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Rubus idaeus L. (red raspberry), is a perennial woody plant species of the Rosaceae family that is widely cultivated in the temperate regions of world and is thus an economically important soft fruit species. It is prized for its flavour and aroma, as well as a high content of healthful compounds such as vitamins and antioxidants. Breeding programs exist globally for red raspberry, but variety development is a long and challenging process. Genomic and molecular tools for red raspberry are valuable resources for breeding. Here, a chromosome-length genome sequence assembly and related gene predictions for the red raspberry cultivar ‘Anitra’ are presented, comprising PacBio long read sequencing scaffolded using Hi-C sequence data. The assembled genome sequence totalled 291.7 Mbp, with 247.5 Mbp (84.8%) incorporated into seven sequencing scaffolds with an average length of 35.4 Mbp. A total of 39,448 protein-coding genes were predicted, 75% of which were functionally annotated. The seven chromosome scaffolds were anchored to a previously published genetic linkage map with a high degree of synteny and comparisons to genomes of closely related species within the Rosoideae revealed chromosome-scale rearrangements that have occurred over relatively short evolutionary periods. A chromosome-level genomic sequence of R. idaeus will be a valuable resource for the knowledge of its genome structure and function in red raspberry and will be a useful and important resource for researchers and plant breeders.

Red raspberry ( Rubus idaeus L.) is an economically valuable soft-fruit species with a relatively small (~300 Mb) but highly heterozygous diploid (2 n = 2 x = 14) genome. Chromosome-scale genome sequences are a vital tool in unravelling the genetic complexity controlling traits of interest in crop plants such as red raspberry, as well as for functional genomics, evolutionary studies, and pan-genomics diversity studies. In this study, we developed genome sequences of a primocane fruiting variety (‘Autumn Bliss’) and a floricane variety (‘Malling Jewel’). The use of long-read Oxford Nanopore Technologies sequencing data yielded long read lengths that permitted well resolved genome sequences for the two cultivars to be assembled. The de novo assemblies of ‘Malling Jewel’ and ‘Autumn Bliss’ contained 79 and 136 contigs respectively, and 263.0 Mb of the ‘Autumn Bliss’ and 265.5 Mb of the ‘Malling Jewel’ assembly could be anchored unambiguously to a previously published red raspberry genome sequence of the cultivar ‘Anitra’. Single copy ortholog analysis (BUSCO) revealed high levels of completeness in both genomes sequenced, with 97.4% of sequences identified in ‘Autumn Bliss’ and 97.7% in ‘Malling Jewel’. The density of repetitive sequence contained in the ‘Autumn Bliss’ and ‘Malling Jewel’ assemblies was significantly higher than in the previously published assembly and centromeric and telomeric regions were identified in both assemblies. A total of 42,823 protein coding regions were identified in the ‘Autumn Bliss’ assembly, whilst 43,027 were identified in the ‘Malling Jewel’ assembly. These chromosome-scale genome sequences represent an excellent genomics resource for red raspberry, particularly around the highly repetitive centromeric and telomeric regions of the genome that are less complete in the previously published ‘Anitra’ genome sequence.

Anthocyanins are phenolic compounds with important technological applications due to its bioactive and color properties. In this study, pomaces from four red berries (blueberries, red raspberries, red currants and blackberries) have been analyzed as sources of anthocyanins. Anthocyanins were determined by high-performance liquid chromatography/mass spectrometry, total phenolic content (TPC) by Folin–Ciocalteu method, antioxidant activity by ABTS assay, and color by tristimulus colorimetry. A total of 15 anthocyanins were identified and quantified in the different pomaces from red berries. Pomaces exhibited different qualitative and quantitative anthocyanin profile and antioxidant activity, depending on type of red berry. The highest amounts of anthocyanins were found in blueberries (1188 mg/100 g); however, red currant pomaces exhibited the highest TPC (3447 mg/100 g) and AA (61 mmol/100 g). Color of extracts was different depending on individual and total content of anthocyanins. Results indicate that these berry pomaces are a natural source of antioxidants and pigments, and they may be useful for industrial purposes. Therefore, the exploitation of these pomaces, such as possible byproducts for their reuse in the food, cosmetics, and drug industries, could be of great interest, considering either the whole pomaces or its individual components.

