Development and validation of a high density SNP array for indigenous Indian pigs

The present study describes the design and development of a high density SNP array for indigenous Indian pigs. Using whole-genome resequencing of eight populations, over 61 million variants were discovered and filtered to produce a final panel of 635,974 high quality bi-allelic SNPs with genome-wide coverage. The technical performance of the customized array was validated by genotyping 96 samples from a diverse set of porcine breeds. The genotyping results identified 553,289 markers as Poly High Resolution, while only 0.819% were Mono High Resolution. Average call rate was 99.636% and 91.121% or 579,504 markers were best and recommended. The array effectively captured population-level diversity and resolved genetic structure among Indian pigs. An in silico evaluation using SNPs of the customized array extracted from whole genome sequences distinguished both indigenous and global pig breeds. The developed customized high density SNP array offers substantial opportunities for advancing pig genomics in India. It provides a powerful platform with improved precision for population genetics and admixture analysis in porcine populations.