Rose is the world's most important ornamental plant, with economic, cultural and symbolic value. Roses are cultivated worldwide and sold as garden roses, cut flowers and potted plants. Roses are outbred and can have various ploidy levels. Our objectives were to develop a high-quality reference genome sequence for the genus Rosa by sequencing a doubled haploid, combining long and short reads, and anchoring to a high-density genetic map, and to study the genome structure and genetic basis of major ornamental traits. We produced a doubled haploid rose line ('HapOB') from Rosa chinensis 'Old Blush' and generated a rose genome assembly anchored to seven pseudo-chromosomes (512 Mb with N50 of 3.4 Mb and 564 contigs). The length of 512 Mb represents 90.1-96.1% of the estimated haploid genome size of rose. Of the assembly, 95% is contained in only 196 contigs. The anchoring was validated using high-density diploid and tetraploid genetic maps. We delineated hallmark chromosomal features, including the pericentromeric regions, through annotation of transposable element families and positioned centromeric repeats using fluorescent in situ hybridization. The rose genome displays extensive synteny with the Fragaria vesca genome, and we delineated only two major rearrangements. Genetic diversity was analysed using resequencing data of seven diploid and one tetraploid Rosa species selected from various sections of the genus. Combining genetic and genomic approaches, we identified potential genetic regulators of key ornamental traits, including prickle density and the number of flower petals. A rose APETALA2/TOE homologue is proposed to be the major regulator of petal number in rose. This reference sequence is an important resource for studying polyploidization, meiosis and developmental processes, as we demonstrated for flower and prickle development. It will also accelerate breeding through the development of molecular markers linked to traits, the identification of the genes underlying them and the exploitation of synteny across Rosaceae.

In vitro chromosome doubling can be induced by several antimitotic agents. The most commonly used are colchicine, oryzalin and trifluralin. The process of induced chromosome doubling in vitro consists of a typical succession of sub-processes, including an induction phase and a confirmation protocol to measure the rate of success. The induction step depends on a large number of variables: media, antimitotic agents, explant types, exposure times and concentrations. Flow cytometry is the pre-eminent method for evaluation of the induced polyploidization. However, alternative confirmation methods, such as chromosome counts and morphological observations, are also used. Since polyploidization has many consequences for plant growth and development, chromosome doubling has been intensively studied over the years and has found its way to several applications in plant breeding. This review gives an overview of the common methods of chromosome doubling in vitro, the history of the technique, and progress made over the years. The applications of chromosome doubling in a broader context are also discussed.

It is becoming increasingly evident that interspecific hybridization is a common event in phytophthora evolution. Yet, the fundamental processes underlying interspecific hybridization and the consequences for its ecological fitness and distribution are not well understood. We studied hybridization events in phytophthora clade 8b. This is a cold-tolerant group of plant pathogenic oomycetes in which six host-specific species have been described that mostly attack winter-grown vegetables. Hybrid characterization was done by sequencing and cloning of two nuclear (ITS and Ypt1) and two mitochondrial loci (Cox1 and Nadh1) combined with DNA content estimation using flow cytometry. Three different mtDNA haplotypes were recovered among the presumed hybrid isolates, dividing the hybrids into three types, with different parental species involved. In the nuclear genes, additivity, i.e. the presence of two alleles coming from different parents, was detected. Hybrid isolates showed large variations in DNA content, which was positively correlated with the additivity in nuclear loci, indicating allopolyploid hybridization followed by a process of diploidization. Moreover, indications of homeologous recombination were found in the hybrids by cloning ITS products. The hybrid isolates have been isolated from a range of hosts that have not been reported previously for clade 8b species, indicating that they have novel pathogenic potential. Next to this, DNA content measurements of the non-hybrid clade 8b species suggest that polyploidy is a common feature of this clade. We hypothesize that interspecific hybridization and polyploidy are two linked phenomena in phytophthora, and that these processes might play an important and ongoing role in the evolution of this genus.

An allopolyploid complex with high genomic integrity has been studied. Dogroses transmit only seven chromosomes (from seven bivalents) through the pollen, whereas 21, 28 or 35 chromosomes (from seven bivalents and 14, 21 or 28 univalents) come from the egg cells. Seedlings derived from two interspecific crosses were analysed with flow cytometry and molecular markers to determine ploidy level, mode of reproduction and genomic constitution. Evidence was obtained for the formation of unreduced male and female gametes, which can take part in fertilization (producing seedlings with higher ploidy than the parental plants) or in apomictic reproduction. Random amplified polymorphic DNA (RAPD) and microsatellite analyses indicated that three seedlings (5%) were derived through apomixis, whereas the other 49 were hybrids. Bivalent formation appears to involve chromosomes that consistently share the same microsatellite alleles. Allele‐sharing between the maternally transmitted and highly conserved univalent‐forming chromosomes reflected the taxonomic distance between different genotypes. The frequently recombining bivalent‐forming chromosomes were taxonomically less informative.

Summary 1.The degree of canopy closure can shape the dynamics of understorey plant populations that rely on clonal and sexual recruitment. Populations are expected to undergo declines in clonal diversity under conditions where recruitment from seed is temporally and spatially restricted. Localized seedling recruitment in clonal populations may also affect spatial genetic structure due to the clumping of genetically related genets. 2. Our major objective was to determine the effect of the degree of canopy closure on clonal diversity and spatial genetic structure in the rhizomatous, dioecious forest perennial Mercurialis perennis . As the distribution of the male and female shoots has been shown to be influenced by canopy openings, we paid special attention to the mediating role of the varying sex ratio. 3. We used genome-wide AFLP markers to fingerprint six populations of M. perennis along a light penetration gradient. 4. The proportion of male shoots in a population increased from 0.51 to 0.81 and male genet diversity decreased from 0.72 to 0.21 with increasing site illumination, in agreement with earlier reports of superior male growth in canopy openings. The most illuminated population, with the highest proportion of male shoots, was dominated by a few outsized, largely aggregated male clones (largest clone spreading over 10 m). 5. Overall clonal diversity (G/N: 0.31-0.74; mean: 0.52) and evenness strongly declined in well-lit sites, suggesting reduced sexual recruitment and the vast vegetative spread of a few locally welladapted male genets under canopy gaps. 6. Fine-scale genetic structure among genets was significant within all populations, but its degree tended to increase with an increased proportion of male shoots and reduced clonal diversity. Very localized recruitment due to a low seed dispersal capacity combined with the aggregated distribution of large gender-specific clones likely incurred this pattern. 7. Synthesis. Forest management practices such as the cutting and removal of trees and the establishment of paths decreased the degree of canopy closure. Many understorey herb populations flourish in these canopy gaps, reflected in a higher clonal diversity. We demonstrated, however, that increased illumination negatively affects genotypic and genetic diversity in the dioecious understorey herb M. perennis .