Dissecting CVYV resistance in cucumber using bulk segregant analysis and next-generation sequencing
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Illumina HiSeq 2000
ORGANISM(S): Cucumis Sativus Var. Sativus
SUBMITTER: IRTA
PROVIDER: PRJEB34274 | EVA | 2019-11-27
REPOSITORIES: EVA
Dataset's files
Items per page: 5 1 - 5 of 7 |
Similar Datasets
Project description:Anopheles gambiae isofemale families from Tororo, Uganda were assayed for resistance to lambda-cyhalothrin (1.5hr exposure). Resistant families were compared to susceptible families. A portion of each family was exposed to 0.05% lambda-cyhalothrin in order to determine the family phenotype. The families used for the array were of known phenotype but were themselves unexposed.
2013-12-03 | E-MTAB-1874 | biostudies-arrayexpress
Project description:Infectious Pancreatic Necrosis (IPN) is a highly contagious birnavirus disease of farmed salmonid fish, which often causes high levels of morbidity and mortality. A large genetic component underlying resistance to this disease has been previously described for Atlantic salmon (Salmo salar L.), which mediates high mortality rates in some families and zero mortality in others. A global comparison of the gene expression profiles of resistant and susceptible Atlantic salmon fry following challenge with the IPN virus was undertaken. Full sibling salmon fry from two IPNV-resistant and two IPNV-susceptible families were challenged with the virus and sampled at 1 day, 7 days and 20 days post-challenge. Significant viral titre was observed in both resistant and susceptible fish at all timepoints, although generally at higher levels in susceptible fish. Microarray interrogations were performed using a custom-designed, oligonucleotide microarray platform (Agilent) with 44 K probes per slide (Salar_2; Agilent Design ID:025520). The design is lodged with ArrayExpress ( under accession number A-MEXP-2065. Dual-label hybridisations were undertaken, with each experimental sample (Cy3 labelled) being competitively hybridised against a pooled reference control (Cy5 labelled) comprising equimolar amounts from each experimental RNA sample. The interrogations comprised 144 separate hybridisations; 2 genotypes (susceptible, resistant) à 2 families for each genotype à 2 challenge states (control, challenged) à 3 timepoints (1, 7, 20 dpi) à 4 biological replicates for resistant (2 from each of two tanks) and 8 biological replicates for susceptible (4 from each of two tanks). A preliminary analysis suggested evidence for a segregating QTL in both the susceptible families and therefore twice as many offspring were screened. It was later established that the evidence for QTL segregation in one of the families was inconclusive and therefore comparisons were made at the family level only. The analyses took the unbalanced design into account.
2016-04-07 | E-MTAB-4275 | biostudies-arrayexpress
Project description:One of the most economically important grapevine diseases is Downy mildew (DM) caused by the oomycete <i>Plasmopara viticola</i>. A strategy to reduce the use of fungicides to compensate for the high susceptibility of <i>V. vinifera</i> is the selection of grapevine varieties showing pathogen-specific resistance. We applied a metabolomics approach to evaluate the metabolic modulation in mono-locus resistant genotypes carrying one locus associated with <i>P. viticola</i> resistance (<i>Rpv</i>) (BC4- <i>Rpv1</i>, Bianca- <i>Rpv3-1</i>, F12P160- <i>Rpv12</i>, Solaris- <i>Rpv10</i>), as well as in pyramided resistant genotypes carrying more than one <i>Rpv</i> (F12P60- <i>Rpv3-1; Rpv12</i> and F12P127- <i>Rpv3-1, Rpv3-3; Rpv10</i>) taking as a reference the susceptible genotype Pinot Noir. In order to understand if different sources of resistance are associated with different degrees of resistance and, implicitly, with different responses to the pathogen, we considered the most important classes of plant metabolite primary compounds, lipids, phenols and volatile organic compounds at 0, 12, 48, and 96 h post-artificial inoculation (hpi). We identified 264 modulated compounds; among these, 22 metabolites were found accumulated in significant quantities in the resistant cultivars compared to Pinot Noir. In mono-locus genotypes, the highest modulation of the metabolites was noticed at 48 and 96 hpi, except for Solaris, that showed a behavior similar to the pyramided genotypes in which the changes started to occur as early as 12 hpi. Bianca, Solaris and F12P60 showed the highest number of interesting compounds accumulated after the artificial infection and with a putative effect against the pathogen. In contrast, Pinot Noir showed a less effective defense response in containing DM growth.
