DRenSeq in potato
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB23708 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR2208680_1.fastq.gz | Fastqsanger.gz | |||
| ERR2208680_2.fastq.gz | Fastqsanger.gz | |||
| ERR2208681_1.fastq.gz | Fastqsanger.gz | |||
| ERR2208681_2.fastq.gz | Fastqsanger.gz | |||
| ERR2208682_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 96 |
Similar Datasets
Project description:Potato wild relatives (Solanum section Petota) are a source of genetic diversity for improving traits in modern cultivars (S. tuberosum) to meet climate challenges. Potatoes are susceptible to multiple abiotic and biotic stresses and have undergone constant improvement through breeding programs worldwide. The allotetraploid S. acaule Bitter has been used to introgress cold tolerance into potato breeding germplasm. The cold challenged transcriptome of S. acaule was compared with that of autotetraploid S. tuberosum cv. Atlantic, and was found to have fewer differentially expressed genes than the latter. Specifically, subgenome 1 has less downregulated alleles compared to subgenome 2 and S. tuberosum.
2025-05-31 | GSE268611 | GEO
Project description:Tuber bruising in tetraploid potatoes (Solanum tuberosum) is a trait of economical importance, as it affects tubers' fitness for sale. Understanding the genetic components affecting tuber bruising is a key step in developing potato lines with increased resistance to bruising. As the tetraploid setting renders genetic analyses more complex, there is still a lot to learn about this complex phenotype. Here, we used genotype by sequencing data on a panel of half-sibling populations from a breeding programme to perform a genome-wide association analysis for tuber bruising. In addition, we collected transcriptomics data to enrich the GWAS results, by performing a differential expression analysis between samples with high- and low-bruising susceptibility.
2022-11-29 | GSE208439 | GEO
Project description:Late blight, caused by the oomycete Phytophthora infestans, is one of the most damaging potato diseases. Genetic resistance is one of the most effective means to control the destruction caused by this pathogen. Transgenic potato lines harboring a resistance gene, RB, confer broad-spectrum, rate-reducing late blight resistance. A microarray approach was used to understand what genes are manipulated in the potato background after the addition of the RB gene that contribute to the late blight resistant phenotype. Keywords: Time course, disease state analysis
2009-10-01 | GSE13341 | GEO
Project description:The potato powdery scab agent Spongospora subterranea causes damage on the skin of tubers and induces root gall formation, precipitating considerable yield and quality losses. Currently, there are no effective chemical treatments for the control of powdery scabs. Understanding the inducible defence responses in roots of potato plants in the resistant and susceptible host environment, particularly during colonisation of the root by S. subterranea is required for the breeding of novel resistant cultivars. Here, we integrated transcriptomics, proteomics and metabolomics datasets to uncover the mechanisms underlying of the potato resistance to powdery scab. This multi-omics approach identified upregulation of glutathione metabolism at the levels of RNA, protein and metabolite in the resistant cultivar but not in the susceptible cultivar. Upregulation of the lignin metabolic process was also specific to in the resistant cultivar at the transcriptome level. In addition, Tthe inositol phosphate pathway was differentially expressed between two cultivars in response to S. subterranea infection, where it was upregulated in the susceptible cultivar but downregulated in the resistant cultivar. We provide, for the first time, large-scale multi-omics data of Spongospora-potato interaction, thereby suggesting the signaling role of glutathione metabolism in the potato resistance against powdery scab
2022-08-12 | PXD029381 | Pride
Project description:We report the application of RNA- sequencing technology for high-throughput profiling of histone modifications in mammalian cellsor identification of expressed genes upon infection by Spongospora subterranea. Using RNA-sequencing (RNA-seq), 2058 differentially expressed genes (DEGs) were identified from two potato cultivars (tolerant and susceptible) in response to Sss infection. Analysis of the expression patterns of ten selected defense-response genes was carried out at two different stages of tuber growth using RT-qPCR to validate the RNA-seq data. Several defense related genes showed contrasting expression patterns between the tolerant and susceptible cultivars, including marker genes involved in the salicylic acid hormonal response pathway (StMRNA, StUDP and StWRKY6). Induction of six defense related genes (StWRKY6, StTOSB, StSN2, StLOX, StUDP and StSN1) persisted until harvest of the tubers, while three other genes (StNBS, StMRNA and StPRF) were highly up-regulated during the initial stages of disease development. The results of this study suggested that the tolerant potato cultivar employs quantitative resistance and salicylic acid pathway hormonal responses against tuber infection by Sss. The identified genes have the potential to be used in the development of molecular markers for selection of powdery scab resistant potato lines in marker assisted breeding programs.
