Abstract
Interspecific hybridization in the genus Rosa (Rosaceae) is a common natural phenomenon. Hybrids often exhibit heterosis and new combinations of traits, which can provide raw materials for horticultural breeding. DNA barcodes and microsatellites have been proposed to facilitate species discrimination and hybrid detection. However, most SSR markers developed for roses have been found unapplicable to Rosa sect. Synstylae because of null alleles or failed amplification. In this study, we designed 15 pairs of microsatellite primers, along with four previously developed primers specifically for Rosa sect. Synstylae; we then analyzed 174 individuals of three closely related and sympatrically distributed Rosa species as a test case to evaluate the consistency between morphological and genetic hybrid identifications and to compare the discrimination efficiency of the DNA barcodes versus SSRs in detecting admixture. Principle coordinate analysis identified several individuals with intermediate phenotypes among the three rose species. Hybridization, intraspecific morphological polymorphism, and sample collection at different growth stages or phenological phases may have hindered species identification based on morphology and distorted the morphological clustering results. The molecular analyses showed that 12 (6.8%), 13 (7.4%), and 15 (8.6%) individuals were identified as admixed by STRUCTURE, NewHybrids, and nrITS sequences, respectively, of which only seven hybrids showed signs of admixture across all three methods. About 81% of the morphologically identifiable hybrids exhibited admixture based on SSRs. Meanwhile, approximately 69% of morphologically identifiable hybrids were detected, but four morphologically pure species individuals were identified as genetically admixed based on nrITS sequences. Some morphologically pure species individuals were genetically identified as hybrids while some morphological hybrids were identified as pure individuals based on certain molecular markers. Overall, EST-SSRs discriminated morphological hybrids more accurately than nrITS. We inferred that there is ongoing interspecific gene exchange among the three wild Rosa species that obscures morphospecies boundaries. Combining multiple data types and analytical approaches offers powerful utility for hybrid detection, regardless of the level of hybridization.
This is a preview of subscription content, log in via an institution to check access.
References
Allendorf FW, Leary RF, Spruell P, Wenburg JK (2001) The problems with hybrids: setting conservation guidelines. Trends Ecol Evol 16:613–622. https://doi.org/10.1016/s0169-5347(01)02290-x
Anderson EC, Thompson EA (2002) A model-based method for identifying species hybrids using multilocus genetic data. Genetics 160:1217–1229. https://doi.org/10.1089/109065702760093951
Arnheim N, Krystal M, Schmickel R, Wilson G, Ryder O, Zimmer E (1980) Molecular evidence for genetic exchanges among ribosomal genes on nonhomologous chromosomes in man and ape. Proc Nat Acad Sci 77:7323–7327. https://doi.org/10.1073/pnas.77.12.7323
Arnold ML (1997) Natural hybridization and evolution. Oxford University Press, Oxford, UK
Beaumont M, Barratt EM, Gottelli D, Kitchener AC, Daniels MJ, Pritchard JK, Bruford MW (2001) Genetic diversity and introgression in the Scottish wildcat. Mol Ecol 10:319–336. https://doi.org/10.1046/j.1365-294X.2001.01196.x
Burgarella C, Lorenzo Z, Jabbour-Zahab R, Lumaret R, Guichoux E, Petit RJ, Soto A, Gil L (2009) Detection of hybrids in nature: application to oaks (Quercus suber and Q. ilex). Heredity 102:442–452. https://doi.org/10.1038/hdy.2009.8
Cerny BA, Kaiser HF (1977) A study of a measure of sampling adequacy for factor-analytic correlation matrices. Multivar Behav Res 12:43–47. https://doi.org/10.1207/s15327906mbr1201_3
Chen YM (2011) Landscape dendrology 2rd edn. China Forestry Publishing House, Bei**g, China, pp 537
Clement M, Snell Q, Walker P, Posada D, Crandall K (2002) TCS: estimating gene genealogies. IEEE Comput Soc. https://doi.org/10.1109/IPDPS.2002.1016585
