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Almost Forgotten or Latest Practice? AFLP applications, analyses and advances

2007; Elsevier BV; Volume: 12; Issue: 3 Linguagem: Inglês

10.1016/j.tplants.2007.02.001

1878-4372

Heidi M. Meudt, Andrew Clarke,

Chromosomal and Genetic Variations

Amplified fragment length polymorphism (AFLP) DNA fingerprinting is a firmly established molecular marker technique, with broad applications in population genetics, shallow phylogenetics, linkage mapping, parentage analyses, and single-locus PCR marker development. Technical advances have presented new opportunities for data analysis, and recent studies have addressed specific areas of the AFLP technique, including comparison to other genotyping methods, assessment of errors, homoplasy, phylogenetic signal and appropriate analysis techniques. Here we provide a synthesis of these areas and explore new directions for the AFLP technique in the genomic era, with the aim of providing a review that will be applicable to all AFLP-based studies. Amplified fragment length polymorphism (AFLP) DNA fingerprinting is a firmly established molecular marker technique, with broad applications in population genetics, shallow phylogenetics, linkage mapping, parentage analyses, and single-locus PCR marker development. Technical advances have presented new opportunities for data analysis, and recent studies have addressed specific areas of the AFLP technique, including comparison to other genotyping methods, assessment of errors, homoplasy, phylogenetic signal and appropriate analysis techniques. Here we provide a synthesis of these areas and explore new directions for the AFLP technique in the genomic era, with the aim of providing a review that will be applicable to all AFLP-based studies. the genetic constitution of an individual inferred from an AFLP fingerprint. alternative form of a genetic locus. For a single marker (locus), plus and null alleles, although different, are deemed to be homologous (i.e. possess a common evolutionary origin). When the term 'allele' is used across different markers (e.g. to refer to any visualized fragment), it should be clear that these alleles will be derived from different loci, and therefore will be mostly non-homologous. an AFLP DNA fragment visualized in a fingerprint (a plus allele). 'Band' is usually applied to a fragment visualized using a gel-based system, and 'peak' to a fragment visualized using a fluorescent system. a marker that is scored in multiple individuals and included in the data matrix. For AFLP, there are two possible character states: '1' (present in an individual; plus allele) or '0' (absent in an individual; null allele). a marker that enables homozygous (AA) and heterozygous (Aa) states to be distinguished. For many applications, particularly in population genetics, codominant markers are more powerful than dominant markers, enabling allele frequencies to be estimated, and require smaller sample sizes to achieve equivalent analytical power. Codominant markers include microsatellites and single nucleotide polymorphisms (SNPs). a marker that is scored as a present (plus) or absent (null) allele. Dominant markers cannot distinguish homozygous (AA) and heterozygous (Aa) states – a band or peak is present in both cases. AFLPs, RAPDs and ISSRs are mostly dominant markers. the complete set of AFLP bands visualized for a given sample. Here we consider 'fingerprint' and 'profile' as synonymous, but the former is sometimes used in a more stringent sense – when the pattern of bands uniquely identifies an individual. a single-stranded AFLP PCR product. Depending on size and strand, not all fragments will be visualized as peaks or bands. a specific region of the chromosome corresponding to the position of a marker; also the DNA at that position. an amplified locus that is identified in AFLP as bands or peaks of equal fragment size across multiple samples. A marker must be polymorphic (i.e. show both plus and null alleles) to be informative. In the AFLP fingerprint, a marker usually occupies a narrow ∼1 bp window (bin), so that, across all samples, visualized fragments of approximately equal mobility are treated as homologous alleles derived from a single locus. Homoplasy occurs when, by chance, non-homologous alleles of equal mobility fall into the same bin and, therefore, are treated as a single marker. In some cases, there can be two or more markers in a fingerprint that are derived from a single locus (e.g. a variable microsatellite). Although these markers should be treated as a single, codominant, marker, this is often not possible (see main text). for a given marker, the inferred allele when the band is absent. an allele present as an amplified DNA fragment (band or peak).