Whole-genome Characterization of Genetic Diversity, Linkage Disequilibrium and Effective Population Size in Four Indian Goat Breeds from Diverse Agroecological Landscapes

Background: Indian goats represent valuable genetic resources adapted to diverse agro-climatic conditions, yet their genome-wide diversity and demographic history remain inadequately characterized. This study assessed genomic variation, genetic diversity, linkage disequilibrium (LD) and historical effective population size (Ne) in Assam Hill, Bhakarwali, Nandidurga and Kutchi goats. Methods: Whole-genome sequencing of 40 unrelated animals (10 from each breed) generated an average coverage of 9.14X. Reads were aligned to the Capra hircus ARS1.2 reference genome, followed by variant calling and quality filtering, yielding 22.22-28.20 million processed variants across breeds. Result: Ts/Tv ratios were consistent (2.3141-2.3175). Observed and expected heterozygosity ranged from 0.2534-0.2746 and 0.2581-0.2763, respectively, while mean MAF ranged from 0.1758-0.1948. Genomic inbreeding was low (-0.0159-0.0323). LD declined progressively with physical distance, with Kutchi showing relatively greater LD persistence. LD-based Ne estimates revealed a substantial decline from historical to recent generations across all breeds. Overall, the breeds exhibited distinct genomic diversity and demographic patterns, providing valuable insights for breed-specific conservation and sustainable genetic utilization of indigenous Indian goats.