MAAP: a Versatile and Universal Tool for Genome Analysis

Overview

Journal Plant Mol Biol

Date 1994 Sep 1

PMID 7919212

Citations 6

Authors

G Caetano-Anolles

Affiliations

Soon will be listed here.

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.

Citing Articles

Population admixtures in medaka inferred by multiple arbitrary amplicon sequencing.

Fujimoto S, Yaguchi H, Myosho T, Aoyama H, Sato Y, Kimura R Sci Rep. 2022; 12(1):19989.

PMID: 36411327 PMC: 9678866. DOI: 10.1038/s41598-022-24498-7.

DNA amplification fingerprinting analysis of bermudagrass (Cynodon): genetic relationships between species and interspecific crosses.

Caetano-Anolles G, Callahan L, Williams P, Weaver K, Gresshoff P Theor Appl Genet. 2013; 91(2):228-35.

PMID: 24169768 DOI: 10.1007/BF00220882.

Molecular phylogeny and DNA amplification fingerprinting of Petunia taxa.

Cerny T, Caetano-Anolles G, Trigiano R, Starman T Theor Appl Genet. 2013; 92(8):1009-16.

PMID: 24166629 DOI: 10.1007/BF00224042.

Phenotypic and genotypic comparison of symbiotic and free-living cyanobacteria from a single field site.

West N, Adams D Appl Environ Microbiol. 2006; 63(11):4479-84.

PMID: 16535734 PMC: 1389290. DOI: 10.1128/aem.63.11.4479-4484.1997.

Molecular variation and fingerprinting of Leucadendron cultivars (Proteaceae) by ISSR markers.

Pharmawati M, Yan G, Finnegan P Ann Bot. 2005; 95(7):1163-70.

PMID: 15790586 PMC: 4246899. DOI: 10.1093/aob/mci127.

References

Ohler L, Rose E . Optimization of long-distance PCR using a transposon-based model system. PCR Methods Appl. 1992; 2(1):51-9. DOI: 10.1101/gr.2.1.51. View

Halward T, Stalker T, LaRue E, Kochert G . Use of single-primer DNA amplifications in genetic studies of peanut (Arachis hypogaea L.). Plant Mol Biol. 1992; 18(2):315-25. DOI: 10.1007/BF00034958. View

Xu Y, Clark M, Pehu E . Use of RAPD markers to screen somatic hybrids between Solanum tuberosum and S. brevidens. Plant Cell Rep. 2013; 12(2):107-9. DOI: 10.1007/BF00241944. View

Kolchinsky A, Funke R, Gresshoff P . DAF-amplified fragments can be used as markers for DNA from pulse field gels. Biotechniques. 1993; 14(3):400-3. View

G Williams J, Reiter R, Young R, Scolnik P . Genetic mapping of mutations using phenotypic pools and mapped RAPD markers. Nucleic Acids Res. 1993; 21(11):2697-702. PMC: 309602. DOI: 10.1093/nar/21.11.2697. View

Torres A, Weeden N, Martin A . Linkage among isozyme, RFLP and RAPD markers in Vicia faba. Theor Appl Genet. 2013; 85(8):937-45. DOI: 10.1007/BF00215032. View

Kazan K, Manners J, Cameron D . Inheritance of random amplified polymorphic DNA markers in an interspecific cross in the genus Stylosanthes. Genome. 1993; 36(1):50-6. DOI: 10.1139/g93-007. View

Parker J, Rabinovitch P, Burmer G . Targeted gene walking polymerase chain reaction. Nucleic Acids Res. 1991; 19(11):3055-60. PMC: 328270. DOI: 10.1093/nar/19.11.3055. View

Michelmore R, Paran I, Kesseli R . Identification of markers linked to disease-resistance genes by bulked segregant analysis: a rapid method to detect markers in specific genomic regions by using segregating populations. Proc Natl Acad Sci U S A. 1991; 88(21):9828-32. PMC: 52814. DOI: 10.1073/pnas.88.21.9828. View

10.

Devos K, Gale M . The use of random amplified polymorphic DNA markers in wheat. Theor Appl Genet. 2013; 84(5-6):567-72. DOI: 10.1007/BF00224153. View

11.

Eskew D, Caetano-Anolles G, Bassam B, Gresshoff P . DNA amplification fingerprinting of the Azolla-Anabaena symbiosis. Plant Mol Biol. 1993; 21(2):363-73. DOI: 10.1007/BF00019951. View

12.

Storck R, ALEXOPOULOS C . Deoxyribonucleic acid of fungi. Bacteriol Rev. 1970; 34(2):126-54. PMC: 408313. DOI: 10.1128/br.34.2.126-154.1970. View

13.

Micheli M, Bova R, Calissano P, DAmbrosio E . Randomly amplified polymorphic DNA fingerprinting using combinations of oligonucleotide primers. Biotechniques. 1993; 15(3):388-90. View

14.

Muralidharan K, Wakeland E . Concentration of primer and template qualitatively affects products in random-amplified polymorphic DNA PCR. Biotechniques. 1993; 14(3):362-4. View

15.

Welsh J, Honeycutt R, McClelland M, Sobral B . Parentage determination in maize hybrids using the arbitrarily primed polymerase chain reaction (AP-PCR). Theor Appl Genet. 2013; 82(4):473-6. DOI: 10.1007/BF00588601. View

16.

Kiss G, Csanadi G, Kalman K, Kalo P, Okresz L . Construction of a basic genetic map for alfalfa using RFLP, RAPD, isozyme and morphological markers. Mol Gen Genet. 1993; 238(1-2):129-37. DOI: 10.1007/BF00279539. View

17.

Akopyanz N, Bukanov N, Westblom T, Kresovich S, Berg D . DNA diversity among clinical isolates of Helicobacter pylori detected by PCR-based RAPD fingerprinting. Nucleic Acids Res. 1992; 20(19):5137-42. PMC: 334296. DOI: 10.1093/nar/20.19.5137. View

18.

Welsh J, Chada K, Dalal S, Cheng R, Ralph D, McClelland M . Arbitrarily primed PCR fingerprinting of RNA. Nucleic Acids Res. 1992; 20(19):4965-70. PMC: 334270. DOI: 10.1093/nar/20.19.4965. View

19.

Caetano-Anolles G . Amplifying DNA with arbitrary oligonucleotide primers. PCR Methods Appl. 1993; 3(2):85-94. DOI: 10.1101/gr.3.2.85. View

20.

Karlin S, Brendel V . Chance and statistical significance in protein and DNA sequence analysis. Science. 1992; 257(5066):39-49. DOI: 10.1126/science.1621093. View