Transcontinental patterns of ancestry and selective sweeps on the X-chromosome evolution in indicine and taurine...

Analyses of genomic diversity across the X-chromosome, and its comparison with autosomal diversity, offer valuable insights into the evolutionary dynamics shaping sex-linked genomic architecture. Investigating X-chromosome linked variation can uncover demographic and selective forces that are often undetectable using autosomal markers. In the present study, 50 individuals representing Indian indicine breeds (Ladakhi, Sahiwal, Kangayam, Nelore, and Gir), Chinese indicine breeds (Guangfeng and Wannan), and taurine breeds (Hereford, Simmental, and Hanwoo) were analysed for Xchromosomal diversity. Variant calling and quality filtering resulted in a total of 1,34,617 high-quality single nucleotide polymorphisms. Principal Component Analysis, Admixture modelling, and Phylogenetic construction, revealed a clear genetic differentiation between indicine and taurine groups. Local ancestry inference on the X-chromosome of Ladakhi cattle revealed region-specific introgression and evidence of adaptive admixture from taurine-derived loci which is linked to TRNAV-CAC gene, which influences milk protein content. Analyses of observed heterozygosity, nucleotide diversity, and linkage disequilibrium revealed lower diversity on the X-chromosome relative to autosomes. Extended haplotype homozygositybased selection signatures, namely the Integrated Haplotype Score for within-population and Cross-population Extended Haplotype Homozygosity for between-population comparisons, identified several regions-involved in metabolism, reproduction, disease resistance, and immune response-located in the distal regions of the X chromosome. Overall, this study is the first of its kind in cattle at large scale and provides a foundational framework for future research in X chromosome specific evolutionary biology and functional genomics.

The online version contains supplementary material available at 10.1007/s13205-026-04724-z.