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Journal of Heredity Advance Access published online on December 15, 2004
Journal of Heredity, doi:10.1093/jhered/esi013
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© 2005 The American Genetic Association
Received May 14, 2004
Accepted July 2, 2004

Brief Communication

Base Composition of Coffea AFLP Sequences and Their Conservation Within the Genus

V. Poncet 1*, P. Hamon 1, M.-B. Sauvage de Saint Marc 1, T. Bernard 1, S. Hamon 1, and M. Noirot 1

1 From UMR 1097 Diversité et Génome des Plantes Cultivées, Centre IRD, 911 avenue Agropolis, BP 64501, 34394 Montpellier Cedex 5, France

* To whom correspondence should be addressed.
V. Poncet, E-mail: poncet{at}mpl.ird.fr


  Abstract

Amplified fragment length polymorphism (AFLP) is often used for genetic mapping and diversity analysis, but very little information is currently available on their sequence characteristics. Species-specific sequences were analyzed from a single Coffea genome (Coffea pseudozanguebariae) associated with clustered or nonclustered AFLP loci of known genetic position. Compared with the expressed sequence tag (EST) sequence composition, their AT content exhibited a bimodal distribution with AT-poor sequences corresponding mainly to putative coding sequences. AT-rich sequences, apart from the EST distribution, were usually clustered on the genetic map and might correspond to noncoding sequences. Conversion of these AFLP markers into sequence-characterized amplified region (SCAR) anchor markers allowed us to assess sequence conservation within Coffea species with respect to species relatedness.


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