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AOBPreview published online on August 1, 2007
Annals of Botany, doi:10.1093/aob/mcm151
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© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Tagging the Signatures of Domestication in Common Bean (Phaseolus vulgaris) by Means of Pooled DNA Samples

Roberto Papa1,*, Elisa Bellucci1, Monica Rossi1, Stefano Leonardi2, Domenico Rau1, Paul Gepts3, Laura Nanni1 and Giovanna Attene4

1 Dipartimento di Scienze degli Alimenti, Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy
2 Dipartimento di Scienze Ambientali, Università di Parma, Parco Area delle Scienze 11A, 43100 Parma, Italy
3 Department of Plant Sciences, Section of Crop and Ecosystem Sciences, UC Davis, 1 Shields Avenue, Davis, CA 95616-8780, USA
4 Dipartimento di Scienze Agronomiche e Genetica Vegetale Agraria, Università di Sassari, Via De Nicola, 07100 Sassari, Italy

* For correspondence. E-mail r.papa{at}univpm.it

Received: 27 September 2006    Returned for revision: 4 December 2006    Accepted: 22 May 2007   

Background and Aims: The main aim of this study was to use an amplified fragment length polymorphism (AFLP)-based, large-scale screening of the whole genome of Phaseolus vulgaris to determine the effects of selection on the structure of the genetic diversity in wild and domesticated populations.

Methods: Using pooled DNA samples, seven each of wild and domesticated populations of P. vulgaris were studied using 2506 AFLP markers (on average, one every 250 kb). About 10 % of the markers were also analysed on individual genotypes and were used to infer allelic frequencies empirically from bulk data. In both data sets, tests were made to determine the departure from neutral expectation for each marker using an FST-based method.

Key Results: The most important outcome is that a large fraction of the genome of the common bean (16 %; P <0·01) appears to have been subjected to effects of selection during domestication. Markers obtained in individual genotypes were also mapped and classified according to their proximities to known genes and quantitative trait loci (QTLs) of the domestication syndrome. Most of the markers that were found to be potentially under the effects of selection were located in the proximity of previously mapped genes and QTLs related to the domestication syndrome.

Conclusions: Overall, the results indicate that in P. vulgaris a large portion of the genome appears to have been subjected to the effects of selection, probably because of linkage to the loci selected during domestication. As most of the markers that are under the effects of selection are linked to known loci related to the domestication syndrome, it is concluded that population genomics approaches are very efficient in detecting QTLs. A method based on bulk DNA samples is presented that is effective in pre-screening for a large number of markers to determine selection signatures.

Key words: AFLP, domestication, Phaseolus vulgaris, population genomics, QTLs, selection


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