Complete chloroplast genome assembly and phylogenetic analysis of blackcurrant (Ribes nigrum), red and white currant (Ribes rubrum), and gooseberry (Ribes uva-crispa) provide new insights into the phylogeny of Grossulariaceae

Background

Blackcurrant (Ribes nigrum), red currant (R. rubrum), white currant (R. rubrum), and gooseberry (R. uva-crispa) belong to Grossulariaceae and are popular small-berry crops worldwide. The lack of genomic data has severely limited their systematic classification and molecular breeding.

Methods

The complete chloroplast (cp) genomes of these four taxa were assembled for the first time using MGI-DNBSEQ reads, and their genome structures, repeat elements and protein-coding genes were annotated. By genomic comparison of the present four and previous released five Ribes cp genomes, the genomic variations were identified. By phylogenetic analysis based on maximum-likelihood and Bayesian methods, the phylogeny of Grossulariaceae and the infrageneric relationships of the Ribes were revealed.

Results

The four cp genomes have lengths ranging from 157,450 to 157,802 bp and 131 shared genes. A total of 3,322 SNPs and 485 Indels were identified from the nine released Ribes cp genomes. Red currant and white currant have 100% identical cp genomes partially supporting the hypothesis that white currant (R. rubrum) is a fruit color variant of red currant (R. rubrum). The most polymorphic genic and intergenic region is ycf1 and trnT-psbD, respectively. The phylogenetic analysis demonstrated the monophyly of Grossulariaceae in Saxifragales and the paraphyletic relationship between Saxifragaceae and Grossulariaceae. Notably, the Grossularia subgenus is well nested within the Ribes subgenus and shows a paraphyletic relationship with the co-ancestor of Calobotrya and Coreosma sections, which challenges the dichotomous subclassification of the Ribes genus based on morphology (subgenus Ribes and subgenus Grossularia). These data, results, and insights lay a foundation for the phylogenetic research and breeding of Ribes species.

[Cloning, structure analysis and functional verification of MYB10 in Ribes L]

This study aims to investigate the molecular mechanism of the transcription factor MYB10, which is involved in anthocyanin biosynthesis, in different colors of Ribes L. fruitification. Rapid amplification of cDNA ends (RACE) was used to clone the MYB10 genes from Ribes nigrum L. (RnMYB10), Ribes rubrum L. (RrMYB10), and Ribes album L. (RaMYB10), respectively. Phylogenetic analysis showed that RnMYB10 and RrMYB10 were evolutionarily homologous. Real-time quantitative PCR (RT-qPCR) showed that the expression of MYB10 in the fruits of Ribes nigrum L. was higher than that of Ribes rubrum L. and much higher than that of Ribes album L. The expression of RnMYB10 and RrMYB10 increased at first and then decreased as the fruit diameter increased and the fruit color deepened (the maximum expression level was reached at 75% of the fruit color change), while the expression level of RaMYB10 was very low. Overexpression of RnMYB10 and RrMYB10 in Arabidopsis thaliana resulted in purple petioles and leaves, whereas overexpression of RaMYB10 resulted in no significant color changes. This indicates that MYB10 gene plays an important role in the coloration of Ribes L. fruit.

[Cloning and expression of dfr in Ribes L. during fruit maturation]

Little is known about the molecular mechanism of currant anthocyanin synthesis. We investigated the effect of dfr, a key gene for anthocyanin synthesis in currant, on anthocyanins of different color currant. Black currant (Ribes nigrum L.), red currant (Ribes rubrum L.) and white currant (Ribes albrum L.) were used as test materials to determine the anthocyanin content at different stages of fruit development. Three full-length cDNA sequences of dfr gene were cloned by RACE (Rapid amplification of cDNA ends), and named as Rndfr, Rrdfr and Radfr. Phylogenetic analysis shows that Rndfr, Rrdfr and Radfr had high homology in evolution. The determination of anthocyanin content in different stages of fruit development shows that the content of anthocyanin in black currant and red currant was higher and gradually increased with the ripening of the fruit. While the content of anthocyanin in white currant was extremely low, and almost no anthocyanin was detected. Quantitative RT-PCR analysis shows that the expression level of dfr in black currant was higher than red currant and white currant in each period of fruit development. As the diameter of the fruit increased and the color of the peel deepened, the expression level of dfr in the black currant showed an increasing trend. In the red currant, the expression level gradually increased until the period of 75% fruit color, then the Rrdfr decreased rapidly. In white currant, the overall trend showed a downward trend, and its expression level was the lowest. All the results suggest that dfr gene plays a role in the process of fruit color.

