title: Genome-wide view of genetic diversity reveals paths of selection and cultivar differentiation in peach domestication.
abstract: Domestication and cultivar differentiation are requisite processes for establishing cultivated crops. These processes inherently involve substantial changes in population structure, including those from artificial selection of key genes. In this study, accessions of peach (Prunus persica) and its wild relatives were analysed genome-wide to identify changes in genetic structures and gene selections associated with their differentiation. Analysis of genome-wide informative single-nucleotide polymorphism loci revealed distinct changes in genetic structures and delineations among domesticated peach and its wild relatives and among peach landraces and modern fruit (F) and modern ornamental (O-A) cultivars. Indications of distinct changes in linkage disequilibrium extension/decay and of strong population bottlenecks or inbreeding were identified. Site frequency spectrum- and extended haplotype homozygosity-based evaluation of genome-wide genetic diversities supported selective sweeps distinguishing the domesticated peach from its wild relatives and each F/O-A cluster from the landrace clusters. The regions with strong selective sweeps harboured promising candidates for genes subjected to selection. Further sequence-based evaluation further defined the candidates and revealed their characteristics. All results suggest opportunities for identifying critical genes associated with each differentiation by analysing genome-wide genetic diversity in currently established populations. This approach obviates the special development of genetic populations, which is particularly difficult for long-lived tree crops.
authors.affiliation: Laboratory of Pomology, Graduate School of Agriculture, Kyoto University, Kita-shirakawa, Oiwake-cho, Kyoto 606-8502, Japan takashia@kais.kyoto-u.ac.jp.
authors.forename: Takashi
authors.initials: T
authors.lastname: Akagi
authors.affiliation: Apple Research Division, NARO Institute of Fruit Tree Science, Morioka 020-0123, Japan.
authors.forename: Toshio
authors.initials: T
authors.lastname: Hanada
authors.affiliation: Breeding and Pest Management Division, NARO Institute, Tsukuba, Ibaragi 305-8605, Japan.
authors.forename: Hideaki
authors.initials: H
authors.lastname: Yaegaki
authors.affiliation: Department of Plant Sciences, University of California Davis, CA 95616, USA.
authors.forename: Thomas M
authors.initials: TM
authors.lastname: Gradziel
authors.affiliation: Laboratory of Pomology, Graduate School of Agriculture, Kyoto University, Kita-shirakawa, Oiwake-cho, Kyoto 606-8502, Japan.
authors.forename: Ryutaro
authors.initials: R
authors.lastname: Tao
mesh_terms: D018745:Genome, Plant; D000069600:Plant Breeding; D011110:Polymorphism, Genetic; D000068239:Prunus persica / Q000235:genetics*; D012641:Selection, Genetic
keywords: artificial selection; cultivar differentiation; domestication; linkage disequilibrium; tree crop