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

Koji Numaguchi, Takashi Akagi, Yuto Kitamura, Ryo Ishikawa, Takashige Ishii

Research output: Contribution to journalArticlepeer-review

14 Citations (Scopus)


Domestication 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 genus Prunus, mainly Japanese apricot (Prunus mume), and apricot (Prunus armeniaca), plum (Prunus salicina), and peach (Prunus persica). Based on their genome-wide single-nucleotide polymorphisms merged with published resequencing data of 79 Chinese P. mume cultivars, we inferred complete and ongoing population differentiation in P. mume. Sliding window characterization of the indexes for genetic differentiation identified interspecific fragment introgressions between P. mume and related species (plum and apricot). These regions often exhibited strong selective sweeps formed in the paths of establishment or formation of substructures of P. mume, suggesting that P. mume has frequently imported advantageous genes from other species in the subgenus Prunus as 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 selections.

Original languageEnglish
Pages (from-to)1551-1567
Number of pages17
JournalPlant Journal
Issue number6
Publication statusPublished - Dec 2020


  • Prunus mume
  • fruit tree
  • introgression
  • population structure
  • selective sweep
  • targeted resequencing

ASJC Scopus subject areas

  • Genetics
  • Plant Science
  • Cell Biology


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