Skim-seq_CE
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB56778 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Transcript profiling of tuber samples of 94 genotypes deriving from a segregating diploid potato population
2011-12-31 | E-MTAB-701 | biostudies-arrayexpress
Project description:Transcription profiling by array of leaf samples of 94 genotypes deriving from a segregating diploid potato population
2011-12-31 | E-MTAB-808 | biostudies-arrayexpress
Project description:Potato genotypes from a diploid potato population were divided in two groups based on their response to Potato virus A (PVA). Plants exhibiting hypersensitive response were compared to plants exhibiting non-necrotic response (i.e. blocking virus movement without cell death).<br>The comparisons were made before inoculation and 12 and 24 hours post-inoculation.<br>
2010-09-30 | E-MEXP-2622 | biostudies-arrayexpress
Project description:BSA pooling experiment for methionine content in a segrating diploid potato population (CxE). RNA of constrasting individuals for methionine content are pooled together based on their tuber methionine content and marker association with either or both of the identified QTLs for methionine content
2009-11-20 | E-MEXP-2441 | biostudies-arrayexpress
Project description:To identify differently expressed proteins in tuber tissue of potato cultivars and diploid interspecific hybrids of Solanum, differing in resistance to Dickeya solani, comparative analysis was performed. Two highly resistant (Bea and Humalda) and three susceptible (Irys, Katahdin, Ulster Supreme) potato cultivars, as well as the highly resistant (DG 00-270) and the susceptible (DG 08-305) diploid clones, were studied. DG 00-270 exhibited higher resistance to D. solani than the cultivars Bea and Humalda. Proteins were extracted from wounded potato tubers inoculated with bacteria at an early symptomatic phase and from controls, i.e., intact tubers and wounded mock-inoculated tubers. Protein profiles were analyzed using nano-liquid chromatography coupled with tandem mass spectrometry (LC-MS-MS/MS).
2019-05-21 | PXD013009 | Pride
Project description:Glycoalkaloids are Solanum bioactive compounds and are involved in allelopathic interactions. To achieve a better understanding of plant–plant interactions, it is essential to deeply examine the trait distribution in a segregating population. In the present paper, we used transcriptomic and metabolomic approaches to recognize the phytotoxic abilities of potato plants originating from a diploid segregating F1 population with particular emphasis on glycoalkaloids in potato groups characterized by a high glycoalkaloid content. In potato F1 individuals, six glycoalkaloids were recognized: solasonine, solamargine, α-solanine, α-chaconine, leptinine I, and leptine II. In the bulk samples characterized by a high total glycoalkaloid content and various phytotoxic potential, high - A’, low - B’ and hormesis - F’, a significant role of the glycoalkaloid composition in the expression of phytotoxic potential was revealed. In particular, leptine II, solasonine and solamargine were present. Based on the RNA-seq analysis of the bulk samples, a flavonol synthase/flavanone 3-hydroxylase-like gene responsible for flavonoid synthesis was upregulated in comparison A’ vs. B’ and A’ vs. F’ (Log2FC=8.30 and 6.40, respectively). The population-level evaluation of phytotoxic potential confirmed a significant negative correlation between total glycoalkaloid content and phytotoxic potential (r=-0.211) but only after correction for total flavonoid content.
2021-10-27 | GSE186482 | GEO
Project description:We report the transcriptional response to Colorado potato beetle herbivory in leaves of the highly beetle resistant Solanum chacoense diploid line USDA8380-1 (80-) and a susceptible F2 individual (EE501F2_093) derived from a cross between 80-1 and a beetle susceptible line S. chacoense M6. Sampling tissue in a time course during adult Colorado potato beetle feeding provides novel insight to the transcriptomic defense response to this important pest.
2023-03-08 | GSE169331 | GEO
Project description:We prepared QTL map of tuber starch content in potato diploid population. Then, we examined expression level of enzyme ADP-glucose pyrophosphorylase (AGPase) taking part in starch biosynthesis (marker AGPaseS-a). Based on starch content and AGPaseS-a expression, we constructed four bulks prepared from RNA isolated from tubers of F1 individuals H1 and H2 consisted of high TSC genotypes, bulks L1 and L2 were made of low TSC genotypes. Plants in bulks H1 and L1 strongly expressed AGPaseS-a, whereas those in bulks H2 and L2 exhibited low levels. Then we used RNA-seq technology for selection of genes displaying differential expression between RNA pools. For selected candidate genes we mapped expression QTL (e-QTL) and found eQTL of eAGPaseS-a and ePGRCRURSE5, were close to the corresponding loci of (AGPaseS-a) and the 12S globulin cruciferin gene (PGCRURSE5). We concluded that the cruciferin gene PGRCRURSE5 is a novel candidate involved in the regulation of starch content in potato tubers and suggests that cruciferin may be a novel PTST protein in potato tubers.
2020-06-24 | GSE153031 | GEO
Project description:Purpose: MicroRNAs (miRNAs) are ubiquitous components of endogenous plant transcriptome. miRNAs are small, single-stranded and ~21 nt long RNAs which regulate gene expression at the post-transcriptional level and are known to play essential roles in various aspects of plant development and growth. Previously, a number of miRNAs have been identified in potato through in silico analysis and deep sequencing approach. However, identification of miRNAs through deep sequencing approach was limited to a few tissue types and developmental stages. This study reports the identification and characterization of potato miRNAs in three different vegetative tissues and four stages of tuber development by high throughput sequencing. Results: Small RNA libraries were constructed from leaf, stem, root and four early developmental stages of tuberization and subjected to deep sequencing, followed by bioinformatics analysis. A total of 89 conserved miRNAs (belonging to 33 families), 147 potato-specific miRNAs (with star sequence) and 112 candidate potato-specific miRNAs (without star sequence) were identified. The digital expression profiling based on TPM (Transcripts Per Million) and qRT-PCR analysis of conserved and potato-specific miRNAs revealed that some of the miRNAs showed tissue specific expression (leaf, stem and root) while a few demonstrated tuberization stage-specific expressions. Targets were predicted for identified conserved and potato-specific miRNAs, and predicted targets of four conserved miRNAs, miR160, miR164, miR172 and miR171, which are ARF16 (Auxin Response Factor 16), NAM (NO APICAL MERISTEM), RAP1 (Relative to APETALA2 1) and HAIRY MERISTEM (HAM) respectively, were experimentally validated using 5′RLM-RACE (RNA ligase mediated rapid amplification of cDNA ends). Gene ontology (GO) analysis for potato-specific miRNAs was also performed to predict their potential biological functions. Conclusions: We report a comprehensive study of potato miRNAs at genome-wide level by high-throughput sequencing and demonstrate that these miRNAs have tissue and/or developmental stage specific expression profile. Also, predicted targets of conserved miRNAs were experimentally confirmed for the first time in potato. Our findings indicate the existence of extensive and complex small RNA population in this crop and suggest their important role in pathways involved in diverse biological processes, including tuber developmental process.
2014-01-09 | GSE52599 | GEO