Solanum tuberosum (Potatoes) Metabolomics Analysis

Solanum tuberosum (Potatoes) Metabolomics Analysis

Service Details Case Study

What is Solanum tuberosum (Potatoes)?

Potato, scientifically known as Solanum tuberosum, is a globally consumed staple crop, rich in starch, vitamins, and minerals. Understanding the intricate metabolic processes governing potato growth, development, and responses to environmental cues is crucial for sustainable agriculture. Solanum tuberosum plays an indispensable role in agriculture, offering adaptability to diverse climates and serving as a primary source of dietary carbohydrates. Its importance is underscored by the need to comprehend the metabolic intricacies of this versatile crop.

Potato metabolism is complex, involving a myriad of biochemical processes. Central to this complexity is starch accumulation in potato tubers, vital for crop yield and quality. Understanding these metabolic pathways is integral to agricultural and nutritional advancements.

Furthermore, Solanum tuberosum, like all living organisms, encounters environmental challenges that necessitate metabolic adaptations. These challenges encompass variations in climate, the presence of pests, and susceptibility to diseases. To address these concerns, metabolomics emerges as an invaluable tool. It enables the profiling and quantification of metabolites in potato plants exposed to different environmental conditions. Through metabolomic analysis, researchers gain insights into how Solanum tuberosum responds at the biochemical level, unveiling the strategies employed by the crop to thrive under adverse circumstances.

Methods for Solanum tuberosum Metabolomic Analysis

Sample Preparation

Sample preparation is a critical first step in potato metabolomics. It involves the collection and extraction of metabolites from potato tissues, such as tubers or leaves. Creative Proteomics employs state-of-the-art techniques to ensure accurate and reproducible sample preparation. Our experts carefully collect samples, freeze them rapidly to preserve metabolite integrity, and subsequently extract metabolites using appropriate solvents.

Metabolite Detection and Identification

Once the metabolites are extracted, the next step is their detection and identification. Creative Proteomics utilizes advanced analytical instruments such as mass spectrometers and nuclear magnetic resonance (NMR) spectrometers for this purpose. Mass spectrometry (MS) enables us to measure the mass-to-charge ratios of metabolites, while NMR spectroscopy provides information on the structural composition of metabolites. By comparing experimental data with comprehensive metabolite databases, we can accurately identify and quantify the metabolites present in potato samples.

Data Analysis and Interpretation

The vast amount of data generated in metabolomic studies necessitates sophisticated data analysis techniques. Creative Proteomics employs bioinformatics tools and statistical methods to process and interpret metabolomic data. This involves identifying significant changes in metabolite levels between different potato samples (e.g., control vs. stress-exposed) and linking these changes to specific metabolic pathways. Such insights are invaluable for understanding how potatoes respond to environmental factors, stressors, or genetic modifications.

Metabolic Pathway Analysis

Metabolomic data can be further analyzed using pathway enrichment analysis. This approach helps identify the metabolic pathways that are most affected by changes in metabolite levels. By pinpointing key pathways, we can uncover potential targets for crop improvement and gain a deeper understanding of potato biology.

Specific Potato Analysis Projects by Creative Proteomics

Metabolite Profiling: We provide comprehensive metabolite profiling services for different potato tissues, helping researchers understand the composition and variation of metabolites under various conditions.

Stress Response Analysis: Creative Proteomics can assess how Solanum tuberosum responds to abiotic or biotic stressors at the metabolome level, aiding in the development of stress-resistant potato varieties.

Nutritional Profiling: We offer nutritional profiling to determine the content of essential nutrients and bioactive compounds in potatoes, contributing to the development of healthier potato-based food products.

Metabolic Engineering Studies: Our team specializes in assisting researchers in metabolic engineering projects for enhanced potato traits, such as increased starch content or altered secondary metabolite profiles.

Customized Metabolomic Studies: We collaborate with researchers to design customized metabolomic experiments tailored to their specific research questions and objectives.

Potatoes Metabolomics Analysis Techniques

1. Liquid Chromatography-Mass Spectrometry (LC-MS)

We employ state-of-the-art liquid chromatography-mass spectrometry (LC-MS) systems, including instruments such as the Thermo Fisher Scientific Q Exactive™ HF-X Hybrid Quadrupole-Orbitrap™ Mass Spectrometer. LC-MS combines the separation capabilities of liquid chromatography with the sensitive detection and high-resolution mass measurement of mass spectrometry. This allows for the precise analysis of a wide range of polar and nonpolar metabolites in potato samples.

