scholarly journals Genetic Diversity of Remaining Populations of Mangaba (Hancornia speciosa Gomes) in Restingas of Brazil

2017 ◽  
Vol 9 (2) ◽  
pp. 46 ◽  
Author(s):  
Ana Veruska Cruz da Silva ◽  
Julie Anne Espíndola Amorim ◽  
Marília Freitas de Vasconcelos Melo ◽  
Ana Da Silva Ledo ◽  
Allivia Rouse Carregosa Rabbani
Keyword(s):  
Genetic Diversity ◽  
Genetic Relationships ◽  
Issr Markers ◽  
Shannon Index ◽  
Conservation Strategies ◽  
Principal Coordinates Analysis ◽  
Fruit Species ◽  
Principal Coordinates ◽  
Hancornia Speciosa ◽  
Brazilian Northeast

Mangaba (Hancornia speciosa Gomes) is a fruit species that is native to Brazil, and has social, economic and cultural importance. Knowledge of the genetic relationships between the remaining populations is essential in order to promote conservation strategies for these genetic resources. In the present study, it was evaluated the genetic diversity of 35 individuals from three remaining restingas areas in the states of Ceará (Iguape and Cascavel) and Pernambuco (Tamandaré), located in the Brazilian Northeast. Nine ISSR primers were used to determine the genetic variability. Sixty-one fully polymorphic fragments (100%) were generated. The largest (10) and smallest (5) number of fragments were obtained with the primers HB14 and HB12, respectively. The Shannon index (I = 0.40), the genetic diversity (H = 0.30), and the percentage of polymorphic loci (%P = 73.77%) were also estimated. Both the methods of UPGMA and the Principal Coordinates Analysis (PCoA) clustered individuals according to their place of origin. Genetic divergence was greater within population (64%) than between them (36%). This may indicate a strong genetic structure, i.e., the gene flow rate between populations is low, favoring inbreeding. ISSR markers were efficient for the analysis of genetic diversity, for the identification of clusters, and for the estimation of the genetic distance between and within populations.

scholarly journals Efficiency of RAPD and ISSR markers in assessing genetic diversity and relationships in black gram (Vigna mungo L. Hepper) vari

2010 ◽  
Vol 90 (4) ◽  
pp. 443-452 ◽  
Author(s):  
T. Karuppanapandian ◽  
H W Wang ◽  
T. Karuppudurai ◽  
J. Rajendhran ◽  
M. Kwon ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Genetic Relationships ◽  
Random Amplified Polymorphic Dna ◽  
Vigna Mungo ◽  
Polymorphic Band ◽  
Black Gram ◽  
Principal Coordinates Analysis ◽  
Principal Coordinates ◽  
Rapd And Issr

The DNA fingerprinting methodologies, random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR), were used to estimate genetic diversity and relationships among 20 black gram (Vigna mungo L. Hepper) varieties. Thirty selected RAPD primers amplified 255 bands, 168 of which were polymorphic (66.5%). On average, these primers produced 8.5 bands, 5.6 of which were polymorphic. Polymorphic band number varied from 2 (A-05) to 10 (OPA-02), with sizes ranging from 100 to 2550 bp. Twenty-four selected ISSR primers produced 238 amplified products, 184 of which were polymorphic (77.8%). On average, these primers generated 9.8 bands, with 7.7 polymorphic bands ranging in number from 4 (ISSR-13) to 11 (ISSR-03), and size from 100-2650 bp. Genetic relationships were estimated using similarity coefficient (Jaccard’s) values between different accession pairs; these varied from 30.7 to 85.0 for RAPD, and from 37.2 to 88.4 with ISSR. UPGMA analysis indicated that the varieties ranged in similarity from 0.50 to 1.00 (mean of 0.75) for RAPD, and from 0.47 to 1.00 (mean of 0.76) with ISSR. Cluster analysis of RAPD and ISSR results identified three clusters with significant bootstrap values, which revealed greater homology between the varieties. Principal coordinates analysis also supported this conclusion. Among the black gram varieties, WBU-108 and RBU-38 were highly divergent, whereas LBG-648 and LBG-623 were genetically similar. The markers generated by RAPD and ISSR assays can provide practical information for the management of genetic resources and these results will also provide useful information for the molecular classification and breeding of new black gram varieties.Key words: Black gram, cluster analysis, genetic diversity, ISSR, molecular markers, RAPD

scholarly journals Genetic diversity in natural populations of Hancornia speciosa Gomes: Implications for conservation of genetic resources

