The Systematics, Reproductive Biology, Biochemistry, and Breeding of Sea Buckthorn-A Review

Both the fruit flesh and seeds of sea buckthorn have multiple uses for medicinal and culinary purposes, including the valuable market for supplementary health foods. Bioactive compounds, such as essential amino acids, vitamins B, C, and E, carotenoids, polyphenols, ursolic acid, unsaturated fatty acids, and other active substances, are now being analyzed in detail for their medicinal properties. Domestication with commercial orchards and processing plants is undertaken in many countries, but there is a large need for improved plant material with high yield, tolerance to environmental stress, diseases, and pests, suitability for efficient harvesting methods, and high contents of compounds that have medicinal and/or culinary values. Applied breeding is based mainly on directed crosses between different subspecies of Hippophae rhamnoides. DNA markers have been applied to analyses of systematics and population genetics as well as for the discrimination of cultivars, but very few DNA markers have as yet been developed for use in selection and breeding. Several key genes in important metabolic pathways have, however, been identified, and four genomes have recently been sequenced.

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.

Combining genetic resources and elite material populations to improve the accuracy of genomic prediction in apple

Genomic selection is an attractive strategy for apple breeding that could reduce the length of breeding cycles. A possible limitation to the practical implementation of this approach lies in the creation of a training set large and diverse enough to ensure accurate predictions. In this study, we investigated the potential of combining two available populations, i.e., genetic resources and elite material, in order to obtain a large training set with a high genetic diversity. We compared the predictive ability of genomic predictions within-population, across-population or when combining both populations, and tested a model accounting for population-specific marker effects in this last case. The obtained predictive abilities were moderate to high according to the studied trait and small increases in predictive ability could be obtained for some traits when the two populations were combined into a unique training set. We also investigated the potential of such a training set to predict hybrids resulting from crosses between the two populations, with a focus on the method to design the training set and the best proportion of each population to optimize predictions. The measured predictive abilities were very similar for all the proportions, except for the extreme cases where only one of the two populations was used in the training set, in which case predictive abilities could be lower than when using both populations. Using an optimization algorithm to choose the genotypes in the training set also led to higher predictive abilities than when the genotypes were chosen at random. Our results provide guidelines to initiate breeding programs that use genomic selection when the implementation of the training set is a limitation.

SSR-Based Analysis of Genetic Diversity and Structure of Sweet Cherry (Prunus avium L.) from 19 Countries in Europe

Sweet cherry (Prunus avium L.) is a temperate fruit species whose production might be highly impacted by climate change in the near future. Diversity of plant material could be an option to mitigate these climate risks by enabling producers to have new cultivars well adapted to new environmental conditions. In this study, subsets of sweet cherry collections of 19 European countries were genotyped using 14 SSR. The objectives of this study were (i) to assess genetic diversity parameters, (ii) to estimate the levels of population structure, and (iii) to identify germplasm redundancies. A total of 314 accessions, including landraces, early selections, and modern cultivars, were monitored, and 220 unique SSR genotypes were identified. All 14 loci were confirmed to be polymorphic, and a total of 137 alleles were detected with a mean of 9.8 alleles per locus. The average number of alleles (N = 9.8), PIC value (0.658), observed heterozygosity (H_o = 0.71), and expected heterozygosity (H_e = 0.70) were higher in this study compared to values reported so far. Four ancestral populations were detected using STRUCTURE software and confirmed by Principal Coordinate Analysis (PCoA), and two of them (K1 and K4) could be attributed to the geographical origin of the accessions. A N-J tree grouped the 220 sweet cherry accessions within three main clusters and six subgroups. Accessions belonging to the four STRUCTURE populations roughly clustered together. Clustering confirmed known genealogical data for several accessions. The large genetic diversity of the collection was demonstrated, in particular within the landrace pool, justifying the efforts made over decades for their conservation. New sources of diversity will allow producers to face challenges, such as climate change and the need to develop more sustainable production systems.

Towards a Joint International Database: Alignment of SSR Marker Data for European Collections of Cherry Germplasm

The objective of our study was the alignment of microsatellite or simple sequence repeat (SSR) marker data across germplasm collections of cherry within Europe. Through the European Cooperative program for Plant Genetic Resources ECPGR, a number of European germplasm collections had previously been analysed using standard sets of SSR loci. However, until now these datasets remained unaligned. We used a combination of standard reference genotypes and ad-hoc selections to compile a central dataset representing as many alleles as possible from national datasets produced in France, Great Britain, Germany, Italy, Sweden and Switzerland. Through the comparison of alleles called in data from replicated samples we were able to create a series of alignment factors, supported across 448 different allele calls, that allowed us to align a dataset of 2241 SSR profiles from six countries. The proportion of allele comparisons that were either in agreement with the alignment factor or confounded by null alleles ranged from 67% to 100% and this was further improved by the inclusion of a series of allele-specific adjustments. The aligned dataset allowed us to identify groups of previously unknown matching accessions and to identify and resolve a number of errors in the prior datasets. The combined and aligned dataset represents a significant step forward in the co-ordinated management of field collections of cherry in Europe.

