Genomic clues to the parental origin of the wild flowering cherry Prunus yedoensis var. nudiflora (Rosaceae)
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.
KeywordsPrunus 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).
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.
- Arnold M (1997) Natural hybridization and evolution, Oxford series in ecology and evolution. Oxford University Press, OxfordGoogle Scholar
- Harn C, Kim Y, Yang S, Chung H (1977) Studies on the origin of Prunus yedoensis Matsumura. I. A comparative electrophoretic study on wild P. subhirtella in Mt. Hanla, cultivated P. yedoensis and P. donarium. Kor J Bot 20:1–5Google Scholar
- Jung Y-H, Oh M-Y (2005) Phylogenetic relationships of Prunus (Rosaceae) in Korea and Japan inferred from chloroplast DNA sequences. Kor J Genet 27:279–288Google Scholar
- Jung Y, Ko M, Oh Y, Kim G, Chung Y, Kim M, Oh M (1997) Phylogenetic relationship among selected taxa of Prunus in Mt. Halla and cultivated Prunus yedoensis by the RAPD analysis. Korean J Plant Taxon 27:415–428Google Scholar
- Jung Y, Ko M, Oh Y, Han S, Kim M, Koh S, Oh M (1998) Genetic relationship of Prunus yedoensis, native and cultivated, based on internal transcribed spacer sequences of ribosomal DNA. Korean J Genet 20:109–116Google Scholar
- Knight R (1969) Abstract bibliography of fruit breeding and genetics to 1965; Prunus. Commonwealth Agricultural Bureaux, Farnham RoyalGoogle Scholar
- Koehne VE (1912) 95 Prunus yedoensis var. nudiflora, nov. var. Von E. Koehne. Repert Specierum Nov Regni Veg 10:507Google Scholar
- Park S, Kim M, Lee S, Sim K (1984) A palynological study of some Prunus in Mt. Halla. Kor J Plant Taxon 14:153–159Google Scholar
- Quraishi UM, Abrouk M, Bolot S, Pont C, Throude M, Guilhot N, Confolent C, Bortolini F, Praud S, Murigneux A, Charmet G, Salse J (2009) Genomics in cereals: from genome-wide conserved orthologous set (COS) sequences to candidate genes for trait dissection. Funct Integr Genom 9:473–484CrossRefGoogle Scholar
- Timms L, Jimenez R, Chase M, Lavelle D, McHale L, Kozik A, Lai Z, Heesacker A, Knapp S, Rieseberg L, Michelmore R, Kesseli R (2006) Analyses of synteny between Arabidopsis thaliana and species in the Asteraceae reveal a complex network of small syntenic segments and major chromosomal rearrangements. Genetics 173:2227–2235CrossRefPubMedPubMedCentralGoogle Scholar
- Wilson E (1916) The cherries of Japan. Univ Press, CambridgeGoogle Scholar
- Zhang Q, Chen W, Sun L, Zhao F, Huang B, Yang W, Tao Y, Wang J, Yuan Z, Fan G, Xing Z, Han C, Pan H, Zhong X, Shi W, Liang X, Du D, Sun F, Xu Z, Hao R, Lv T, Lv Y, Zheng Z, Sun M, Luo L, Cai M, Gao Y, Wang J, Yin Y, Xu X, Cheng T, Wang J (2012) The genome of Prunus mume. Nat Commun 3:1318CrossRefPubMedPubMedCentralGoogle Scholar