Development and validation of a high-density SNP chip tailored for genomic analysis in Indian backyard chickens

1. Indian backyard chicken breeds are well adapted to local climatic conditions and possess distinct genetic characteristics, necessitating a dedicated SNP chip to address their unique genetic diversity, breed identification and conservation needs. In this study, a high-density SNP chip, Axiom_Kukkut was developed with SNP markers derived from genomes of 16 indigenous chicken breeds, Red Jungle Fowl and White Leghorn.2. A total of 622,376 markers and an inter-marker distance of 1.9 kb, the Axiom_Kukkut provided a denser marker distribution compared to existing arrays. The chip was validated by genotyping a set of samples from diverse Indian chicken breeds. All the SNPs were used for validation. An average call rate of 99.92% and 91.28%, as high resolution polymorphic markers, demonstrated the high precision of the designed array.3. Population stratification analysis revealed high genetic diversity and distinct linkage disequilibrium patterns among various breeds. Multivariate principal component analysis confirmed the genetic distinctiveness of Red Jungle Fowl and Uttara, suggesting low genetic diversity due to geographic isolation or specific breeding practices.4. The customised SNP chip allows a multitude of possibilities, including applications in genome-wide association analysis, identification of selection signatures, population genetics and breed improvement programmes for Indian chicken. Continued refinement will expand its utility to include exotic and commercial breeds as well, enhancing its overall applicability across a wider range of chicken populations.