Solanum tuberosum
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PROVIDER: PRJNA107945 | ENA |
REPOSITORIES: ENA
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Project description:Total RNA sequencing for potato tuberization
| PRJNA589236 | ENA
Project description:A tuberization inhibitor has long been postulated, but not yet found. We found that blue light inhibits tuberization in Norland, a day-neutral variety of Solanum tuberosum L. Tissue-cultured plants formed tubers within 8 weeks under continuous darkness, and white, red, or far-red light. Preliminary experiments indicated that a one- or two-day exposure to blue light after 3-4 weeks of dark treatment will inhibit tuber formation in ‘Norland’ plants. Using this system and expression profiling, we may be able to identify candidate tuberization inhibitors. 'Norland' plants (subcultured from existing cultures and grown for two weeks under continuous 100 umol/m2-s white fluorescent light) were placed in tuber-inducing media containing 6% sucrose, vitamins, MS salts, and kinetin (2.5 mg/L). Tubes containing plants were wrapped in two layers of aluminum foil. After 3 weeks and 2 days, half of the tubes were exposed to 6-7 umol/m2-s blue light. The other half of the tubes were left in darkness (controls). After 2 days, all plants were harvested and frozen in liquid nitrogen. Plants exposed to blue light were harvested under blue light. Control plants were harvested under < 2 umol/m2-s light conditions. All plant transfers were done at 1700 (5 PM) to avoid possible complications due to circadian effects. Experiments were performed four times, from subculture to harvest. RNA was extracted from stem and leaf tissue of plants using the Qiagen RNeasy Plant Mini kit. Extracted RNA was then converted to dsDNA using the Invitrogen protocol and reagents for double stranded cDNA synthesis. The resulting dsDNA was in vitro transcribed into amplified RNA using the Ambion procedure and reagents for in vitro transcription. cDNA was purified using Qiagen MinElute columns and protocol. Amplified RNA was purified using Ambion columns or Qiagen RNeasy columns and the Ambion protocol, and quantified using RiboGreen dye fluorometry. Keywords: Direct comparison
2008-02-13 | GSE10491 | GEO
Project description:RNA-sequencing of Apical Rooted Cuttings and Microplants for tuberization
| PRJNA836250 | ENA
Project description:Potato, S. tuberosum, is one of the most important global crops, but has high levels of waste due to tuber greening under light, which is associated with the accumulation of neurotoxic glycoalkaloids. Here, we have investigated the effect of monochromatic far-red, red, and blue light on the regulation of chlorophyll and glycoalkaloid accumulation in tubers of a commercial variety, King Edward. Transcriptomic analysis of tubers exposed to red, blue, and white light showed that light induction of photosynthesis and tetrapyrrole-related genes grouped into two distinct patterns with one group showing much stronger induction in blue at 6 h and 24 h and a second group showing only red induction at 24 h.
2020-02-25 | E-MTAB-7707 | biostudies-arrayexpress
Project description:Transcriptome analysis in potato for tuberization under different N conditions in aeroponics
| PRJNA818293 | ENA
Project description:The potato is susceptible to water stress at all stages of development. We examined four clones of tetraploid potato, Cardinal, Desirée, Clone 37 FB and Mije, from the germplasm bank of the National Institute of Agricultural Research (INIA) in Chile. Water stress was applied by suspending irrigation at the beginning of tuberization. Stomatal conductance, tuber and plant fresh and dry weight was used to categorize water stress tolerance. Cardinal had high susceptibility to water stress. Desirée was less suscepetible than Cardinal and had some characteristics of tolerance. Mije had moderate and Clon 37 FB high tolerance. Differential gene expression in leaves from plants with and without water stress were examined using transcriptome sequencing. Water stress susceptible Cardinal had the fewest differentially expressed genes at 101, compared to Desirée at 1867, Clon 37 FB at 1179 and Mije at 1010. Water stress tolerance was associated with up-regulation of expression of transcription factor genes and genes involved in osmolyte and polyamine biosynthesis. Increased expression of genes encoding late embryogenesis abundant (LEA) and dehydrin proteins along with decreased expression of genes involved in nitrate assimilation and amino acid metabolism were found for clones showing water stress tolerance. The results also show that water deficit was associated with reduced biotic stress responses. Additionally, heat shock protein genes were differentially expressed in all clones except for highly susceptible Cardinal. Together the gene expression study demonstrates variation in the molecular pathways and biological processes in response to water stress contributing to tolerance and susceptibility.