Dakin EE, Avise JC (2004) Microsatellite null alleles in parentage analysis. Heredity 93:504–509. https://doi.org/10.1038/sj.hdy.6800545
de Candolle AP (1813) Catalogus plantarum Horti botanici monspeliensis. Ex typis J. Martel natus majoris, Apud Am., Koenig, Bibliopolam., Monspelii. (1813) Parisiis ett Argentorati, pp 113
Degnan JH, Rosenberg NA (2009) Gene tree discordance, phylogenetic inference and the multispecies coalescent. Trends Ecol Evol 24:332–340. https://doi.org/10.1016/j.tree.2009.01.009
Earl DA, von Holdt BM (2012) STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv Genet Resour 4:359–361. https://doi.org/10.1007/s12686-011-9548-7
Esselink GC, Smulders MJM, Vosman B (2003) Identification of cut rose (Rosa Hybrida) and rootstock varieties using robust sequence tagged microsatellite site markers. Theor Appl Genet 106:277–286. https://doi.org/10.1007/s00122-002-1122-y
Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE.: a simulation study. Mol Ecol 14:2611–2620. https://doi.org/10.1111/j.1365-294x.2005.02553.x
Falush D, Stephens M, Pritchard JK (2003) Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164:1567–1587
Fan Q, Chen SF, Li MW, Guo W, **g HJ, Wu W, Zhou RC, Liao WB (2014) Molecular evidence for natural hybridization between wild loquat (Eriobotrya japonica) and its relative E. prinoides. BMC Plant Biol 14:275. https://doi.org/10.1186/s12870-014-0275-6
Gao YD, Zhang Y, Gao XF, Zhu ZM (2015) Pleistocene glaciations, demographic expansion and subsequent isolation promoted morphological heterogeneity: a phylogeographic study of the alpine Rosa sericea complex (Rosaceae). Sci Rep 5:11698. https://doi.org/10.1038/srep11698
Grant P, Grant B, Markert J, Keller L, Petren K (2004) Convergent evolution of Darwin’s finches caused by introgressive hybridization and selection. Evolution 58:1588–1599. https://doi.org/10.1111/j.0014-3820.2004.tb01738.x
Grimaldi MC, Crouau-Roy B (1997) Microsatellite allelic homoplasy due to variable flanking sequences. J Mol Evol 44:336–340. https://doi.org/10.1007/PL00006151
Grimm GW, Denk T (2008) ITS evolution in Platanus (Platanaceae): homoeologues, pseudogenes and ancient hybridization. Ann Bot 101:403–419. https://doi.org/10.1093/aob/mcm305
Gu CZ (2003) Flora of China 9. Science, Bei**g, pp 360–455
Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser 41:95–98
Harrison H (1921) The genus Rosa, its hybridology and other genetical problem. Trans Nat Hist Soc 5:244–298
Hibrand-Saint Oyant L, Crespel L, Rajapakse S, Zhang L, Fouche F (2008) Genetic linkage maps of rose constructed with new microsatellite markers and locating QTL controlling flowering traits. Tree Genet Genomes 4:11–23. https://doi.org/10.1007/s11295-007-0084-2
Hodkinson TR, Chase MW, Takahashi C, Leitch IJ, Bennett MD, Renvoize SA (2002) The use of dna sequencing (ITS and trnL-F), AFLP, and fluorescent in situ hybridization to study allopolyploid Miscanthus (Poaceae). Am J Bot 89:279–286. https://doi.org/10.3732/ajb.89.2.279
Huang TC (1994) Flora of Taiwan 1, 2rd edn. National Taiwan University, Taipei, Taiwan, China
Hung LY (2011) A taxonomic study of Rosa L. (Rosaceae) in Taiwan. National Taiwan Normal University, Taipei, Taiwan, China
Hung LY, Wang JC (2022) A revision of Rosa transmorrisonensis Hayata and allied species in Taiwan. Taiwania 67:484–496. https://doi.org/10.6165/tai.2022.67.484
Iwatsuki K, Boufford DE, Ohba H (2001) Flora of Japan 2b. Kodansha, Tokyo, Japan, pp 171
Jakobsson M, Rosenberg NA (2007) CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics 23:1801–1806. https://doi.org/10.1093/bioinformatics/btm233
Kalinowski ST, Taper ML, Marshall TC (2007) Revising how the computer program CERVUS accommodates genoty** error increases success in paternity assignment. Mol Ecol 16:1099–1106. https://doi.org/10.1111/j.1365-294X.2007.03089.x
Keim P, Paige KN, Whitham TG, Lark KG (1989) Genetic analysis of an interspecific hybrid swarm of Populus occurrence of unidirectional introgression. Genetics 123:557. https://doi.org/10.1101/gad.3.11.1801
