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

Abstract

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.

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Acknowledgements

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).

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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.

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Correspondence to Jeong-Hwan Mun.

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The authors declare that they have no conflict of interest.

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Cho, A., Baek, S., Kim, GB. et al. Genomic clues to the parental origin of the wild flowering cherry Prunus yedoensis var. nudiflora (Rosaceae). Plant Biotechnol Rep 11, 449–459 (2017). https://doi.org/10.1007/s11816-017-0465-4

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Keywords

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