scholarly journals Assessment of genetic diversity for some Iraqi date palms (Phoenix dactylifera L.) using amplified fragment length polymorphisms (AFLP) markers

2011 ◽  
Vol 10 (47) ◽  
pp. 9570-9576 ◽  
Author(s):  
Khierallah ◽  
H ◽  
Bader ◽  
S ◽  
Baum ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Fragment Length ◽  
Phoenix Dactylifera ◽  
Aflp Markers ◽  
Date Palms ◽  
Phoenix Dactylifera L ◽  
Length Polymorphisms ◽  
Amplified Fragment Length Polymorphisms

Selection criteria for scoring amplified fragment length polymorphisms (AFLPs) positively affect the reliability of population genetic parameter estimates

Genome ◽  
2010 ◽  
Vol 53 (4) ◽  
pp. 302-310 ◽  
Author(s):  
Doris Herrmann ◽  
Bénédicte N. Poncet ◽  
Stéphanie Manel ◽  
Delphine Rioux ◽  
Ludovic Gielly ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Fragment Length ◽  
Population Genetic ◽  
Selection Criteria ◽  
Genetic Parameters ◽  
Data Set ◽  
Marker Selection ◽  
Length Polymorphisms ◽  
Amplified Fragment Length Polymorphisms ◽  
Population Genetic Parameters

A reliable data set is a fundamental prerequisite for consistent results and conclusions in population genetic studies. However, marker scoring of genetic fingerprints such as amplified fragment length polymorphisms (AFLPs) is a highly subjective procedure, inducing inconsistencies owing to personal or laboratory-specific criteria. We applied two alternative marker selection algorithms, the newly developed script scanAFLP and the recently published AFLPScore, to a large AFLP genome scan to test how population genetic parameters and error rates were affected. These results were confronted with replicated random selections of marker subsets. We show that the newly developed marker selection criteria reduced the mismatch error rate and had a notable influence on estimates of genetic diversity and differentiation. Both effects are likely to influence biological inference. For example, genetic diversity (HS) was 29% lower while genetic differentiation (FST) was 8% higher when applying scanAFLP compared with AFLPScore. Likewise, random selections of markers resulted in substantial deviations of population genetic parameters compared with the data sets including specific selection criteria. These randomly selected marker sets showed surprisingly low variance among replicates. We conclude that stringent marker selection and phenotype calling reduces noise in the data set while retaining patterns of population genetic structure.

scholarly journals Genetic Relationships among Schizolobium parahybum (Vell.) Blake (Leguminosae) Ecotypes from Ecuador and other Countries

2007 ◽  
Vol 56 (1-6) ◽  
pp. 214-221 ◽  
Author(s):  
H. F. Canchignia-Martínez ◽  
S. Hernández-Delgado ◽  
M. González-Paz ◽  
E. Motte ◽  
N. Mayek-Pérez
Keyword(s):  
Costa Rica ◽  
Fragment Length ◽  
Geographical Origin ◽  
Genetic Relationships ◽  
Random Amplified Polymorphic Dna ◽  
Aflp Markers ◽  
Diversity Patterns ◽  
Length Polymorphisms ◽  
Amplified Fragment Length Polymorphisms ◽  
Genetic Status

Abstract Fifteen ecotypes of Schizolobium parahybum (Vell.) Blake collected in Ecuador (9), Brazil (3), Bolivia (1) Costa Rica (1), and Peru (1) were analyzed using Random Amplified Polymorphic DNA (RAPDs), Amplified Fragment Length Polymorphisms (AFLPs) and microsatellites (SSRs) in order to determine their genetic relationships and diversity patterns among ecotypes and to identify the origin of cultivated germplasm in Ecuador. Although AFLP markers were the most informative technique based on amplified products, SSRs clearly differentiated the ecotypes of Ecuador based on their geographical origin or genetic status into two groups: commercial ecotypes growing at western Ecuador very similar to the ecotype from Costa Rica, and native germplasm from eastern Ecuador and ecotypes from Brazil, Peru and Bolivia.

Genetic diversity of the Andean blackberry (Rubus glaucus Benth.) in Ecuador assessed by AFLP markers

2020 ◽  
Vol 18 (4) ◽  
pp. 243-250
Author(s):  
Patricia Garrido ◽  
Eduardo Morillo ◽  
Wilson Vásquez-Castillo
Keyword(s):  
Genetic Diversity ◽  
Genetic Resources ◽  
Basic Research ◽  
Aflp Markers ◽  
Issr Primer ◽  
Inter Simple Sequence Repeats ◽  
Length Polymorphisms ◽  
Amplified Fragment Length Polymorphisms ◽  
Main Production ◽  
Production Areas

AbstractAndean blackberry (Rubus glaucus Benth.) is an emerging fruit crop with significant commercial potential. Despite its growing popularity, basic research about its genetic resources and breeding remains insufficient. The aim of this study was to assess the genetic diversity of Andean blackberry cultivars and related berries species from the main production areas in Ecuador. We analysed a total of 106 samples and performed DNA screening with different molecular markers: random-amplified polymorphic DNAs (RAPDs), inter-simple sequence repeats (ISSRs) and a set of representative samples with amplified fragment length polymorphisms (AFLPs). The tested RAPD primers did not reveal any differentiation among accessions identified as R. glaucus, however one ISSR primer was useful to find polymorphisms allowing the selection of 29 accessions for the analysis with AFLP markers. AFLP-M13 technology was used for screen genetic variations among these accessions and eight wild Rubus accessions. We scored 203 bands using five primer combinations; out of these 152 were informative in R. glaucus. AFLP markers clearly distinguish R. glaucus from the screened wild Rubus species, also an unexpected genetic structure was revealed among R. glaucus cultivars. This genetic differentiation and detection of admixed genotypes suggest a possible introgression of wild Rubus species in R. glaucus. Our findings are relevant for blackberry genetic breeding and use of these genetic resources.

The Use of ISSR Marker for Analyzing the Genetic Diversity of Nigerian Date Palms (Phoenix dactylifera L.)

2017 ◽  
Vol 1 (3) ◽  
pp. 133-137
Author(s):  
Beatrice Emoghene ◽  
◽  
Chukwuemeka Eke ◽  
Omorefe Asemota ◽  
McDonald Idu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phoenix Dactylifera ◽  
Issr Marker ◽  
Date Palms ◽  
Phoenix Dactylifera L

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.

Assessing Rosa persica genetic diversity using amplified fragment length polymorphisms analysis

2009 ◽  
Vol 120 (4) ◽  
pp. 538-543 ◽  
Author(s):  
T. Basaki ◽  
M. Mardi ◽  
M. Jafarkhani Kermani ◽  
S.M. Pirseyedi ◽  
M.R. Ghaffari ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Fragment Length ◽  
Length Polymorphisms ◽  
Amplified Fragment Length Polymorphisms
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