Abstract: | BackgroundRecently, many studies utilizing next generation sequencing have investigated
plant evolution and domestication in annual crops. Peach, Prunus persica, is a typical perennial fruit crop that has
ornamental and edible varieties. Unlike other fruit crops, cultivated peach
includes a large number of phenotypes but few polymorphisms. In this study, we
explore the genetic basis of domestication in peach and the influence of humans on
its evolution.ResultsWe perform large-scale resequencing of 10 wild and 74 cultivated peach
varieties, including 9 ornamental, 23 breeding, and 42 landrace lines. We identify
4.6 million SNPs, a large number of which could explain the phenotypic variation
in cultivated peach. Population analysis shows a single domestication event, the
speciation of P. persica from wild peach.
Ornamental and edible peach both belong to P.
persica, along with another geographically separated subgroup,
Prunus ferganensis.We identify 147 and 262 genes under edible and ornamental selection,
respectively. Some of these genes are associated with important biological
features. We perform a population heterozygosity analysis in different plants that
indicates that free recombination effects could affect domestication history. By
applying artificial selection during the domestication of the peach and
facilitating its asexual propagation, humans have caused a sharp decline of the
heterozygote ratio of SNPs.ConclusionsOur analyses enhance our knowledge of the domestication history of perennial
fruit crops, and the dataset we generated could be useful for future research on
comparative population genomics.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-014-0415-1) contains supplementary material, which is available to authorized
users. |