Exon capture resequencing of Japanese apricot (Prunus mume)

Japanese apricot (Prunus mume Sieb. et Zucc.) is a kind of deciduous fruit tree species, which belongs to the same genus as apricot (P. armeniaca) , Japanese plum (P. salicina) and peach (P. persica). Although this is a culturally and agronomically popular tree crop in East Asia, its evolutional nature remains unknown. Therefore, we conducted exon capture resequencing of 112 Japanese and 5 Taiwanese accessions of Japanese apricot, 7 accessions of apricot, 4 accessions of Japanese plum and an accession of peach to reveal current population structure of East Asian cultivars of Japanese apricot. We also detected selective sweeps based on cultivar differentiations and signals for inter-specific introgressions from apricots or Japanese plums. These findings shed light on complicated nature of evolution with inter-specific introgressions and natural or artificial selection in a fruit tree crop. These data based on exon capture is also available for genome-wide association study (GWAS). Because the majority of polymorphism is located around coding regions, we can efficiently catch informative signals, even if the covered genomic proportions were much less than that of whole genome sequencing (WGS).