Quantitative trait loci mapping of polyphenol metabolites in blackcurrant (Ribes nigrum L.)

INTRODUCTION

Commercially, blackcurrants (Ribes nigrum L.) are grown mainly for processing, especially for juice production. They are valued for their high levels of polyphenols, especially anthocyanins, which contribute to their characteristic deep colour, but also as a good source of vitamin C. Recently, evidence has accrued that polyphenols, such as anthocyanins, may have specific human health benefits.

OBJECTIVE

The aims of this study were to investigate the genetic control of polyphenols and other key juice processing traits in blackcurrants.

METHODS

The levels, over 2 years, of vitamin C, citrate, malate, succinate, total organic acids, total anthocyanins and total phenolics together with 46 mainly polyphenol metabolites were measured in a blackcurrant biparental mapping population. Quantitative trait loci (QTLs) for these traits were mapped onto a high-density SNP linkage map.

RESULTS

At least one QTL was detected for each trait, with good consistency between the 2 years. Clusters of QTLs were found on each of the eight linkage groups (LG). For example, QTLs for the major anthocyanidin glucosides, delphinidin-3-O-glucoside and cyanidin-3-O-glucoside, co-localised with a QTL for total anthocyanin content on LG3 whereas the major anthocyanidin rutinosides, delphinidin-3-O-rutinoside and cyanidin-3-O-rutinoside, had QTLs on LG1 and LG2. Many of the QTLs explained a high proportion of the trait variation, with the most significant region, on LG3 at ~ 35 cM, explaining more than 60% of the variation in the coumaroylated metabolites, Cyanidin-coumaroyl-glucose, Delphinidin-coumaroyl-glucose, Kaempferol-coumaroyl-glucose and Myricetin-coumaroyl-glucose.

CONCLUSION

The identification of robust QTLs for key polyphenol classes and individual polyphenols in blackcurrant provides great potential for marker-assisted breeding for improved levels of key components.

Application of HPLC-PDA-MS metabolite profiling to investigate the effect of growth temperature and day length on blackcurrant fruit

INTRODUCTION

Blackcurrant (Ribes nigrum L.) is an excellent example of a "super fruit" with potential health benefits. Both genotype and cultivation environment are known to affect the chemical composition of blackcurrant, especially ascorbic acid and various phenolic compounds. Environmental conditions, like temperature, solar radiation and precipitation can also have significant impact on fruit chemical composition. The relevance of the study is further accentuated by the predicted and ongoing changes in global climate.

OBJECTIVES

The aim of the present study was to provide new knowledge and a deeper understanding of the effects of post flowering environmental conditions, namely temperature and day length, on fruit quality and chemical composition of blackcurrant using an untargeted high performance liquid chromatography-photo diode array-mass spectrometry (HPLC-PDA-MS) metabolomics approach.

METHODS

A phytotron experiment with cultivation of single-stemmed potted plants of blackcurrant cv. Narve Viking was conducted using constant temperatures of 12, 18 or 24 °C and three different photoperiods (short day, short day with night interruption, and natural summer daylight conditions). Plants were also grown under ambient outdoor conditions. Ripe berries were analysed using an untargeted HPLC-PDA-MS metabolomics approach to detect the presence and concentration of molecules as affected by controlled climatic factors.

RESULTS

The untargeted metabolomics dataset contained a total of 7274 deconvolved retention time-m/z pairs across both electrospray ionisation (ESI) positive and negative polarities, from which 549 metabolites were identified or minimally annotated based upon accurate mass MS. Conventional principal component analysis (PCA) in combination with the Friedman significance test were applied to first identify which metabolites responded to temperature in a linear fashion. Multi-block hierarchical PCA in combination with the Friedman significance test was secondly applied to identify metabolites that were responsive to different day length conditions. Temperature had significant effect on a total of 365 metabolites representing a diverse range of chemical classes. It was observed that ripening of the blackcurrant berries under ambient conditions, compared to controlled conditions, resulted in an increased accumulation of 34 annotated metabolites, mainly anthocyanins and flavonoids. 18 metabolites were found to be regulated differentially under the different daylength conditions. Moreover, based upon the most abundant anthocyanins, a comparison between targeted and untargeted analyses, revealed a close convergence of the two analytical methods. Therefore, the study not just illustrates the value of non-targeted metabolomics approaches with respect to the huge diversity and numbers of significantly changed metabolites detected (and which would be missed by conventional targeted analyses), but also shows the validity of the non-targeted approach with respect to its precision compared to targeted analyses.

