scholarly journals Molecular Characterization of Mulberry Accessions in Turkey by AFLP Markers

2008 ◽  
Vol 133 (4) ◽  
pp. 593-597 ◽  
Author(s):  
Salih Kafkas ◽  
Mustafa Özgen ◽  
Yıldız Doğan ◽  
Burcu Özcan ◽  
Sezai Ercişli ◽  
...  
Keyword(s):  
Fragment Length Polymorphism ◽  
Polymorphic Information Content ◽  
Arithmetic Mean ◽  
Fruit Color ◽  
Aflp Markers ◽  
Group Method ◽  
Upgma Dendrogram ◽  
Pair Group ◽  
Principle Coordinate Analysis

Mulberries (Morus L.) show a great deal of genetic variability and adaptability to various environments. There are more than 24 species of mulberries in cultivated and wild forms. In Turkey, three Morus species, M. alba L., M. nigra L., and M. rubra L., are grown. In this study, we attempted to characterize 43 Morus accessions originating from distinct regions of Turkey using fluorescent dye amplified fragment length polymorphism (AFLP) markers and capillary electrophoresis. The accessions belonged to M. alba, M. nigra, and M. rubra; M. alba consisted of white- and purple-fruited samples. Eight primer combinations generated a total of 416 bands, 337 of which were polymorphic (80.5%). Resolving powers of the AFLP primers ranged from 0.410 to 0.942 making a total of 5.015, whereas the polymorphic information content ranged from 0.662 to 0.898 with an average of 0.812. Unweighted pair-group method of arithmetic mean (UPGMA) clustering of the accessions showed three major groups representing M. nigra, M. rubra, and M. alba accessions. The M. alba group had two subgroups that were not correlated with fruit color. The UPGMA dendrogram of average taxonomic differences confirmed these results. The principle coordinate analysis demonstrated that M. nigra accessions had limited genetic variation. In conclusion, our study indicated that M. nigra and M. rubra are molecularly distinct from M. alba. Our results also suggest that M. nigra accessions having a low level of morphological variation are molecularly similar.

scholarly journals Polymorphism and Genetic Relationships among Tea Genotypes from Turkey Revealed by Amplified Fragment Length Polymorphism Markers

2009 ◽  
Vol 134 (4) ◽  
pp. 428-434 ◽  
Author(s):  
Salih Kafkas ◽  
Sezai Ercişli ◽  
Yıldız Doğan ◽  
Yaşar Ertürk ◽  
Ayhan Haznedar ◽  
...  
Keyword(s):  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Polymorphic Information Content ◽  
Genetic Relationships ◽  
Amplified Fragment Length Polymorphism ◽  
Group Method ◽  
Aflp Analysis ◽  
Black Sea Region ◽  
Pair Group

Individuals in most countries around the world drink tea (Camellia sinensis). Tea drinking has attained ceremonial status in many places as a social and medicinal beverage. Although tea is of great importance in Turkey's economy, little is known about the pattern of genetic variation among the various tea genotypes grown in Turkey. A total of 32 tea genotypes found at the Ataturk Tea and Horticulture Research Institute in the eastern Black Sea region of Turkey were sampled. Fluorescent dye amplified fragment length polymorphism (AFLP) markers and capillary electrophoresis were applied for molecular characterization. The AFLP analysis with six primer combinations generated 835 fragments of which 567 were polymorphic, corresponding to 69.8% polymorphism. Resolving powers of the AFLP primers ranged from 62.6 to 81.9, yielding a total of 437.8; the polymorphic information content (PIC) ranged from 0.76 to 0.83, with an average of 0.79. Genetic similarity values ranged from 0.68 to 0.92, with an average of 0.76. The dendrogram derived by unweighted pair group method with arithmetic mean algorithm (UPGMA) and principal coordinate analysis (PCoA) revealed that all tea genotypes could be clearly divided into four distinct clusters. The results of this study will provide valuable information to the tea cultivar breeding program for the purpose of parental selection.

scholarly journals Evaluation of Genetic Diversity among Persian Fig Cultivars by Morphological Traits and RAPD Markers

