Plant Biotechnology Reports

, Volume 11, Issue 6, pp 449–459 | Cite as

Genomic clues to the parental origin of the wild flowering cherry Prunus yedoensis var. nudiflora (Rosaceae)

  • Ara Cho
  • Seunghoon Baek
  • Goon-Bo Kim
  • Chang-Ho Shin
  • Chan-Soo Kim
  • Kyung Choi
  • Youngje Kang
  • Hee-Ju Yu
  • Joo-Hwan Kim
  • Jeong-Hwan MunEmail author
Original Article


Prunus yedoensis Matsumura is one of the popular ornamental flowering cherry trees native to northeastern Asia, and its wild populations have only been found on Jeju Island, Korea. Previous studies suggested that wild P. yedoensis (P. yedoensis var. nudiflora) is a hybrid species; however, there is no solid evidence on its exact parental origin and genomic organization. In this study, we developed a total of 38 nuclear gene-based DNA markers that can be universally amplifiable in the Prunus species using 586 Prunus Conserved Orthologous Gene Set (Prunus COS). Using the Prunus COS markers, we investigated the genetic structure of wild P. yedoensis populations and evaluated the putative parental species of wild P. yedoensis. Population structure and phylogenetic analysis of 73 wild P. yedoensis accessions and 54 accessions of other Prunus species revealed that the wild P. yedoensis on Jeju Island is a natural homoploid hybrid. Sequence-level comparison of Prunus COS markers between species suggested that wild P. yedoensis might originate from a cross between maternal P. pendula f. ascendens and paternal P. jamasakura. Moreover, approximately 81% of the wild P. yedoensis accessions examined were likely F1 hybrids, whereas the remaining 19% were backcross hybrids resulting from additional asymmetric introgression of parental genotypes. These findings suggest that complex hybridization of the Prunus species on Jeju Island can produce a range of variable hybrid offspring. Overall, this study makes a significant contribution to address issues of the origin, nomenclature, and genetic relationship of ornamental P. yedoensis.


Prunus COS Gene-based marker Wild Prunus yedoensis Genome Homoploid hybrid 



This work was supported by grants from the Next-Generation Biogreen21 program (PJ01108601), the Korea National Arboretum (KNA1-2-13, 14 -2), and the National Institute of Forest Science, Korea (FG0802-2011-01).

Authors’ contribution

JHM conceived the projects, designed research, analyzed data, and wrote manuscript. AC performed the experiments, analyzed data, and wrote the manuscript. SB and GBK performed bioinformatics analysis and designed molecular makers. HJY and JHK analyzed data and participated in manuscript preparation. CHS, CSK, KC, and YK prepared plant samples.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

11816_2017_465_MOESM1_ESM.docx (15.7 mb)
Supplementary material 1 (DOCX 16047 KB)
11816_2017_465_MOESM2_ESM.docx (75 kb)
Supplementary material 2 (DOCX 75 KB)


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Copyright information

© Korean Society for Plant Biotechnology and Springer Japan KK, part of Springer Nature 2017

Authors and Affiliations

  • Ara Cho
    • 1
  • Seunghoon Baek
    • 1
  • Goon-Bo Kim
    • 1
  • Chang-Ho Shin
    • 2
  • Chan-Soo Kim
    • 3
  • Kyung Choi
    • 2
  • Youngje Kang
    • 3
  • Hee-Ju Yu
    • 4
  • Joo-Hwan Kim
    • 5
  • Jeong-Hwan Mun
    • 1
    Email author
  1. 1.Department of Bioscience and BioinformaticsMyongji UniversityYonginSouth Korea
  2. 2.Korea National ArboretumPocheonSouth Korea
  3. 3.Warm Temperate and Subtropical Forest Research CenterNational Institute of Forest ScienceJejuSouth Korea
  4. 4.Department of Life ScienceThe Catholic University of KoreaBucheonSouth Korea
  5. 5.Department of Life ScienceGachon UniversitySeongnamSouth Korea

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