CONCLUSIONS

Blackcurrant maturation under controlled ambient conditions revealed a number of insightful relationships between environment and chemical composition of the fruit. A prominent reduction of the most abundant anthocyanins under the highest temperature treatments indicated that blackcurrant berries in general may accumulate lower total anthocyanins in years with extreme hot summer conditions. HPLC-PDA-MS metabolomics is an excellent method for broad analysis of chemical composition of berries rich in phenolic compounds. Moreover, the experiment in controlled phytotron conditions provided additional knowledge concerning plant interactions with the environment.

Polyphenol metabolism in differently colored cultivars of red currant (Ribes rubrum L.) through fruit ripening

Rare red currants colors caused by low anthocyanin content in the pink and a lack of anthocyanins in the white cultivar correlated with low ANS gene expression, enzyme activity, and increased sugar/acid ratios. Changes in the contents of polyphenols, sugars, and organic acids in berries of the three differently colored Ribes rubrum L. cultivars ('Jonkheer van Tets', 'Pink Champagne', and 'Zitavia') were determined by LC-MS and HPLC at 4 sampling times during the last month of fruit ripening. The activities of the main flavonoid enzymes, chalcone synthase/chalcone isomerase (CHS/CHI), flavanone 3-hydroxylase (FHT), and dihydroflavonol 4-reductase (DFR), and the expression of anthocyanidin synthase (ANS) were additionally measured. Despite many attempts, activities of flavonol synthase and glycosyltransferase did not show reliable results, the reason of which they could not be demonstrated in this study. The pink fruited cultivar 'Pink Champagne' showed generally lower enzyme activity than the red cultivar 'Jonkheer van Tets'. The white cultivar 'Zitavia' showed very low CHS/CHI activity and ANS expression and no FHT and DFR activities were detected. The DFR of R. rubrum L. clearly preferred dihydromyricetin as substrate although no 3',4',5'-hydroxylated anthocyanins were present. The anthocyanin content of the red cultivar slightly increased during the last three weeks of ripening and reached a maximum of 890 mg kg^-1 FW. Contrary to this, the pink cultivar showed low accumulation of anthocyanins; however, in the last three weeks of ripening, their content increased from 14 to 105 mg kg^-1 FW. Simultaneously, the content of polyphenols slightly decreased in all 3 cultivars, while the sugar/acid ratio increased. The white cultivar had no anthocyanins, but the sugar/acid ratios were the highest. In the white and pink cultivars, reduction/lack of anthocyanins was mainly compensated by increased relative concentrations of hydroxycinnamic acids and flavonols.

Ascorbate pool, sugars and organic acids in black currant (Ribes nigrum L.) berries are strongly influenced by genotype and post-flowering temperature

BACKGROUND

Marked effects of the climatic environment on fruit chemical composition have often been demonstrated in field experiments. However, complex covariations of several climatic factors in the natural environment complicate the interpretation of such experiments and the identification of the causal factors. This can be better achieved in a phytotron where the various climatic factors can be varied systematically. Therefore, we grew four black currant cultivars of contrasting origin in a phytotron under controlled post-flowering temperature and photoperiod conditions and analysed the berries for their ascorbic acid, sugar and organic acid contents.

RESULTS

The analyses revealed significant effects of genotype on all investigated compounds. Particularly large cultivar differences were observed in the concentrations of l-ascorbic acid (AA) and sucrose. The concentrations of both AA and dehydroascorbic acid (DHAA), as well as the concentrations of all major sugars, decreased consistently with an increasing temperature over the temperature range 12-24 °C. Fructose and glucose were the predominant sugars with concentrations several fold higher than that for sucrose. AA was the main contributor to the total ascorbate pool in black currant berries. The AA/DHAA ratio varied from 5.6 to 10.3 among the studied cultivars. The concentration of citric acid, which was the predominant organic acid in black currant berries, increased with an increasing temperature, whereas the opposite trend was observed for malic and shikimic acid. Quninic acid was always present at relatively low concentrations. By contrast, photoperiod had no significant effect on berry content of any of the investigated compounds.

