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.

Background: Recently, 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. Results: We 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.

Anthocyanins are natural pigments that exhibit a wide range of protective effects with potential benefits for human health related to their antioxidant activities. Grape berries are rich anthocyanins, and these compounds have considerable influence on wine quality. However, these pigments are known to only be present in coloured grape berries. In the present study, we investigated three distinctive grapes, in which only a few reports of mutant strains on the skin colour of the grape berry were reported. Anthocyanin and non-anthocyanin phenolic profiles of grape berry skin, pulp, and seeds at different growth stages were analysed using high performance liquid chromatography of flight mass spectrometry (HPLC-ESI-MS/MS). Meanwhile, grape antioxidant properties were evaluated at growth stages, including the early stage, veraison, and mature stage. The results showed that some anthocyanins contents, such as malvidin 3-Oglucoside, are significantly different between white skin grapes and their corresponding coloured genotypes, with high content in coloured but not in white skin grapes. However, other anthocyanins, such as delphinidin 3-O-glucoside, showed no significant differences between white skin grapes and their corresponding coloured genotypes. Moreover, non-anthocyanin phenolic profiles and antioxidant properties, except cultivars Pinot Blanc and Pinot Noir, showed no significant differences between white skin grapes and their corresponding coloured genotypes at any growth stage, including the pulp and seeds. However, significant differences were noted between different cultivars, for example, white-ciputao and Pinot Noir, Pinot Blanc and Muscat Rouge, and coloured-ciputao and Muscat Blanc, showing that the antioxidant capacity was not always in correlation with skin colour of grape berries.

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Crown gall disease caused by Agrobacterium tumefaciens affects a wide range of horticultural plants, and has no effective treatment. During the evaluation of crown gall resistance of peach germplasm resources, we observed enhanced resistance to subsequent invasion that was activated by virulence of A. tumefaciens in two peach cultivars. To further verify the phenotype observed in field experiments, systemic acquired resistance (SAR)-related salicylic acid (SA) and PR1 genes were investigated. The levels of SA were elevated in two cultivars, and these high levels were maintained for 35 days postinoculation. Compared with mock-inoculated controls, eight of the 22 candidate PpPR1 genes in A. tumefaciens-inoculated samples were significantly upregulated and three were downregulated in response to inoculation with A. tumefaciens. These data suggested that SA-induced SAR was activated in two peach cultivars by virulent A. tumefaciens infection. In addition, the eight induced PpPR1 genes can be used as molecular markers in defense studies in peach.