title: Linkage disequilibrium and population structure in wild and domesticated populations of Phaseolus vulgaris L.
abstract: Together with the knowledge of the population structure, a critical aspect for the planning of association and/or population genomics studies is the level of linkage disequilibrium (LD) that characterizes the species and the population used for such an analysis. We have analyzed the population structure and LD in wild and domesticated populations of Phaseolus vulgaris L. using amplified fragment length polymorphism markers, most of which were genetically mapped in two recombinant inbred populations. Our results reflect the previous knowledge of the occurrence of two major wild gene pools of P. vulgaris, from which two independent domestication events originated, one in the Andes and one in Mesoamerica. The high level of LD in the whole sample was mostly due to the gene pool structure, with a much higher LD in domesticated compared to wild populations. In relation to association studies, our results also suggest that whole-genome-scan approaches are feasible in the common bean. Interestingly, an excess of inter-chromosomal LD was found in the domesticated populations, which suggests an important role for epistatic selection during domestication. Moreover, our results indicate the occurrence of a strong bottleneck in the Andean wild population before domestication, suggesting a Mesoamerican origin of P. vulgaris. Finally, our data support the occurrence of a single domestication event in Mesoamerica, and the same scenario in the Andes.
authors.affiliation: Scienze Ambientali e delle Produzioni Vegetali, Università Politecnica delle Marche Ancona, Italy.
authors.forename: Monica
authors.initials: M
authors.lastname: Rossi
authors.affiliation: Scienze Ambientali e delle Produzioni Vegetali, Università Politecnica delle Marche Ancona, Italy.
authors.forename: Elena
authors.initials: E
authors.lastname: Bitocchi
authors.affiliation: Scienze Ambientali e delle Produzioni Vegetali, Università Politecnica delle Marche Ancona, Italy.
authors.forename: Elisa
authors.initials: E
authors.lastname: Bellucci
authors.affiliation: Scienze Ambientali e delle Produzioni Vegetali, Università Politecnica delle Marche Ancona, Italy.
authors.forename: Laura
authors.initials: L
authors.lastname: Nanni
authors.affiliation: Scienze Agronomiche e Genetica Vegetale Agraria, Università degli Studi di Sassari Sassari, Italy.
authors.forename: Domenico
authors.initials: D
authors.lastname: Rau
authors.affiliation: Scienze Agronomiche e Genetica Vegetale Agraria, Università degli Studi di Sassari Sassari, Italy.
authors.forename: Giovanna
authors.initials: G
authors.lastname: Attene
authors.affiliation: Scienze Ambientali e delle Produzioni Vegetali, Università Politecnica delle Marche Ancona, Italy.
authors.forename: Roberto
authors.initials: R
authors.lastname: Papa
keywords: AFLP; Common Bean; Crop Evolution; Domestication; Epistatic Selection; Leguminosae