2018-12-11 | GSE123545 | GEO
Project description:The causal agent of bacterial wilt is Ralstonia solanacearum (Rs) with an unusually wide host range including potato. Bacterial wilt is the most destructive bacterial disease of plants that seriously reduce crop yield word-wide. Control of Rs through resistance breeding and biotechnology is considered to be very important and necessary. Rs resistance has been reported in a few potato cultivars and hybrids. Identification of defense mechanism underlying resistance is a prerequisite of biotechnological approaches. In this study, two resistant cultivars, ‘Calalo Gaspar’ (CG) and ‘Cruza 148’ (CR), and a sensitive cultivar, ‘Désirée’, were analysed and compared to each other at molecular level before-, and a few days after Rs infection. The transcriptome analysis of roots revealed up-regulation of chitin interaction and cell wall related genes in CR and DES. The phenylpropanoid biosynthesis and glutathione metabolism pathways were induced only CR. Microscopic analysis detected lignification over the whole stele in CR roots. In CG roots, concentrations of chlorogenic acid and quercetin derivatives were highly increased upon Rs infection. A characteristic increase at the transcript level of MAP kinase signalling pathway genes and concentrations of jasmonic-, salicylic-, abscisic and indoleacetic acid was detected in DES roots. These results indicate a different mechanism of defence both in the two tested resistant and the sensitive potato cultivar.
2023-01-20 | GSE211973 | GEO
Project description:The cultivar Desirée and the breeding line SW93-1015 were challenged with potato cyst nematodes and transcriptomes analysed after 8h and 48 h.
2018-04-02 | E-MTAB-5215 | biostudies-arrayexpress
Project description:The use of phosphites in disease control management and abiotic stress has proven to be effective. Although the mechanisms underlying their effect remain unclear, it has been postulated that miRNAs could be involved. In order to understand these mechanisms we performed NGS sequencing in potato leaves treated or not with KPhi to identify miRNAs responsive to this biocompatible compound. The aim of the present work is to identify miRNAs that are involved in the regulation of potato defense responses after phosphite treatment.
2019-08-30 | GSE132232 | GEO
Project description:Potato (Solanum tuberosum L.), as an important food crop on the Qinghai-Tibet Plateau, is prone to low temperature and frost damage during the seedling stage, causing economic losses for farmers. In this study, transcriptome analyses were conducted on the leaves of Atlantic, KY130 and KY140 potato varieties following exposure to cold stress (CS). The genes StPAL(Soltu.Atl.09_2G005110) and StGAD(Soltu.Atl.11_3G000340), suggesting their involvement in the regulation of cold resistance in potato. “Flavonoid-related metabolism,” “lipid metabolism,” “amino acid metabolism,” “carbohydrate metabolism,” “nucleotide metabolism,” and “energy metabolism” might play an important role in the cold resistance of potato. Our results provided novel insights into the molecular mechanisms underlying cold resistance in potato.
2025-03-12 | GSE291340 | GEO
Project description:we performed de novo transcriptome assembly and digital gene expression (DGE) profiling analyses of sweet potato challenged with Fob using Illumina Hiseq technology. A total of 89,944,188 clean reads were generated and were assembled into 101,988 unigenes with an average length of 666bp, 62,605(61.38%) of them were functional annotated in the non-redundant(nr) protein database from NCBI by using BLASTX with a cut-off E-value of 10-5, and COG,GO and KEGG annotations were examined for better understand their functions. Five DGE libraries were constructed from the sweet potato cultivar JS57 (high resistance) and XZH (high susceptible) challenged with pathogenic and Nonpathogenic Fob. The differentially expressed genes including up- and down-regulation in five libraries were identified and calculated based on comparisons of transcriptomes, showing differences in gene expression profiles among the samples. A set of differentially expressed genes involved disease response were identified, including 40 WRKY and seven NAC transcription factors, four resistance genes, 22 pathogenesis-related genes, and six genes involved in SA signal pathway. Our study is the first to provide the transcriptome sequence resource of sweet potato challenged with pathogenic and non-pathogenic Fob and demonstrate its digital expression profiling. We discovered a set of genes involved in disease resistance. These data provides comprehensive sequence resource of sweet potato for genetic and genomic studies and will accelerate the understanding of molecular mechanism of disease resistance.
2018-02-13 | GSE89290 | GEO