Comparative DCMS analysis reveals a novel breed-specific X-linked selection signature in Changthangi sheep

Introduction The X chromosome contributes to important adaptive and fitness-related traits in livestock, but it has received relatively limited attention in sheep genomics, particularly in studies of indigenous Indian breeds. Methods We utilised the de-correlated composite of multiple signals (DCMS) approach, which integrates five individual statistics including FST, H1, H12, Tajima’s D, and π, to identify selection signatures within breeds on the X chromosome in Changthangi (n = 29), Deccani (n = 24), and Garole (n = 26) sheep, genotyped with the Illumina OvineSNP50 BeadChip. Candidate genes and quantitative trait loci (QTLs) in significant regions (FDR 0.05) were annotated using the GALLO package, followed by prioritisation and visualisation through protein–protein interaction networks. Results Our analysis identified a significant genomic region on the X chromosome (∼55.9–57.2 Mb; ∼1.396 Mb) in Changthangi sheep, whereas no comparable signal was detected in Deccani or Garole. This region includes 31 genes, with the top-prioritized genes being OTUD5 , CACNA1F , ZNF182 , and GRIPAP1 . The QTL annotation indicated enrichment for traits related to milk production, body weight, and reproduction, while protein-protein interaction networks identified OTUD5 as a prioritized and relatively well-connected node within the candidate interval. Conclusion This study identifies a breed-specific X-linked candidate selection region in Changthangi sheep and supports the view that X-linked variation may contribute to local adaptation at high altitudes. These findings highlight the value of within-breed composite approaches for investigating the X chromosome in indigenous sheep populations and provide a basis for future validation of candidate genes relevant to adaptation and breeding.