2021-07-07 | MTBLS2876 | MetaboLights
Project description:Infectious pancreatic necrosis (IPN) is widespread disease with global distribution and highly contagious, which leads to severe economic problems both freshwater and saltwater, particularly in the Atlantic salmon (Salmo salar). In this work we analyzed and evaluated gene expression profiles in resistant and susceptible families associated to S. salar exposed to IPNV in order to understand the defense mechanisms mounted by resistant fish in combating infection. Experimentally, 29 families with known pedigree and variability were infected by immersion with 1x106 PFU/ml of IPNV, and a gamma frailty model analysis based on Kaplan-Meier mortality curves were obtained to identify and classify families as susceptible or resistant. Samples of head kidney tissue were obtained at day 1 and 5 post-infection from susceptible and resistant families and pooled to analyse their expression pattern with realt-ime PCR and one-color salmon-specific oligonucleotide microarray (21K). The microarray results showed clear differences in both families, where resistant fish presented an over-expression of genes associated with endocrine function, and a down-regulation of genes associated principally with tissue differentiation, metabolism protein degradation, cell signaling and immunological process. Moreover qPCR analysis using as target a number of transcripts associated with immunological processes showed the same trend observing a higher expression in susceptible than resistant families, indicating significant differences for CCL-19, CCRM-NM-3c, IL-12, IFN-M-NM-1, and IFN-M-NM-3. The one-color oligonucleotide microarrays included in this study was performed using pooled samples from each families at two different post-infection time condition. In the case of susceptible families were chosen at 1 day post-infection (dpi) the families 5352 (n = 2) and 5469 (n = 2) and at 5 dpi the families 5629 (n = 2) and 5637 (n = 2), whereas in resistant families were selected at 1 dpi the families 5459 (n =3) and 5761 (n =3), and at 5 dpi the families 5463 (n =3) and 5764 (n =3).
2012-09-05 | E-GEOD-40575 | biostudies-arrayexpress
Project description:Infectious pancreatic necrosis (IPN) is widespread disease with global distribution and highly contagious, which leads to severe economic problems both freshwater and saltwater, particularly in the Atlantic salmon (Salmo salar). In this work we analyzed and evaluated gene expression profiles in resistant and susceptible families associated to S. salar exposed to IPNV in order to understand the defense mechanisms mounted by resistant fish in combating infection. Experimentally, 29 families with known pedigree and variability were infected by immersion with 1x106 PFU/ml of IPNV, and a gamma frailty model analysis based on Kaplan-Meier mortality curves were obtained to identify and classify families as susceptible or resistant. Samples of head kidney tissue were obtained at day 1 and 5 post-infection from susceptible and resistant families and pooled to analyse their expression pattern with realt-ime PCR and one-color salmon-specific oligonucleotide microarray (21K). The microarray results showed clear differences in both families, where resistant fish presented an over-expression of genes associated with endocrine function, and a down-regulation of genes associated principally with tissue differentiation, metabolism protein degradation, cell signaling and immunological process. Moreover qPCR analysis using as target a number of transcripts associated with immunological processes showed the same trend observing a higher expression in susceptible than resistant families, indicating significant differences for CCL-19, CCRγc, IL-12, IFN-α, and IFN-γ.
2012-09-05 | GSE40575 | GEO
Project description:Anthelmintic resistance is a major problem in the global fight against parasitic nematodes., Most previous studies have focused on the analysis of potential candidate genes that may have a role in resistance. Here we take a novel approach in the important parasite, Haemonchus contortus, by investigating changes in microRNA expression between resistant and susceptible parasites. The resistant worms included two geographically distinct strains and two lines generated by multiple rounds of backcrossing between susceptible and resistant parents, with ivermectin selection. All four resistant strains showed increased abundance of a single miRNA, hco-miR-9551, compared to the susceptible strain. hco-miR-9551 is enriched in female worms, is likely to be located on the X chromosome and is found only in clade V parasitic nematodes. Approximately 5-10% of the genomes of the resistant parental strains are introgressed into the respective backcrosses, suggesting that hco-miR-9551, or genes regulated by the miRNA, may be genetically linked to a locus that determines resistance. Genes containing predicted binding sites for hco-miR-9551 were identified computationally and refined based on differential expression in a transcriptomic dataset. These findings advance our conceptual understanding of the molecular mechanisms of anthelmintic resistance in H. contortus and indicate that altered miRNA expression may be linked with drug resistance. All samples were carried out using three biological replicates
2016-03-25 | E-GEOD-79542 | biostudies-arrayexpress
Project description:European grapevine cultivars (Vitis vinifera spp.) are highly susceptible to the downy mildew pathogen Plasmopara viticola. Breeding of resistant V. vinifera cultivars is a promising strategy to reduce the impact of disease management. Most cultivars that have been bred for resistance to downy mildew, rely on resistance mediated by the Rpv3 (Resistance to P. viticola) locus. However, despite the extensive use of this locus, little is known about the mechanism of Rpv3-mediated resistance. In this study, Rpv3-mediated defense responses were studied in Rpv3+ and Rpv3ˉ grapevine cultivars following inoculation with two distinct P. viticola isolates avrRpv3+ and avrRpv3ˉ, with the latter being able to overcome Rpv3 resistance. Based on comparative microscopic, metabolomic and transcriptomic analyses, our results show that the Rpv3-mediated resistance is associated with a defense mechanism that triggers synthesis of fungi-toxic stilbenes and programmed cell death (PCD), resulting in reduced but not suppressed pathogen growth and development. Functional annotation of the encoded protein sequence of genes significantly upregulated during the Rpv3-mediated defense response revealed putative roles in pathogen recognition, signal transduction and defense responses.
