MAAP: a versatile and universal tool for genome analysis

Abstract

Multiple arbitrary amplicon profiling (MAAP) uses one or more oligonucleotide primers (> or = 5 nt) of arbitrary sequence to initiate DNA amplification and generate characteristic fingerprints from anonymous genomes or DNA templates. MAAP markers can be used in general fingerprinting as well as in mapping applications, either directly or as sequence-characterized amplified regions (SCARs). MAAP profiles can be tailored in the number of monomorphic and/or polymorphic products. For example, multiple endonuclease digestion of template DNA or the use of mini-hairpin primers can enhance detection of polymorphic DNA. Comparison of the expected and actual number of amplification products produced with primers differing in length, sequence and GC content from templates of varying complexity reveal severe departures from theoretical formulations with interesting implications in primer-template interaction. Extensive primer-template mismatching can occur when using templates of low complexity or long primers. Primer annealing and extension appears directed by an 8 nt 3'-terminal primer domain, requires sites with perfect homology to the first 5-6 nt fom the 3' terminus, and involves direct physical interaction between amplicon annealing sites.

Genetic diversity of chickpea (Cicer arietinum L.) germplasm in Pakistan as revealed by RAPD analysis

“…Polymorphisms could be caused by the difference of a single-nucleotide sequence at the priming sites (such as point mutations), or by structural arrangements within the amplified sequence (e.g., insertions, deletions, inversions) (Williams et al, 1990;Welsh and McClelland, 1990). RAPD analysis has been used in many applications and various organisms, especially in plant science (Caetano-Anolles, 1994;Sharma and Mohapatra, 1996).…”

Molecular Markers as a Tool for Analyses of Genetic Relatedness and Selection in Ornamentals

“…In the early 1990s, several research groups independently suggested the use of PCR strategies based on random primers for the detection of polymorphisms which do not require prior knowledge of target sequences (Welsh and McClelland, 1990;Williams et al, 1990;Caetano-Anolles et al, 1991;Caetano-Anolles, 1994). Though the term RAPD is the most widely used, DAF Q!NA Amplification !…”

R-ISSR marker as a useful tool for detection of new genomic loci in Arthrocnemum macrostachyum

“…There was no band found to be polymorphic when ISSR primer (AG) 8 GTG was combined with RAPD OPR12. Since primer specificity determinants are located within the first eight nucleotides at the 3' end (Caetano-Anollés 1994), anchoring primers at their 3' ends will lower the number of sequences which have homology to the primers, thus producing distinct bands (Parsons et al 1997). The success in specific amplified bands also depends on the anchoring motif.…”