HortScience ◽  
2018 ◽  
Vol 53 (5) ◽  
pp. 613-619 ◽  
Author(s):  
Ghazal Baziar ◽  
Moslem Jafari ◽  
Mansoureh Sadat Sharifi Noori ◽  
Samira Samarfard
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
Polymorphic Information Content ◽  
Random Amplified Polymorphic Dna ◽  
Hierarchical Cluster ◽  
Fruit Trees ◽  
Group Method ◽  
Fars Province ◽  
Pair Group

Ficus carica L. is one of the most ancient fruit trees cultivated in Persia (Iran). The conservation and characterization of fig genetic resources is essential for sustainable fig production and food security. Given these considerations, this study characterizes the genetic variability of 21 edible F. carica cultivars in the Fars Province using random amplified polymorphic DNA (RAPD) markers. The collected cultivars were also characterized for their morphological features. A total of 16 RAPD primers produced 229 reproducible bands, of which, 170 loci (74.43%) were polymorphic with an average polymorphic information content (PIC) value of 0.899. Genetic analysis using an unweighted pair-group method with arithmetic averaging (UPGMA) revealed genetic structure and relationships among the local germplasms. The dendrogram resulting from UPGMA hierarchical cluster analysis separated the fig cultivars into five groups. These results demonstrate that analysis of molecular variance allows for the partitioning of genetic variation between fig groups and illustrates greater variation within fig groups and subgroups. RAPD-based classification often corresponded with the morphological similarities and differences of the collected fig cultivars. This study suggests that RAPD markers are suitable for analysis of diversity and cultivars’ fingerprinting. Accordingly, understanding of the genetic diversity and population structure of F. carica in Iran may provide insight into the conservation and management of this species.

Molecular variation of Trypanosoma brucei subspecies as revealed by AFLP fingerprinting

Parasitology ◽  
2002 ◽  
Vol 124 (4) ◽  
pp. 349-358 ◽  
Author(s):  
E. E. C. AGBO ◽  
P. A. O. MAJIWA ◽  
H. J. H. M. CLAASSEN ◽  
M. F. W. TE PAS
Keyword(s):  
Trypanosoma Brucei ◽  
Reliable Method ◽  
Fragment Length Polymorphism ◽  
Genetic Characterization ◽  
Pearson Correlation ◽  
Group Method ◽  
Aflp Fingerprinting ◽  
Pair Group ◽  
Definition Of

Genetic analysis of Trypanosoma spp. depends on the detection of variation between strains. We have used the amplified fragment length polymorphism (AFLP) technique to develop a convenient and reliable method for genetic characterization of Trypanosome (sub)species. AFLP accesses multiple independent sites within the genome and would allow a better definition of the relatedness of different Trypanosome (sub)species. Nine isolates (3 from each T. brucei subspecies) were tested with 40 AFLP primer combinations to identify the most appropriate pairs of restriction endonucleases and selective primers. Primers based on the recognition sequences of EcoRI and BglII were chosen and used to analyse 31 T. brucei isolates. Similarity levels calculated with the Pearson correlation coefficient ranged from 15 to 98%, and clusters were determined using the unweighted pair-group method using arithmetic averages (UPGMA). At the intraspecific level, AFLP fingerprints were grouped by numerical analysis in 2 main clusters, allowing a clear separation of T. b. gambiense (cluster I) from T. b. brucei and T. b. rhodesiense isolates (cluster II). Interspecies evaluation of this customized approach produced heterogeneous AFLP patterns, with unique genetic markers, except for T. evansi and T. equiperdum, which showed identical patterns and clustered together.

scholarly journals Morphometric and Genetic Variation in Three Populations of Indian Salmon (Polydactylus plebeius)

