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.
Highlights
Many studies utilizing generation sequencing have investigated plant evolution and domestication in annual crops
Ferganensis Kost. et Riab., 70 of P. persica (L.) Batsch, and 1 of P. persica × P. davidiana (Table S1 in Additional file 1). These peach lines were chosen from 837 accessions in the National Germplasm Repository of China, which includes more than 80% of the peach varieties worldwide
As there is no sexual barrier between wild and cultivated peach, the available diversity in the wild germplasm could be an important tool to expand the allelic pool of cultivated peach through introgression, to enhance the resistance of peach to adverse conditions and insect pests
Summary
Many studies utilizing generation sequencing have investigated plant evolution and domestication in annual crops. Prunus persica, is a typical perennial fruit crop that has ornamental and edible varieties. We explore the genetic basis of domestication in peach and the influence of humans on its evolution. These species produce fruits of very poor eating quality except for P. ferganensis, they could be valuable as a source of disease-resistance traits or as rootstocks. Some variations (flat shape, glabrous surface, double flower, and colorful anther) exist in peach but not in other close fruit species, such as apricot (Prunus armeniaca), plum (Prunus salicina), apple (Malus domestica), and grape (Vitis vinifera), peach has a lower level of genetic variability compared with the other Prunus crops due to selfing as well as important bottlenecks in its recent breeding history [4]
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