CONCLUSION

It is concluded that the post-flowering temperature has marked effects on the concentration of important chemical compounds responsible for taste and nutritional value of black currant berries, whereas photoperiod has no such effect in the studied cultivars. © 2016 Society of Chemical Industry.

Conservation genetics of two island endemic Ribes spp. (Grossulariaceae) of Sardinia: survival or extinction?

Measuring levels of population genetic diversity is an important step for assessing the conservation status of rare or endangered plant species and implementing appropriate conservation strategies. Populations of Ribes multiflorum subsp. sandalioticum and R. sardoum, two endangered endemic species from Sardinia, representing the whole genus on the island, were investigated using ISSR and SSR markers to determine levels and structure of genetic variability in their natural populations. Results indicated medium to low genetic diversity at the population level: Nei's gene diversity for ISSR markers ranged from 0.0840 to 0.1316; the expected heterozygosity (HE ) for SSR ranged from 0.4281 to 0.7012. In addition, only one remnant population of R. sardoum showed a high level of inbreeding, in accordance with its very small size. Regarding the structure of the six R. sandalioticum populations, both principal coordinates analysis (PCoA) and STRUCTURE analysis of ISSR and SSR data highlighted low population structure, although two populations appeared to be clearly distinct from the others. The genetic pattern of the two taxa associated with their different ecological positions indicated resilience of R. sandalioticum populations in fresh and humid habitats and uncertain future resistance for the residual R. sardoum population in xeric calcareous stands. Hence, this study highlights the importance of an integrated conservation approach (genetic plus in situ and ex situ conservation studies/measures) for activating management programmes in these endemic and threatened taxa that can be considered as crop wild relatives of cultivated Ribes species.

Berry antioxidants: small fruits providing large benefits

Small berry fruits are consumed because of their attractive colour and special taste, and are considered one of the richest sources of natural antioxidants. Their consumption has been linked to the prevention of some chronic and degenerative diseases. The term 'berry fruits' encompasses the so-called 'soft fruits', primarily strawberry, currants, gooseberry, blackberry, raspberry, blueberry and cranberry. The objective of this review is to highlight the nutraceutical value of berries and to summarize the factors affecting berry fruit antioxidants. Particular attention is given to postharvest and processing operation factors that may affect fruit phytochemical content. The structure-antioxidant relationships for phenolic compounds - the main group of antioxidants in this fruit group - are presented and major areas for future research are identified.

Analysis and sensory evaluation of jostaberry (Ribes x nidigrolaria Bauer) volatiles

Volatiles of jostaberries (Ribes x nidigrolaria Bauer)--a hybrid of black currant (Ribes nigrum L.) and gooseberry (Ribes uva-crispa L.)--were isolated via vacuum headspace extraction and analyzed by capillary gas chromatographic methods for the first time. (E)-Hex-2-enal, (E)-hex-2-en-1-ol, (Z)-hex-3-enal, (Z)-hex-3-en-1-ol, methyl butanoate, ethyl butanoate, 2-methylbut-3-en-2-ol, and 1,8-cineol turned out to be the most dominant volatiles. The variability of the volatile profile was shown by the analysis of jostaberries harvested from different locations in Southern Germany and in different years. In addition to ripe jostaberries, underripe berries were also investigated and changes in the volatile profile were followed during the ripening process. By using sensory analysis, key aroma compounds were elucidated. An aroma model prepared by mixing most odor active compounds ((Z)-hex-3-enal, 1,8-cineol, ethyl butanoate, (E)-hex-2-enal, (E)-hex-3-enal, hexanal, pent-1-en-3-one, methyl butanoate, ethyl hexanoate, and oct-1-en-3-one) in their naturally occurring concentrations showed an overall aroma very similar to that of fresh jostaberries.

Anthocyanins profile, total phenolics and antioxidant activity of black currant ethanolic extracts as influenced by genotype and ethanol concentration

