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 10K SNP array for chickens based on 55K 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 10K array effectively captured major genetic diversity and clearly distinguished among groups. Genomic relationship estimates derived from the 10K and 55K 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 10K to the 55K array largely restored predictive accuracy to high-density levels, especially when the reference panel contained full-sibling individuals. These results indicate that the 10K 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.
Ma et al. (Sun,) studied this question.