title: Evolutionary Genomics of Peach and Almond Domestication.
abstract: The domesticated almond [Prunus dulcis (L.) Batsch] and peach [P. persica (Mill.) D. A. Webb] originated on opposite sides of Asia and were independently domesticated ∼5000 yr ago. While interfertile, they possess alternate mating systems and differ in a number of morphological and physiological traits. Here, we evaluated patterns of genome-wide diversity in both almond and peach to better understand the impacts of mating system, adaptation, and domestication on the evolution of these taxa. Almond has around seven times the genetic diversity of peach, and high genome-wide [Formula: see text] values support their status as separate species. We estimated a divergence time of ∼8 MYA (million years ago), coinciding with an active period of uplift in the northeast Tibetan Plateau and subsequent Asian climate change. We see no evidence of a bottleneck during domestication of either species, but identify a number of regions showing signatures of selection during domestication and a significant overlap in candidate regions between peach and almond. While we expected gene expression in fruit to overlap with candidate selected regions, instead we find enrichment for loci highly differentiated between the species, consistent with recent fossil evidence suggesting fruit divergence long preceded domestication. Taken together, this study tells us how closely related tree species evolve and are domesticated, the impact of these events on their genomes, and the utility of genomic information for long-lived species. Further exploration of this data will contribute to the genetic knowledge of these species and provide information regarding targets of selection for breeding application, and further the understanding of evolution in these species.
authors.affiliation: Department of Plant Sciences, University of California, Davis, California 95616 dmvelasco@ucdavis.edu.|United States Department of Agriculture, Agricultural Research Service, National Clonal Germplasm Repository, Davis, California 95616.
authors.forename: Dianne
authors.identifier: 0000-0003-1432-0630
authors.initials: D
authors.lastname: Velasco
authors.affiliation: Department of Plant Sciences, University of California, Davis, California 95616.
authors.forename: Josh
authors.initials: J
authors.lastname: Hough
authors.affiliation: United States Department of Agriculture, Agricultural Research Service, National Clonal Germplasm Repository, Davis, California 95616.
authors.forename: Mallikarjuna
authors.initials: M
authors.lastname: Aradhya
authors.affiliation: Department of Plant Sciences, University of California, Davis, California 95616.|Center for Population Biology, University of California, Davis, California 95616.|Genome Center, University of California, Davis, California 95616.
authors.forename: Jeffrey
authors.identifier: 0000-0003-1656-4954
authors.initials: J
authors.lastname: Ross-Ibarra
mesh_terms: D000071278:Domestication; D019143:Evolution, Molecular; D017343:Genes, Plant; D056726:Genetic Association Studies; D014644:Genetic Variation; D005828:Genetics, Population; D018745:Genome, Plant; D023281:Genomics / Q000379:methods; D007178:Inbreeding; D009154:Mutation; D000068181:Prunus dulcis / Q000235:genetics*; D000068239:Prunus persica / Q000235:genetics*; D040641:Quantitative Trait Loci
keywords: Prunus dulcis; Prunus persica; almond; domestication; mating system; peach