If a gene or QTL controlling an agronomic trait is already mapped and described in the literature, you don’t always need SNP arrays or sequencing to use it in your breeding program.
If your lab already works with SSR markers, you can develop a gene-linked SSR using public resources.
Here’s a practical, generic workflow 👇
1️⃣ Start from a known gene or locus
Select a gene or genomic region already associated with a trait of interest (yield, resistance, quality, adaptation). This information typically comes from publications or public databases.
2️⃣ Retrieve the genomic sequence around the locus
-Obtain the gene sequence from a public nucleotide database, like NCBI.
-Use this sequence to locate the gene in the reference genome of the species via a BLAST search.
-Select a high-confidence genomic hit (e.g. E-value ≈ 0).
-Once the genomic location is identified:
-Open the species’ public genome browser.
-Locate the locus in the browser by using the coordinates generated by the BLAST analysis.
-Extract a genomic window around the locus (for example, ~50–100 kb upstream and downstream) and download a decorated FASTA file.
This region will be used to search for SSRs linked to the gene.
3️⃣ Identify SSRs and design primers (web-based tools)
– Use public, web-based SSR tools to scan the extracted genomic sequence.
Tools such as WebSat or MegaSSR are publicly available.
– Visit the tool of your choice and submit the FASTA sequence.
– The program reports repeat length and position of the identified SSRs.
-Automatically design PCR primers flanking the repeat (or you can adjust the PCR parameters)
4️⃣ Genotype and validate
Amplify the SSR using PCR and visualize allele size differences by gel or capillary electrophoresis. Validate the marker across contrasting genotypes to confirm polymorphism and linkage to the trait.
✅ Why this approach works
Uses existing genomic knowledge
Low-cost and PCR-based
Compatible with standard molecular labs
Very effective for marker-assisted selection
💡 Want to learn more? If you found this tip useful and want to dive deeper into developing molecular markers join our course: “How to Set a Marker-Assisted Selection Pipeline”.
👉 Discover the full program:
https://lnkd.in/esqGj4kD
BLOG ON MOLECULAR BREEDING
How to Develop a PCR-Detectable SSR Marker for a Known Gene or Trait?
Discover how to develop gene-linked SSR markers from published QTLs using public genomic resources—without the need for SNP arrays or sequencing.
Estimación de la Heredabilidad - Mide con precisión qué proporción de la variación de un trait es genética, lo que guía a los mejoradores a centrarse en traits con mayor potencial de ganancia genética.
