0.327 by RAPD and 0.296 by SSR markers. Genetic distance produced by SSR markers was higher than distance produced by RAPD marker. These landraces were from two districts and therefore have shown intermediate diversity. These molecular marker-based findings should would be more useful if we could link with agromorphological traits. Inclusion of large number of landraces collected from different areas are required to get higher level diversity in addition to associate genetic diversity with geographical sites. Groupings of these landraces could be useful for selecting landraces in breeding program as well as planning conservation program.

scholarly journals Genetic diversity of four cattle breeds using microsatellite markers

2003 ◽  
Vol 32 (1) ◽  
pp. 93-98 ◽  
Author(s):  
Marco Antonio Machado ◽  
Ivan Schuster ◽  
Mário Luiz Martinez ◽  
Ana Lúcia Campos
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Distance Matrix ◽  
Average Heterozygosity ◽  
Informative Locus ◽  
Holstein Breed ◽  
Cattle Breeds ◽  
Genetic Distance Matrix ◽  
Hardy Weinberg Equilibrium ◽  
Nei's Genetic Distance

Four cattle breeds (Gyr, Nellore, Guzerat and Holstein) were analyzed by amplification of genomic DNA using microsatellite loci to evaluate the genetic diversity within and among them. DNA samples of 18 animals from each breed were collected to access the genetic content of them. Allele frequencies were calculated and used to generate a Nei's genetic distance matrix what was used to build a dendrogram following UPGMA clustering. As expected, Holstein breed was the most distinct from the other breeds: 1.15 in relation to Gyr, 1.12 in relation to Nellore and 0.94 in relation to Guzerat. The closest genetic distance was 0.25 between Guzerat and Nellore. A total of 64 alleles in all four breeds were detected using nine microsatellite primers. Each breed showed 53% of the total number of alleles. The average number of alleles per locus was 7.11 ± 3.21. The most informative locus was BMS1237 with 53% of observed heterozygosity and the least informative locus was BMS3004 with 12% only. The average heterozygosity detected for the nine loci were 35% and the expected value for Hardy-Weinberg equilibrium was 53%. This low heterozygosity suggests a high endogamy level among the animals sampled within each breed.

scholarly journals Molecular Diversity Analysis of Somaclonal Variants of Potato (Solanum tuberosum L.) by Random Amplified Polymorphic DNA Markers

2021 ◽  
pp. 63-76
Author(s):  
Md Shamsuzzaman ◽  
Debu Kumar Bhattacharjya ◽  
Md. Shariful Islam ◽  
Md. Ekramul Hoque
Keyword(s):  
Genetic Diversity ◽  
Solanum Tuberosum ◽  
Genetic Distance ◽  
Solanum Tuberosum L ◽  
Random Amplified Polymorphic Dna ◽  
Somaclonal Variants ◽  
Somaclonal Variations ◽  
Similarity Indices ◽  
Young Leaves ◽  
Nei's Genetic Distance

Aims: An experiment was conducted to analyze the DNA fingerprinting and genetic diversity of nine potato (Solanum tuberosum L.) somaclonal variants and three check varieties. Place and Duration of Study: The experiment was carried out at the Biotechnology laboratory of the Department of Biotechnology, Faculty of Agriculture, Sher-e-Bangla Agricultural University, Dhaka-1207, Bangladesh during November, 2013 to December, 2014. Methodology: The somaclonal variants investigated were SIP-3, SIP-5, SVP-6, SVP-18, SVP-19, SVP-25, SVP-55, SVP-56 and SVP-68, while the check varieties were Cardinal, Diamant and Asterix. Six RAPD primers were used to perform PCR reaction after genomic DNA was extracted from young leaves. Results: The selected 6 primers produced total 54 distinct and differential amplified DNA bands of size range 88 bp to 3265 bp, where 47 bands (~87%) were polymorphic and 7 bands (~13%) were monomorphic. The pair-wise inter-genotype similarity indices were ranged from 61.59% to 93.55% with an average of 74.31%. The Nei’s genetic distance among 12 potato genotypes was estimated from 0.0972 to 0.6217 whereas, genetic identity was between 0.5370 and 0.9074. Here, the distantly linked accessions among the somaclonal variations with check varieties were SVP-6 (to Cardinal and Diamant) and SVP-25 (to Asterix). In addition, the UPGMA dendrogram segregated the 12 potato genotypes into two broad clusters containing 8 and 4 genotypes, respectively. Furthermore, the dendrogram also displayed the highest genetic distance between SVP-6 vs SVP-68 genotype pair. Conclusion: Significant relationship and diversity were found among the studied 12 genotypes. This genetic diversity among the potato genotypes would be utilized for further potato improvement.

