title: High Level of Nonsynonymous Changes in Common Bean Suggests That Selection under Domestication Increased Functional Diversity at Target Traits.
abstract: Crop species have been deeply affected by the domestication process, and there have been many efforts to identify selection signatures at the genome level. This knowledge will help geneticists to better understand the evolution of organisms, and at the same time, help breeders to implement successful breeding strategies. Here, we focused on domestication in the Mesoamerican gene pool ofPhaseolus vulgarisby sequencing 49 gene fragments from a sample of 45P. vulgariswild and domesticated accessions, and as controls, two accessions each of the closely related speciesPhaseolus coccineusandPhaseolus dumosus. An excess of nonsynonymous mutations within the domesticated germplasm was found. Our data suggest that the cost of domestication alone cannot explain fully this finding. Indeed, the significantly higher frequency of polymorphisms in the coding regions observed only in the domesticated plants (compared to noncoding regions), the fact that these mutations were mostly nonsynonymous and appear to be recently derived mutations, and the investigations into the functions of their relative genes (responses to biotic and abiotic stresses), support a scenario that involves new functional mutations selected for adaptation during domestication. Moreover, consistent with this hypothesis, selection analysis and the possibility to compare data obtained for the same genes in different studies of varying sizes, data types, and methodologies allowed us to identify four genes that were strongly selected during domestication. Each selection candidate is involved in plant resistance/tolerance to abiotic stresses, such as heat, drought, and salinity. Overall, our study suggests that domestication acted to increase functional diversity at target loci, which probably controlled traits related to expansion and adaptation to new agro-ecological growing conditions.
authors.affiliation: Department of Agricultural, Food and Environmental Sciences, Università Politecnica delle Marche Ancona, Italy.
authors.forename: Elena
authors.initials: E
authors.lastname: Bitocchi
authors.affiliation: Department of Agriculture, Università degli Studi di Sassari Sassari, Italy.
authors.forename: Domenico
authors.initials: D
authors.lastname: Rau
authors.affiliation: Department of Life Sciences and Biotechnology, Università degli Studi di Ferrara Ferrara, Italy.
authors.forename: Andrea
authors.initials: A
authors.lastname: Benazzo
authors.affiliation: Department of Agricultural, Food and Environmental Sciences, Università Politecnica delle Marche Ancona, Italy.
authors.forename: Elisa
authors.initials: E
authors.lastname: Bellucci
authors.affiliation: Department of Agricultural, Food and Environmental Sciences, Università Politecnica delle MarcheAncona, Italy; Department of Plant Physiology, Umeå Plant Science Centre, Umeå UniversityUmeå, Sweden.
authors.forename: Daniela
authors.initials: D
authors.lastname: Goretti
authors.affiliation: Department of Agricultural, Food and Environmental Sciences, Università Politecnica delle Marche Ancona, Italy.
authors.forename: Eleonora
authors.initials: E
authors.lastname: Biagetti
authors.affiliation: Department of Life Sciences and Biotechnology, Università degli Studi di Ferrara Ferrara, Italy.
authors.forename: Alex
authors.initials: A
authors.lastname: Panziera
authors.affiliation: Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria, Centro di Ricerca per la Cerealicoltura Foggia, Italy.
authors.forename: Giovanni
authors.initials: G
authors.lastname: Laidò
authors.affiliation: Department of Agriculture, Università degli Studi di Sassari Sassari, Italy.
authors.forename: Monica
authors.initials: M
authors.lastname: Rodriguez
authors.affiliation: Scuola di Scienze Agrarie, Forestali, Alimentari ed Ambientali, Università degli Studi della Basilicata Potenza, Italy.
authors.forename: Tania
authors.initials: T
authors.lastname: Gioia
authors.affiliation: Department of Agriculture, Università degli Studi di Sassari Sassari, Italy.
authors.forename: Giovanna
authors.initials: G
authors.lastname: Attene
authors.affiliation: Department of Plant Sciences, North Dakota State University Fargo, ND, USA.
authors.forename: Phillip
authors.initials: P
authors.lastname: McClean
authors.affiliation: Department of Plant Sciences, North Dakota State University Fargo, ND, USA.
authors.forename: Rian K
authors.initials: RK
authors.lastname: Lee
authors.affiliation: Center for Applied Genetic Technologies, University of Georgia Athens, GA, USA.
authors.forename: Scott A
authors.initials: SA
authors.lastname: Jackson
authors.affiliation: Department of Life Sciences and Biotechnology, Università degli Studi di Ferrara Ferrara, Italy.
authors.forename: Giorgio
authors.initials: G
authors.lastname: Bertorelle
authors.affiliation: Department of Agricultural, Food and Environmental Sciences, Università Politecnica delle Marche Ancona, Italy.
authors.forename: Roberto
authors.initials: R
authors.lastname: Papa
keywords: adaptation; cost of domestication; deleterious mutations; recombination rate; selection