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

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

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

Increasing the precision in selection by targeting genes or genomic regions associated with those traits.

Allowing Early Trait Detection at the seed or seedling stage, saving time and resources.

Providing higher selection accuracy especially for traits whose expression is influenced by environmental factors or they are assayed by challenging protocols .

Accelerating breeding progress by enhancing selection accuracy and efficiency.