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The recent completion of the rose genome sequence is not the end of a process, but rather a starting point that opens up a whole set of new and exciting activities. Next to a high-quality genome sequence other genomic tools have also become available for rose, including transcriptomics data, a high-density single-nucleotide polymorphism array and software to perform linkage and quantitative trait locus mapping in polyploids. Rose cultivars are highly heterogeneous and diverse. This vast diversity in cultivated roses can be explained through the genetic potential of the genus, introgressions from wild species into commercial tetraploid germplasm and the inimitable efforts of historical breeders. We can now investigate how this diversity can best be exploited and refined in future breeding work, given the rich molecular toolbox now available to the rose breeding community. This paper presents possible lines of research now that rose has entered the genomics era, and attempts to partially answer the question that arises after the completion of any draft genome sequence: ‘Now that we have “the” genome, what’s next?’. Having access to a genome sequence will allow both (fundamental) scientific and (applied) breeding-orientated questions to be addressed. We outline possible approaches for a number of these questions.

AbstractWe studied the petal number trait in a population obtained after self-pollination of R. x damascenaf. trigintipetala following analysis of molecular markers which have previously been mapped near the major dominant locus Blfo/d6determining this trait in other rose species including R. multifloraand R. hybrida. The results showed that the same genetic mechanism, which determines the petal number trait in R. multifloraand R. hybridaalso controls the trait in R. x damascenaf. trigintipetala and is related to the dominant effect of a single copy allele in the tetraploid genome of this species. We also analyzed the expression of several flower homeotic genes including R. x damascena APETALA1/FUL-like(paleo AP1 type), R. x damascena euAPETALA 3(euAP3 line) and R. x damascena AGAMOUSin early stage flower buds corresponding to plants with double and simple flowers. The obtained results showed that only R. x damascena AGAMOUSwas differentially expressed between the samples of double and simple flowers, its relative expression being upregulated 3.5-fold in simple flowers. We further cloned and sequenced the four genomic clones of R. x damascena AGAMOUSand studied the potential additive effect of this gene by analysing the segregation of its four alleles in the population of self-pollinated R. x damascena. Analysis of variance of the data for petal number and allele segregation did not show a statistically significant effect of any allele configuration of the AGAMOUSgene on the petal number trait in R. x damascenaf. trigintipetala.

ABSTRACTAfrican nightshades are becoming more important as leafy vegetables in sub-Saharan Africa. Previously considered as food for the poor, their cultivation is now being promoted, and some cultivars are commercialised; however, most farmers use self-produced seeds, leading to low and varying yields. Improvement through conventional breeding depends on the available genetic diversity, the possible breeding systems, and the nutritional value of the accessions. Therefore, we review the information on these topics with the following main outcomes: the most commonly discussed species, S. nigrum, S. scabrum, S. villosum, and S. americanum, could be differentiated using molecular markers, but further sub-clustering was rarely possible, and statistical support often missing. S. nigrumand S. scabrumseem to be most closely related to each other. The mainly self-pollinating African nightshades form a polyploidy series with diploid (2n = 2x = 24) to hexaploid taxa. Interploidy hybridisations between diploids and tetraploids are possible, whereas the hexaploid S. nigrumand S. scabrumcould not be crossed to genotypes of lower ploidies. Solanine, solamargine, solasonine, and chaconine are the major steroidal alkaloid glucosides in African nightshades. Amounts are age and environment dependant. Mineral and vitamin contents in leaves are at least as high as in Brassica oleraceaor Spinacia oleracea, underlining their relevance as local vegetables.

This study aims to: (i) identify the Rosa S-locus controlling self-incompatibility (SI); (ii) test the genetic linkage of the S-locus with other loci controlling important ornamental traits, such as the continuous-flowering (CF) characteristic; (iii) identify the S-alleles (SC) of old Chinese CF cultivars (e.g, Old Blush, Slater’s Crimson China) and examine the changes in the frequency of cultivars with Scthrough the history of breeding; (iv) identify wild species carrying the Sc-alleles to infer wild origins of CF cultivars. We identified a new S-RNase(SC2) of Rosa chinensisin a contig from a genome database that has not been integrated into one of the seven chromosomes yet. Genetic mapping indicated that SC2is allelic to the previously-identified S-RNase(SC1) in chromosome 3. Pollination experiments with half-compatible pairs of roses confirmed that they are the pistil-determinant of SI. The segregation analysis of an F1-population indicated genetic linkage between the S-locus and the floral repressor gene KSN.The non-functional allele ksnis responsible for the CF characteristic. A total of five S-alleles (SC1–5) were identified from old CF cultivars. The frequency of cultivars with SCdramatically increased after the introgression of ksnfrom Chinese to European cultivars and remains high (80%) in modern cultivars, suggesting that S-genotyping is helpful for effective breeding. Wild individuals carrying SCwere found in Rosa multiflora(SC1), Rosa chinensisvar. spontanea(SC3), and Rosa gigantea(SC2, SC4), supporting the hypothesis of hybrid origins of CF cultivars and providing a new evidence for the involvement of Rosa multiflora.