Ten Years of VINQUEST: First Insight for Breeding New Apple Cultivars With Durable Apple Scab Resistance

Apple scab, caused by Venturia inaequalis, is a major fungal disease worldwide. Cultivation of scab-resistant cultivars would reduce the chemical footprint of apple production. However, new apple cultivars carrying durable resistances should be developed to prevent or at least slow the breakdown of resistance against races of V. inaequalis. One way to achieve durable resistance is to pyramid multiple scab resistance genes in a cultivar. The choice of the resistance genes to be combined in the pyramids should take into account the frequency of resistance breakdown and the geographical distribution of apple scab isolates able to cause such breakdowns. In order to acquire this information and to make it available to apple breeders, the VINQUEST project (www.vinquest.ch) was initiated in 2009. Ten years after launching this project, 24 partners from 14 countries regularly contribute data. From 2009 to 2018, nearly 9,000 data points have been collected. This information has been used to identify the most promising apple scab resistance genes for developing cultivars with durable resistance, which to date are: Rvi5, Rvi11, Rvi12, Rvi14, and Rvi15. As expected, Rvi1, together with Rvi3 and Rvi8, were often overcome, and have little value for scab resistance breeding. Rvi10 may also belong to this group. On the other hand, Rvi2, Rvi4, Rvi6, Rvi7, Rvi9, and Rvi13 are still useful for breeding, but their use is recommended only in extended pyramids of ≥3 resistance genes.

Review of the Impact of Apple Fruit Ripening, Texture and Chemical Contents on Genetically Determined Susceptibility to Storage Rots

Fungal storage rots like blue mould, grey mould, bull's eye rot, bitter rot and brown rot destroy large amounts of the harvested apple crop around the world. Application of fungicides is nowadays severely restricted in many countries and production systems, and these problems are therefore likely to increase. Considerable variation among apple cultivars in resistance/susceptibility has been reported, suggesting that efficient defence mechanisms can be selected for and used in plant breeding. These are, however, likely to vary between pathogens, since some fungi are mainly wound-mediated while others attack through lenticels or by infecting blossoms. Since mature fruits are considerably more susceptible than immature fruits, mechanisms involving fruit-ripening processes are likely to play an important role. Significant associations have been detected between the susceptibility to rots in harvested fruit and various fruit maturation-related traits like ripening time, fruit firmness at harvest and rate of fruit softening during storage, as well as fruit biochemical contents like acidity, sugars and polyphenols. Some sources of resistance to blue mould have been described, but more research is needed on the development of spore inoculation methods that produce reproducible data and can be used for large screenings, especially for lenticel-infecting fungi.

Using whole-genome SNP data to reconstruct a large multi-generation pedigree in apple germplasm

BACKGROUND

Apple (Malus x domestica Borkh.) is one of the most important fruit tree crops of temperate areas, with great economic and cultural value. Apple cultivars can be maintained for centuries in plant collections through grafting, and some are thought to date as far back as Roman times. Molecular markers provide a means to reconstruct pedigrees and thus shed light on the recent history of migration and trade of biological materials. The objective of the present study was to identify relationships within a set of over 1400 mostly old apple cultivars using whole-genome SNP data (~ 253 K SNPs) in order to reconstruct pedigrees.

RESULTS

Using simple exclusion tests, based on counting the number of Mendelian errors, more than one thousand parent-offspring relations and 295 complete parent-offspring families were identified. Additionally, a grandparent couple was identified for the missing parental side of 26 parent-offspring pairings. Among the 407 parent-offspring relations without a second identified parent, 327 could be oriented because one of the individuals was an offspring in a complete family or by using historical data on parentage or date of recording. Parents of emblematic cultivars such as 'Ribston Pippin', 'White Transparent' and 'Braeburn' were identified. The overall pedigree combining all the identified relationships encompassed seven generations and revealed a major impact of two Renaissance cultivars of French and English origin, namely 'Reinette Franche' and 'Margil', and one North-Eastern Europe cultivar from the 1700s, 'Alexander'. On the contrary, several older cultivars, from the Middle Ages or the Roman times, had no, or only single, identifiable offspring in the set of studied accessions. Frequent crosses between cultivars originating from different European regions were identified, especially from the nineteenth century onwards.

CONCLUSIONS

The availability of over 1400 apple genotypes, previously filtered for genetic uniqueness and providing a broad representation of European germplasm, has been instrumental for the success of this large pedigree reconstruction. It enlightens the history of empirical selection and recent breeding of apple cultivars in Europe and provides insights to speed-up future breeding and selection.

Tandem Mass Tag Based Quantitative Proteomics of Developing Sea Buckthorn Berries Reveals Candidate Proteins Related to Lipid Metabolism

Sea buckthorn ( Hippophae L.) is an economically important shrub or small tree distributed in Eurasia. Most of its well-recognized medicinal and nutraceutical products are derived from its berry oil, which is rich in monounsaturated omega-7 (C16:1) fatty acid and polyunsaturated omega-6 (C18:2) and omega-3 (C18:3) fatty acids. In this study, tandem mass tags (TMT)-based quantitative analysis was used to investigate protein profiles of lipid metabolism in sea buckthorn berries harvested 30, 50, and 70 days after flowering. In total, 8626 proteins were identified, 6170 of which were quantified. Deep analysis results for the proteins identified and related pathways revealed initial fatty acid accumulation during whole-berry development. The abundance of most key enzymes involved in fatty acid and triacylglycerol (TAG) biosynthesis peaked at 50 days after flowering, but TAG synthesis through the PDAT (phospholipid: diacylglycerol acyltransferase) pathway mostly occurred early in berry development. In addition, the patterns of proteins involved in lipid metabolism were confirmed by combined quantitative real-time polymerase chain reaction, enzyme-linked immunosorbent assay, and parallel reaction monitoring analyses. Our data on the proteomic spectrum of sea buckthorn berries provide a scientific basic for understanding lipid metabolism and related pathways in the developing berries.