2019-08-21 | GSE128865 | GEO
Project description:Anthelmintic resistance is a major problem in the global fight against parasitic nematodes., Most previous studies have focused on the analysis of potential candidate genes that may have a role in resistance. Here we take a novel approach in the important parasite, Haemonchus contortus, by investigating changes in microRNA expression between resistant and susceptible parasites. The resistant worms included two geographically distinct strains and two lines generated by multiple rounds of backcrossing between susceptible and resistant parents, with ivermectin selection. All four resistant strains showed increased abundance of a single miRNA, hco-miR-9551, compared to the susceptible strain. hco-miR-9551 is enriched in female worms, is likely to be located on the X chromosome and is found only in clade V parasitic nematodes. Approximately 5-10% of the genomes of the resistant parental strains are introgressed into the respective backcrosses, suggesting that hco-miR-9551, or genes regulated by the miRNA, may be genetically linked to a locus that determines resistance. Genes containing predicted binding sites for hco-miR-9551 were identified computationally and refined based on differential expression in a transcriptomic dataset. These findings advance our conceptual understanding of the molecular mechanisms of anthelmintic resistance in H. contortus and indicate that altered miRNA expression may be linked with drug resistance.
2016-03-25 | GSE79542 | GEO
Project description:Aim:To characterise a recently discovered stem rust resistance locus on wheat chromosome 7AL. Transcriptome analysis by RNA-sequencing, in association with microscopic observations, was used to compare responses to the Puccinia graminis f. sp. tritici pathogen of the susceptible line Columbus, and two independent backcrossed resistant lines containing the locus, Columbus-NS765 and Columbus-NS766. Results: Microscopic observations of infected leaves revealed that the resistance conferred by the 7AL resistance locus was initiated by two days post-inoculation, upon the entry of the stem rust fungus into the plant through the stoma. Death of guard and epidermal cells adjacent to the fungal points of entry was observed to be clearly more frequent in resistant lines than in the susceptible genotype, suggesting that the resistance response is similar in all genotypes, but enhanced in the resistant lines. Transcriptomic analysis, combined with assignment of genes to wheat chromosomes, revealed a disporportionately high number of differentially expressed genes were located on chromosomes 7AL and 6A. A number of genes annotated as cysteine-rich receptor-like kinases were located on chromosome 7AL. Closer investigation indicated that the encoded proteins were in fact putative receptor-like cytoplasmic kinases (RLCKs). One of the putative RLCK genes contained a SNP marker previously shown to co-segregate with the 7AL resistance locus. The large number of differentially expressed genes on chromosome 6A indicated the presence of a large introgression on this chromosome that co-segregated with stem rust resistance in the two independent resistant lines, but its role in the resistance response is currently unclear. Conclusions: This study represents the first transcriptome analysis of responses to stem rust in wheat, and the first investigation of the resistance conferred by the newly-discovered wheat 7AL stem rust resistance locus. Microscopy showed the resistance response was associated with pre-haustorial cell death. Results of the RNA-seq, which has the resolution to discriminate between homeologous wheat genes, along with assignment of differentially expressed genes to wheat chromosomes, suggested putative receptor-like cytoplasmic kinases linked to the 7AL locus as candidate resistance genes for further investigation.
2017-02-22 | GSE83149 | GEO
Project description:By exploring the large-scale transcriptome analysis, we aim to identify differentially expressed genes in the comparison between resistant and susceptible families.
2022-07-12 | GSE200311 | GEO