Genomic signals on the X chromosome reveal local adaptations in Ethiopian cattle

Abstract

Background In livestock, understanding the genetic basis of adaptation to the environment is essential for enhancing resilience to climate change and sustaining productivity in diverse environments. Indigenous Ethiopian cattle represent an ideal model for such studies, as they have evolved across a wide range of environments from the cool, oxygen-limited highlands to the hot, pathogen-rich lowlands. These environmental gradients imposed intense selective pressures, shaping their genomic landscape. In this study, we performed the first comprehensive analysis of X-linked adaptive signatures in Ethiopian indigenous cattle using whole-genome sequencing data. Results Population structure analysis revealed clear genetic differentiations between Abigar and Barka cattle, while the remaining populations showed substantial shared ancestry and admixtures. Pairwise fixation index (\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\:{F}_{ST})$$\end{document} estimates, runs of homozygosity (ROH) patterns, and linkage disequilibrium (LD) decay further supported historical isolation and stronger selection pressure in Barka, contrasting with the greater diversity and faster LD decay in Gojjam Highland cattle. Complementary selection signature detections (\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\:{F}_{ST}$$\end{document}, XP-EHH, and\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\:\:iHS$$\end{document}) revealed population-specific and shared genomic regions under selection on the X chromosome. Notably, signals associated with high-altitude adaptation were detected near the RBM3, RPS4X, and TSC22D3 loci. Additional signals were observed in genes related to thermoregulation and oxidative stress response (EDA, SUV39H1, and HDAC8), as well as immune regulation (IRAK1, BDA20, and IL1RAPL1), suggesting adaptation to hot and pathogen-rich environments. Functional enrichment analysis highlighted genes involved in extracellular matrix organization and immune signaling pathways, underscoring their roles in environmental adaptation. Conclusions This study provides the first genome-wide evidence of X-linked adaptive divergence in the Ethiopian cattle. The findings highlight the contribution of the X chromosome to heat tolerance, hypoxia adaptation, and immune resilience, offering valuable genomic insights for breeding programs aimed at enhancing productivity and climate adaptability in tropical cattle. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-026-12817-5.