2018 ◽  
Vol 42 (6) ◽  
pp. 623-630
Author(s):  
Cristiane Gouvêa Fajardo ◽  
Daniel Ferreira da Costa ◽  
Kyvia Pontes Teixeira das Chagas ◽  
Fábio de Almeida Vieira
Keyword(s):  
Genetic Diversity ◽  
Genetic Resources ◽  
In Situ Conservation ◽  
Natural Populations ◽  
Allelic Diversity ◽  
Shannon Index ◽  
Conservation Strategies ◽  
Effective Population ◽  
Infinite Allele Model ◽  
Hancornia Speciosa

ABSTRACT The continuing fragmentation of forests has been a threat to the maintenance of genetic resources. Genetic diversity is fundamental to the survival of species in natural environments in the long term, as well as being the basis for genetic improvement. The objective of this study was to evaluate the genetic diversity in natural populations of Hancornia speciosa and to contribute to the development of conservation strategies. We sampled 105 individuals of H. speciosa, distributed in seven populations. The ISSR (Inter-Simple Sequence Repeat) markers provided 70 loci, of which 81% were polymorphic. The mean genetic diversity of Nei (h) was 0.19, and the Shannon index (I) was 0.27. The h and I diversity indices ranged respectively from 0.16 to 0.24 in the PAD (Parque das Dunas) population and from 0.21 to 0.29 in MAC (Macaíba) population. Resulting from a Bayesian analysis, the genotypes were divided into four groups (K = 4). The allelic diversity patterns observed indicated the occurrence of the genetic bottleneck in all populations, according to the stepwise mutation model (SMM). The infinite allele model (IAM) revealed an imbalance between mutation and genetic drift only in the PAD population. Genetic conservation strategies for H. speciosa should cover each genetic group that was differentially structured. We recommend in situ conservation and the creation of germplasm banks, especially with the PAD population which demonstrated the lower genetic diversity and decreased effective population size according to the two mutational models.

Genetic diversity analysis using simple sequence repeat markers in soybean

2014 ◽  
Vol 12 (S1) ◽  
pp. S87-S90 ◽  
Author(s):  
Zhenbin Hu ◽  
Guizhen Kan ◽  
Guozheng Zhang ◽  
Dan Zhang ◽  
Derong Hao ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Simple Sequence Repeat ◽  
Genetic Relationships ◽  
Wild Soybean ◽  
Sequence Repeat ◽  
Principal Coordinates Analysis ◽  
Principal Coordinates ◽  
Cultivated Soybean ◽  
Simple Sequence ◽  
Nei's Genetic Distance

To evaluate the genetic diversity (GD) of wild and cultivated soybeans and determine the genetic relationships between them, in this study, 127 wild soybean accessions and 219 cultivated soybean accessions were genotyped using 74 simple sequence repeat (SSR) markers. The results of the study revealed that the GD of the wild soybeans exceeded that of the cultivated soybeans. In all, 924 alleles were detected in the 346 soybean accessions using 74 SSRs, with an average of 12.49 alleles per locus. In the 219 cultivated soybean accessions, 687 alleles were detected, with an average of 9.28 alleles per locus; in the 127 wild soybean accessions, 835 alleles were detected, with an average of 11.28 alleles per locus. We identified 237 wild-soybean-specific alleles and 89 cultivated-soybean-specific alleles in the 346 soybean accessions, and these alleles accounted for 35.28% of all the alleles in the sample. Principal coordinates analysis and phylogenetic analysis based on Nei's genetic distance indicated that all the accessions could be classified into two major clusters, corresponding to wild and cultivated soybeans. These results will increase our understanding of the genetic differences and relationships between wild and cultivated soybeans and provide information to develop future breeding strategies to improve soybean yield.