Genome-Wide Association Mapping of Flowering and Ripening Periods in Apple

Deciphering the genetic control of flowering and ripening periods in apple is essential for breeding cultivars adapted to their growing environments. We implemented a large Genome-Wide Association Study (GWAS) at the European level using an association panel of 1,168 different apple genotypes distributed over six locations and phenotyped for these phenological traits. The panel was genotyped at a high-density of SNPs using the Axiom®Apple 480 K SNP array. We ran GWAS with a multi-locus mixed model (MLMM), which handles the putatively confounding effect of significant SNPs elsewhere on the genome. Genomic regions were further investigated to reveal candidate genes responsible for the phenotypic variation. At the whole population level, GWAS retained two SNPs as cofactors on chromosome 9 for flowering period, and six for ripening period (four on chromosome 3, one on chromosome 10 and one on chromosome 16) which, together accounted for 8.9 and 17.2% of the phenotypic variance, respectively. For both traits, SNPs in weak linkage disequilibrium were detected nearby, thus suggesting the existence of allelic heterogeneity. The geographic origins and relationships of apple cultivars accounted for large parts of the phenotypic variation. Variation in genotypic frequency of the SNPs associated with the two traits was connected to the geographic origin of the genotypes (grouped as North+East, West and South Europe), and indicated differential selection in different growing environments. Genes encoding transcription factors containing either NAC or MADS domains were identified as major candidates within the small confidence intervals computed for the associated genomic regions. A strong microsynteny between apple and peach was revealed in all the four confidence interval regions. This study shows how association genetics can unravel the genetic control of important horticultural traits in apple, as well as reduce the confidence intervals of the associated regions identified by linkage mapping approaches. Our findings can be used for the improvement of apple through marker-assisted breeding strategies that take advantage of the accumulating additive effects of the identified SNPs.

Assessment of diversity and genetic relationships of Neonectria ditissima: the causal agent of fruit tree canker

BACKGROUND

Neonectria ditissima is one of the most important fungal pathogens of apple trees, where it causes fruit tree canker. Information about the amount and partitioning of genetic variation of this fungus could be helpful for improving orchard management strategies and for breeding apple cultivars with high levels of genetically determined resistance. In this study single-spore Neonectria isolates originating from both the same and from different perithecia, apple cultivars and apple orchards in Sweden and Belgium, were evaluated for AFLP- and SSR-based genetic similarity and for mating system.

RESULTS

Seven SSR loci produced a total of 31 alleles with an average of 4 alleles per locus, while 11 AFLP primer combinations produced an average of 35 fragments per primer combination and 71 % polymorphic fragments. An AFLP-based analysis of molecular variance (AMOVA) revealed that 89 % of the variation was found within orchards and 11 % between orchards. Genetic similarity among the studied isolates was illustrated with a principal coordinate analyseis (PCoA) and a dendrogram. AFLP-based Jaccard's similarity coefficients were the highest when single-ascospore isolates obtained from the same perithecium were compared, medium-high for isolates from different perithecia on the same tree, and lowest when isolates from different trees were compared.

CONCLUSIONS

Based on the results of PCoA and AMOVA analysis, isolates from the same or geographically close orchards did not group together. Since AFLP profiles differed also when single-ascospore isolates from the same perithecium were compared, the mating system of N. ditissima is most likely heterothallic.

Analysis of the genetic diversity and structure across a wide range of germplasm reveals prominent gene flow in apple at the European level

BACKGROUND

The amount and structure of genetic diversity in dessert apple germplasm conserved at a European level is mostly unknown, since all diversity studies conducted in Europe until now have been performed on regional or national collections. Here, we applied a common set of 16 SSR markers to genotype more than 2,400 accessions across 14 collections representing three broad European geographic regions (North + East, West and South) with the aim to analyze the extent, distribution and structure of variation in the apple genetic resources in Europe.

RESULTS

A Bayesian model-based clustering approach showed that diversity was organized in three groups, although these were only moderately differentiated (FST = 0.031). A nested Bayesian clustering approach allowed identification of subgroups which revealed internal patterns of substructure within the groups, allowing a finer delineation of the variation into eight subgroups (FST = 0.044). The first level of stratification revealed an asymmetric division of the germplasm among the three groups, and a clear association was found with the geographical regions of origin of the cultivars. The substructure revealed clear partitioning of genetic groups among countries, but also interesting associations between subgroups and breeding purposes of recent cultivars or particular usage such as cider production. Additional parentage analyses allowed us to identify both putative parents of more than 40 old and/or local cultivars giving interesting insights in the pedigree of some emblematic cultivars.

CONCLUSIONS

The variation found at group and subgroup levels may reflect a combination of historical processes of migration/selection and adaptive factors to diverse agricultural environments that, together with genetic drift, have resulted in extensive genetic variation but limited population structure. The European dessert apple germplasm represents an important source of genetic diversity with a strong historical and patrimonial value. The present work thus constitutes a decisive step in the field of conservation genetics. Moreover, the obtained data can be used for defining a European apple core collection useful for further identification of genomic regions associated with commercially important horticultural traits in apple through genome-wide association studies.

Assessment of diversity in Harpagophytum with RAPD and ISSR markers provides evidence of introgression

The genus Harpagophytum has two species: H. procumbens which is an important medicinal plant in southern Africa, and H. zeyheri. Genetic diversity in 96 samples, obtained by germinating seeds collected from Botswana, was assessed using six inter-simple sequence repeat (ISSR) and 10 random amplified polymorphic DNA (RAPD) primers. These DNA markers yielded a total of 138 polymorphic bands. Polymorphism information content (PIC) ranged from 0.06 to 0.39 for ISSR primers, and from 0.09 to 0.43 for RAPD primers. Jaccard's similarity coefficients were highest when seedlings derived from the same fruit capsule were compared, while seedlings from different fruits on the same plant had intermediate values. The lowest values were recorded among seedlings from different plants. These results were consistent with an outcrossing breeding system in Harpagophytum. Analysis of molecular variance revealed significant differentiation (P<0.01) between taxonomic units within Harpagophytum. About 39% of the variability occurred between the two species, H. procumbens and H. zeyheri. Plants with an intermediate morphology, i.e. putative hybrids (PH), showed 21% differentiation when compared with H. procumbens ssp. procumbens (PP), and 19% when compared with H. procumbens ssp. transvaalense (PT) or with H. zeyheri (ZZ). In addition, a deviating variant of PT was identified, here termed 'procumbens new variety' (PN). PN showed only 9% differentiation when compared with PT, 22% when compared with PP or with PH, and 41% when compared with ZZ. Considerable differentiation between the two Harpagophytum species was revealed also by a cluster analysis. Introgression was, however, suggested by the intermediate position of the putative hybrid plants in a principal component analysis while inter-specific gene flow was shown by a Bayesian genetic structure analysis.