Kimura TC, Nishitani HI, Ban Y, Yamamoto T (2006) Development of microsatellite markers in rose. Mol Ecol Notes 6:810–812. https://doi.org/10.1111/j.1471-8286.2006.01352.x
Koressaar T, Remm M (2007) Enhancements and modifications of primer design program Primer3. Bioinf 23:1289–1291. https://doi.org/10.1093/bioinformatics/btm091
MacPhail VJ, Kevan PG (2009) Review of the breeding systems of wild roses (Rosa spp.). Floriculture and Ornamental Biotechnology: 6–7
Matthews JR (1920) Hybridism and classification in the Genus Rosa. New Phytol 19:153–171
Meng J, Li DZ, Yi TS, Yang JB, Zhao XF (2009) Development and characterization of microsatellite loci for Rosa odorata var. gigantea Rehder & E. H. Wilson (Rosaceae). Conserv Genet 10:1973–1976. https://doi.org/10.1007/s10592-009-9871-7
Mikanagia Y, Ohbab H (2011) Rosa × Mikawamontana Mikanagi and H. Ohba (Rosaceae), a new hybrid between R. sambucina var. pubescens and R. paniculigera from Aichi Prefecture, Central Japan. J Jpn Bot 86:240–252
Ohba H, Akiyama S, Mikanagi Y (2007) Interspecific hybrids between the Japanese species in Rosa Section Synstylae (Rosaceae). J Jpn Bot 82:45–53
Peakall R, Smouse PE (2012) GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research– an update. Bioinformatics 28:2537–2539
Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959. https://doi.org/10.1093/genetics/164.4.1567
Rieseberg LH, Ellstrand NC, Arnold M (1993) What can molecular and morphological markers tell us about plant hybridization? Crit Rev Plant 12:213–241. https://doi.org/10.1080/0735268930970190
Rieseberg LH, Soltis DE (1991) Phylogenetic consequences of cytoplasmic gene flow in plants. Evol Trends 5:65–83. https://doi.org/10.1007/BF00021248
Rozas J, Ferrer-Mata A, Sánchez-DelBarrio JC, Guirao-Rico S, Librado P, Ramos-Onsins SE, Sáncher-Gracia A (2017) DnaSP 6: DNA sequence polymorphism analysis of large data sets. Mol Biol Evol 34:3299–3302. https://doi.org/10.1093/molbev/msx248
Rusanov K, Kovacheva N, Vosman B, Zhang L, Rajapakse S, Atnanssov A, Atanassov I (2005) Microsatellite analysis of Rosa Damascena Mill. Accessions reveals genetic similarity between genotypes used for rose oil production and old Damask rose varieties. Theor Appl Genet 111:804–809. https://doi.org/10.1007/s00122-005-2066-9
Sang T (2002) Utility of low-copy nuclear gene sequences in plant phylogenetics. Crit Rev Biochem Mol Biol 37:121–147. https://doi.org/10.1080/10409230290771474
Shaw J, Lickey EB, Schilling EE, Small RL (2007) Comparison of whole chloroplast genome sequences to choose noncoding regions for phylogenetic studies in angiosperms: the tortoise and the hare III. Am J Bot 94:275–288. https://doi.org/10.3732/ajb.94.3.275
Stougaard (1983) Pollination in Rosa multiflora. Tidsskrift Planteavl 87:633–642
Taberlet P, Gielly L, Pautou G, Bouvet J (1991) Universal primers for amplification of three non-coding regions of chloroplast DNA. Plant Mol Biol 17:1105–1109. https://doi.org/10.1007/BF00037152
Thiel T, Michalek W, Varshney R, Graner A (2003) Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L). Thero Appl Genet 106:411–422. https://doi.org/10.1007/s00122-002-1031-0
Thompson JD, Higgins DG (1994) Clustal W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680
Ueda Y, Akimoto S (2001) Cross- and self-compatibility in various species of the Genus Rosa. J Hortic Sci Biotech 76:392–395. https://doi.org/10.1080/14620316.2001.11511382
Untergasser A, Cutcutache I, Koressaar T, Ye J, Faircloth BC, Remm M, Rozen SG (2012) Primer3– new capabilities and interfaces. Nucleic Acids Res 40:e115. https://doi.org/10.1093/nar/gks596
van Buuren S, Groothuis-Oudshoorn K (2011) Mice: Multivariate imputation by chained equations in R. J Stat Softw 45:1–67. https://doi.org/10.18637/jss.v045.i03
Vähä JP, Primmer CR (2006) Efficiency of model-based bayesian methods for detecting hybrid individuals under different hybridization scenarios and with different numbers of loci. Mol Ecol 15:63–72. https://doi.org/10.1111/j.1365-294X.2005.02773.x