Ethanolic extracts prepared from the fruits of three cultivars of black currant ('Record', 'Blackdown' and 'Ronix') macerated in three concentrations (40%, 60% and 96%) of aqueous ethanol were investigated for their anthocyanins profile, total phenolics and antioxidant activity. Nine individual anthocyanins were detected and quantified by using HPLC-MS in ethanolic extracts of black currants, i.e. delphinidin 3-glucoside, delphinidin 3-rutinoside, cyanidin 3-glucoside, cyanidin 3-rutinoside, petunidin 3-rutinoside, pelargonidin 3-rutinoside, peonidin 3-rutinoside, petunidin 3-(6-coumaroyl)-glucoside and cyanidin 3-(6-coumaroyl)-glucoside. The antioxidant activity of the alcoholic extracts was investigated by the 2,2'-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging method while the total phenolic content was determined by using the Folin-Ciocalteu assay. The highest anthocyanins content was found in the extracts made in 60% ethanol while total phenolics content was highest at 96% ethanol concentration. The extraction yield of individual anthocyanins was differently influenced by the rise of the ethanolic concentration. Maximum extraction yield of most individual anthocyanins was reached at 60% ethanol concentration except the 3-(6-coumaroyl)-glucoside of cyanidin and petunidin whose maximum extraction occurred at 96% ethanol concentration.

Phenolics, antioxidative activity and characterization of anthocyanins in berries of blackcurrant interspecific hybrids

The interest in phenols and anthocyanins has increased due to their antioxidant properties and to their potential usage as dietary antioxidants in human nutrition. Total phenols and anthocyanin content, composition and stability in berry extracts of blackcurrant interspecific hybrids, and antioxidative activity of extracts was evaluated. Berries of interspecific hybrids accumulated 530 to 614 mg 100 g(-1) FW of total phenolic compounds, while 621 mg 100 g(-1) FW of phenolics was established in berries of control Ribes nigrum cultivar 'Ben Tirran'. 'Ben Tirran' berries accumulated 444 mg 100 g(-1) FW of anthocyanins and higher amount was identified in berries of interspecific hybrids No. 11-13 (R. nigrum × R. petraeum) and No. 57 (R. nigrum × R. aureum), 522 and 498 mg100 g(-1) FW respectively. Berry extracts of hybrid No. 11-13 distinguished by the highest antioxidative activity (80%) and it was higher than antioxidant activity of 'Ben Tirran' (70%). Antioxidative activity of all tested berry extracts (70-80%) was twice higher compared to synthetic antioxidant BHT (39%). However correlation between phenolics or total anthocyanin content and antioxidative activity degree was not established. Amount of cyanidin 3-O-glucoside and cyanidin 3-O-rutinoside in berries of hybrids No. 57, No. 11-13 and No. 8 ((R. nigrum × R. americanum) × (R. nigrum × R. americanum)) was higher than in berries of 'Ben Tirran'. It was established that cyanidins are more stable anthocyanins in all studied temperature and irradiation conditions. Therefore interspecific hybrids No. 57 and No. 11-13 were the most agronomically valuable hybrids.

An approach to the determination of winter chill requirements for different Ribes cultivars

Winter chilling is critical for flowering and fruiting of many temperate fruits, with evidence that blackcurrant (Ribes nigrum L.) cropping has been adversely affected by warm winters. Accurate models of chill accumulation in blackcurrant are required so that breeding strategies can be formulated for the generation of new cultivars with resilience to future climates. Existing models for chill accumulation have largely been derived from statistical correlation; here we report the derivation of improved models for blackcurrant using controlled environment treatments. Hardwood cuttings from a diverse set of cultivars were exposed to constant or varying chilling temperatures and the effects on bud break after transfer to a warm, permissive environment evaluated. The impact of different combinations of temperature and chilling periods were described in terms of their overall 'Effectiveness' (E). Clear genotypic differences were found, with excessive chilling often inhibiting bud break. There was a significant interaction between observed chilling response and the period of low temperature exposure. A number of chilling models to explain observed interactions between chilling temperature and time of exposure on bud break were compared; the most effective involved an optimal response to increasing chill accumulation. The effects of varying temperatures during chilling on bud break were complex, with warm temperature breaks substantially inhibiting bud development and cooler temperature breaks tending to enhance bud burst. The relevance of these models to generic studies of endodormancy is discussed, together with their potential application to the development of phenotyping screens for future breeding using diverse blackcurrant germplasm.

Identification, utilisation and mapping of novel transcriptome-based markers from blackcurrant (Ribes nigrum)

BACKGROUND

Deep-level second generation sequencing (2GS) technologies are now being applied to non-model species as a viable and favourable alternative to Sanger sequencing. Large-scale SNP discovery was undertaken in blackcurrant (Ribes nigrum L.) using transcriptome-based 2GS 454 sequencing on the parental genotypes of a reference mapping population, to generate large numbers of novel markers for the construction of a high-density linkage map.