scholarly journals Genetic diversity and relationships of Chinese donkeys using microsatellite markers

2019 ◽  
Vol 62 (1) ◽  
pp. 181-187 ◽  
Author(s):  
Lulan Zeng ◽  
Ruihua Dang ◽  
Hong Dong ◽  
Fangyu Li ◽  
Hong Chen ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Genetic Relationships ◽  
Mean Value ◽  
Principal Coordinates Analysis ◽  
Expected Heterozygosity ◽  
Principal Coordinates ◽  
Baseline Information ◽  
Grouping Pattern ◽  
The Mean

Abstract. Donkeys are one important livestock in China because of their nourishment and medical values. To investigate the genetic diversity and phylogenetic relationships of Chinese donkey breeds, a panel of 25 fluorescently labeled microsatellite markers was applied to genotype 504 animals from 12 Chinese donkey breeds. A total of 226 alleles were detected, and the expected heterozygosity ranged from 0.6315 (Guanzhong) to 0.6999 (Jiami). The mean value of the polymorphism information content, observed number of alleles, and expected number of alleles for all the tested Chinese donkeys were 0.6600, 6.890, and 3.700, respectively, suggesting that Chinese indigenous donkeys have relatively abundant genetic diversity. Although there were abundant genetic variations found, the genetic differentiation between the Chinese donkey breeds was relatively low, which displayed only 5.99 % of the total genetic variance among different breeds. The principal coordinates analysis clearly splits 12 donkey breeds into two major groups. The first group included Xiji, Xinjiang, Liangzhou, Kulun, and Guanzhong donkey breeds. In the other group, Gunsha, Dezhou, Biyang, Taihang, Jiami, Qingyang, and Qinghai donkeys were clustered together. This grouping pattern was further supported by structure analysis and neighbor-joining tree analysis. Furthermore, genetic relationships between different donkey breeds identified in this study were corresponded to their geographic distribution and breeding history. Our results provide comprehensive and precise baseline information for further research on preservation and utilization of Chinese domestic donkeys.

scholarly journals Determination of genetic diversity among some almond accessions

Genetika ◽  
2015 ◽  
Vol 47 (1) ◽  
pp. 13-22 ◽  
Author(s):  
Hasan Pinar ◽  
Sezai Ercisli ◽  
Mustafa Unlu ◽  
Mustafa Bircan ◽  
Aydın Uzun ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Cultivar Identification ◽  
Genetic Relationships ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Geographical Isolation ◽  
Fruit Species ◽  
Rapd And Issr ◽  
Simple Sequence

More recently the use of different molecular markers in fruit species to determine particularly genetic diversity, genetic relationships and cultivar identification has been gained more importance. In the study, 13 randomly amplified polimorfic DNA (RAPD) and 4 inter-simple sequence repeat (ISSR) markers were used to evaluate genetic relationships among 95 almong accessions (26 foreign cultivars and 69 national cultivars and selections). The all plant material found in Almond Germplasm Repository in Gaziantep, Turkey. Both RAPD and ISSR markers distinguished the almond cultivars and selections in various levels. 17 RAPD and ISSR markers yielded a total of 73 scorable bands, which 51 are polymorphic. The two marker system exhibited variation with regard to average band sizes and polymorphism ratio. The average polymorphism was higher in ISSR (88%) compared to RAPD (74%). RAPD and ISSR marker systems were found to be useful for determining genetic diversity among almong genotypes and cultivars. Combining of two dendrograms obtained through these markers show different clustering of 96 almond specimens without geographical isolation. These results supported that almonds in Turkey indicated considerable genetic diversity.

