Abstract
BACKGROUND: Natural and artificial selection are believed to have left traces on the genomes of livestock, often characterized by the fixation of variants linked to traits under selection. These footprints differentiate populations genetically. The selection signatures of four Italian island cattle breeds — Sarda, Sardo Bruna, Sardo Modicana, and Limousine — were studied here using Integrated Haplotype Score, Cross-population Extended Haplotype Homozygosity, and Fixation Index analysis. RESULTS: Several signals of positive selection have been identified in the four beef cattle breeds, with many overlapping regions (31.6% of genes found on recurrent haplotypes). The cross-population extended haplotype homozygosity analysis revealed three notable regions recurring in pairwise comparisons: from 36,681,743 to 38,001,622 bp on BTA6, containing 66 SNPs; from 66,502,254 to 70,354,943 bp on BTA11 with 42 markers; and from 22,781,305 to 24,452,175 bp on BTA14 with 26 SNPs. In total, 134 SNPs were identified as potentially useful discriminant variables across the four breeds. More precisely, SAM and SAR differentiated from the other breeds for the selection signature on BTA6,while SAB for that on BTA11, and finally LIM presented a breed-specific region on BTA14. The region on BTA 6 appears to be the most promising for the genes located there (e.g., LAP3, MED28 , FAM184B, DCAF16, NCAPG, and LCORL), which have been identified in multiple studies as candidate genes for body and bone weight, as well as growth development. CONCLUSIONS: This comprehensive genomic analysis of selection signatures in four beef cattle breeds reared within the same geographic area reveals distinct patterns shaped by both local adaptation and long-term selection pressures. Shared selective sweeps involving key growth and development genes underscore common functional targets across breeds, while unique breed-specific regions highlight their genetic distinctiveness and adaptive strategies. This study could lay the foundation for future valorization and traceability strategies that will be cheap for farmers' and breeders’ associations. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-025-12204-6.