RESULTS

Over 700,000 reads were produced, from which a total of 7,000 SNPs were found. A subset of polymorphic SNPs was selected to develop a 384-SNP OPA assay using the Illumina BeadXpress platform. Additionally, the data enabled identification of 3,000 novel EST-SSRs. The selected SNPs and SSRs were validated across diverse Ribes germplasm, including mapping populations and other selected Ribes species.SNP-based maps were developed from two blackcurrant mapping populations, incorporating 48% and 27% of assayed SNPs respectively. A relatively high proportion of visually monomorphic SNPs were investigated further by quantitative trait mapping of theta score outputs from BeadStudio analysis, and this enabled additional SNPs to be placed on the two maps.

CONCLUSIONS

The use of 2GS technology for the development of markers is superior to previously described methods, in both numbers of markers and biological informativeness of those markers. Whilst the numbers of reads and assembled contigs were comparable to similar sized studies of other non-model species, here a high proportion of novel genes were discovered across a wide range of putative function and localisation. The potential utility of markers developed using the 2GS approach in downstream breeding applications is discussed.

Development and characterization of microsatellite markers for the Cape gooseberry Physalis peruviana

Physalis peruviana, commonly known as Cape gooseberry, is an Andean Solanaceae fruit with high nutritional value and interesting medicinal properties. In the present study we report the development and characterization of microsatellite loci from a P. peruviana commercial Colombian genotype. We identified 932 imperfect and 201 perfect Simple Sequence Repeats (SSR) loci in untranslated regions (UTRs) and 304 imperfect and 83 perfect SSR loci in coding regions from the assembled Physalis peruviana leaf transcriptome. The UTR SSR loci were used for the development of 162 primers for amplification. The efficiency of these primers was tested via PCR in a panel of seven P. peruviana accessions including Colombia, Kenya and Ecuador ecotypes and one closely related species Physalis floridana. We obtained an amplification rate of 83% and a polymorphic rate of 22%. Here we report the first P. peruviana specific microsatellite set, a valuable tool for a wide variety of applications, including functional diversity, conservation and improvement of the species.

Multi-environment QTL mapping in blackcurrant (Ribes nigrum L.) using mixed models

The first genetic linkage map of blackcurrant, published by Brennan et al. (Euphytica 161:19-34, 2008), identified regions where quantitative trait loci (QTLs) for some important traits were located. The analysis was complicated by the fact that the mapping population was found to contain two subgroups, with segregation ratios consistent with these being crossed and selfed offspring. The QTL analysis was based on the trait mean over 3 years and focused on the crossed offspring. Here we proposed a mixed model multi-environment approach for this population. The 3 years are considered as three separate environments, the data from both the selfed and crossed offspring are combined and different residual terms are explored to model the correlation between the years. This permits tests for interactions between the QTLs, the year and the type of offspring (selfed or crossed). This is applied to re-analyse two important traits, anthocyanin concentration and budbreak. Several additional QTLs were identified, some affecting the trait in both the selfed and crossed offspring, others in just one.

Candidate genes associated with bud dormancy release in blackcurrant (Ribes nigrum L.)

BACKGROUND

The detrimental effects of mild winter temperatures on the consistency of cropping of blackcurrant (Ribes nigrum L.) in parts of Europe have led to increasing interest in the genetic control of dormancy release in this species. This study examined patterns of gene expression in leaf buds of blackcurrant to identify key differential changes in these profiles around the time of budbreak.

RESULTS

Using leaf bud tissue of blackcurrant, a cDNA library was generated as a source of blackcurrant ESTs for construction of a custom microarray, which was used to identify differential gene expression during dormancy release. Gene activity was lowest in early stages of dormancy, increasing to reach a maximum around the time of budbreak. Genes with significantly changing expression profiles were clustered and evidence is provided for the transient activity of genes previously associated with dormancy processes in other species. Expression profiling identified candidate genes which were mapped onto a blackcurrant genetic linkage map containing budbreak-related QTL. Three genes, which putatively encode calmodulin-binding protein, beta tubulin and acetyl CoA carboxylase respectively, were found to co-localise with budbreak QTL.

CONCLUSIONS

This study provides insight into the genetic control of dormancy transition in blackcurrant, identifying key changes in gene expression around budbreak. Genetic mapping of ESTs enabled the identification of genes which co-localise with previously-characterised blackcurrant QTL, and it is concluded that these genes have probable roles in release of dormancy and can therefore provide a basis for the development of genetic markers for future breeding deployment.