2019-12-18 | GSE140083 | GEO
Project description:For expression profiling analyses of early stages of tuber induction, plants of Solanum tuberosum ssp andigena (7540) were used. This wild subspecies is strictly dependent on photoperiod for tuberisation, such that short days (SD) inductive conditions are required in order to trigger tuber induction in the stolons. Andigena plants were grown in the greenhouse under LD non-inductive conditions until a 10-leaf stage. They were subsequently transferred to inductive SD conditions (8 h light/16 h dark), and sampled at 0, 2, 4, 6 and 8 days after transfer to SDs. Tuber swelling was visible approximately 6-8 days after transfer to inductive conditions. The apical region of the stolons (2 cm) was collected one hour before the beginning of the light period.
2011-10-06 | GSE31336 | 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
Project description:Solanum lycopersicum and Solanum tuberosum are agriculturally important crop species as they are rich sources of starch, protein, antioxidants, lycopene, beta-carotene, vitamin C, and fiber. The genomes of S. lycopersicum and S. tuberosum are currently available. However the linear strings of nucleotides that together comprise a genome sequence are of limited significance by themselves. Computational and bioinformatics approaches can be used to exploit the genomes for fundamental research for improving their varieties. The comparative genome analysis, Pfam analysis of predicted reviewed paralogous proteins was performed. It was found that S. lycopersicum proteins belong to more families, domains and clans in comparison with S. tuberosum. It was also found that mostly intergenic regions are conserved in two genomes followed by exons, intron and UTR. This can be exploited to predict regions between genomes that are similar to each other and to study the evolutionary relationship between two genomes, leading towards the development of disease resistance, stress tolerance and improved varieties of tomato.
| S-EPMC3842579 | biostudies-literature
Project description:Light is a major environmental factor that affects metabolic pathways and stimulates the production of secondary metabolites in potato. However, adaptive changes in potato metabolic pathways and physiological functions triggered by light are partly explained by gene expression changes. Regulation of secondary metabolic pathways in potato has been extensively studied at transcriptional level, but little is known about the mechanisms of post-transcriptional regulation by miRNAs. To identify light-responsive miRNAs/mRNAs and construct putative metabolism pathways regulated by the miRNA-mRNA pairs, an integrated omics (sRNAome and transcriptome) analysis was performed to potato under light stimulus. A total of 31 and 48 miRNAs were identified to be differentially expressed in the leaves and tubers, respectively. Among the DEGs, 1353 genes in the leaves and 1841 genes in the tubers were upregulated, while 1595 genes in the leaves and 897 genes in the tubers were downregulated by light. Mapman enrichment analyses showed that genes related to MVA pathway, alkaloids-like, phenlypropanoids, flavonoids, and carotenoids metabolism were significantly upregulated, while genes associated with major CHO metabolism were repressed in the leaves and tubers. Integrated miRNA and mRNA profiles revealed that light-responsive miRNAs are important regulators in alkaloids metabolism, UMP-salvage, lipid biosynthesis, and cellulose catabolism. Moreover, several miRNAs may participate in glycoalkaloids metabolism via JA signaling pathway, UDP-glucose biosynthesis and hydroxylation reaction. This study provides a global view of transcriptome response in potato response to light, our results suggest that miRNAs might play important roles in secondary metabolic pathways, especially in glycoalkaloid biosynthesis. The findings will enlighten us on the genetic regulation of secondary metabolite pathways and pave the way for future application of genetically engineered potato.
2016-09-28 | GSE79984 | GEO