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

Area of Science:

• Animal Genetics
• Quantitative Genetics
• Genomic Selection

Background:

• Genomic selection (GS) accelerates genetic improvement in poultry.
• High costs of high-density SNP arrays hinder large-scale GS application in commercial poultry lines.

Purpose of the Study:

• Develop and validate a cost-effective 10K SNP array for chickens.
• Assess the performance of the 10K array for genomic prediction and population structure analysis.

Main Methods:

• Developed a 10K SNP array using 55K array data from 58,496 individuals across 16 commercial lines.
• Integrated fixation index (FST), parentage-informative markers, and linkage disequilibrium (LD) pruning for SNP selection.
• Validated the 10K array against a 55K array for genomic relationships and genomic estimated breeding values (GEBVs).

Main Results:

• The 10K SNP array captured major genetic diversity and distinguished between population groups.
• Genomic relationship estimates from 10K and 55K arrays were highly concordant (r=0.992).
• GEBVs for seven traits showed strong correlations between the 10K and 55K platforms (r≈0.97).
• Imputation from 10K to 55K largely restored predictive accuracy, especially with full-sibling reference panels.

Conclusions:

• The 10K SNP array offers a cost-effective solution for poultry GS, balancing cost and performance.
• A low-density SNP array combined with imputation is effective for GS when a high-quality reference panel is available.