Browse
Submit Data
Databases
API
Help

Dataset Information

5 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

An Effective Method of Ribes spp. Inoculation with Blackcurrant Reversion Virus under In Vitro Conditions.

ABSTRACT: Blackcurrant reversion virus (BRV) is the most destructive currant-infecting and mite-transmitted pathogen from the genus Nepovirus. In this work, BRV transmission in the system Ribes ex vitro-Ribes in vitro was applied for the first time. Triple infection of BRV identified in blackcurrant cv. Gojai was used for phylogenetic analysis and inoculation assay. Transmission of BRV was successful due to its stability in the inoculum for up to 8 days at 4 °C; all BRV isolates were infectious. Our suggested inoculation method through roots was applied in six Ribes spp. genotypes with 100.0% reliability, and the expression levels of defence-related gene PR1 to biotic stress was observed. The prevalence of the virus in microshoots after 2-14 days post-inoculation (dpi) was established by PCR. In resistant genotypes, the BRV was identified up to 8 dpi; meanwhile, infection remained constant in susceptible genotypes. We established that BRV transmission under controlled conditions depends on the inoculum quality, post-inoculation cultivation temperature, and host-plant susceptibility to pathogen. This in vitro inoculation method opens possibilities to reveal the resistance mechanisms or response pathways to BRV and can be used for the selection of resistant Ribes spp. in breeding programs.

SUBMITTER: Juskyte AD

PROVIDER: S-EPMC9269295 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Analysis of R Genes Related to Blackcurrant Reversion Virus Resistance in the Comparative Transcriptome of Ribes nigrum cv. Aldoniai

Project description:Blackcurrant reversion virus (BRV) is the most destructive mite-transmitted pathogen in blackcurrants. The understanding of the resistance to BRV is limited, hindering and delaying the selection process. To identify the resistance (R) gene for BRV resistance, a gene expression analysis based on de novo blackcurrant cv. Aldoniai comparative transcriptome analysis (mock- and BRV-inoculated samples at 2 and 4 days post-inoculation (dpi)) was performed. In this study, 111 annotated clusters associated with pathogenesis according to conservative R gene domains were identified. In virus-infected samples, only Cluster-12591.33361 showed significant expression at 4 dpi. The expression profiles of this cluster were significantly associated with the presence of BRV particles in plant tissues, making it a putative R gene in the dominant resistance strategy in the BRV–Ribes nigrum interaction. The newly identified gene R.nigrum_R belongs to the CC-NBS-LRR class and has 63.9% identity with RPM1 in Populus spp. This study provides new insights on dominant putative R genes related to resistance to BRV in R. nigrum, which could aid targeted research and genetic improvement in breeding programs of blackcurrants.

| S-EPMC9692259 | biostudies-literature

Compositional Diversity among Blackcurrant ( Ribes nigrum) Cultivars Originating from European Countries.

Project description:Berries representing 21 cultivars of blackcurrant were analyzed using liquid chromatographic, gas chromatographic, and mass spectrometric methods coupled with multivariate models. This study pinpointed compositional variation among cultivars of different origins cultivated in the same location during two seasons. The chemical profiles of blackcurrants varied significantly among cultivars and growing years. The key differences among cultivars of Scottish, Lithuanian, and Finnish origins were in the contents of phenolic acids (23 vs 16 vs 19 mg/100 g on average, respectively), mainly as 5- O-caffeoylquinic acid, 4- O-coumaroylglucose, ( E)-coumaroyloxymethylene-glucopyranosyloxy-( Z)-butenenitrile, and 1- O-feruloylglucose. The Scottish cultivars were grouped on the basis of the 3- O-glycosides of delphinidin and cyanidin, as were the Lithuanian cultivars. Among the Finnish samples, the content of myricetin 3- O-glycosides, 4- O-caffeoylglucose, 1- O-coumaroylglucose, and 4- O-coumaroylglucose were significantly different between the two green-fruited cultivars and the black-fruited cultivars. The samples from the studied years differed in the content of phenolic acid derivatives, quercetin glycosides, monosaccharides, and citric acid.

| S-EPMC6750745 | biostudies-literature

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

Project description: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.

| S-EPMC2956551 | biostudies-literature

Profiles of Volatile Compounds in Blackcurrant ( Ribes nigrum) Cultivars with a Special Focus on the Influence of Growth Latitude and Weather Conditions.

Project description:The volatile profiles of three blackcurrant ( Ribes nigrum L.) cultivars grown in Finland and their responses to growth latitude and weather conditions were studied over an 8 year period by headspace solid-phase microextraction (HS-SPME) followed by gas-chromatographic-mass-spectrometric (GC-MS) analysis. Monoterpene hydrocarbons and oxygenated monoterpenes were the major classes of volatiles. The cultivar 'Melalahti' presented lower contents of volatiles compared with 'Ola' and 'Mortti', which showed very similar compositions. Higher contents of volatiles were found in berries cultivated at the higher latitude (66° 34' N) than in those from the southern location (60° 23' N). Among the meteorological variables, radiation and temperature during the last month before harvest were negatively linked with the volatile content. Storage time had a negative impact on the amount of blackcurrant volatiles.

| S-EPMC6221373 | biostudies-literature

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

Project description: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.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.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.

| S-EPMC3217869 | biostudies-other

Blackcurrant (<i>Ribes nigrum</i>) Extract Prevents Dyslipidemia and Hepatic Steatosis in Ovariectomized Rats.

