ISSR Molecular Marker Analysis Service – High-Resolution Genetic Diversity Profiling
Service Highlights
The ISSR (Inter-Simple Sequence Repeat) marker assay offers a powerful means of revealing genome-wide polymorphisms by targeting regions between simple sequence repeats, without the need for reference genome information. Applicable to plants, animals, and microorganisms, ISSR generates highly polymorphic, reproducible banding patterns with minimal DNA input. Its ability to capture rich genetic diversity data makes it an invaluable tool for biodiversity assessment, germplasm characterization, and population structure studies — providing researchers with a cost-effective and dependable platform for molecular ecology and breeding research.
Request a QuoteWhy ISSR Matters
Inter-Simple Sequence Repeat (ISSR) analysis is a PCR-based molecular marker technology designed to detect genetic variation across individuals, populations, or species without requiring prior genome information. By amplifying the DNA regions between simple sequence repeats, ISSR combines the simplicity of RAPD with the high polymorphism potential of SSR, offering a robust and cost-efficient way to profile genetic diversity.
For researchers, ISSR opens the door to precise genotype discrimination and population-level insights, even in non-model organisms with limited genomic resources. It has been successfully applied to studies in biodiversity assessment, germplasm characterization, phylogenetics, and conservation genetics, providing clear, reproducible data that can guide both basic and applied research.
When projects require scalable, reproducible, and adaptable genetic analysis—whether for rare medicinal plants, crop varieties, or wild animal populations—ISSR offers a proven balance between accessibility and analytical depth.
Core Advantages – Tailored for Researchers
What sets ISSR apart is its combination of technical reliability and practical flexibility, making it a trusted choice for diverse research environments.
- High-Resolution Genetic Differentiation
Detects subtle polymorphisms that other dominant markers may miss, enabling fine-scale discrimination.
- Cost-Efficient Workflow
Avoids expensive probe synthesis, cloning, or high-throughput sequencing while still delivering rich datasets.
- Low DNA Input with High Data Yield
Generates robust profiles from minimal DNA quantities, allowing work with precious or limited samples.
- Optimized Reproducibility
Our refined protocols produce consistent, comparable results across runs and sample sets.
- Flexible Detection Platforms
Options for standard agarose gel, high-resolution PAGE, or capillary electrophoresis to match research needs.
By combining these strengths, ISSR technology delivers actionable genetic insights that support critical decisions in breeding, taxonomy, and conservation—without overburdening budgets or timelines.
Research-Friendly Applications
ISSR technology has proven to be a highly adaptable genetic marker platform, making it suitable for a broad spectrum of research objectives across multiple disciplines. Its flexibility allows researchers to design projects that balance resolution, cost, and sample availability, without compromising scientific rigor.
Common and High-Impact Use Cases
- Biodiversity and Conservation Genetics
Assess genetic diversity within and between populations to guide conservation priorities, monitor genetic erosion, and identify unique genetic lineages for protection.
- Germplasm Characterization and Fingerprinting
Generate molecular "fingerprints" to differentiate closely related varieties or strains, ensuring accurate labeling, resource management, and protection of breeding lines.
- Phylogenetic and Taxonomic Studies
Resolve evolutionary relationships at intra- and interspecific levels, even in taxa with limited genomic information, enabling more precise classification.
- Breeding Program Support
Screen parental lines, monitor genetic uniformity, and track inheritance patterns to accelerate selection and maintain desired traits in cultivated populations.
- Authentication of Medicinal and Economic Plants
Verify plant identity and origin, ensuring quality control in the production and trade of high-value botanical materials.
Our Customized ISSR Workflow
We tailor each ISSR project to your species, sample type, and research goals — ensuring data that is accurate, reproducible, and directly relevant to your study.
Sample Requirements
To ensure high-quality and reproducible ISSR results, please follow these guidelines when preparing your samples:
Genomic DNA
- Concentration: 50–100 ng/μL
- Purity: OD260/OD280 between 1.8–2.0; no visible contamination
- Condition: Intact, no degradation (check via 2% agarose gel)
- Storage: Dissolved in TE buffer or nuclease-free water, shipped on ice or dry ice
Plant Material
- Fresh, silica-dried, or frozen leaves/tissue
- Avoid mold or physical damage during storage and shipping
Animal Material
- Fresh tissue preserved in ethanol (95–100%)
- Keep at low temperature during transport
Note: All samples should be free of PCR inhibitors (e.g., polysaccharides, phenolic compounds) to ensure optimal amplification quality.
Deliverables – What You Receive
Upon completion of the ISSR analysis, you will receive:
- High-Resolution Gel Images or Electropherograms
Clear, reproducible banding patterns displaying polymorphisms across all analyzed samples.
- Polymorphism Analysis Report
Includes a binary presence/absence matrix, diversity indices, and similarity or distance analysis relevant to your research objectives.
- Optional Data Interpretation Outputs
Phylogenetic trees, clustering diagrams, or population structure analysis based on ISSR banding data.
- All Raw Data Files
Complete datasets in accessible formats (e.g., TIFF, XLSX, FSA) for archival and further analysis.
