Genome assemblies of five Prunus species and GWASs for key agronomic traits in peach

The Rosaceae family includes many genera with different types of fruit, of which the Prunus genus contains several fruit tree species with important economic value, such as peach (Prunus persica), plum (Prunus japonica Thunb.), and apricot (Prunus armeniaca L.), as well as wild peach species such as Tibetan peach (Prunus mira Koehne) and Chinese wild peach (Prunus davidiana). These species all produce drupes, a fruit whose endocarp gradually hardens throughout development, which are unique to the Prunus crops. The fleshy fruit of Prunus crops offers an abundance of nutrients, such as carbohydrates, organic acids, vitamins, and minerals, extensive phenotypic variation contributing to these fruit characteristics exist within or between species. Although these species have considerable economic value, the genetic mechanisms underlying favorable traits are poorly understood. That is, to some extent, attributed to the scarcity of genomic resources, which severely limits efforts to improve Prunus crops, particularly for plum, Prunus mira Koehne, and Prunus davidiana. Here, we report de novo genome assemblies for these five organisms, analysed whole-genome re-sequencing data of 417 peach accessions and performed a structural variant-based genome-wide association study (GWAS) of key agricultural traits.