Genome wide copy number diversity in Indian goat breeds scaled to world-wide breeds

Copy number variations (CNVs), heritable chromosomal structural changes characterized by deletions or insertions exceeding 50 base pairs, is an emerging area in genetic diversity research due to their significant roles in morphological, metabolic, and adaptive traits. Despite the global exploration of CNVs across various species, limited attention has been given to goats, particularly Indian breeds. This study utilized whole-genome resequencing (WGRS) data from Indian goat breeds in comparison to transboundary and global breeds/populations, including wild relatives, to investigate copy number variation regions (CNVRs) as markers of genetic diversity and population structure. A total of 103 sequences from indigenous breeds and nine publicly available trans-boundary sequences representing Black Bengal and Beetal goats were analyzed as Dataset-I, while Dataset-II comprised 262 whole genome sequences from global breeds and wild relatives. CNVRs were identified using CNVcaller, leveraging normalized read depth across sliding windows, resulting in 63,728 CNVRs in Dataset-I and 48,869 CNVRs in Dataset-II. These numbers surpass previous reports, attributed to refined resolution, larger sample sizes, and advanced detection algorithms. Principal component analysis (PCA) and admixture analyses leveraged by CVerror (https://github.com/chau-mau/CVerror) revealed clustering patterns, demonstrating genetic uniqueness among Indian breeds while highlighting admixture with transboundary populations. Phylogenetic analysis using custom pipeline named Plink2Phylo (https://github.com/kkokay07/pq-genetics/tree/main/Plink2Phylo; Kanaka 2025), identified distinct evolutionary nodes, with Uttarakhand Hill and Black Bengal showing unique clustering patterns, affirming rich genetic diversity. This research provides a comprehensive framework for understanding CNVR-based genetic diversity in Indian goats, positioning them within the global genetic landscape.