{"id":6201,"date":"2026-05-06T09:33:23","date_gmt":"2026-05-06T09:33:23","guid":{"rendered":"https:\/\/agrosynapsis.com\/?p=6201"},"modified":"2026-05-06T09:33:27","modified_gmt":"2026-05-06T09:33:27","slug":"how-to-turn-a-published-snp-qtl-into-a-diagnostic-kasp-marker","status":"publish","type":"post","link":"https:\/\/agrosynapsis.com\/es\/how-to-turn-a-published-snp-qtl-into-a-diagnostic-kasp-marker\/","title":{"rendered":"How to turn a published SNP\u2013QTL into a diagnostic KASP marker"},"content":{"rendered":"\n

At AgroSynapsis<\/a>, we have successfully completed two editions of our e-course \u201cHow to set up a Marker-Assisted Selection Pipeline\u201d. During these courses \u2014 and in the individual consulting sessions that followed \u2014 we started receiving recurrent questions from students and breeders.<\/p>\n\n\n\n

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.<\/p>\n\n\n\n

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.<\/p>\n\n\n\n

In this post, we address the following common question:<\/p>\n\n\n\n

\u201cI 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?\u201d<\/p>\n\n\n\n

\ud83d\udca1 Short answer:<\/p>\n\n\n\n

You need the exact genomic coordinates of the SNP and its flanking sequence in the reference genome.<\/p>\n\n\n\n

\ud83d\udd2c Practical step-by-step approach<\/p>\n\n\n\n

1\ufe0f\u20e3 Identify the SNP coordinates<\/p>\n\n\n\n

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).<\/p>\n\n\n\n

2\ufe0f\u20e3 Use a public genome browser<\/p>\n\n\n\n

Go to a public genome browser (e.g. Ensembl Plants, NCBI, species-specific databases) and locate the SNP using its coordinates.<\/p>\n\n\n\n

3\ufe0f\u20e3 Extract flanking sequences<\/p>\n\n\n\n

Retrieve ~50 bp upstream and ~50 bp downstream of the SNP.<\/p>\n\n\n\n

4\ufe0f\u20e3 Format the SNP for KASP design<\/p>\n\n\n\n

Insert the SNP in brackets within the sequence, for example:<\/p>\n\n\n\n

\u2026ACTG[A\/G]TCCA\u2026<\/p>\n\n\n\n

5\ufe0f\u20e3 Send the sequence into a genotyping service provider<\/p>\n\n\n\n

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.<\/p>\n\n\n\n

\ud83d\udccc Tip: Always confirm that the SNP is stable, validated and technically robust before investing in large-scale genotyping.<\/p>\n\n\n\n

\ud83d\udc49 If you\u2019d like to be informed about the upcoming workshops organized by AgroSynapsis<\/a>, and receive early access and discounts, \ud835\uddf3\ud835\uddf6\ud835\uddf9\ud835\uddf9 \ud835\uddfc\ud835\ude02\ud835\ude01 \ud835\uddfc\ud835\ude02\ud835\uddff \ud835\ude00\ud835\uddf5\ud835\uddfc\ud835\uddff\ud835\ude01 \ud835\ude01\ud835\uddff\ud835\uddee\ud835\uddf6\ud835\uddfb\ud835\uddf6\ud835\uddfb\ud835\uddf4 \ud835\uddf6\ud835\uddfb\ud835\ude01\ud835\uddf2\ud835\uddff\ud835\uddf2\ud835\ude00\ud835\ude01 \ud835\uddf3\ud835\uddfc\ud835\uddff\ud835\uddfa here:<\/p>\n\n\n\n

https:\/\/lnkd.in\/g3tApqPz<\/a><\/p>\n

<\/div>","protected":false},"excerpt":{"rendered":"

Discover how to convert a published SNP into a practical KASP marker by extracting genomic coordinates and flanking sequences for reliable genotyping.<\/p>","protected":false},"author":2,"featured_media":6204,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_jetpack_memberships_contains_paid_content":false,"footnotes":""},"categories":[68],"tags":[],"class_list":["post-6201","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-tips"],"yoast_head":"\nHow to turn a published SNP\u2013QTL into a diagnostic KASP marker - AgroSynapsis<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/agrosynapsis.com\/es\/how-to-turn-a-published-snp-qtl-into-a-diagnostic-kasp-marker\/\" \/>\n<meta property=\"og:locale\" content=\"es_ES\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"How to turn a published SNP\u2013QTL into a diagnostic KASP marker - 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