Promotion of wound healing by Plantago major L. leaf extracts--ex-vivo experiments confirm experiences from traditional medicine

The wound-healing properties of Plantago major L. (plantain) were evaluated using an ex-vivo porcine wound-healing model. Ethanol- and water-based extracts were prepared from greenhouse-grown and freeze-dried leaves of P. major. Both types of extracts stimulated wound healing in porcine skin, but the ethanol-based extracts had a somewhat stronger effect. A concentration of 1.0 mg/mL (on dry weight basis) produced the best results for both types of extracts.

High penetrance of a pan-canina type rDNA family in intersection Rosa hybrids suggests strong selection of bivalent chromosomes in the section Caninae

All dogroses (Rosa sect. Caninae) are characterized by the peculiar canina meiosis in which genetic material is unevenly distributed between female and male gametes. The pan-canina rDNA family (termed beta) appears to be conserved in all dogroses analyzed so far. Here, we have studied rDNAs in experimental hybrids obtained from open pollination of F1 plants derived from 2 independent intersectional crosses between the pentaploid dogrose species (2n = 5x = 35) Rosa rubiginosa as female parent (producing 4x egg cells due to the unique asymmetrical canina meiosis) and the tetraploid (2n = 4x = 28) garden rose R. hybrida 'André Brichet' as male parent (producing 2x pollen after normal meiosis). We analyzed the structure of rDNA units by molecular methods [CAPS and extensive sequencing of internal transcribed spacers (ITS)] and determined the number of loci on chromosomes by FISH. FISH showed that R. rubiginosa and 'André Brichet' harbored 5 and 4 highly heteromorphic rDNA loci, respectively. In the second generation of hybrid lines, we observed a reduced number of loci (4 and 5 instead of the expected 6). In R. rubiginosa and 'André Brichet', 2-3 major ITS types were found which is consistent with a weak homogenization pressure maintaining high diversity of ITS types in this genus. In contrast to expectation (the null hypothesis of Mendelian inheritance of ITS families), we observed reduced ITS diversity in some individuals of the second generation which might derive from self-fertilization or from a backcross to R. rubiginosa. In these individuals, the pan-canina beta family appeared to be markedly enriched, while the paternal families were lost or diminished in copies. Although the mechanism of biased meiotic transmission of certain rDNA types is currently unknown, we speculate that the bivalent-forming chromosomes carrying the beta rDNA family exhibit extraordinary pairing efficiency and/or are subjected to strong selection in Caninae polyploids.

DNA fingerprinting in botany: past, present, future

Almost three decades ago Alec Jeffreys published his seminal Nature papers on the use of minisatellite probes for DNA fingerprinting of humans (Jeffreys and colleagues Nature 1985, 314:67-73 and Nature 1985, 316:76-79). The new technology was soon adopted for many other organisms including plants, and when Hilde Nybom, Kurt Weising and Alec Jeffreys first met at the very First International Conference on DNA Fingerprinting in Berne, Switzerland, in 1990, everybody was enthusiastic about the novel method that allowed us for the first time to discriminate between humans, animals, plants and fungi on the individual level using DNA markers. A newsletter coined "Fingerprint News" was launched, T-shirts were sold, and the proceedings of the Berne conference filled a first book on "DNA fingerprinting: approaches and applications". Four more conferences were about to follow, one on each continent, and Alec Jeffreys of course was invited to all of them. Since these early days, methodologies have undergone a rapid evolution and diversification. A multitude of techniques have been developed, optimized, and eventually abandoned when novel and more efficient and/or more reliable methods appeared. Despite some overlap between the lifetimes of the different technologies, three phases can be defined that coincide with major technological advances. Whereas the first phase of DNA fingerprinting ("the past") was dominated by restriction fragment analysis in conjunction with Southern blot hybridization, the advent of the PCR in the late 1980s gave way to the development of PCR-based single- or multi-locus profiling techniques in the second phase. Given that many routine applications of plant DNA fingerprinting still rely on PCR-based markers, we here refer to these methods as "DNA fingerprinting in the present", and include numerous examples in the present review. The beginning of the third phase actually dates back to 2005, when several novel, highly parallel DNA sequencing strategies were developed that increased the throughput over current Sanger sequencing technology 1000-fold and more. High-speed DNA sequencing was soon also exploited for DNA fingerprinting in plants, either in terms of facilitated marker development, or directly in the sense of "genotyping-by-sequencing". Whereas these novel approaches are applied at an ever increasing rate also in non-model species, they are still far from routine, and we therefore treat them here as "DNA fingerprinting in the future".

Oral challenges with four apple cultivars result in significant differences in oral allergy symptoms

BACKGROUND

We analyzed the hypoallergenic potential of a recently bred apple selection with unusually low content of Mal d 1, using an oral challenge model with three additional apple cultivars for comparison.

METHODS

Sixty-six birch pollen-allergic individuals with a history of oral allergy syndrome after apple intake were subjected to a double-blind oral provocation with two apple cultivars (B:0654 and 'Discovery'). Thirteen also tested two other apple cultivars ('Ingrid Marie' and 'Gloster'). Three doses were given consecutively, 30 min apart: 10 g without peel, and 10 and 50 g with peel. A final assessment was conducted 30 min after the last intake. Oral symptoms were graded from 0 to 5. Total oral symptom score (TOS) included all scores for each cultivar at all time points.

