Interspecific introgression and natural selection in the evolution of Japanese apricot (Prunus mume)

SummaryDomestication and population differentiation in crops involve considerable phenotypic changes. The logs of these evolutionary paths, including natural/artificial selection, can be found in the genomes of the current populations. However, these profiles have been little studied in tree crops, which have specific characters, such as long generation time and clonal propagation, maintaining high levels of heterozygosity.We conducted exon-targeted resequencing of 129 genomes in the genusPrunus, mainly Japanese apricot (Prunus mume), and apricot (P. armeniaca), plum (P. salicina), and peach (P. persica). Based on their genome-wide single nucleotide polymorphisms merged with published resequencing data of 79 ChineseP. mumecultivars, we inferred complete and ongoing population differentiation inP. mume.Sliding window characterization of the indexes for genetic differentiation identified interspecific fragment introgressions betweenP. mumeand related species (plum and apricot). These regions often exhibited strong selective sweeps formed in the paths of establishment or formation of substructures ofP. mume, suggesting thatP. mumehas frequently imported advantageous genes from other species in the subgenusPrunusas adaptive evolution.These findings shed light on the complicated nature of adaptive evolution in a tree crop that has undergone interspecific exchange of genome fragments with natural/artificial selection.