Identification and functional analysis of the genes encoding Delta6-desaturase from Ribes nigrum

Gamma-linolenic acid (gamma-linolenic acid, GLA; C18:3 Delta(6, 9, 12)) belongs to the omega-6 family and exists primarily in several plant oils, such as evening primrose oil, blackcurrant oil, and borage oil. Delta(6)-desaturase is a key enzyme involved in the synthesis of GLA. There have been no previous reports on the genes encoding Delta(6)-desaturase in blackcurrant (Ribes nigrum L.). In this research, five nearly identical copies of Delta(6)-desaturase gene-like sequences, named RnD8A, RnD8B, RnD6C, RnD6D, and RnD6E, were isolated from blackcurrant. Heterologous expression in Saccharomyces cerevisiae and/or Arabidopsis thaliana confirmed that RnD6C/D/E were Delta(6)-desaturases that could use both alpha-linolenic acids (ALA; C18:3 Delta(9,12,15)) and linoleic acid (LA; C18:2 Delta(9,12)) precursors in vivo, whereas RnD8A/B were Delta(8)-sphingolipid desaturases. Expression of GFP tagged with RnD6C/D/E showed that blackcurrant Delta(6)-desaturases were located in the mitochondrion (MIT) in yeast and the endoplasmic reticulum (ER) in tobacco. GC-MS results showed that blackcurrant accumulated GLA and octadecatetraenoic acids (OTA; C18:4 Delta(6,9,12,15)) mainly in seeds and a little in other organs and tissues. RT-PCR results showed that RnD6C and RnD6E were expressed in all the tissues at a low level, whereas RnD6D was expressed at a high level only in seeds, leading to the accumulation of GLA and OTA in seeds. This research provides new insights to our understanding of GLA synthesis and accumulation in plants and the evolutionary relationship of this class of desaturases, and new clues as to the amino acid determinants which define precise enzyme activity.

Detection of 8-hydroxy-2-deoxyguanosine as a marker of oxidative damage in DNA and germplasm exposed to cryogenic treatments

An HPLC method has been optimised to measure 8-hydroxy-2-deoxyguanosine (8OHdG) in DNA and germplasm with the objective of using the adduct as a marker of cryostorage stability. The encapsulation-dehydration cryopreservation protocol was adapted as a model system for assessing the formation of 8OHdG from alginate-encapsulated DNA of calf thymus (CT) and currant species (Ribes) exposed to temperatures of -20 and -196 degree C. The presence of H2O2 exacerbated the formation of 8OHdG in encapsulated CT and Ribes DNA. Production of the oxidized adduct was lower in the plant system. A reduction in residual water following osmotic dehydration and evaporative desiccation was associated with reduced adduct formation in encapsulated DNA. No significant differences in 8OHdG adduct formation were observed in plants regenerated from cryopreserved Ribes meristems derived from genotypes known to have differential tolerance to cryopreservation.

Cryopreservation induces temporal DNA methylation epigenetic changes and differential transcriptional activity in Ribes germplasm

The physiological and molecular mechanisms associated with acclimation and survival have been examined in four Ribes genotypes displaying differential cryotolerance. Changes in DNA methylation, nucleic acid and nucleoside composition were determined during acclimation and recovery of in vitro shoot-meristems from cryopreservation. DNA methylation was induced in the tolerant genotype, while demethylation was evident in sensitive genotypes. This response initially occurred during sucrose simulated acclimation, with progressive changes as shoots recovered from successive stages of the encapsulation-dehydration protocol. These methylation patterns existed in the initial vegetative cycle but regressed to control values following subculture, indicating the changes in DNA methylation to be a reversible epigenetic mechanism. RNA levels indicating transcriptional activity during the acclimation of nodal tissue are inversely linked to methylation changes, where activity appears to be up-regulated in the cryosensitive genotypes. Conversely, cryopreserved shoots show increased levels of both RNA and DNA methylation in the cryotolerant genotypes. Other nucleosides show post-transcriptional activity corresponds with tolerance during acclimation and cryopreservation. These observations connect physiological attributes to differential molecular changes in Ribes, the implications of which are discussed in relation to cryopreservation-induced apoptosis and genetic stability.