2013 ◽  
Vol 5 (3) ◽  
pp. 275-281
Author(s):  
Ramakrishnan THIRUMARAISELVI ◽  
Muthusamy THANGARAJ ◽  
Vellaichamy RAMANADEVI
Keyword(s):  
Univariate Analysis ◽  
Arithmetic Mean ◽  
Group Method ◽  
Morphometric Character ◽  
Clear Pattern ◽  
Arbitrary Primers ◽  
Upgma Dendrogram ◽  
Pair Group ◽  
Morphometric Analyses ◽  
The Status

Morphometric character analyses and RAPD was used to discriminate and ratify the status of three populations of Indian salmon, Polydactylus plebeius along the coromandel coast of India. Morphometric analyses showed a clear pattern of differentiation between the stocks and revealed the discreteness of two groups, southern stock (Pazhayar) and northern stock (Cuddalore). The univariate analysis of variance showed significant differences between means of the samples for most morphometric descriptors. A total of 1077 scorable bands were produced using all ten arbitrary primers in three populations. An un-weighted pair-group method with arithmetic mean (UPGMA) dendrogram was constructed based on genetic values to show the genetic relationship among the three populations. The genetic diversity (H) of P. plebeius in Cuddalore was more (0.0733 ± 0.0648) than Pazhayar (0.0609 ± 0.0416) and Vellar (0.0613 ± 0.0344) populations. All the three populations had significantly (p

scholarly journals Genetic Diversity and Origin of Slovene Common Bean (Phaseolus vulgaris L.) Germplasm as Revealed by AFLP Markers and Phaseolin Analysis

2006 ◽  
Vol 131 (2) ◽  
pp. 242-249 ◽  
Author(s):  
Jelka Šustar-Vozlič ◽  
Marko Maras ◽  
Branka Javornik ◽  
Vladimir Meglič
Keyword(s):  
Genetic Diversity ◽  
Phaseolus Vulgaris ◽  
Common Bean ◽  
Seed Protein ◽  
Fragment Length Polymorphism ◽  
Aflp Markers ◽  
Group Method ◽  
Phaseolus Vulgaris L ◽  
Pair Group ◽  
High Level

There is a long tradition of common bean cultivation in Slovenia, which has resulted in the development of numerous landraces in addition to newly established cultivars. The genetic diversity of 100 accessions from the Genebank of the Agricultural Institute of Slovenia (AIS) were evaluated with amplified fragment length polymorphism (AFLP) markers and phaseolin seed protein. Twenty-seven standard accessions of known Mesoamerican and Andean origin, 10 wild Phaseolus vulgaris accessions and two related species, P. coccineus L. and P. lunatus L., were also included. Ten AFLP primer combinations produced 303 polymorphic bands, indicating a relatively high level of genetic diversity. Based on the marker data, unweighted pair group method with arithmethic mean (UPGMA) analysis and principal coordinate analysis (PCoA) all P. vulgaris accessions were separated into three well-defined groups. Two groups consisted of accessions of Mesoamerican and Andean origin, while the third was comprised of only four wild P. vulgaris accessions. A set of Slovene accessions formed a well-defined sub-group within the Andean cluster, showing their unique genetic structure. These data were supported by phaseolin analysis, which also revealed additional variants of “C” and “T” phaseolin types. The results are in agreement with previous findings concerning diversification of common bean germplasm introduced in Europe.

scholarly journals GENETIC DIVERSITY OF Brassica rapa GERMPLASM OF KHYBER PAKHTUNKHWA PAKISTAN REVEALED BY MOLECULAR MARKERS

2019 ◽  
Vol 18 (6) ◽  
pp. 57-65
Author(s):  
Naushad Ali ◽  
Sardar Ali ◽  
Naqib Ullah Khan ◽  
Sohail Ahmad Jan ◽  
Malik Ashiq Rabbani ◽  
...  
Keyword(s):  
Genetic Variability ◽  
Ssr Markers ◽  
Brassica Rapa ◽  
Arithmetic Mean ◽  
Group Method ◽  
Khyber Pakhtunkhwa ◽  
Upgma Dendrogram ◽  
Pair Group ◽  
Ssr Primers ◽  
Simple Sequence

