Abstract
Genome scans based on anonymous Amplified Fragment Length Polymorphism (AFLP) markers scattered throughout the genome are becoming an increasingly popular approach to study the genetic basis of adaptation and speciation in natural populations. A shortcoming of this approach is that despite its efficiency to detect signatures of selection, it can hardly help pinpoint the specific genomic region(s), gene(s), or mutation(s) targeted by selection. Here, we present two methods to be undertaken after performing an AFLP-based genome scan to easily obtain the sequences of AFLP loci detected as outliers by population genomics approaches. The first one is based on the gel excision of the target AFLP fragment, after simplification of the AFLP fingerprint and separation of the fragments by migration. The second one is a combination of classical AFLP protocol and 454 pyrosequencing.
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Acknowledgments
We are grateful to Cécile Godé and Pierre Saumitou-Laprade for technical assistance and to Martin C. Fischer and Aurélie Bonin for helpful comments on an earlier version of this work. M.P. and L.D. were supported by a grant from the French Rhône-Alpes region (grant 501545401) and by the French National Research Agency (project ANR-08-CES-006-01 DIBBECO). C.L.M. was funded by the French Ministry of Research and Technology.
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Paris, M., Meyer, CL., Blassiau, C., Coissac, E., Taberlet, P., Després, L. (2012). Two Methods to Easily Obtain Nucleotide Sequences from AFLP Loci of Interest. In: Pompanon, F., Bonin, A. (eds) Data Production and Analysis in Population Genomics. Methods in Molecular Biology, vol 888. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-61779-870-2_6
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DOI: https://doi.org/10.1007/978-1-61779-870-2_6
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