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

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

2️⃣ 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
✔️ High reproducibility
✔️ Low missing data
✔️ Standardized workflows and QC
👉 Customized SNP arrays allow you to focus on:
Trait-linked markers
Breeding-specific germplasm
Long-term program consistency
👉 Widely used for:
Routine selection
Genomic selection (especially arrays)
Seed purity and quality control

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

⚖️ How platforms compare on key parameters
GBS:
High throughput ✅ | Missing data ❌ | Reproducibility ⚠️
→ Powerful, but requires strict filtering and careful interpretation
SSRs:
Moderate throughput ⚠️ | Low missing data ✅ | Reproducibility ❌
→ Informative but difficult to standardize
SNP arrays / KASP panels:
High throughput ✅ | Low missing data ✅ | High reproducibility ✅
→ The most robust option for routine decisions

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

👉 Discovery & early-stage selection:
Use GBS
✔️ Explore diversity, discover markers, screen large populations ay low cost

👉 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:

https://lnkd.in/g3tApqPz

How to choose the right genotyping platform for my breeding program?