AFLP MARKER IN GENETIC DIVERSITYASSESSMENT OF FIG (Ficus carica L.) POPULATIONS IN KURDISTAN REGION – IRAQ.

In this study, the genetic relatedness of 12 cultivars of fig from different populations in Kurdistan region- Iraq were analyzed using eleven AFLP primers pairs combinations by using the technology of molecular analysis the DNA. Genetic similarity matrices were produced for the AFLP data to calculate genetic distances among their cultivars. Genetic similarity coefficient ranged from 0.1261 to 0.3905. The lowest genetic similarity was observed between Kola and Gala Zard (0.1261). The Hejeera Rash and Shela cultivars were most similar ones with a coefficient of 0.3905. Clustering based on AFLP data for the 12 fig cultivars was identified at the 0.32 similarity level. In the developed dendogram two main groups were found, the first one combined Ketek and Shela together, while the second group contained two sub group Shingaly and Benatty combined together, while in the other sub group cluster three other sub-group were identified. The results of this study may help in the formulation of appropriate strategies for conservation and cultivar improvement in figs, for which limited knowledge of the genetic diversity is available.

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Genetic similarity of Jatropha curcas accessions based on AFLP markers

Cropp Breeding and Applied Biotechnology ◽

10.1590/s1984-70332010000400012 ◽

2010 ◽

Vol 10 (4) ◽

pp. 364-369 ◽

Cited By ~ 9

Author(s):

Carlos Antonio Fernandes Santos ◽

Marcos Antonio Drumond ◽

Marciene Amorim Rodrigues ◽

Marcio Rannieri Viana Evangelista

Keyword(s):

Genetic Variability ◽

Jatropha Curcas ◽

Genetic Similarity ◽

Aflp Marker ◽

Genetic Relationships ◽

Molecular Data ◽

Genetic Distances ◽

Similarity Coefficient ◽

High Variability ◽

Upgma Dendrogram

The genetic relationships between accessions of Jatropha (Jatropha curcas) were determined based on AFLP marker. A set of 50 plants from 12 accessions of J. curcas was analyzed with molecular data from 164 loci generated from 17 AFLP primer combinations. Molecular variance of data was analyzed by total decomposition between and within accessions. An UPGMA dendrogram was constructed based on genetic distances estimated by Jaccard's similarity coefficient. The well-defined dendrogram showed a cophenetic value of 0.91. Groups of plants were observed in six of the 12 accessions studied with similarity of over 30 %, indicating high genetic variability. The variation among accessions was estimated to be 0.275, also indicating high variability. These results show that the genetic variability of the studied J. curcas accessions is structured according to the origin and that a greater number of populations should be sampled to increase the genetic diversity of the studied genebank.

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Identification of Pecan Cultivars and Their Genetic Relatedness as Determined by Randomly Amplified Polymorphic DNA Analysis

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.126.4.474 ◽

2001 ◽

Vol 126 (4) ◽

pp. 474-480 ◽

Cited By ~ 13

Author(s):

Patrick J. Conner ◽

Bruce W. Wood

Keyword(s):

Genetic Similarity ◽

Rapd Markers ◽

Dna Analysis ◽

Genetic Relatedness ◽

Genetic Relationships ◽

Genetic Distances ◽

Similarity Coefficient ◽

Carya Illinoinensis ◽

Randomly Amplified Polymorphic Dna ◽

Average Value

Genetic variation among pecan [Carya illinoinensis (Wangenh.) C. Koch] cultivars was studied using randomly amplified polymorphic DNA (RAPD) markers. Using a combination of primers, a unique fingerprint is presented for each of the pecan genotypes studied. The genetic relatedness between 43 cultivars was estimated using 100 RAPD markers. Genetic distances, based on the similarity coefficient of Nei & Li, varied from 0.91 to 0.46, with an average value of 0.66 among all cultivars. The phenetic dendrogram developed from cluster analysis showed relatively weak grouping association. However, cultivars with known pedigrees usually grouped with at least one of the parents and genetic similarity estimates appear to agree with known genetic relationships.

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Correlation between geographic distance and genetic similarity in an international collection of bovine faecal Escherichia coli O157[ratio ]H7 isolates

Epidemiology and Infection ◽

10.1017/s0950268803008884 ◽

2003 ◽

Vol 131 (2) ◽

pp. 923-930 ◽

Cited By ~ 28

Author(s):

M. A. DAVIS ◽

D. D. HANCOCK ◽

T. E. BESSER ◽

D. H. RICE ◽

C. J. HOVDE ◽

...