RESULTS

B:0654 induced significantly higher TOS than 'Discovery' when tested by 66 individuals, in spite of its lower Mal d 1 content. TOS values were higher in females and increased with increasing age of the individuals when challenged with 'Discovery'. Among the 13 individuals who tested all four cultivars, B:0654 produced a higher score after the second dose compared to 'Ingrid Marie'. This was also the case after the third dose compared to 'Ingrid Marie' and 'Gloster', and again 30 min after the last intake compared to each of the other three cultivars, as well as a higher TOS compared to each of the other three cultivars (all p < 0.01).

CONCLUSIONS

Our test was safe and well tolerated, and produced significant differences among the apple cultivars. Contrary to expectations, B:0654 was less well tolerated than the other three cultivars.

AFLP-based population structure analysis as a means to validate the complex taxonomy of dogroses (Rosa section Caninae)

Within the genus Rosa numerous species have been described. Circumscription of the dogrose section Caninae is straightforward, but the delineation of species and subsections within this section is less clear, partly due to hybridisation between species. We have investigated the extent to which DNA marker-based information of wild populations corroborates present-day dogrose taxonomy and hypotheses about the origination of taxa. Sampling was conducted in a transect across Europe, collecting over 900 specimens of all encountered dogrose taxa. For comparison, we also included more than 200 samples of species belonging to other sections. Two lines of statistical analyses were used to investigate the genetic structure based on AFLP data: (1) an unstructured model with principal coordinate analysis and hierarchical clustering, and (2) a model with a superimposed taxonomic structure based on analysis of genetic diversity using a novel approach combining assignment tests with canonical discriminant analysis. Support was found for five of the seven subsections, whereas R. balsamica apparently belongs to subsection Caninae thus omitting the need for recognising subsection Tomentellae. For R. stylosa, a hybridogenic origin with a non-dogrose section member has been suggested, and it can be treated either as a separate subsection or within subsection Caninae. Within the subsection Rubigineae, a species cluster with low support for the taxa R. micrantha, R. rubiginosa and the putatively hybridogenous R. gremlii was identified. Similarly, several species in the subsection Caninae overlapped considerably, and are best regarded as one common species complex. This population genetic approach provides a general method to validate the taxonomic system in complex and polyploid taxa.

Effects of Plantago major L. leaf extracts on oral epithelial cells in a scratch assay

ETHNOPHARMACOLOGICAL RELEVANCE

The present study was undertaken to evaluate the effects from different leaf extracts of the traditional medicinal herb Plantago major L. (plantain) on cell proliferation and migration in vitro, as a test for potential wound healing properties.

MATERIALS AND METHODS

Water and ethanol-based extracts were prepared from Plantago major fresh and dried leaves, and tested in vitro in a scratch assay with oral epithelial cells.

RESULTS

The scratch assay produced reliable results after 18 h. Most of the tested extracts increased the proliferation/migration of the oral epithelial cells compared to the negative control. A concentration of 1.0 mg/mL (on dry weight basis) appears to be optimal regardless of type of extract, and among the alternatives, 0.1 mg/mL was always better than 10 mg/mL. Ethanol-based extracts with a concentration of 10 mg/mL had very detrimental effects on cell proliferation/migration. At the other two concentrations, ethanol-based extracts had the most beneficial effect, followed by water extracts of fresh leaves, ethanol plus water extracts of dried leaves and, finally, water extracts of dried leaves.

CONCLUSIONS

This study suggests that both the water extracts and the more polyphenol-rich ethanol-based extracts of Plantago major leaves have medicinal properties. Further research is, however, needed to determine what compounds are responsible for the wound healing effects.

Advances in improvement of quality and resistance in a multipurpose crop: sea buckthorn

Sea buckthorn is a berry crop with multiple uses. The berries are highly appreciated for their unique taste but are also very rich in bioactive compounds with powerful nutritional and medicinal values. In addition, the plants grow well under adverse conditions, and are often used to fight soil erosion. Utilization of sea buckthorn has therefore increased around the world but serious problems have, nevertheless, been encountered due to drought, salinity, diseases and insect pests. This review covers important aspects of sea buckthorn research, such as heritable and environmentally induced variation in biochemical compounds, causes and effects of the devastating dried-shrink disease, susceptibility to insect pests, methods for conventional breeding, and the utilization of DNA markers for taxonomical and population genetic analyses, and for investigating the inheritance of quality and resistance traits. We also present possibilities to implement innovative biotechnological breeding methods, especially metabolite profiling and MAS/GRC-based markers, for fast and efficient development of elite genotypes with specific nutritional- and health-related bioactive compounds and strong resistance to biotic and abiotic stress.

Genetic diversity in watermelon (Citrullus lanatus) landraces from Zimbabwe revealed by RAPD and SSR markers

Low polymorphism in cultivated watermelon has been reported in previous studies, based mainly on US Plant Introductions and watermelon cultivars, most of which were linked to breeding programmes associated with disease resistance. Since germplasm sampled in a putative centre of origin in southern Africa may harbour considerably higher variability, DNA marker-based diversity was estimated among 81 seedlings from eight accessions of watermelon collected in Zimbabwe; five accessions of cow-melons (Citrullus lanatus var. citroides) and three of sweet watermelons (C. lanatus var. lanatus). Two molecular marker methods were used, random amplified polymorphic DNA (RAPD) and simple sequence repeats (SSR) also known as microsatellite DNA. Ten RAPD primers produced 138 markers of which 122 were polymorphic. Nine SSR primer pairs detected a total of 43 alleles with an average of 4.8 alleles per locus. The polymorphic information content (PIC) ranged from 0.47 to 0.77 for the RAPD primers and from 0.39 to 0.97 for the SSR loci. Similarity matrices obtained with SSR and RAPD, respectively, were highly correlated but only RAPD was able to provide each sample with an individual-specific DNA profile. Dendrograms and multidimensional scaling (MDS) produced two major clusters; one with the five cow-melon accessions and the other with the three sweet watermelon accessions. One of the most variable cow-melon accessions took an intermediate position in the MDS analysis, indicating the occurrence of gene flow between the two subspecies. Analysis of molecular variation (AMOVA) attributed most of the variability to within-accessions, and contrary to previous reports, sweet watermelon accessions apparently contain diversity of the same magnitude as the cow-melons.

