Identification of commercial chicory cultivars for hydroponic forcing and their phenetic relationships revealed by random amplified polymorphic DNAs and amplified fragment length polymorphisms

AFLP is a combination restriction fragment/PCR molecular marker technique which detects polymorphisms due to changes at or in the vicinity of restriction enzyme sites. The technique detects multiple polymorphic loci throughout the genome and may be used for fingerprinting and mapping purposes. The main advantages of the method are the consistency and reliability of the technique due to stringent PCR conditions and the ability to rapidly detect many polymorphic loci.

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Amplified fragment length polymorphisms, the evolution of the land snail genus Theba (Stylommatophora: Helicidae), and an objective approach for relating fossils to internal nodes of a phylogenetic tree using geometric morphometrics

Zoological Journal of the Linnean Society ◽

10.1111/zoj12123 ◽

2014 ◽

Keyword(s):

Phylogenetic Tree ◽

Geometric Morphometrics ◽

Fragment Length ◽

Land Snail ◽

Length Polymorphisms ◽

Amplified Fragment Length Polymorphisms

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Genetic diversity of Echinacea species based upon amplified fragment length polymorphism markers

Genome ◽

10.1139/g03-086 ◽

2004 ◽

Vol 47 (1) ◽

pp. 102-111 ◽

Cited By ~ 17

Author(s):

D -H Kim ◽

D Heber ◽

D W Still

Keyword(s):

Genetic Diversity ◽

Genetic Distance ◽

Fragment Length ◽

Echinacea Purpurea ◽

Morphological Characters ◽

Pairwise Distance ◽

Neighbor Joining ◽

Aflp Data ◽

Phenetic Relationships ◽

Length Polymorphisms

The taxonomy of Echinacea is based on morphological characters and has varied depending on the monographer. The genus consists of either nine species and four varieties or four species and eight varieties. We have used amplified fragment length polymorphisms (AFLP) to assess genetic diversity and phenetic relationships among nine species and three varieties of Echinacea (sensu McGregor). A total of 1086 fragments, of which approximately 90% were polymorphic among Echinacea taxa, were generated from six primer combinations. Nei and Li's genetic distance coefficient and the neighbor-joining algorithm were employed to construct a phenetic tree. Genetic distance results indicate that all Echinacea species are closely related, and the average pairwise distance between populations was approximately three times the intrapopulation distances. The topology of the neighbor-joining tree strongly supports two major clades, one containing Echinacea purpurea, Echinacea sanguinea, and Echinacea simulata and the other containing the remainder of the Echinacea taxa (sensu McGregor). The species composition within the clades differs between our AFLP data and the morphometric treatment offered by Binns and colleagues. We also discuss the suitability of AFLP in determining phylogenetic relationships.Key words: Echinacea, AFLP, genetic distance, phylogeny.

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Analysis of Amplified Fragment-Length Polymorphisms (VNTRISTR Loci) for Human Identity Testing

Forensic DNA Profiling Protocols ◽

10.1385/0-89603-443-7:155 ◽

2003 ◽

pp. 155-172

Author(s):

Bruce Budowle ◽

Robert C. Allen

Keyword(s):

Fragment Length ◽

Human Identity ◽

Identity Testing ◽

Length Polymorphisms ◽

Amplified Fragment Length Polymorphisms

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

Genome ◽

10.1139/g10-006 ◽

2010 ◽

Vol 53 (4) ◽

pp. 302-310 ◽

Cited By ~ 32

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.

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