The initial set of finger millet mid-density panel was developed using 3,730 SNP markers validated on 470 diverse finger millet accessions including 182 African and 288 Asian lines. A total of 2,606 SNPs (69.9%) with robust performance were retained.
All selected SNPs are distributed across 18 chromosomes of the A and B genomes and are located within genic regions, enhancing relevance for trait association studies.
SNP distribution plot with 2,606 SNPs on the finger millet genome
Overall Marker Performance
| Mean call rate | Median call rate | Mean MAF | Mean heterozygosity | Mean PIC | |
|---|---|---|---|---|---|
| Overall | 0.88 | 0.95 | 0.12 | 0.18 | 0.15 |
| African lines | 0.93 | 0.98 | 0.07 | 0.10 | 0.08 |
| Asian lines | 0.84 | 0.94 | 0.15 | 0.22 | 0.18 |
Marker Filtering Criteria
- Call rate ≥ 0.8 (80%)
- Minor allele frequency (MAF) ≥ 0.05 (5%)
Quality Metrics of Markers
| Metric | Number | Percentage |
|---|---|---|
| Call rate ≥ 95% | 1,225 | 48% |
| Call rate ≥ 80% | 2,026 | 78% |
| Polymorphic (MAF >5%) | 2,127 | 82% |
| High quality (CR ≥80% & MAF >5%) | 1,789 | 69% |
Principal Component Analysis of African and Asian germplasm
The clear separation observed along the principal components indicates a distinct population structure between African and Asian finger millet lines.