Keyword(s):

Escherichia Coli ◽

Gel Electrophoresis ◽

Genetic Similarity ◽

Genetic Relatedness ◽

Geographic Distance ◽

Similarity Coefficient ◽

Pulsed Field Gel Electrophoresis ◽

Dice Similarity Coefficient ◽

Escherichia Coli O157 ◽

Molecular Studies

Evidence from epidemiological and molecular studies of bovine Escherichia coli O157[ratio ]H7 suggests that strains are frequently transmitted across wide geographic distances. To test this hypothesis, we compared the geographic and genetic distance of a set of international bovine Escherichia coli O157[ratio ]H7 isolates using the Mantel correlation. For a measure of genetic relatedness, pulsed-field gel electrophoresis of six different restriction enzyme digests was used to generate an average Dice similarity coefficient for each isolate pair. Geographic distance was calculated using latitude and longitude data for isolate source locations. The Mantel correlation between genetic similarity and the logarithm of geographic distance in kilometers was −0·21 (P<0·001). The low magnitude of the Mantel correlation indicates that transmission over long distances is common. The occurrence of isolates from different continents on the same cluster of the dendrogram also supports the idea that Escherichia coli O157[ratio ]H7 strains can be transferred with considerable frequency over global distances.

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An ISSR-based genetic diversity analysis of Malus sieversii in Tienshan Mountains in Xinjiang, China and Kyrgyzstan

10.36811/ijpsh.2019.110004 ◽

2019 ◽

pp. 40-48

Author(s):

Meiling Yang ◽

Shiyou Che ◽

Hong Long ◽

Guorong Yan ◽

Weiwei Yu

Keyword(s):

Genetic Diversity ◽

Genetic Similarity ◽

Inter Simple Sequence Repeat ◽

Similarity Coefficient ◽

Malus Sieversii ◽

Long Time ◽

Polymorphism Rate ◽

Different Populations ◽

Xinjiang Of China ◽

Issr Primers

Malus sieversii constitute a valuable genetic resource in wild apple ecosystems. The aim of this study was to use inter-simple sequence repeat (ISSR) primers as an accessible tool to investigate the genetic diversity in Malus sieversii species. The experimental materials include 34 samples from Kyrgyzstan and Xinjiang of China. A total of 125 bands and 98 polymorphic bands were amplified using 47 ISSR primers. The polymorphism rate was 78.4%. The genetic similarity coefficient of Kyrgyzstan and Xinjiang of China population was 0.68; the genetic similarity coefficient of various populations in Xinjiang was 0.72~0.94. The samples in same population got into a category, but some samples in faraway geographic locations have cross clustering. Geographical isolation hindered the gene exchange of Malus sieversii in different populations for a long time, and Malus sieversii developed along the natural selection environment direction and generate genetic differentiation after that.

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Genetic Relatedness among Dendrobium (Orchidaceae) Species and Hybrids Using Morphological and AFLP Markers

HortScience ◽

10.21273/hortsci.49.5.524 ◽

2014 ◽

Vol 49 (5) ◽

pp. 524-530

Author(s):

Lydia E. Wahba ◽

Nor Hazlina ◽

A. Fadelah ◽

Wickneswari Ratnam

Keyword(s):

Genetic Relatedness ◽

Morphological Characters ◽

Similarity Coefficient ◽

Aflp Analysis ◽

Jaccard Similarity ◽

Aflp Data ◽

Data Set ◽

Combined Analysis ◽

Jaccard Similarity Coefficient ◽

Combined Data

Dendrobium is one of the largest genera in the Orchidaceae family. Information on the genetic diversity and relationships among species and hybrids is important for breeding purposes and species conservation. The objectives of this study were to assess genetic relatedness and to determine whether morphological, molecular, or combined analysis can discriminate among Dendrobium species, commercial hybrids, and interspecific hybrids. A total of 81 Dendrobium accessions were characterized with 12 amplified fragment length polymorphism (AFLP) primer pairs and 21 morphological characters. Mean genetic relatedness for morphological characters, AFLP analysis, and combined analysis were 0.61, 0.37, and 0.43, respectively. Dendrograms were generated using an unweighted pair group method with arithmetic averages (UPGMA); the analysis was performed on a Jaccard similarity coefficient matrix. The data from morphological characters revealed that the Jaccard similarity coefficient ranged from 0.20 to 1.0, where the tested 81 Dendrobium accessions could be grouped into four clusters. For the AFLP analysis, the number of polymorphic fragments for each primer varied from 80 to 284 with 78% average percentage of polymorphic loci and the similarity coefficient ranging from 0.125 to 1.0 with Dendrobium accessions grouped into three clusters. The similarity coefficients estimated through a combined analysis of morphological and AFLP data ranged from 0.21 to 1.0 and the Dendrobium accessions appeared clustered into two groups. The results revealed some similarities among the three data sets. The combined data set was the most useful in discriminating Dendrobium accessions based on species sections and relationship among species and their hybrids. The correlation between the AFLP data and the combined data was highly significant (r = 0.98, P > 0.001), indicating the usefulness of AFLP data for species discrimination and hybrid identity in the absence of floral morphological characters.