A total of 96 indigenous Brassica rapa accessions were collected from different locations of Khyber Pakhtunkhwa, Pakistan. Simple Sequence Repeats (SSR) markers were used to identify the most diverse genotypes among the collected lots. Twenty six (26) different SSR primers were used for (genetic) variability among collected genotypes. These primers were selected from literature based on their previous results. These primers produced 135 scorable bands of which 75 were polymorphic, with an average of 55.5% polymorphic loci, and reflected the broader genetic background of the collected genotypes. An average 2.88 polymorphic bands with an average PIC value of 0.49 was recorded. Unweighted Pair Group Method with Arithmetic Mean (UPGMA) divided all genotypes into three main groups. Group one contained three clusters, while group two and three had four and two clusters each. Based on the UPGMA dendrogram, genotypes collected from Kohat, Bannu, Swat and Haripur showed considerable amount of variation. From the present study, it is concluded that SSR markers can be proved as the best tool for the genetic variability of other local and exotic B. rapa genotypes.

scholarly journals Diversidad genética de aislados de Phytophthora infestans colectados en zonas productoras de papa y tomate de Guatemala

2018 ◽  
Vol 5 (2) ◽  
pp. 151-161
Author(s):  
Jose Alejandro Ruiz-Chutan ◽  
Julio E. Berdúo-Sandoval ◽  
Amilcar Sánchez-Pérez
Keyword(s):  
Phytophthora Infestans ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Amplified Fragment Length Polymorphism ◽  
Arithmetic Mean ◽  
Group Method ◽  
Pair Group ◽  
Unweighted Pair Group Method

Phytophthora infestans (Mont) DeBary es el agente causal de la enfermedad conocida como tizón tardío, la cual ha sido catalogada como la enfermedad de plantas más devastadora reportada en la historia de la humanidad. Este patógeno afecta plantas de importancia económica de la familia Solanaceae, como el tomate y la papa. P. infestans es un oomicete heterotálico y necesita de dos tipos de apareamiento, A1 y A2, para presentar una reproducción sexual, la cual es la principal vía por la que este patógeno incrementa su grado de diversidad, a través de una recombinación de su material genético, que representa el mayor desafío para el manejo de la enfermedad. Este estudio determinó el nivel de variabilidad genética, a través del marcador molecular amplified fragment length polymorphism (AFLP), de 22 aislados de P. infestans colectados en diferentes zonas productoras de papa y tomate. Con el perfil de bandas generado por el marcador molecular, se realizó un análisis cluster creando un dendograma de tipo unweighted pair group method with arithmetic mean (UPGMA), con el índice de Dice, mediante una matriz de distancias genéticas. Los aislados fueron situados en tres grupos principales, los cuales responden al lugar de procedencia y al tipo de planta hospedera. 

Assessing inter- and intra-cultivar variation in Greek Prunus avium by SSR markers

2010 ◽  
Vol 8 (3) ◽  
pp. 242-248 ◽  
Author(s):  
Ioannis V. Ganopoulos ◽  
Evagellia Avramidou ◽  
Dionisia A. Fasoula ◽  
Grigorios Diamantidis ◽  
Filippos A. Aravanopoulos
Keyword(s):  
Sweet Cherry ◽  
Prunus Avium ◽  
Polymorphic Information Content ◽  
Arithmetic Mean ◽  
Group Method ◽  
Northern Greece ◽  
Pair Group ◽  
Expected Heterozygosity ◽  
Cultivar Variation ◽  
Simple Sequence

Prunus avium cultivars widely used in northern Greece were investigated in terms of inter- and intra-cultivar genetic variation and DNA fingerprinting. Based on 11 simple sequence repeats loci, the average number of alleles per locus (Na = 2.82), probability of identity (PID = 0.327), polymorphic information content (0.451) and expected heterozygosity (He = 0.494) were within the range reported in similar studies. The most informative markers were BPPCT039 and EMPa018. The cultivars were clearly separated in both an unweighted pair group method with arithmetic mean dendrogram and a multivariate space ordination. Any two cultivars differed on the average at 6.30 loci. The null hypothesis of zero intra-cultivar variability was tested and could not be rejected. Two cultivars (Tragana Edessis and Tragana Sarakinon) were genetically similar, but not identical. This study, the first of its kind for sweet cherry in Greece, presents a useful molecular tool for resolving issues of intra-cultivar variability and synonimity and provides a warranty of genetic identity in the handling and management of local traditional germplasm.