Frequent silencing of rDNA loci on the univalent-forming genomes contrasts with their stable expression on the bivalent-forming genomes in polyploid dogroses (Rosa sect. Caninae)

The polyploid species in Rosa section Caninae (2n=21, 28 or 35) are characterized by an unusual reproductive system known as odd (or asymmetric) meiosis. Only two chromosome sets form bivalents in meiosis, whereas the remaining chromosomes are transmitted as univalents through the female germline. Evolution of ribosomal rRNA genes (rDNA) does not seem to be significantly affected by interlocus homogenization in dogroses. As a consequence, most species contain several rDNA families falling into two main clades (beta and gamma) thought to be differentially distributed between bivalent and univalent chromosomes, respectively. Here, we have investigated expression of rRNA gene families in five pentaploid species (R. canina, R. rubiginosa, R. dumalis, R. sherardii and R. caesia, 2n=35) and in one tetraploid (R. mollis, 2n=28). Using extensive sequencing of ITS clones and cleaved amplified polymorphism sequence (CAPS) analysis, we found that the beta-family was constitutively expressed in all species. However, there was large variation in the expression patterns of families constituting the gamma-clade. In addition, a single family can be active in one species, whereas silenced in another. The data show that the families on bivalent-forming chromosomes dominate rDNA expression in all dogrose species. We hypothesize that genes on bivalent genomes are stably expressed, whereas those on univalent genomes undergo variable levels of epigenetic silencing. Nonetheless, mosaic expression of univalent genomes could contribute to phenotypic variation between the species.

Molecular characterisation of indigenous Swedish apple cultivars based on SSR and S-allele analysis

Trees of 68 apple cultivars, aimed for preservation by the 'National Program for diversity of cultivated plants' as mandate cultivars, were analysed using a set of 10 SSR (simple sequence repeat) primer pairs and the self-incompatibility (S-)locus to evaluate genetic diversity and reveal inter-cultivar relationships. The 12 polymorphic SSR loci exhibited 2 to 15 alleles, with expected heterozygozity (H(e)) ranging from 0.36 to 0.88 and a mean of 0.74. Numerous alleles were classified as rare or unique (35% and 18% respectively). For the S-locus, a total of 14 alleles were identified in this study. Five alleles, S1-S3, S5 and S7 had frequencies ranging from 11 to 18%, whereas the remaining 9 alleles were below 6%. All sexually obtained cultivars could be distinguished with the set of SSR loci. Sports were identical with their progenitors in two cases, but differed in one SSR allele in a third case. An SSR-based dendrogram, based on Roger's genetic distances, did not reveal any clear pattern of clustering. The genetic distances were, however, correlated with a corresponding matrix obtained in a previously conducted RAPD-based study of the same cultivars. Non-mandate parents of Swedish mandate cultivars together with some other reference cultivars were included in this study to check the accuracy of allele scoring, verify parentage and compare the results of this study with those presented in previously published studies. Some discrepancies in allele sizing were revealed and the possibilities of avoiding this problem are discussed.

The asymmetric meiosis in pentaploid dogroses (Rosa sect. Caninae) is associated with a skewed distribution of rRNA gene families in the gametes

In pentaploid dogroses, Rosa section Caninae (2n=5x=35), the pollen transmits one basic genome (x=7) derived from the seven segregating bivalents, whereas the egg transmits four basic genomes (4x=28) one set derived from the segregation of seven bivalents and three sets of univalent-forming chromosomes. Chromosomes from all five genomes carry 18-5.8-26S nuclear ribosomal DNA (rDNA) sites. This mode of sexual reproduction, known as permanent odd polyploidy, can potentially lead to the independent evolution of rDNA on bivalent- and univalent-forming chromosomes. To test this hypothesis, we analyzed rRNA gene families in pollen and somatic leaf tissue of R. canina, R. rubiginosa and R. dumalis. Six major rRNA gene families (alpha, beta, beta' gamma, delta and epsilon) were identified based on several highly polymorphic sites in the internal transcribed spacers (ITSs). At least two of the major rRNA gene families were found in each species indicating that rDNAs have not been homogenized across subgenomes. A comparison of ITS1 sequences from leaf and pollen showed differences: the shared beta rRNA gene family was more abundant among pollen clones compared to leaf clones and must constitute a major part of the rDNA loci on bivalent-forming chromosomes. The gamma and delta families were underrepresented in pollen genomes and are probably located predominantly (or solely) on the univalents. The results support the hypothesis that pentaploid dogroses inherited a bivalent-forming genome from a common proto-canina ancestor, a likely donor of the beta rDNA family. Allopolyploidy with distantly related species is likely to have driven evolution of Rosa section Caninae.