scholarly journals Molecular characterization of sesame germplasms of West Bengal, India using RAPD markers

2019 ◽  
Vol 63 (1) ◽  
pp. 15-24
Author(s):  
Soumen Saha ◽  
Tarak Nath Dhar ◽  
Parthadeb Ghosh ◽  
Tulsi Dey
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
West Bengal ◽  
Genetic Relationships ◽  
Random Amplified Polymorphic Dna ◽  
Group Method ◽  
Similarity Coefficients ◽  
Principal Coordinates Analysis ◽  
High Genetic Diversity ◽  
Principal Coordinates

The aim of this research was to assess the genetic diversity of sesame (Sesamum indicum L.) and also to reveal the genetic relationships using the Random Amplified Polymorphic DNA (RAPD) markers. Fifteen sesame germplasms were collected from seven districts or four zones of West Bengal, India. A high genetic diversity was revealed by ten RAPD primers within and among the fifteen germplasms. The value of Jaccard’s similarity coefficients among and within the fifteen germplasms ranged from 0.287 to 0.725 which indicated high degree of genetic variability. Cluster analysis using Unweighted Pair Group Method with Arithmetic Mean (UPGMA) grouped all the germplasms into three main clusters. Analysis of various genetic diversity indices strongly indicated high level of genetic diversity among the populations of four different regions. UPGMA analysis of four populations resulted into two groups and the results of Principal Coordinates Analysis (PCoA) depicted a clear distinction among the germplasms.

scholarly journals Analysis of genetic relationships of genotypes of the genus Rosa L. from the collection of Nikita Botanical Gardens using ISSR and IRAP DNA markers

2020 ◽  
Vol 24 (5) ◽  
pp. 474-480
Author(s):  
I. I. Suprun ◽  
S. A. Plugatar ◽  
I. V. Stepanov ◽  
T. S. Naumenko
Keyword(s):  
Genetic Diversity ◽  
Bayesian Methods ◽  
Dna Markers ◽  
Wild Species ◽  
Genetic Similarity ◽  
Genetic Relationships ◽  
Issr Markers ◽  
The Other ◽  
Clustering Methods ◽  
Botanical Gardens

In connection with the development of breeding and the creation of new plant varieties, the problem of their genotyping and identification is becoming increasingly important, therefore the use of molecular methods to identify genetic originality and assess plant genetic diversity appears to be relevant. As part of the work performed, informative ISSR and IRAP DNA markers promising for the study of genetic diversity of the Rosa L. genus were sought and applied to analysis of genetic relationships among 26 accessions of the genus Rosa L. from the gene pool collection of Nikita Botanical Gardens. They included 18 cultivated varieties and 8 accessions of wild species. The species sample included representatives of two subgenera, Rosa and Platyrhodon. The subgenus Platyrhodon was represented by one accession of the species R. roxburghii Tratt. Cultivated roses were represented by varieties of garden groups hybrid tea, floribunda, and grandiflora. The tested markers included 32 ISSRs and 13 IRAPs. Five ISSR markers (UBC 824, ASSR29, 3A21, UBC 864, and UBC 843) and three IRAPs (TDK 2R, Сass1, and Сass2) were chosen as the most promising. They were used for genotyping the studied sample of genotypes. In general, they appeared to be suitable for further use in studying the genetic diversity of the genus Rosa L. The numbers of polymorphic fragments ranged from 12 to 31, averaging 19.25 fragments per marker. For markers UBC 864 and UBC 843, unique fingerprints were identified in each accession studied. The genetic relationships of the studied species and varieties of roses analyzed by the UPGMA, PCoA, and Bayesian methods performed on the basis of IRAP and ISSR genotyping are consistent with their taxonomic positions. The genotype of the species R. roxburghii of the subgenus Platyrhodon was determined genetically as the most distant. According to clustering methods, the representative of the species R. bengalensis did not stand out from the group of cultivated varieties. When assessing the level of genetic similarity among the cultivated varieties of garden roses, the most genetically isolated varieties were ‘Flamingo’, ‘Queen Elizabeth’, and ‘Kordes Sondermeldung’; for most of the other varieties, groups of the greatest genetic similarity were identified. This assessment reflects general trends in phylogenetic relationships, both among the studied species of the genus and among cultivated varieties.