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Estimating Genetic Similarity Matrices using Phylogenies

10.1101/2020.07.30.229286 ◽

2020 ◽

Author(s):

Shijia Wang ◽

Shufei Ge ◽

Caroline Coljin ◽

Liangliang Wang ◽

Lloyd T Elliott

Keyword(s):

Genetic Similarity ◽

Phylogenetic Trees ◽

Genetic Relatedness ◽

Poor Quality ◽

Morphological Data ◽

Inner Product ◽

Simulation Studies ◽

Genetic Traits ◽

Genetic Sequences ◽

Similarity Matrices

AbstractGenetic similarity is a measure for the genetic relatedness among individuals. The standard method for computing similarity matrices involves the inner product of observed genetic variant matrices. Such an approach is inaccurate or impossible if genotypes are not available, or not densely sampled, or of poor quality (for example, genetic analysis of extinct species). We provide a new method for computing genetic similarities among individuals using phylogenetic trees. Our method can supplement (or stand in for) computations based on genetic sequences. We show that the genetic similarity matrices computed from trees are consistent with those computed from genotypes. Quantitative analysis on genetic traits and analysis of heritability and co-heritability can be conducted directly using genetic similarity matrices and so in the absence of genotype data, and the presence of phylogenetic trees derived from morphological data or geological dates, such analyses can be undertaken using our methods. We use simulation studies to demonstrate the advantages of our method, and we provide an application to ancient hominin data.

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Molecular Analysis for Conservation of Georgia Plume, a Threatened Endemic, Using Random Amplified Polymorphic DNA

HortScience ◽

10.21273/hortsci.47.5.563 ◽

2012 ◽

Vol 47 (5) ◽

pp. 563-569

Author(s):

Justin A. Porter ◽

Hazel Y. Wetzstein ◽

David Berle ◽

Phillip A. Wadl ◽

Robert N. Trigiano

Keyword(s):

Genetic Similarity ◽

Genetic Relatedness ◽

Genetic Relationships ◽

Random Amplified Polymorphic Dna ◽

Conservation Priorities ◽

Gps Survey ◽

Large Numbers ◽

In The Wild ◽

Different Populations ◽

Number Of Individuals

Georgia plume, Elliottia racemosa (Ericaceae), is a small tree endemic only to the state of Georgia, where it is listed as a threatened species. Information about genetic relatedness is critical for establishing approaches for safeguarding, reintroduction, and conservation of this rare species. The genetic relationships among and within selected georgia plume populations were evaluated using random amplified polymorphic DNA (RAPD) in conjunction with site visits at which time a census and GPS survey were conducted. Populations ranged from those containing eight to over 1000 individuals with most populations containing few plants (less than 50 individuals). With one exception, small populations with less than 50 individuals had more genetic similarity than populations with greater numbers of plants. Two protected populations containing large numbers of individuals were sampled extensively. Genetic similarity of individuals was not associated with plant proximity within a population. The small number of individuals and geographic isolation characteristic of many populations were associated with high within-population genetic similarity. Conservation priorities should be given to preserving as many different populations as possible to retain the genetic diversity of the species. Whether the narrow genetic variation found in some populations may be contributing to lack of sexual reproduction in the wild is an area for further study.