AFLP markers as a tool to reconstruct complex relationships: A case study in Rosa (Rosaceae)

The genus Rosa has a complex evolutionary history caused by several factors, often in conjunction: extensive hybridization, recent radiation, incomplete lineage sorting, and multiple events of polyploidy. We examined the applicability of AFLP markers for reconstructing (species) relationships in Rosa, using UPGMA clustering, Wagner parsimony, and Bayesian inference. All trees were well resolved, but many of the deeper branches were weakly supported. The cluster analysis showed that the rose cultivars can be separated into a European and an Oriental cluster, each being related to different wild species. The phylogenetic analyses showed that (1) two of the four subgenera (Hulthemia and Platyrhodon) do not deserve subgeneric status; (2) section Carolinae should be merged with sect. Cinnamomeae; (3) subsection Rubigineae is a monophyletic group within sect. Caninae, making sect. Caninae paraphyletic; and (4) there is little support for the distinction of the five other subsections within sect. Caninae. Comparison of the trees with morphological classifications and with previous molecular studies showed that all methods yielded reliable trees. Bayesian inference proved to be a useful alternative to parsimony analysis of AFLP data. Because of their genome-wide sampling, AFLPs are the markers of choice to reconstruct (species) relationships in evolutionary complex groups.

Unique genomic configuration revealed by microsatellite DNA in polyploid dogroses, Rosa sect. Caninae

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.

RAPD analysis of diploid and tetraploid populations of Aronia points to different reproductive strategies within the genus

Plant breeding in black chokeberry (Aronia melanocarpa) is based mainly on seedlings derived from domesticated Russian plants. Previous studies have, however, demonstrated very low levels of phenotypic variation within this gene pool. The present investigation was undertaken in order to study the genetic structure in native populations growing in North America. Random amplified polymorphic DNA (RAPD) marker variation was analysed in eight populations (three or five mother plants/population and five seedlings/mother plant) and compared with the variation in four cultivars and 15 seedlings derived from a Russian plantation. The four cultivars and all the Russian seedlings turned out to have identical RAPD profiles. In the native plant material, there were two types of mother plants: diploid plants that produced very heterogeneous offspring and tetraploid plants that produced homogeneous offspring. Partitioning of variability based on Shannon's diversity index attributed approx. 22% of the variation to the among-population level in diploids, compared to approx. 55% in the tetraploids. However, the diploid populations and the tetraploid populations did not differ significantly in within-population variation. These results prompted a second set of RAPD analyses, which were carried out on offspring obtained through open pollination of the initially examined material when growing in an experimental field. The analyses showed that tetraploid plants produced tetraploid offspring that, with few exceptions, were identical, indicating apomixis, whereas offspring of diploid plants were diploid or triploid, and highly heterogeneous, indicating outcrossing. Presumably, the tetraploid form of Aronia is an allopolyploid, with A. melanocarpa as one of the parents.

Microsatellite DNA marker inheritance indicates preferential pairing between two highly homologous genomes in polyploid and hemisexual dog-roses, Rosa L. Sect. Caninae DC

According to previous cytological evidence, the hemisexual dog-rose species, Rosa sect. Caninae, transmit only seven chromosomes (derived from seven bivalents) through their pollen grains, whereas egg cells contain 21, 28 or 35 chromosomes (derived from seven bivalents and 14, 21 or 28 univalents) depending on ploidy level. Two sets of reciprocal pairwise interspecific crosses involving the pentaploid species pair R. dumalis and R. rubiginosa, and the pentaploid/tetraploid species pair R. sherardii and R. villosa, were analysed for 13 and 12 microsatellite DNA loci, respectively. Single loci were represented by a maximum of three simultaneously occurring alleles in R. villosa, and four alleles in the other three parental plants. In the experimentally derived offspring, the theoretical maximum of five alleles was found for only one locus in the pentaploid progenies. Microsatellite DNA allele composition was identical with that of the maternal parent in 10 offspring plants, which were probably derived through apomixis. Almost all microsatellite DNA alleles were shared with the maternal parent also in the remaining offspring, but 1-4 alleles shared only with the paternal parent, indicating sexual seed formation. Analysis of quantitative peak differences allowed a tentative estimation of allelic configuration in the individual plants, and suggested that bivalent formation preferentially takes place between chromosomes that consistently share the same microsatellite alleles and therefore appear to be highly homologous. Moreover, alleles that were shared between the species in each cross combination comparatively often appear to reside on the bivalent-forming chromosomes, whereas species-specific alleles instead occur comparatively often on the univalent-forming chromosomes and are therefore inherited through the maternal parent only. Recombination then takes place between very similar genomes also in interspecific crosses, resulting in a reproduction system that is essentially a mixture between apomixis and selfing.

Assignment of allelic configuration in polyploids using the MAC-PR (microsatellite DNA allele counting-peak ratios) method

Polysomic inheritance frequently results in the simultaneous occurrence of several microsatellite DNA alleles on a single locus. The MAC-PR (microsatellite DNA allele counting-peak ratios) method was recently developed for the analysis of polyploid plants and makes use of the quantitative values for microsatellite allele peak areas. To date, this approach has only been used in plants with known genetic relationships. We report here the application of MAC-PR for the first time to random samples of unknown pedigrees. We analysed six microsatellite loci using a set of tetraploid ornamental rose ( Rosa x hybrida L.) varieties. For each locus, all alleles were analysed in pairwise combinations in order to determine their copy number in the individual samples. This was accomplished by calculating the ratios between the peak areas for two alleles in all of the samples where these two alleles occurred together. The allele peak ratios observed were plotted in a histogram, and those histograms that produced at least two well-separated groups were selected for further analysis. Mean allelic peak ratio values for these groups were compared to the relationships expected between alleles in hypothetical configurations of the locus investigated. Using this approach, we were able to assign precise allelic configurations (the actual genotype) to almost all of the varieties analysed for five of the six loci investigated. MAC-PR also appears to be a very effective tool for detecting 'null' alleles in polyploid species.