Background Red raspberry ( Rubus idaeus L.) is a renowned fruit plant with significant medicinal value. Its nuclear genome and chloroplast genome (plastome) have been reported, while there is a lack of genetic information on its mitogenome. We sequenced and assembled the complete mitogenome of R. idaeus , and conducted a series of genetic investigations comparing it with the nuclear and chloroplast genomes, so as to better gain a comprehensive understanding of the species’ genetic background. Results The mitogenome is represented by one circular chromosome of 438,947 bp. Twenty-four core genes, nine variable genes, 26 tRNAs, and three rRNAs were annotated. A total of 52 SSRs and 38 tandem repeat sequences were identified. 533 pairs of dispersed repeats were detected, among which three pairs were found to have mediated the homologous recombination, resulting in one major conformation and seven minor conformations. Furthermore, 52 homologous sequences between the mitogenome and plastome were identified, including six complete protein-coding genes and 12 tRNA genes. We also detected 828 homologous fragments between the nuclear genome and mitogenome, including one trn M-CAU gene. Conclusions In this study, we presented the mitogenome of R. idaeus for the first time based on data obtained from Illumina and Oxford Nanopore sequencing platforms. Key characteristics of the mitogenome were examined, including its gene composition, repetitive elements, and homologous DNA fragments. Additionally, we identified multiple recombination events in the mitogenome mediated by repetitive sequences The high-quality and well-annotated mitogenome for the known fruit red raspberry will provide essential genetic information for species classification, evolution analysis, and even genetic improvement in Rubus in the future.

The estimated global production of raspberry from year 2016 to 2020 averaged 846,515 tons. The most common cultivated Rubus spp. is European red raspberry (Rubus idaeus L. subsp. idaeus). Often cultivated for its high nutritional value, the red raspberry (Rubus idaeus) is susceptible to multiple viruses that lead to yield loss. These viruses are transmitted through different mechanisms, of which one is invertebrate vectors. Aphids and nematodes are known to be vectors of specific raspberry viruses. However, there are still other potential raspberry virus vectors that are not well-studied. This review aimed to provide an overview of studies related to this topic. All the known invertebrates feeding on raspberry were summarized. Eight species of aphids and seven species of plant-parasitic nematodes were the only proven raspberry virus vectors. In addition, the eriophyid mite, Phyllocoptes gracilis, has been suggested as the natural vector of raspberry leaf blotch virus based on the current available evidence. Interactions between vector and non-vector herbivore may promote the spread of raspberry viruses. As a conclusion, there are still multiple aspects of this topic that require further studies to get a better understanding of the interactions among the viral pathogens, invertebrate vectors, and non-vectors in the raspberry agroecosystem. Eventually, this will assist in development of better pest management strategies.

Background Red raspberry fruit color is a key driver of consumer preference and a major target of breeding programs worldwide. Screening for fruit color typically involves the determination of anthocyanin content and/or the assessment of color through a colorimeter. However, both procedures are time-consuming when the analyses involve hundreds or thousands of samples. The objectives of this study were to develop a high-throughput method for red raspberry puree color measurement and to test the correlations between color parameters and total anthocyanin content. Color coordinates were collected with a colorimeter on 126 puree samples contained in Petri dishes and with the Tomato Analyzer Color Test (TACT) module to assess the same samples prepared in Petri dishes and in 96-well plates. An additional 425 samples were analyzed using only 96-well plates. Total anthocyanins were extracted from all 551 samples. Results Regression models for L*, a*, b* measured with the colorimeter and TACT using Petri dishes were all significant ( p  < 0.001), but very consistent only for L* ( R 2  = 0.94). Significant ( p  < 0.001) and very consistent regressions ( R 2  = 0.94 for L* and b*, R 2  = 0.93 for a*) were obtained for color parameters measured with TACT using Petri dishes and TACT using plates. Of the color parameters measured with the colorimeter, only L*, a*/b*, and hue significantly correlated with total anthocyanins ( p  < 0.05), but, except for L* ( R = − 0.79), the correlations were weak ( R = − 0.23 for a*/b* and R  = 0.22 for hue). Conversely, all correlations with total anthocyanins and color parameters measured with TACT were significant ( p  < 0.001) and moderately strong (e.g., R = − 0.69 for L* and R  = 0.55 for a*/b*). These values were indicative of darker colors as total anthocyanin content increased. Conclusions While the colorimeter and TACT-based methods were not fully interchangeable, TACT better captured color differences among raspberry genotypes than the colorimeter. The correlations between color parameters measured with TACT and total anthocyanins were not strong enough to develop prediction models, yet the use of TACT with 96-well plates instead of Petri dishes would enable the high-throughput measurement of red raspberry puree color.