2. Gas Chromatography-Mass Spectrometry (GC-MS)

Creative Proteomics also utilizes gas chromatography-mass spectrometry (GC-MS) techniques, employing instruments like the Agilent 7890A GC System coupled with the Agilent 5977A Mass Spectrometer. GC-MS is particularly effective for the analysis of volatile and thermally stable compounds in potato samples. It offers excellent separation and identification capabilities, making it a valuable tool for comprehensive metabolomic studies.

3. Nuclear Magnetic Resonance (NMR) Spectroscopy

In addition to mass spectrometry, we harness the power of nuclear magnetic resonance (NMR) spectroscopy for Solanum tuberosum metabolomics analysis. High-field NMR spectrometers like the Bruker Avance III HD 600 MHz NMR Spectrometer provide insights into the structural composition of metabolites, offering complementary data to MS-based techniques.

Workflow for Metabolomics ServiceWorkflow for Metabolomics Service

Sample Requirements for Potatoes Metabolomics

Sample Requirements Details
Sample Type Potato tissues (e.g., tubers, leaves, roots)
Sample Quantity Minimum 50 grams of fresh tissue
Sample Storage Freeze immediately in liquid nitrogen, then store at -80°C
Sample Preparation Cryogenically grind tissues to a fine powder
Sample Replication Prepare multiple biological replicates for statistical robustness

Case. Metabolomic Analysis Reveals Key Compounds Associated with Quantitative Resistance to Black Dot Disease in Potato Tubers


Quantitative resistance in plants is a complex trait involving multiple mechanisms that collectively limit the progression of pathogen infections. Unlike qualitative resistance, which relies on specific resistance genes, quantitative resistance is influenced by various structural and biochemical factors. Potato tubers are susceptible to black dot disease, caused by the fungus Colletotrichum coccodes, and understanding the mechanisms underlying quantitative resistance in potato cultivars is essential for sustainable potato production.


The study focused on five different potato cultivars with varying degrees of resistance to black dot disease. These cultivars included Lady Felicia (highly susceptible), Gwenne and Erika (moderately resistant), and Agria and Cheyenne (partially resistant). The researchers analyzed the skin and suberin composition, as well as the metabolite profiles of these cultivars, to identify factors associated with resistance.

Technological Methods

Structural Analysis:

  • Phellem Thickness: Phellem, the outermost layer of potato skin, was measured to assess its potential correlation with black dot resistance. Lady Felicia, with the thinnest skin, served as a critical reference point.
  • Suberin Analysis: The study investigated suberin, a cell wall component, in potato skins to determine if its amount or composition played a role in resistance. This analysis aimed to identify structural factors associated with resistance.

Metabolite Profiling:

  • Untargeted Metabolomics: Metabolites in potato skin samples were analyzed using untargeted metabolomics. This technique allows for the comprehensive profiling of a wide range of metabolites without prior knowledge of their identities.
  • Mass Spectrometry: Mass spectrometry was employed to identify and quantify metabolites present in the potato skin samples.
  • Multivariate Data Analysis: Advanced statistical methods, such as AMOPLS (adducts and multivariate orthogonal projections to latent structures), were used to analyze the complex data generated by metabolomics.


Phellem Thickness: Overall, there was no significant correlation between phellem thickness and resistance to black dot disease. However, the highly susceptible cultivar Lady Felicia had the thinnest skin, suggesting a potential minimum skin thickness requirement for resistance.

Suberin Composition: The amount and composition of suberin in potato skins did not correlate with black dot resistance, in contrast to their role in resistance to other potato pathogens.

Metabolite Composition: Metabolite profiles of the five cultivars differed significantly, and certain metabolites were identified as Resistant-Related Constitutive (RRC) compounds. These included alpha-chaconine, hydroxycinnamic acids (HCAs), and hydroxycoumarins.

Alpha-Chaconine: This glycoalkaloid, known for its antifungal properties, appeared to be involved in resistance to black dot disease.

HCAs: Hydroxycinnamic acids, particularly chlorogenic acid and its derivatives, were found in higher levels in resistant cultivars. Although chlorogenic acid did not inhibit C. coccodes growth, its role in resistance was suggested.

Hydroxycoumarins: Hydroxycoumarins, including scopoletin and esculetin, were specifically induced in resistant cultivars upon C. coccodes inoculation and exhibited antifungal activity.

Overview of the metabolomics strategy.Overview of the metabolomics strategy.


  1. Massana-Codina, Josep, et al. "Insights on the structural and metabolic resistance of potato (Solanum tuberosum) cultivars to tuber black dot (Colletotrichum coccodes)." Frontiers in plant science 11 (2020): 1287.