The development of a PCR-based marker linked to resistance to the blackcurrant gall mite (Cecidophyopsis ribis Acari: Eriophyidae)

Gall mite (Cecidophyopsis ribis) is the most serious pest of blackcurrant (Ribes nigrum L.), causing the damaging condition known as 'big bud' and also transmitting blackcurrant reversion virus (BRV) within and between plantations. The identification of resistant germplasm is at present a time-consuming and expensive process, dependent on field infestation plots. Resistance based on gene Ce introgressed from gooseberry has been used in UK breeding programmes for blackcurrant. Using a bulked segregant analysis, 90 AFLP primer combinations were screened and a linkage map constructed around the resistance locus controlled by Ce. Sixteen of the primer combinations produced a fragment in the resistant bulked progeny and the gall mite-resistant parent, but not in the susceptible bulked progeny and parent; subsequent testing on individual progeny identified an AFLP fragment closely linked to gall mite resistance. This fragment, designated E41M88-280, was converted to a PCR-based marker based on sequence-specific primers, amplifying only in resistant individuals. Validation of this marker across a range of susceptible and resistant blackcurrant germplasm with different genetic backgrounds confirmed its reliability in the identification of mite-resistant germplasm containing gene Ce. The conversion of an AFLP fragment to a sequence-based PCR marker simplifies its application and therefore increases its utility for selection of mite-resistant germplasm in high-throughput breeding programmes for blackcurrant.

Biochemical profiling and chemometric analysis of seventeen UK-grown black currant cultivars

Black currant fruits are recognized as being an important dietary source of health-related compounds, such as anthocyanins and ascorbic acid. In the present study, the biochemical composition (viz., nonstructural carbohydrates, individual anthocyanins, total anthocyanins, total phenolics, and organic acids, including ascorbic acid) from 17 UK-grown black currant cultivars was analyzed. Berry composition was significantly affected by genotype. Nonstructural carbohydrates ranged from 85.09 to 179.92 mg g(-1) on a fresh weight (FW) basis, while concentration for organic acids ranged from 36.56 to 73.35 mg g(-1) FW. Relative concentrations of cyanidin 3-glucoside, cyanidin 3-rutinoside, delphinidin 3-glucoside and delphinidin 3-rutinoside were 3.1-7.9%, 35.4-47.0%, 7.6-12.5% and 36.9-50.9%, respectively. Differences in the biochemical profile among cultivars were emphasized by principal component analysis (PCA) and hierarchical cluster analysis (HCA). PCA was able to discriminate between cultivars, especially on the basis of health-related compounds. Initial exploration revealed that individual anthocyanins, total phenolics, and ascorbic acid could be used to characterize and classify different cultivars. HCA showed that the biochemical composition of the different cultivars was related to parentage information.

Fatty acid content and juice characteristics in black currant (Ribes nigrum L.) genotypes

The fatty acid compositions of seeds from 29 black currant genotypes were determined using a rapid small-scale procedure. There was interest in alpha-linolenic, stearidonic, and, especially, gamma-linolenic acid (GLA) contents, and most samples showed values between 11.1 and 18.7%, between 2.5 and 4.5%, and between 11.6 and 17.4%, respectively. However, six genotypes exhibited gamma-linolenic contents >18%, and values >20% were recorded in four of these genotypes. The fatty acid contents of the six genotypes were also analyzed by using a conventional procedure, and only slight differences in fatty acid composition were found between the two methods. Although GLA content was not strongly correlated with juice parameters, some genotypes had both high GLA contents and desirable juice characteristics. The results obtained provide evidence that it is possible to select for GLA contents without negatively affecting juice quality, and both aspects can be combined in a single cultivar, thereby increasing the added value of the whole fruit.

Fruit plant germplasm characterisation using molecular markers generated in RAPD and ISSR-PCR

The genotypes of the strawberry (Fragaria x ananassa), apple (Malus domestica) and Ribes species (R. nigrum, R. rubrum and R. glossularia), maintained in our Institute's collection and used in breeding programs, were screened for DNA markers. Twenty primers for RAPD (among 60 tested) and seven for ISSR (among 10 tested) were chosen as creating polymorphic DNA bands differentiating the investigated genotypes. Based on those identity markers, the genetic distance between genotypes was determined, and their relatedness was estimated. In many cases, both RAPD- and ISSR-based genetic similarity confirmed relatedness connected with biological origin and with the place where the cultivar was developed. However, some diversity connected with the technique used for molecular marker generation was observed. Generally, the similarity values based on ISSR data were higher than those based on RAPD. Parallel study using two data sets seems to enable a reduction in the number of potential mistakes connected with each method's, technical limitations and ensures more precise relatedness determination.