The time delay in receiving conventional tissue nutrient analysis results caused red raspberry ( Rubus idaeus L.) growers to be interested in rapid sap tests to provide real-time results to guide immediate nutrient management practices. However, sap analysis has never been conducted in raspberry. The present work aimed to evaluate the relationship of petiole sap nitrate (NO 3 – ), potassium (K + ), and calcium (Ca 2+ ) concentrations measured using compact ion meters and leaf tissue total nitrogen (TN), potassium (K), and calcium (Ca) concentrations measured using conventional tissue nutrient analysis. The relationship of petiole sap NO 3 – and leaf tissue TN concentrations with plant growth and production variables was also explored. Fertilizer treatments of urea were surface applied to raised beds of established “Meeker” floricane red raspberry plots at control, low, medium, and high rates (0, 34, 67, and 101 kg N ha –1 , respectively) in 2019 and 2020. The experiment was arranged in a randomized complete block design with three replications. Whole leaves were collected from representative primocanes in mid- and late- July and August 2019 and 2020 (i.e., four sampling time points per year). At each sampling time point, a subsample of leaves was used for petiole sap analyses of NO 3 – , K + , and Ca 2+ concentrations using compact ion meters, and conventional tissue testing of leaf tissue TN, K, and Ca concentrations, respectively. There were no interactions between N fertilizer rate and year nor between N fertilizer rate and sampling time. No significant differences were found due to N fertilizer rate for petiole sap NO 3 – , K + , Ca 2+ nor leaf tissue TN, K, Ca concentrations. However, significant year and sampling time effects occurred in measured petiole sap and leaf tissue nutrient concentrations. Overall, the correlations between petiole sap NO 3 – and leaf tissue TN, petiole sap Ca 2+ and leaf tissue Ca, petiole sap K + and leaf tissue K concentrations were non-strong and inconsistent. Future research is warranted as the interpretation of correlations between raspberry petiole sap and leaf tissue nutrient concentrations were inconclusive.

Red raspberry (Rubus idaeus L.) represents a relevant crop which production has largely increased worldwide during the last decade. Cane blight is one of the most common diseases of red raspberry and it can produce considerable losses. During 2019–2021, surveys were conducted in red raspberry orchards in Cuneo province, Northern Italy, to investigate the etiology and pathogen diversity in association with cane blight. Eleven isolates were collected from symptomatic plants of the cultivars ‘Diamond Jubilee’ and ‘Grandeur’, and were identified through multi-locus phylogenies and morphological features. Three fungal species were identified: Paraconiothyrium fuckelii, Diaporthe eres and Neocosmospora parceramosa. Four different genomic regions were included in the molecular analyses: ITS, tef1, tub2 and rpb2. The species pathogenicity was confirmed and P. fuckelii was revealed as the most aggressive. This study provides an insight into raspberry cane blight in Italy and the genomic loci sequencing lay the basis to develop specific diagnostic protocols to monitor the presence of pathogens and to prevent disease spread, adopting effective integrated control strategies.

ObjectiveThe objective of this study was to investigate the genetic control of polyphenol accumulation in red raspberry (Rubus idaeus L).MethodsThe levels of total anthocyanins and 37 individual polyphenol metabolites were measured over three years in a raspberry biparental mapping population. Quantitative trait loci (QTLs) for these traits were mapped onto a high-density SNP linkage map.ResultsAt least one QTL was detected for each trait, with good consistency among the years. On four linkage groups (LG), there were major QTLs affecting several metabolites. On LG1, a QTL had large effects on anthocyanins and flavonols containing a rutinoside or rhamnose group. On LG4, a QTL had large effects on several flavonols and on LG5 and LG6 QTLs had large effects on ellagic acid derivatives. Smaller QTLs were found on LG2 and LG3.ConclusionThe identification of robust QTLs for key polyphenols in raspberry provides great potential for marker-assisted breeding for improved levels of potentially health beneficial components.

The anti-oxidative phenolic compounds in plant extracts possess multiple pharmacological functions. However, the phenolic characterization and in vitro bio-activities in various parts of raspberry (Rubus idaeus L.) have not been investigated systematically. In the present study, the phenolic profiles of leaves (LE), fruit pulp (FPE), and seed extracts (SE) in raspberry were analyzed by HR-HPLC-ESI-qTOF-MS/MS method, and their antioxidant activities and digestive enzymes inhibitory abilities were also investigated. The molecular docking analysis was used to delineate their inhibition mechanisms toward type II diabetes related digestive enzymes. Regardless of LE, FPE, or SE, 50% methanol was the best solvent for extracting high contents of phenolic compounds, followed by 50% ethanol and 100% methanol. The LE of raspberry displayed the highest total phenolic content (TPC) and total flavonoid content (TFC). A total of nineteen phenolic compounds were identified. The quantitative results showed that gallic acid, ellagic acid, and procyanidin C3 were the major constituents in the three extracts. The various parts extracts of raspberry all exhibited the strong antioxidant activities, especially for LE. Moreover, the powerful inhibitory effects of the three extracts against digestive enzymes (α-glucosidase and α-amylase) were observed. The major phenolic compounds of the three extracts also showed good inhibitory activities of digestive enzyme in a dose-dependent manner. The underlying inhibitory mechanisms of the main phenolic compounds against digestive enzymes were clarified by molecular docking analysis. The present study demonstrated that the various parts of raspberry had strong antioxidant activities and inhibitory effects on digestive enzymes, and can potentially prevent oxidative damage or diabetes-related problems.