Project description:Estrogen is involved in lipid metabolism. Menopausal women with low estrogen secretion usually gain weight and develop steatosis associated with abnormal lipid metabolism. A previous study showed that blackcurrant (Ribes nigrum L.) extract (BCE) had phytoestrogen activity. In this study, we examined whether BCE improved lipid metabolism abnormalities and reduced liver steatosis in ovariectomized rats, as a menopausal animal model. Twelve-week-old ovariectomized (OVX) rats were fed a regular diet (Ctrl) or a 3% BCE supplemented diet while sham rats were fed a regular diet for three months. Body weight, visceral fat weight, levels of serum triglycerides, total cholesterol, and LDL cholesterol decreased in the BCE-treated OVX and sham rats, but not in OVX Ctrl rats. The results of hematoxylin and eosin staining revealed that BCE decreased the diameters of adipocytes and the nonalcoholic fatty liver disease activity score. Furthermore, quantitative RTPCR indicated a decreased expression of hepatitis-related genes, such as tumor necrosis factor-?, IL-6, and IL-1? in OVX rats after BCE treatment. This is the first study that reported improvement of lipid metabolism abnormalities in OVX rats by BCE administration. These results suggest that the intake of BCE alleviated dyslipidemia and prevented nonalcoholic steatohepatitis during menopause in this animal model.

| S-EPMC7284623 | biostudies-literature

Hypocholesterolemic Effect of Blackcurrant (Ribes nigrum) Extract in Healthy Female Subjects: A Pilot Study.

Project description:Blackcurrant extract (BCE) ameliorates dyslipidemia in menopausal model animals and in elderly women at a risk of dyslipidemia. However, it is unknown whether the daily intake of BCE can prevent lipid abnormalities in healthy individuals. Lipids are essential for the body, but they also cause arteriosclerosis. In this noncomparative pilot study, we examined the effects of BCE administered for 29 days on serum lipids in young healthy women. Blood samples were collected before and on days 4 and 29 after BCE intake, and 20 lipoprotein fractions in the serum were separated using a gel-permeation high-performance liquid chromatography method to measure the triacylglycerol and cholesterol levels in lipoproteins. There were no effects on lipids on day 4 of BCE intake, but the total cholesterol level decreased on day 29. Furthermore, the levels of total very-low-density lipoprotein (VLDL) cholesterol, small VLDL cholesterol, and large low-density lipoprotein cholesterol were significantly decreased. These results suggest that the daily intake of BCE has a hypocholesterolemic effect in healthy women, and that it is effective in preventing atherosclerosis.

| S-EPMC8272003 | biostudies-literature

Data on free and bound volatile compounds in six Ribes nigrum L. blackcurrant cultivars.

Project description:The data investigated 198 volatile compounds of six currant cultivars grown in China which is analyzed by SPME-GC-MS. Volatile compounds in these currant samples were identified by two methods, comparing retention indices with reference standards and matching mass spectrum in the NST11 library. A synthetic currant matrix prepared according to the currant juice condition were extracted and analyzed using the same extraction procedure as the currant samples. The standard curve was generated for quantification of volatile compounds. For the volatiles without the available standard, the data provided consulting standards that had the same carbon atom or the similar functional structure for quantification. Further interpretation and discussion can be seen in article entitled "Characterization of Free and Bound Volatile Compounds in Six Ribes nigrum L. Blackcurrant Cultivars" (Liu et al., 2018) [1].

| S-EPMC5988502 | biostudies-literature

A new method for the inoculation of <i>Phytophthora palmivora</i> (Butler) into cacao seedlings under greenhouse conditions.

Project description:BackgroundThe black pod disease affects cacao plantations worldwide; it is caused by the oomycete species of the genus Phytophthora. The resistance of cacao plants to the black pod is commonly evaluated by artificial inoculation of the pathogen and the monitoring of the disease symptoms. However, it is difficult to identify resistant plants because the commonly used methods for the inoculation of the pathogens produce inconsistent results. Therefore, this study aimed to develop an efficient and reliable method to evaluate the resistance of Theobroma cacao seedlings to the infection by Phytophthora palmivora.ResultsSeedlings of different cacao genotypes were inoculated with P. palmivora under greenhouse conditions using the previously reported inoculation methods and a newly proposed method, the agar-water solution method. While none of the previously reported methods was effective, the agar-water solution method ensured a 100% seedling infection under greenhouse conditions. The proposed agar-water methodology is fast, simple and reproducible. Furthermore, the evaluation of this method in susceptible (CCN-51) and tolerant (SCA-6) T. cacao genotypes produced the expected contrasting results.ConclusionsThe agar-water solution method presented in this study is an efficient alternative inoculation protocol for the identification of cacao genotypes that are resistant to black pod under greenhouse conditions.

| S-EPMC7437064 | biostudies-literature

An efficient in vitro-inoculation method for Tomato yellow leaf curl virus.

Project description:BackgroundTomato yellow leaf curl virus (TYLCV) is a member of the family Geminiviridae, genus Begomovirus. To test the infectivity of TYLCV in tomato plants, an improved protocol for inoculation of in vitro-cultured tomato plants was developed.ResultsA TYLCV isolate was cloned, sequenced and used to construct a 1.8-mer infectious clone. Three weeks old microshoots of TYLCV-susceptible tomato plants were inoculated with Agrobacterium tumefaciens harboring the infectious clone for the TYLCV isolate. After two weeks, the TYLCV symptoms started to appear on the in vitro-inoculated plants and the symptoms became more severe and pronounced eight weeks post-inoculation. The method was used efficiently to uncover the resistance mechanism against TYLCV in Solanum habrochaites accession LA 1777, a wild tomato known for its high resistance to whitefly and TYLCV.ConclusionsThe reported in vitro-inoculation method can be used to screen tomato genotypes for their responses to TYLCV under controlled conditions and it will be a useful tool for better understanding of the TYLCV biology in tomato plants.

| S-EPMC2874538 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data