Untangling the hedge: Genetic diversity in clonally and sexually transmitted genomes of European wild roses, Rosa L.

While European wild roses are abundant and widely distributed, their morphological taxonomy is complicated and ambiguous. In particular, the polyploid Rosa section Caninae (dogroses) is characterised by its unusual meiosis, causing simultaneous clonal and sexual transmission of sub-genomes. This hemisexual reproduction, which often co-occurs with vegetative reproduction, defies the standard definition of species boundaries. We analysed seven highly polymorphic microsatellite loci, scored for over 2 600 Rosa samples of differing ploidy, collected across Europe within three independent research projects. Based on their morphology, these samples had been identified as belonging to 21 dogrose and five other native rose species. We quantified the degree of clonality within species and at individual sampling sites. We then compared the genetic structure within our data to current rose morpho-systematics and searched for hemisexually co-inherited sets of alleles at individual loci. We found considerably fewer copies of identical multi-locus genotypes in dogroses than in roses with regular meiosis, with some variation recorded among species. While clonality showed no detectable geographic pattern, some genotypes appeared to be more widespread. Microsatellite data confirmed the current classification of subsections, but they did not support most of the generally accepted dogrose microspecies. Under canina meiosis, we found co-inherited sets of alleles as expected, but could not distinguish between sexually and clonally inherited sub-genomes, with only some of the detected allele combinations being lineage-specific

Principal coordinate analyses of all investigated samples.

One copy per MLG per species, based on a total of 236 alleles at seven microsatellite loci. Colours indicate species/subsections; symbols indicate estimated ploidy level. (A) all taxonomic units; (B) subsection Caninae only; (C) subsection Rubigineae only; (D) subsection Vestitae only.</p

Dataset and metadata.

While European wild roses are abundant and widely distributed, their morphological taxonomy is complicated and ambiguous. In particular, the polyploid Rosa section Caninae (dogroses) is characterised by its unusual meiosis, causing simultaneous clonal and sexual transmission of sub-genomes. This hemisexual reproduction, which often co-occurs with vegetative reproduction, defies the standard definition of species boundaries. We analysed seven highly polymorphic microsatellite loci, scored for over 2 600 Rosa samples of differing ploidy, collected across Europe within three independent research projects. Based on their morphology, these samples had been identified as belonging to 21 dogrose and five other native rose species. We quantified the degree of clonality within species and at individual sampling sites. We then compared the genetic structure within our data to current rose morpho-systematics and searched for hemisexually co-inherited sets of alleles at individual loci. We found considerably fewer copies of identical multi-locus genotypes in dogroses than in roses with regular meiosis, with some variation recorded among species. While clonality showed no detectable geographic pattern, some genotypes appeared to be more widespread. Microsatellite data confirmed the current classification of subsections, but they did not support most of the generally accepted dogrose microspecies. Under canina meiosis, we found co-inherited sets of alleles as expected, but could not distinguish between sexually and clonally inherited sub-genomes, with only some of the detected allele combinations being lineage-specific.</div

Results of AMOVA analyses regarding different taxonomic levels within European roses.

Results of AMOVA analyses regarding different taxonomic levels within European roses.</p

Clonal richness R of each investigated species.

0 = all plants identical, 1 = all plants unique. Dashes denote mean values per subsection in section Caninae, or the mean across all other sections. Ploidy levels after species names refer to the majority of our samples (see Table 1).</p

Most frequent allele combinations (MFACs) per locus and group.

Caninae (5x) 958 samples; Rubigineae (5x) 315 samples; Vestitae (5x) 176 and (4x) 166 samples. Category–A: MFAC of ploidy-1 alleles; B: MFAC of less than ploidy-1 alleles; BC: MFAC hardly discernible; C: MFAC not discernible. Triangle: example for MFAC category shown in Fig 2; bold: MFAC / allele specific to subsection; underlined: allele proposed as bivalent in literature [28, 35]. ANA–apparent number of alleles in proposed MFAC; cf(ANA)–frequency of samples with at least ANA alleles in group (grey bar); f(MFAC)–frequency of MFAC in group (orange bar). ***: MFAC more frequent than random (p ≤ 0.001); °: MFAC more frequent in group than in entire dataset (p ≤ 0.01).</p

Laboratory methods.

While European wild roses are abundant and widely distributed, their morphological taxonomy is complicated and ambiguous. In particular, the polyploid Rosa section Caninae (dogroses) is characterised by its unusual meiosis, causing simultaneous clonal and sexual transmission of sub-genomes. This hemisexual reproduction, which often co-occurs with vegetative reproduction, defies the standard definition of species boundaries. We analysed seven highly polymorphic microsatellite loci, scored for over 2 600 Rosa samples of differing ploidy, collected across Europe within three independent research projects. Based on their morphology, these samples had been identified as belonging to 21 dogrose and five other native rose species. We quantified the degree of clonality within species and at individual sampling sites. We then compared the genetic structure within our data to current rose morpho-systematics and searched for hemisexually co-inherited sets of alleles at individual loci. We found considerably fewer copies of identical multi-locus genotypes in dogroses than in roses with regular meiosis, with some variation recorded among species. While clonality showed no detectable geographic pattern, some genotypes appeared to be more widespread. Microsatellite data confirmed the current classification of subsections, but they did not support most of the generally accepted dogrose microspecies. Under canina meiosis, we found co-inherited sets of alleles as expected, but could not distinguish between sexually and clonally inherited sub-genomes, with only some of the detected allele combinations being lineage-specific.</div

Fig 2 -

Examples of network plots for loci sorted into categories A, B, BC and C (see text). Allele combinations differing by only one allele are connected by lines. Circle diameter corresponds to the frequency of the respective allele combination, relative to the most frequent combination (MFAC, in red, maximum diameter). The frequency of the MFAC is displayed in the centre of the network, marked by stars if significantly higher than random (* p ≤ 0.05, ** p ≤ 0.01, *** p ≤ 0.001), and additionally by a degree sign if significantly elevated within the respective subsection (° p ≤ 0.001).</p

Additional figures.

While European wild roses are abundant and widely distributed, their morphological taxonomy is complicated and ambiguous. In particular, the polyploid Rosa section Caninae (dogroses) is characterised by its unusual meiosis, causing simultaneous clonal and sexual transmission of sub-genomes. This hemisexual reproduction, which often co-occurs with vegetative reproduction, defies the standard definition of species boundaries. We analysed seven highly polymorphic microsatellite loci, scored for over 2 600 Rosa samples of differing ploidy, collected across Europe within three independent research projects. Based on their morphology, these samples had been identified as belonging to 21 dogrose and five other native rose species. We quantified the degree of clonality within species and at individual sampling sites. We then compared the genetic structure within our data to current rose morpho-systematics and searched for hemisexually co-inherited sets of alleles at individual loci. We found considerably fewer copies of identical multi-locus genotypes in dogroses than in roses with regular meiosis, with some variation recorded among species. While clonality showed no detectable geographic pattern, some genotypes appeared to be more widespread. Microsatellite data confirmed the current classification of subsections, but they did not support most of the generally accepted dogrose microspecies. Under canina meiosis, we found co-inherited sets of alleles as expected, but could not distinguish between sexually and clonally inherited sub-genomes, with only some of the detected allele combinations being lineage-specific.</div

Summary of sampled wild rose species originating from three different data sets.

Summary of sampled wild rose species originating from three different data sets.</p