At AgroSynapsis, we have successfully completed two editions of our e-course “How to set up a Marker-Assisted Selection Pipeline”. During these courses — and in the individual consulting sessions that followed — we started receiving recurrent questions from students and breeders.
Many of these questions are simple but critical, while others are more technical or methodological, especially around molecular markers, their development, and their practical use in breeding programs.
To address these recurring topics and share practical, field-oriented guidance, we are launching this short series of AgroSynapsis Tips, based directly on real questions from real breeding or research programs.
In this post, we address the following common question:
“I found a SNP reported in a publication and linked to a QTL. How can I convert it into a diagnostic lab test using KASP technology?”
💡 Short answer:
You need the exact genomic coordinates of the SNP and its flanking sequence in the reference genome.
🔬 Practical step-by-step approach
1️⃣ Identify the SNP coordinates
From the publication (or supplementary data), retrieve the chromosome and physical position of the SNP in the reference genome of the species of interest (pay attention to use the correct version of the genome).
2️⃣ Use a public genome browser
Go to a public genome browser (e.g. Ensembl Plants, NCBI, species-specific databases) and locate the SNP using its coordinates.
3️⃣ Extract flanking sequences
Retrieve ~50 bp upstream and ~50 bp downstream of the SNP.
4️⃣ Format the SNP for KASP design
Insert the SNP in brackets within the sequence, for example:
…ACTG[A/G]TCCA…
5️⃣ Send the sequence into a genotyping service provider
This formatted sequence is sent to a genotyping facility, which will design allele-specific primers and perform PCR and fluorescence detection using KASP (Kompetitive Allele-Specific PCR) technology.
📌 Tip: Always confirm that the SNP is stable, validated and technically robust before investing in large-scale genotyping.
👉 If you’d like to be informed about the upcoming workshops organized by AgroSynapsis, and receive early access and discounts, 𝗳𝗶𝗹𝗹 𝗼𝘂𝘁 𝗼𝘂𝗿 𝘀𝗵𝗼𝗿𝘁 𝘁𝗿𝗮𝗶𝗻𝗶𝗻𝗴 𝗶𝗻𝘁𝗲𝗿𝗲𝘀𝘁 𝗳𝗼𝗿𝗺 here:
Heritability Estimation – we accurately measures how much of a trait’s variation is genetic, guiding breeders in focusing on traits with higher genetic gain potential.