Distinction between wild and cultivated enset (Ensete ventricosum) gene pools in Ethiopia using RAPD markers

In southwest Ethiopia, the cultivation area of Ensete ventricosum (enset) overlaps with the natural distribution area of this species. Analyses of genetic diversity were undertaken using RAPD to provide information for conservation strategies as well as evidence of possible gene flow between the different gene pools, which can be of interest for future improvement of cultivated enset. The extent of RAPD variation in wild enset was investigated in 5 populations in the Bonga area (Kefficho administrative region) and 9 cultivated clones. Comparisons were also made with some Musa samples of potential relevance for crop improvement. Nine oligonucleotide primers amplified 72 polymorphic loci. Population differentiation was estimated with the Shannon index (G'(ST)=0.10), Nei's G(ST) (0.12) and AMOVA (Phi(ST)=0.12), and appears to be relatively low when compared with outbreeding, perennial species in general. Cluster analysis (UPGMA) and principal component analysis (PCA) similarly indicated low population differentiation, and also demonstrated that cultivated clones essentially clustered distinctly from wild enset samples, suggesting that the present-day cultivated enset clones have been introduced to domestication from a limited number of wild progenitors. In addition, subsequent gene flow between wild and cultivated enset may have been prohibited by differences between modes of propagation and harvesting time; cultivated enset is propagated vegetatively through sucker production and the plant is generally harvested before maturity or flower set, thereby hindering pollination by wild enset or vice versa. A significant correlation was not found between genetic and geographical distances. The relatively high total RAPD diversity suggests that wild enset populations in the Bonga area harbour genetic variability which could potentially act as a source for useful or rare genes in the improvement of cultivated enset. As expected, E. ventricosum was clearly differentiated from the analysed Musa samples, that clustered in accordance with the present morphology- and molecular marker-based taxonomy of the genus.

Comparison of different nuclear DNA markers for estimating intraspecific genetic diversity in plants

A compilation was made of 307 studies using nuclear DNA markers for evaluating among- and within-population diversity in wild angiosperms and gymnosperms. Estimates derived by the dominantly inherited markers (RAPD, AFLP, ISSR) are very similar and may be directly comparable. STMS analysis yields almost three times higher values for within-population diversity whereas among-population diversity estimates are similar to those derived by the dominantly inherited markers. Number of sampled plants per population and number of scored microsatellite DNA alleles are correlated with some of the population genetics parameters. In addition, maximum geographical distance between sampled populations has a strong positive effect on among-population diversity. As previously verified with allozyme data, RAPD- and STMS-based analyses show that long-lived, outcrossing, late successional taxa retain most of their genetic variability within populations. By contrast, annual, selfing and/or early successional taxa allocate most of the genetic variability among populations. Estimates for among- and within-population diversity, respectively, were negatively correlated. The only major discrepancy between allozymes and STMS on the one hand, and RAPD on the other hand, concerns geographical range; within-population diversity was strongly affected when the former methods were used but not so in the RAPD-based studies. Direct comparisons between the different methods, when applied to the same plant material, indicate large similarities between the dominant markers and somewhat lower similarity with the STMS-based data, presumably due to insufficient number of analysed microsatellite DNA loci in many studies.

Skewed distribution of morphological character scores and molecular markers in three interspecific crosses in Rosa section Caninae

The dogroses, Rosa section Caninae, are all polyploid and characterised by their unbalanced meiosis; the pollen parent contributes one genome, whereas the seed parent contributes 3-5 genomes depending upon ploidy level of the species. As a result, genetically determined traits are expected to be matroclinally inherited. In the present study, the transmittal of genetic material was studied using manually scored reproductive characters (ovary and sepals), automated image analysis of leaflet shape (Fourier coefficients), and molecular markers (RAPD). The plant material consisted of a pair of reciprocal crosses between R. sherardii and R. villosa, a R. rubiginosa x R. sherardii cross and offspring obtained from selfing or within-population crosses of the parental species. All but one of the maternal markers were transmitted to all the offspring plants, whereas only 41% of the paternal markers were transmitted to all of them, 23% were never transmitted and 36% reached only one or two of the offspring plants. Canonical variates analyses (CVA) based on the vegetative characters could easily separate the offspring groups representing parental species and also all three hybridogenous offspring groups from each other, whereas CVA based on reproductive characters failed to separate R. sherardii x R. villosa from its seed parent, but otherwise distinguished all offspring groups. The study shows that the expression of characters as well as molecular marker inheritance is dependent upon the direction of the cross, and on the species involved. It also demonstrates the importance of employing several different types of character sets for an improved comprehension of the effects of the peculiar canina meiosis.

Combined analyses of RAPDs, cpDNA and morphology demonstrate spontaneous hybridization in the plant genus Chaenomeles

Evidence of spontaneous hybridization between two partially sympatric species of Chaenomeles, C. cathayensis and C. speciosa, has been obtained through analysis of offspring families from these two species, as well as from two presumed interspecific hybrid populations. A combination of different methods was applied. Analysis of diagnostic RAPD markers and of chloroplast DNA haplotypes supported the notion of spontaneous hybridization, and suggested that there has been symmetrical, rather than unidirectional, introgression between C. cathayensis and C. speciosa. RAPDs and morphological characters revealed concordant patterns of genetic relatedness among the studied offspring families. Some putative hybrid families had mainly intermediate characters, whereas others appeared to be later generation hybrids as they were genetically and phenotypically rather similar to families that appeared to represent pure species. The RAPD-based proportion of between-family variability was considerably higher in the putatively hybridogenous populations than in populations of the pure species. Within-family gene diversity estimates ranged from C. speciosa (max. Hj = 0.235) to C. cathayensis (min. Hj = 0.094) with the presumed hybrid families taking intermediate values.