Molecular Breeding

, Volume 34, Issue 3, pp 1245–1260 | Cite as

The status of AFLP in the genomics era and a pipeline for converting AFLPs into single-locus markers



Even though next-generation sequencing (NGS) has now become the predominant state-of-the-art technique for genotyping populations, amplified fragment length polymorphism (AFLP) DNA fingerprinting is still a relevant method, thanks to its versatility, cost-effectiveness, independence of prior sequence information and broad applicability. Even though the number of AFLP studies reached its peak in 2012, it is still applied extensively for phylogenetic analysis, genotyping or identifying non-model species, which often feature complex and large genomes. For these purposes, tools continue to be developed for designing AFLP studies, scoring AFLPs or handling AFLP data. Moreover, AFLP studies embrace the NGS technology; for example, the whole-genome sequence of model species is used to design more efficient AFLP studies for non-model species. Conversely, in complexity reduction of polymorphic sequences and restriction site-associated DNA sequencing studies, polymorphisms are often found to be present in many restriction sites, which can still be studied as AFLPs. We discuss the latest advances in AFLP-based studies in the era of NGS and anticipate that AFLP will remain a relevant method in the near future, even for species with a known genome, owing to its many promising new features such as methylation-sensitive-AFLP. Here, we also present an optimized pipeline for converting AFLP markers into single-locus markers, which can be applied in both traditional AFLP and NGS studies.


AFLP Next-generation sequencing MS-AFLP Single-locus marker Conversion 



We thank all the reviewers and the editors for their useful and constructive comments and suggestions concerning our manuscript. This work was supported financially by the National Natural Science Foundation of China (Code: 31000116 and 30800680) and the Fundamental Research Funds for the Central Universities (Grant No. 2012ZYTS045).

Supplementary material

11032_2014_113_MOESM1_ESM.docx (25 kb)
Supplementary material 1 (DOCX 24 kb)


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Copyright information

© Springer Science+Business Media Dordrecht 2014

Authors and Affiliations

  1. 1.Hubei Key Laboratory of Genetic Regulation and Integrative Biology, College of Life SciencesCentral China Normal UniversityWuhanPeople’s Republic of China
  2. 2.Institute for Agricultural and Fisheries Research (ILVO)MelleBelgium
  3. 3.College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanPeople’s Republic of China

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