Allozyme variations in six natural populations of scots pine (Pinus sylvestris) in Turkey

Biologia ◽  
2007 ◽  
Vol 62 (6) ◽  
Author(s):  
Behiye Bilgen ◽  
Nuray Kaya
Keyword(s):  
Genetic Variation ◽  
Pinus Sylvestris ◽  
Genetic Distance ◽  
Scots Pine ◽  
Natural Populations ◽  
Mean Value ◽  
Population Variation ◽  
Starch Gel Electrophoresis ◽  
The Mean ◽  
Nei's Genetic Distance

AbstractGenetic variation in six natural populations of Scots pine (Pinus sylvestris L.) was determined with isoenzyme analyses. For this purpose, haploid female gametophytes of seeds and horizontal starch gel electrophoresis technique were used. A total of 17 loci and 58 alleles were observed in studying 10 enzyme systems. The average proportion of polymorphic loci for populations ranged from 58.8% to 70.6%. The average number of alleles per locus per population was 2.65. The mean estimated expected heterozygosity (He) of populations was 0.294. A rather high proportion of genetic diversity (96.4%) was due to within-population variation and the remaining (3.6%) was due to variation among populations. The level of gene flow (Nem) was found to be 6.69 per generation. Nei’s genetic distance coefficient ranged from 0.006 to 0.027 (mean 0.017) among all possible population pairs. The mean value of Nei’s genetic distance is similar to the values reported for other European Scots pine populations. The low mean value of Nei’s genetic distance among populations is enough to explain low interpopulation variation. According to genetic variation parameters, three out of six populations (Akdagmadeni-Yozgat, Refahiye-Erzincan and Vezirkopru-Samsun) appear to be preferable populations for genetic conservation and forest tree breeding programs.

scholarly journals Comparing the effectiveness between issr and ssr markers in assessing genetic diversity of natural populations of Dacrydium elatum in Tay Nguyen, Vietnam

2018 ◽  
Vol 15 (2) ◽  
pp. 293-305
Author(s):  
Trần Thị Liễu ◽  
Vũ Thị Thu Hiền ◽  
Nguyễn Thị Liễu ◽  
Đinh Thị Phòng
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Ssr Markers ◽  
Genetic Similarity ◽  
Natural Populations ◽  
Population Level ◽  
Polymorphic Markers ◽  
Similarity Matrix ◽  
Similarity Coefficients ◽  
Molecular Variance

The two techniques, ISSR (27 markers) and SSR (20 markers), were used to compare the effectiveness and to assess genetic diversity of 70 Dacrydium elatum samples collected in Lam Dong, Kon Tum, Dak Lak, and Gia Lai. The results showed 38/47 polymorphic markers (23/27 ISSR and 15/20 SSR markers) and 180 amplified DNA fragments, in which 85/127 (66.93%) and 46/53 (86.79%) were polymorphic for ISSR and SSR markers, respectively. Generally, the average values among the genetic diversity parameters of the populations for SSR (Hj = 0.213; Ne = 1.566, I = 0.444; He = 0.301; h = 0.228; and PPB = 72.50%) were higher than those for ISSR (Hj = 0.155; Ne = 1.142, I = 0.125; He = 0.083; h = 0.074 and PPB = 25.07%). The correlation coefficient between genetic distance measured with ISSR and combining ISSR + SSR was higher (r = 0.92) than that measured with SSR and combining ISSR + SSR (r = 0.65). There was not much difference in the total level of molecular variance (AMOVA) among populations and among individuals when analyzing ISSR and SSR data separately or combining both data. The three dendrograms constructed based on similarity matrix generated by ISSR, SSR and ISSR + SSR data were similar and they all divided the 70 D. elatum samples into two main groups with genetic similarity coefficients ranged from 74 to 99%, 78.4 to 100% and 76 to 96.6%, respectively. The obtained results indicated D. elatum species should be protected at the population level.

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