Wang J, Luo J, Ma YZ, Mao XX, Liu JQ (2019) Nuclear simple sequence repeat markers are superior to DNA barcodes for identification of closely related Rhododendron species on the same mountain. J Syst Evol 57:278–286. https://doi.org/10.1111/jse.12460
Wang Y, Lim K-B, Kim ST, Kim WH, Hwang Y-J (2021) Chromosome information on domestic rose cultivars in Korea. Flower Res J 29:47–54. https://doi.org/10.11623/frj.2021.29.2.01
White TJ, Bruns T, Lee S (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. PCR Protocols: Guide Methods Appl 38:315–322
Wickham H (2016) ggplot2: Elegant graphics for data analysis. Springer-Verlag, New York. https://ggplot2.tidyverse.org
Wickham H, Averick M, Bryan J, Chang W, McGowan LD, François R, Grolemund G, Hayes A, Henry L, Hester J, Kuhn M, Pedersen TL, Miller E, Bache SM, Müller K, Ooms J, Robinson D, Seidel DP, Spinu V, Takahashi K, Vaughan D, Wilke C, Woo K, Yutani H (2019) Welcome to the tidyverse. J Open Source Softw. 4:1686. https://doi.org/10.21105/joss.01686
Williams JGK, Kubelik AR, Livak KJ, Rafalski JA, Tingey SV (1990) DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res 18:6531–6535. https://doi.org/10.1093/nar/18.22.6531
Wu GQ (2019) Investigation of wild parent of Chinese old garden roses based on SSR molecular markers. Yunnan University, Kunming, China
**ao LQ, Zhu H (2009) Incomplete nrDNA ITS concerted evolution in plants and its evolutionary implications. Acta Bot Boreal-Occident Sin 29:1708–1713
Zhang C (2019) Evolutionary and systematic studies of Rosa sects. Synstylae and Chinenses (Rosaceae). Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
Zhang C, Li SQ, **e HH, Liu JQ, Gao XF (2022) Comparative plastid genome analyses of Rosa: insights into the phylogeny and gene divergence. Tree Genet Genomes 18:20. https://doi.org/10.1007/s11295-022-01549-8
Zhang C, Li SQ, Zhang Y, Liu JQ, Gao XF (2020) Molecular and morphological evidence for hybrid origin and matroclinal inheritance of an endangered wild rose, Rosa × pseudobanksiae (Rosaceae) from China. Conserv Genet 21:1–11. https://doi.org/10.1007/s10592-019-01227-8
Zhu ZM (2015) Molecular phylogenetics of Rosa sects. Chinenses and Synstylae (Rosaceae). Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
Zhu ZM, Gao XF (2015) Molecular evidence for the hybrid origin of Rosa lichiangensis (Rosaceae). Phytotaxa 222:221–228. https://doi.org/10.11646/phytotaxa.222.3.5
Zhu ZM, Gao XF, Fougère-Danezan M (2015) Phylogeny of Rosa sections Chinenses and Synstylae (Rosaceae) based on chloroplast and nuclear markers. Mol Phylogenet Evol 87:50–64. https://doi.org/10.1016/j.ympev.2015.03.014
Acknowledgements
We sincerely thank Professor Ching-I Peng and his staff at the Biodiversity Research Center of Academia Sinica and Dr. Shih-Wen Chung, Dr. Zai-Wen Hsu, and their staff at the Taiwan Forestry Research Institute for their assistance during fieldwork in Taiwan. The research was partially supported by the National Natural Science Foundation of China (Grant No. 31670192) and the Second Tibetan Plateau Scientific Expedition and Research Program (2019QZKK0502) to X.-F. G.
Author information
Authors and Affiliations
Contributions
G.X.F. contributed to identification of Rosa species, manuscript revision, and securing funding. Z.C. conceived and designed the experiments, analyzed the data, and wrote the manuscript. L.S.Q. and L.L.Y. helped conduct the experiments.
Corresponding author
Ethics declarations
Conflict of interest
The authors declare that they have no conflict of interest.
Additional information
Publisher’s Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Electronic supplementary material
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Zhang, C., Li, SQ., Li, LY. et al. Morphology-based genetic diversity analysis reveals introgressive hybridizations obscure species boundaries of three wild roses endemic to Taiwan Island. Hortic. Environ. Biotechnol. (2024). https://doi.org/10.1007/s13580-024-00619-1
Received:
Revised:
Accepted:
Published:
DOI: https://doi.org/10.1007/s13580-024-00619-1