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

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.

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.

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.

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.