Decreased Nucleotide and Expression Diversity and Modified Coexpression Patterns Characterize Domestication in the Common Bean.
Using RNA sequencing technology and de novo transcriptome assembly, we compared representative sets of wild and domesticated accessions of common bean (Phaseolus vulgaris) from Mesoamerica. RNA was extracted at the first true-leaf stage, and de novo assembly was used to develop a reference transcriptome; the final data set consists of ∼190,000 single nucleotide polymorphisms from 27,243 contigs in expressed genomic regions. A drastic reduction in nucleotide diversity (∼60%) is evident for the domesticated form, compared with the wild form, and almost 50% of the contigs that are polymorphic were brought to fixation by domestication. In parallel, the effects of domestication decreased the diversity of gene expression (18%). While the coexpression networks for the wild and domesticated accessions demonstrate similar seminal network properties, they show distinct community structures that are enriched for different molecular functions. After simulating the demographic dynamics during domestication, we found that 9% of the genes were actively selected during domestication. We also show that selection induced a further reduction in the diversity of gene expression (26%) and was associated with 5-fold enrichment of differentially expressed genes. While there is substantial evidence of positive selection associated with domestication, in a few cases, this selection has increased the nucleotide diversity in the domesticated pool at target loci associated with abiotic stress responses, flowering time, and morphology.
Department of Agricultural, Food, and Environmental Sciences, Università Politecnica delle Marche, 60131 Ancona, Italy.
Elisa
E
Bellucci
Department of Agricultural, Food, and Environmental Sciences, Università Politecnica delle Marche, 60131 Ancona, Italy.
Elena
E
Bitocchi
Department of Biotechnology, University of Verona, 37134 Verona, Italy.
Alberto
A
Ferrarini
Department of Life Sciences and Biotechnology, University of Ferrara, 44100 Ferrara, Italy.
Andrea
A
Benazzo
Department of Agricultural, Food, and Environmental Sciences, Università Politecnica delle Marche, 60131 Ancona, Italy.
Eleonora
E
Biagetti
Genes and Small Molecules Group, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany.
Sebastian
S
Klie
Department of Biotechnology, University of Verona, 37134 Verona, Italy.
Andrea
A
Minio
Department of Agriculture, University of Sassari, 07100 Sassari, Italy.
Domenico
D
Rau
Department of Agriculture, University of Sassari, 07100 Sassari, Italy.
Monica
M
Rodriguez
Department of Life Sciences and Biotechnology, University of Ferrara, 44100 Ferrara, Italy Department of Biodiversity and Molecular Ecology, Fondazione Edmund Mach, 38010 S. Michele all'Adige, Italy.
Alex
A
Panziera
Department of Biotechnology, University of Verona, 37134 Verona, Italy.
Luca
L
Venturini
Department of Agriculture, University of Sassari, 07100 Sassari, Italy.
Giovanna
G
Attene
Department of Applied Biology, University of Perugia, 06121 Perugia, Italy.
Emidio
E
Albertini
Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia 30602.
Scott A
SA
Jackson
Department of Agricultural, Food, and Environmental Sciences, Università Politecnica delle Marche, 60131 Ancona, Italy.
Laura
L
Nanni
Central Metabolism Group, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany.
Alisdair R
AR
Fernie
Systems Biology and Mathematical Modeling Group, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany.
Zoran
Z
Nikoloski
Department of Life Sciences and Biotechnology, University of Ferrara, 44100 Ferrara, Italy.
Giorgio
G
Bertorelle
Department of Biotechnology, University of Verona, 37134 Verona, Italy.
Massimo
M
Delledonne
Department of Agricultural, Food, and Environmental Sciences, Università Politecnica delle Marche, 60131 Ancona, Italy Consiglio per la Ricerca e Sperimentazione in Agricoltura, Cereal Research Centre (CRA-CER), 71122 Foggia, Italy r.papa@univpm.it.
Roberto
http://orcid.org/0000-0001-9598-3131
R
Papa