scholarly journals Morphological and genetic diversity of Senecio vulgaris L. (Asteraceae) in Iran

2021 ◽  
Vol 80 (2) ◽  
Author(s):  
Mostafa Ebadi ◽  
Rosa Eftekharian
Keyword(s):  
Genetic Diversity ◽  
Principal Component ◽  
Morphological Characters ◽  
Mantel Test ◽  
Morphological Data ◽  
Principal Coordinates Analysis ◽  
Cauline Leaf ◽  
Senecio Vulgaris ◽  
Molecular Features ◽  
Principal Coordinates

Senecio vulgaris L., an annual herb belonging to the Asteraceae, is widely distributed in different regions of the world. There is no information on the intraspecific variations of the morphological and molecular features of this species. In the present investigation, we studied the morphological and genetic diversity of 81 accessions of S. vulgaris collected from 10 geographical populations. Eleven inter simple sequence repeat (ISSR) primers were used for the examination of genetic variations among the populations. Analysis of molecular variance (AMOVA) and GST analyses revealed significant differences among the investigated populations. A significant correlation between genetic distance and geographical distance was revealed by the Mantel test. However, reticulation analysis indicated the occurrence of gene flow among most of the populations studied. Principal component analysis (PCA) plot showed that the number of capitula, length of the cauline leaf and plant height were the most variable morphological characters. Principal coordinates analysis (PCoA) plot revealed two groups of populations, according to molecular and morphological data. The results suggested the existence of possible intraspecific taxonomic ranks within this species.

scholarly journals The genetic diversity and population structure of two endemic Amazonian quillwort (Isoetes L.) species

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10274 ◽  
Author(s):  
Mirella Pupo Santos ◽  
João V.S. Rabelo Araujo ◽  
Arthur V. Sant’anna Lopes ◽  
Julio Cesar Fiorio Vettorazzi ◽  
Marcela Santana Bastos Boechat ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variation ◽  
Geographical Location ◽  
Inter Simple Sequence Repeat ◽  
Shannon Index ◽  
Conservation Strategies ◽  
Amazon Forest ◽  
Mass Extinctions ◽  
Effective Conservation

Background Two endemic lycophyte species Isoetes cangae and Isoetes serracarajensis have been recently described in the State of Pará in the Amazon forest located in northern Brazil. Isoetes L. has survived through three mass extinctions. Plants are considered small-sized, heterosporous, and can display a great diversity of physiological adaptations to different environments. Thus, the current study aimed to estimate the genetic variation of the populations of I. cangae and I. serracarajensis to generate information about their different mechanisms for survival at the same geographical location that could point to different reproductive, adaptative and dispersal strategies and should be considered for effective conservation strategies. Methods The genetic diversity and population structure of I. cangae and I. serracarajensis were investigated using Inter Simple Sequence Repeat (ISSR) molecular markers. Total genomic DNA was isolated, and the genetic diversity parameters were calculated. Results The sixteen primers produced 115 reproducible bands, 87% of which were polymorphic. A high level of polymorphic loci (81.74% and 68.48%) and a high Shannon index (Sh = 0.376 and 0.289) were observed for I. cangae and I. serracarajensis, respectively. The coefficient of genetic differentiation between population areas (GST) showed a higher value in I. serracarajensis (0.5440). Gene flow was higher in I. cangae (1.715) and lower in I. serracarajensis populations (0.419). Overall, the results further show that I. serracarajensis and I. cangae are two species with considerable genetic variation and that these differences may reflect their habitats and modes of reproduction. These results should be considered in the development of effective conservation strategies for both species.

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.

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