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090 Identification and Genetic Relatedness among Pecan Cultivars Detected by Randomly Amplified Polymorphic DNA (RAPD) Analysis

HortScience ◽

10.21273/hortsci.35.3.404b ◽

2000 ◽

Vol 35 (3) ◽

pp. 404B-404

Author(s):

Patrick J. Conner ◽

Bruce W. Wood

Keyword(s):

Cluster Analysis ◽

Genetic Variation ◽

Genetic Similarity ◽

Rapd Markers ◽

Genetic Relatedness ◽

Rapd Analysis ◽

Genetic Relationships ◽

Genetic Distances ◽

Carya Illinoinensis ◽

Randomly Amplified Polymorphic Dna

Genetic variation among pecan [Carya illinoinensis (Wangenh.) K. Koch] cultivars was studied using randomly amplified polymorphic DNA (RAPD) markers. Using a combination of primers, a unique fingerprint was produced for each of the pecan genotypes studied. The genetic relatedness between 44 cultivars was estimated using more than 100 RAPD markers. Genetic distances based on the simple matching coefficient varied from 0.91 to 0.59. The phenetic dendogram developed from cluster analysis showed relatively weak grouping association. However, cultivars with known pedigrees usually grouped with at least one of the parents and genetic similarity estimates appear to agree with known genetic relationships. Using RAPD information in determining genetic relationships among pecan cultivars with unknown or questionable pedigrees and the integration of that knowledge into the breeding program is discussed.

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Genetic diversity of Scots pine (Pinus sylvestris L.) populations in Serbia revealed by SSR markers

Archives of Biological Sciences ◽

10.2298/abs1404485l ◽

2014 ◽

Vol 66 (4) ◽

pp. 1485-1492 ◽

Cited By ~ 1

Author(s):

Aleksandar Lucic ◽

Vladan Popovic ◽

Marija Nevenic ◽

Danijela Ristic ◽

Ljubinko Rakonjac ◽

...

Keyword(s):

Pinus Sylvestris ◽

Ssr Markers ◽

Scots Pine ◽

Correspondence Analysis ◽

Genetic Similarity ◽

Genetic Distances ◽

Spatial Distance ◽

Population Genetic Differentiation ◽

Ssr Analysis ◽

Interpopulation Variability

This paper presents the results of analysis of the genetic variability of seven Scots pine (Pinus sylvestris L.) populations in Serbia using SSR markers. Genomic DNA was isolated from seed tissue of all seven populations. The concentration of DNA samples was within the range of 1-4 mg/ml. Different PCR protocols were used depending on the type of SSR markers. The total number of fragments obtained by SSR analysis with 4 selected primers was 17 (only bands of strong and medium intensity were considered), of which 6 fragments were polymorphic (35.29%). In order to analyze the genetic similarity of the analyzed populations, graphs of correspondence analysis and UPGMA clusters were produced. By comparative analysis of the obtained dendrograms, the dependence of population genetic differentiation and spatial distance was observed, i.e. their isolation by natural barriers. The results indicate that in further research of interpopulation variability it is necessary, when graphically interpreting genetic distances, to use both methods of statistical analysis (UPGMA analysis and correspondence analysis).

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EVALUATION OF GENETIC DIVERSITY IN CACAO COLLECTED FROM KOLAKA, SOUTHEAST SULAWESI, USING SSR MARKERS

Indonesian Journal of Agricultural Science ◽

10.21082/ijas.v16n2.2015.pp.71-78 ◽

2016 ◽

Vol 16 (2) ◽

pp. 71

Author(s):

Rubiyo Rubiyo ◽

Nur Kholilatul Izzah ◽

Indah Sulistiyorini ◽

Cici Tresniawati

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Gel Electrophoresis ◽

Genetic Similarity ◽

Similarity Coefficient ◽

Breeding Program ◽

New Variety ◽

Average Value ◽

The Third ◽

Ctab Method

Kolaka, which is located in Southeast Sulawesi, has long been known as one of cacao production centers in Indonesia. Therefore, many different cacao germplasms can be found in this region. The study aimed to evaluate genetic diversity and relationships of 12 cacao genotypes collected from Kolaka. Genomic DNA was extracted by using a modified CTAB method. Meanwhile, genetic diversity was analyzed based on 16 SSR markers, which then separated by 6% non-denaturing polyacryl-amide gel electrophoresis. The result showed that all of those markers, 14 markers exhibited polymorphism and subsequently used for data analysis using NTSYS and PowerMarker program. About 70 different alleles were generated from 12 cacao genotypes analyzed with an average of 5 alleles per locus. Average value of polymorphism information content (PIC) resulted in this study was 0.59. The cluster analysis using UPGMA method based on the genetic similarity coefficient revealed that all cacao genotypes were separated into three major groups. The first group consisted of five cacao genotypes, the second one held four cacao genotypes, whereas the third group contained three genotypes. This result indicates that three genotypes that clustered separately from the others could be used as a good clonal candidate for cacao breeding program. The information resulted from this present study would be useful for future cacao breeding program, especially in efforts to release a new variety.

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