{"id":6238,"date":"2026-05-06T10:13:54","date_gmt":"2026-05-06T10:13:54","guid":{"rendered":"https:\/\/agrosynapsis.com\/?p=6238"},"modified":"2026-05-06T10:13:58","modified_gmt":"2026-05-06T10:13:58","slug":"how-to-choose-the-right-genotyping-platform-for-my-breeding-program","status":"publish","type":"post","link":"https:\/\/agrosynapsis.com\/es\/how-to-choose-the-right-genotyping-platform-for-my-breeding-program\/","title":{"rendered":"How to choose the right genotyping platform for my breeding program?"},"content":{"rendered":"

First, we should focus on what really defines a genotyping platform:
\ud83d\udc49 Reproducibility (across batches, labs, and years)
\ud83d\udc49 Throughput (how many samples you can process efficiently)
\ud83d\udc49 Missing data rate (and how much cleaning\/imputation you\u2019ll need)
These three factors determine the data quality as tool of decision making.

\ud83e\uddec Main genotyping platforms in plant breeding
1\ufe0f\u20e3 SSRs (Simple Sequence Repeats)
PCR-based markers targeting repeat regions in the genome.
Moderate throughput
Low missing data
\u26a0\ufe0f Limited reproducibility across labs (allele calling can vary)
\ud83d\udc49 Still useful for: parentage, diversity, legacy datasets

2\ufe0f\u20e3 SNPs (KASP assays \/ SNP arrays)
Targeted genotyping of predefined SNPs at known genomic positions.
KASP (targeted SNP panels): flexible, low-to-medium throughput
SNP arrays (fixed or customized panels): scalable, high-throughput platforms
\u2714\ufe0f High reproducibility
\u2714\ufe0f Low missing data
\u2714\ufe0f Standardized workflows and QC
\ud83d\udc49 Customized SNP arrays allow you to focus on:
Trait-linked markers
Breeding-specific germplasm
Long-term program consistency
\ud83d\udc49 Widely used for:
Routine selection
Genomic selection (especially arrays)
Seed purity and quality control

3\ufe0f\u20e3 GBS (Genotyping-by-Sequencing)
A reduced-representation sequencing approach using restriction enzymes and barcoding to sample SNPs across the genome.
\u2714\ufe0f Very high throughput
\u2714\ufe0f Low cost per sample
\u2757 High missing data
\u2757 Lower reproducibility across runs
\u2757 Requires bioinformatics pipelines and stringent QC
\ud83d\udc49 Typical uses:
Very large early-generation populations
Species without SNP arrays
GWAS and biparental QTL mapping
Diversity panels
Entry-level genomic selection

\u2696\ufe0f How platforms compare on key parameters
GBS:
High throughput \u2705 | Missing data \u274c | Reproducibility \u26a0\ufe0f
\u2192 Powerful, but requires strict filtering and careful interpretation
SSRs:
Moderate throughput \u26a0\ufe0f | Low missing data \u2705 | Reproducibility \u274c
\u2192 Informative but difficult to standardize
SNP arrays \/ KASP panels:
High throughput \u2705 | Low missing data \u2705 | High reproducibility \u2705
\u2192 The most robust option for routine decisions

\ud83c\udfaf So\u2026 which platform for which objective?
\ud83d\udc49 Routine selection (MAS):
Use targeted SNP panels (KASP) or customized SNP arrays
\u2714\ufe0f Focus on a compact set of validated, trait-linked markers
\u2714\ufe0f More effective than hundreds of dispersed genome-wide SNPs
\ud83d\udc49 Genomic selection (advanced programs):
Use medium- to high-density SNP arrays
\u2714\ufe0f Consistent, comparable data across years and environments

\ud83d\udc49 Discovery & early-stage selection:
Use GBS
\u2714\ufe0f Explore diversity, discover markers, screen large populations ay low cost


\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:

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

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

Discover how to choose the right genotyping platform by balancing reproducibility, throughput, and data quality for your breeding decisions<\/p>","protected":false},"author":2,"featured_media":6215,"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-6238","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-tips"],"yoast_head":"\nHow to choose the right genotyping platform for my breeding program? - 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-choose-the-right-genotyping-platform-for-my-breeding-program\/\" \/>\n<meta property=\"og:locale\" content=\"es_ES\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"How to choose the right genotyping platform for my breeding program? 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