A versatile high-density customized SNP array for augmenting genomic analysis in sheep

We designed a genome-wide high-density SNP array using genetically diverse sheep of the Indian subcontinent. The array includes 627 509 biallelic markers and was validated on 522 individuals from diverse breeds of the Indian peninsula. The average call rate for samples passing quality control was 99.6%, with 96.15% (603 523) markers classified as best and recommended. The high-density SNP array offers dense genomic coverage with an average intermarker distance of 4.6 kb, effectively delineates breed-specific clusters and reveals population stratification, underscoring its utility for genetic analysis, selection, and conservation in sheep. This array addresses the limited representation of Asian and African ovine diversity of the commercially available SNP arrays for sheep. Its applicability across global breeds further supports its value in international ovine genomics.