Service Description
| Service Name | Service Content | Deliverables & Standards |
|---|---|---|
| ISSR Polymorphism Detection | Sample quality check and DNA extraction (if required) | DNA quality report including concentration and purity assessment |
| ISSR primer selection and PCR amplification | High-resolution gel images or capillary electropherograms clearly showing polymorphic band patterns | |
| Polymorphism analysis and data processing | Binary presence/absence matrix (0/1), polymorphism statistics, similarity/distance matrix | |
| Optional bioinformatics analysis | Cluster diagrams, phylogenetic trees, population structure analysis charts | |
| Project reporting and data delivery | Comprehensive experimental report (methods, results, data interpretation), all raw data files (TIFF, XLSX, FSA, etc.) |
Why Choose CD Genomics
Choosing the right partner for ISSR analysis can make the difference between a dataset that is simply "usable" and one that is research-grade, reproducible, and publication-ready. At CD Genomics, we focus exclusively on serving the scientific research community, ensuring that every project is approached with precision and care.
- Tailored Solutions
Every ISSR project is customized to your species, sample type, and study goals. We adapt primer strategies, detection methods, and analysis depth to fit your objectives.
- Proven Data Reliability
Our optimized protocols deliver consistent, reproducible banding patterns, allowing for confident comparisons across experiments and datasets.
- Transparent Communication
From initial consultation to final delivery, we maintain open, clear communication so you always know the status of your project.
- End-to-End Support
We provide not just raw results but also analysis, interpretation options, and guidance to help you integrate the data into your research.
By partnering with CD Genomics, you gain a dedicated technical ally committed to producing molecular data that drives impactful scientific outcomes.
Case Study – ISSR & RAPD for Species Differentiation in Artemisia
Journal: BMC Plant Biology (2025)
Methods Compared: ISSR vs RAPD (with DNA barcoding and SCAR marker development)
Using 5 ISSR primers on wild Egyptian Artemisia species, researchers generated 41 polymorphic bands (100% polymorphism). To resolve closely related species (A. herba-alba vs A. judaica), 27 RAPD primers were applied, yielding 212 bands (99.5% polymorphism). Two RAPD primers, OPA-10 and OPK-07, achieved superior species discrimination and were instrumental in developing eco-specific SCAR markers for reliable species authentication and quality control of medicinal plants.
ISSR profiles of the studied Artemisia species using 5 ISSR primers.
FAQ – Addressing Researcher Concerns
Q1: Can ISSR be applied to species without a reference genome?
A: Yes. ISSR does not require prior genome information, making it ideal for non-model organisms and poorly characterized species.
Q2: How much DNA is needed for ISSR analysis?
A: Typically 50–100 ng/μL of high-quality DNA is sufficient. Lower concentrations may be acceptable, but intact, inhibitor-free DNA ensures optimal results.
Q3: Can ISSR be combined with other marker systems in the same project?
A: Yes. We can integrate ISSR with SSR, RAPD, or other markers to enhance genetic resolution and dataset robustness.
Q4: How reproducible are ISSR results?
A: With optimized primers and PCR conditions, ISSR delivers consistent, high-quality banding patterns across runs and replicates.
Q5: Do you provide data interpretation in addition to raw results?
A: Yes. We offer optional bioinformatics outputs such as clustering analysis, diversity indices, and phylogenetic trees to support your research conclusions.
More About This Service
1. Technical Principle – How ISSR Works
ISSR markers exploit the abundance of simple sequence repeats (microsatellites) in the genome. Primers are designed to target the regions flanking SSR motifs, often with 1–4 anchored bases at the 5' or 3' end to increase specificity. When the SSRs are in opposite orientations within a suitable genomic distance, PCR amplification produces distinct fragments. The resulting polymorphic banding patterns reflect variations in the number, distribution, and orientation of SSRs among samples, enabling precise detection of genetic diversity without the need for prior sequence information.
2. ISSR Compared with Other Molecular Marker Techniques
| Feature | ISSR | RAPD | SSR | AFLP |
|---|---|---|---|---|
| Prior Sequence Info Required | No | No | Yes | No |
| Polymorphism Detection | High | Moderate | High | Very High |
| Reproducibility | High | Low–Moderate | High | High |
| Technical Complexity | Low–Moderate | Low | Moderate | High |
| Cost Efficiency | High | High | Moderate | Low–Moderate |
Key Takeaway: ISSR combines the simplicity of RAPD with the high reproducibility and informativeness of SSR, making it a powerful choice for rapid, cost-effective, and genome-wide polymorphism analysis.
3. Technical Limitations & Considerations
- DNA Quality Matters – Degraded or impure DNA can reduce amplification efficiency and reproducibility.
- Primer Selection – Choice of primer sequence and anchor bases significantly influences polymorphism resolution.
- Band Scoring – Manual scoring of faint or ambiguous bands may introduce subjectivity; using automated gel documentation and software-based analysis improves consistency.
- Limited Functional Insight – Like most neutral markers, ISSR detects variation but does not directly reveal gene function or expression differences.
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