Development and application of a 10 K low-density whole-genome SNP array for chickens

Genomic selection (GS) accelerates genetic improvement in poultry, but the high cost of high-density SNP arrays limits its large-scale application. Here, we developed and validated a cost-effective 10 K SNP array for chickens based on 55 K array data from 58,496 individuals across 16 commercial lines. The genome-wide panel comprises 10,000 SNPs using a multi-step strategy that integrated the fixation index (F_ST), parentage-informative markers, and linkage disequilibrium (LD) pruning. Population genetic analyses showed that the 10 K array effectively captured major genetic diversity and clearly distinguished among groups. Genomic relationship estimates derived from the 10 K and 55 K arrays were highly concordant (r = 0.992), and genomic estimated breeding values (GEBVs) for seven traits showed strong correlations between the two platforms (r ≈ 0.97). Imputation from the 10 K to the 55 K array largely restored predictive accuracy to high-density levels, especially when the reference panel contained full-sibling individuals. These results indicate that the 10 K SNP array achieves an effective balance between cost and performance, and that a low-density plus imputation strategy is effective when a high-quality reference panel is available.