Journal of Horticultural Science & Biotechnology (2013) 88 (1) 85-92
The diploid origins of allopolyploid rose species studied using single nucleotide polymorphism haplotypes flanking a microsatellite repeat


The taxonomy of the genus Rosa is complex, not least because of hybridisations between species. We aimed to develop a method to connect the diploid Rosa taxa to the allopolyploid taxa to which they contributed, based on the sharing of haplotypes. For this we used an SNPSTR marker, which combines a short tandem repeat (STR; microsatellite) marker with single nucleotide polymorphisms (SNPs) in the flanking sequences. In total, 53 different sequences (haplotypes) were obtained for the SNPSTR marker, Rc06, from 20 diploid and 35 polyploid accessions from various species of Rosa. Most accessions of the diploid species had only one allele, while accessions of the polyploid species each contained two-to-five different alleles. Twelve SNPs were detected in the flanking sequences, which alone formed a total of 18 different haplotypes. A maximum likelihood dendrogram revealed five groups of haplotypes. Diploid species in the same Section of the genus Rosa contained SNP haplotypes from only one haplotype group. In contrast, polyploid species contained haplotypes from different haplotype groups. Identical SNP haplotypes were shared between polyploid species and diploid species from more than one Section of the genus Rosa. There were three different polymorphic repeat regions in the STR region. The STR repeat contained eight additional SNPs, but these contributed little to the resolution of the haplotype groups. Our results support hypotheses on diploid Rosa species that contributed to polyploid taxa. Finding different sets of haplotypes in different groups of species within the Sections Synstylae and Pimpinellifoliae supports the hypothesis that these may be paraphyletic.

Bootstrap values in the ML dendrogram were relatively low, probably due to the low number of informative sites. We tentatively distinguished five Groups of related haplotypes, but only haplotype Groups III, IV, and V were supported by somewhat higher bootstrap values (i.e., 70, 71, and 78 of 100 replications, respectively). Group III and Group IV haplotypes were found in species from the Section Pimpinellifoliae. Group III haplotypes were present in the tetraploid R. foetida (in various variants, see above) and in R. hemispaerica; while Group IV haplotypes were found in various diploid species from this Section, including R. hugonis, plus diploid R. roxburgii from the sub-genus Platyrhodon. R. roxburgii and R. hugonis were also the most similar species in the most parsimonous tree based on the AFLP data in Koopman et al. (2008). Therefore, our data support the conclusions of these authors and those of several others (Matsumoto et al., 1998:Wu et al., 2001; Wissemann and Ritz, 2005; Bruneau et al., 2007) that R. roxburgii was incorrectly classified into the separate sub-genus, Plathyrodon. The fact that Section Pimpinellifoliae haplotypes in Group IV were not found in any polyploid species may mean that these species did not contribute to the polyploid Rosa species, or that we did not include the polyploid species concerned. On the other hand, the fact that haplotypes from diploid and polyploid species did not resemble each other closely was consistent with the hypothesis (Matsumoto et al., 2001; Bruneau et al., 2007) that Section Pimpinellifoliae was a polyphyletic group.

Group V included haplotype H1, plus three other haplotypes. The group contained all haplotypes obtained from the seven diploid species of the Section Cinnamomeae, and a diploid species of the Section Carolineae that was included in this study, as well as haplotypes from various polyploid Sections, notably various species of the Section Caninae.

Fifty-five accessions of Rosa species used in this study
Code No.¶
Species name Location Ploidy
50 R. acicularis Lindl. 2
22 R. arvensis Germany 2
23 R. arvensis Germany 2
39 R. arvensis 2
44 R. blanda Aiton 2
18 R. caesia Nyman Switzerland 5,6
2 R. canina L. Iran 5
6 R. canina L. Iran 5
11 R. canina L. Switzerland 5
19 R. canina L. Germany 5
27 R. canina L. Netherlands 5
28 R. canina L. Netherlands 5
51 R. chinensis 'spontanea' Jacq China 2
14 R. columnifera Switzerland 4
34 R. corymbifera Netherlands 5
20 R. corymbifera Borkh. Germany 5
21 R. corymbifera Borkh. Germany 5
4 R. damascene L. Iran 4
15 R. dumalis Bechst. Switzerland 5
26 R. dumalis Bechst. Netherlands 5
5 R. foetida 'double' Herrm. Iran 4
3 R. foetida Herrm. Iran 4
9 R. hemisphaerica Herrm. Iran 4
40 R. hugonis Hemsl. 2
I R. iberica Steven ex M. Bieb. Iran 5
7 R. iberica Steven ex M. Bieb. Iran 5
13 R. inodora Switzerland 5
Code No.¶
Species name Location Ploidy
46 R. majalis Herrm. 2
29 R. micrantha Borr. ex Sm. Netherlands 4,5,6
41 R. moschata L. 2
45 R. multiflora '117'* 2
37 R. multiflora Thunb. 2
43 R. nitida 2
10 R. orientalis Iran 5
48 R. pendulina 2
8 R. pimpinellifolia L. Iran 4
42 R. roxburghii 2
35 R. rubiginosa L. Switzerland 5
47 R. rugosa Thunb. 2
53 R. sericea Lindl. China 2
54 R. sericea subsp. Omeiensis (Rolfe) A.V. Roberts China 2
55 R. sericea subsp. Omeiensis (Rolfe) A.V. Roberts China 2
49 R. sertata Rolfe 2
16 R. sherardii Davies Switzerland 4,5,6
31 R. sherardii Davies Netherlands 4,5,6
24 R. spinosissima L. Germany 4
30 R. spinosissima L. Netherlands 4
25 R. tomentella Léman Netherlands 5
33 R. tomentella Léman Netherlands 5
12 R. villosa subsp. mollis Switzerland 4
17 R. villosa subsp. mollis Switzerland 4
52 R. wichurana Crép. 2
36 R. wichurana Crép. 2
38 R. woodsii Lindl. 2
32 R. x irregularis Déségl. & Guillon§ Netherlands Unknown
Accessions 1-19 were from Samiei et al. (2010). Accessions 11-35 were also used in Koopman et al. (2008)
* R. multiflora ‘hybrid 117’ is a diploid rose from a cross between Rosa multiflora and an unknown garden rose.
§ R. x irregularis is morphologically intermediate between R. arvensis and R. canina (Vander Mijnsbrugge et al., 2010).


Haplotypes that occurred in polyploid Rosa species were shared with those in diploid Rosa species, indicating that these diploid species may have been involved in the formation of allopolyploid roses with higher ploidy levels. Nevertheless, our study should only be considered as a proof-of-concept, as we did not include a complete set of accessions from all diploid species, and used only a single SNPSTR locus. Multiple accessions per taxon may be necessary if there is heterogeneity in the chromosomal segments present in polyploids. In that case, more loci would have to be included in order to cover the genomes involved. Next-generation sequencing will facilitate this, as it becomes cheaper to generate sequences from a large variety of samples without the need to clone the sequences. It is essential that multiple haplotypes with SNPs are obtained, as only this would generate the necessary resolving power.