Characterization of genotypes and genetic relationships of cili (Rosa roxburghii) and its relatives using RAPD markers

2004 ◽  
Vol 1 (2) ◽  
pp. 79-84
Author(s):  
Wen Xiao-Peng ◽  
Deng Xiu-Xin
Keyword(s):  
Rapd Markers ◽  
Genetic Relationships ◽  
Arithmetic Mean ◽  
Group Method ◽  
Arbitrary Primers ◽  
Pair Group ◽  
Rosa Roxburghii ◽  
Widespread Interest ◽  
Unweighted Pair Group Method

AbstractCili (Rosa roxburghii Tratt), characterized by containing the highest vitamin C content among fruits and showing attractive senescence-retarding and cancer-preventing effects, has gained widespread interest. RAPD markers were applied to identify the seven genotypes of cili and to evaluate the genetic relationships within cili, as well as among its relatives. Sixteen arbitrary primers screened from 154 were adopted to analyse polymorphism in RAPD profiles for the 15 samples. A total of 137 RAPD bands ranging in size from 480 bp to 3.3 kb were obtained, among which 95 were polymorphic, covering 69.3% of the total bands obtained; and an average of 8.6 bands/primer was scored. The genotypes of cili and seedless cili could be identified efficiently by 14 genotype-specific bands, which were obtained from the polymorphic primers OPB-11, OPAF-16 and OPW-02. Additionally, using the unweighted pair group method with arithmetic mean, a dendrogram showing genetic relationships among the 15 samples was constructed based on cluster analysis of genetic distance. The possible origin of seedless cili and multiple-corolla cili is also discussed.

Evaluation of AFLPs for germplasm fingerprinting and assessment of genetic diversity in cultivars of tomato (Lycopersicon esculentum L.)

Genome ◽  
2004 ◽  
Vol 47 (3) ◽  
pp. 510-518 ◽  
Author(s):  
Young Hoon Park ◽  
Marilyn A.L West ◽  
Dina A St. Clair
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Lycopersicon Esculentum ◽  
Fragment Length Polymorphism ◽  
Aflp Markers ◽  
Group Method ◽  
Similarity Coefficients ◽  
Pair Group ◽  
Phenetic Relationships ◽  
High Bootstrap

Cultivated tomato (L. esculentum L.) germplasm exhibits limited genetic variation compared with wild Lycopersicon species. Amplified fragment length polymorphism (AFLP) markers were used to evaluate genetic variation among 74 cultivars, primarily from California, and to fingerprint germplasm to determine if cultivar-specific patterns could be obtained. All 74 cultivars were genotyped using 26 AFLP primer combinations; of the 1092 bands scored, 102 AFLP bands (9.3%) were polymorphic. Pair-wise genetic similarity coefficients (Jaccard and Nei–Li) were calculated. Jaccard coefficients varied from 0.16 to 0.98 among cultivar pairs, and 72% of pair-wise comparisons exceeded 0.5. UPGMA (unweighted pair-group method with arithmetic averaging) clustering and principle component analysis revealed four main clusters, I–IV; most modern hybrid cultivars grouped in II, whereas most vintage cultivars grouped in I. Clusters III and IV contained three and two cultivars, respectively. Some groups of cultivars closely related by pedigree exhibited high bootstrap values, but lower values (<50%) were obtained for cluster II and its four subgroups. Unique fingerprints for all 74 cultivars were obtained by a minimum of seven AFLP primer pairs, despite inclusion of some closely related cultivars. This study demonstrated that AFLP markers are effective for obtaining unique fingerprints of, and assessing genetic diversity among, tomato cultivars.Key words: Lycopersicon esculentum, AFLPs, DNA fingerprinting, genetic diversity, phenetic relationships.

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