Estimating genetic diversity of Arabidopsis thaliana ecotypes with amplified fragment length polymorphisms (AFLP)

2000 ◽  
Vol 100 (3-4) ◽  
pp. 633-640 ◽  
Author(s):  
S. Erschadi ◽  
G. Haberer ◽  
M. Schöniger ◽  
R. A. Torres-Ruiz
Keyword(s):  
Genetic Diversity ◽  
Arabidopsis Thaliana ◽  
Fragment Length ◽  
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.

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

scholarly journals Detection of Genetic Variation in Wild Populations of Three Allium Species Using Amplified Fragment Length Polymorphisms

HortScience ◽  
2008 ◽  
Vol 43 (3) ◽  
pp. 637-643 ◽  
Author(s):  
Nathan C. Phillips ◽  
Steven R. Larson ◽  
Daniel T. Drost
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Fragment Length ◽  
Genetic Divergence ◽  
Isolation By Distance ◽  
The United States ◽  
Length Polymorphisms ◽  
Amplified Fragment Length Polymorphisms ◽  
Geographical Regions ◽  
Collection Sites

Three wild onion species native to the intermountain west in the United States—Allium acuminatum, A. brandegei, and A. passeyi—show horticultural potential, but little is known about patterns of genetic diversity among localized populations and geographical regions. We examined amplified fragment length polymorphisms (AFLP) within and among five Allium acuminatum, four A. brandegei, and three A. passeyi collection sites in Utah. These three congeners with contrasting abundance and distribution patterns provide an opportunity to investigate the role of geographic distance, altitude, and rarity in patterns of genetic divergence. The collection sites were selected along an altitudinal gradient to reflect ecogeographic variation. Individual plants from each of the 12 sites were genotyped using six AFLP primer combinations detecting DNA variation within and among all three species. Genetic differences between species were high enough to render comparisons among species impractical, so each species was analyzed separately for differences between populations and variability within populations. Similarity coefficients were significantly greater within collection sites versus among collection sites indicating divergence between populations. Within-population genetic diversity was not correlated with elevation for any of the three species. Analysis of molecular variance revealed that 66% (A. acuminatum), 83% (A. passeyi), and 64% (A. brandegei) of observed variation is found within populations. Genetic divergence among populations (ФST) was higher in the widely distributed species, suggesting that interpopulation gene flow may be negatively correlated with range size. Allium acuminatum and A. brandegei individuals cluster into groups corresponding strictly to collection sites based on neighbor-joining analysis of the total number of DNA polymorphisms between individual plants. Allium passeyi populations, however, had less overall genetic variation between populations. Genetic isolation by distance appeared responsible for much of the variability among populations, although there was one notable exception showing significant differences between two geographically close populations in A. acuminatum.

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