Selection signatures in Gir and Holstein cattle

Natural and artificial selection leave footprints on the genome, known as selection signatures, that can indicate regions related to adaptive and economically important traits. The recurrent use of a limited number of sires and increased selection pressure may affect genetic diversity, potentially affecting long-term breeding programs. Among dairy cattle, the Holstein breed has been intensively selected to maximize productivity, particularly in Canada and the United States. In the dairy industry, the Gir breed plays an important role in milk production in tropical regions such as India and Latin America. Gir cattle were introduced into Brazil in the 19th and 20th centuries, and since 1985, this breed has been intensively selected for milk production. This study aimed to assess the genetic diversity and characterize the selection signatures in Holstein cattle from the United States and Canada (HOL), Gir cattle from India (GIR_IN), and Dairy Gir cattle from Brazil (GIR_BR). Genetic diversity was assessed by nucleotide diversity, single nucleotide variant density analysis, minor allele frequency, observed and expected heterozygosity, and the inbreeding coefficient. Selection signatures were identified via Tajima's D, the integrated haplotype score (iHS), the fixation index, and the cross-population extended haplotype homozygosity test for autosomes. Additionally, the analysis of selection signatures using Tajima's D and iHS was conducted for the X chromosome. Lower genetic diversity was observed in the HOL population, whereas the GIR_IN and GIR_BR populations presented greater diversity. Several genes previously related to economically important traits were identified as being under selection, including DNAJC18, FSHR, HELB, HMGA2, PLAG1, GAB3, and PTEN. In conclusion, the genes identified within the selection signatures were linked to several traits, including growth, reproduction, mastitis, milk production, heat tolerance, health, and adaptation.