Investigation of selection signatures provides key insights into genetic differences between Holstein and Sarabi dairy cattle breeds

Articles in Press

Document Type : Research Article (Regular Paper)

Authors

1 Department of Animal Science, Faculty of Agriculture, College of Agriculture and Natural Resources, University of Tehran, Karaj, 7787131587, Iran

2 Assistant Professor, Department of Animal Science, Faculty of Agricultural Science, Urmia university, Urmia, Iran

Abstract

Abstract
Selection increases the frequency of beneficial alleles in subpopulations, leaving genomic signatures associated with genes and QTLs controlling economic traits. Genomic data from 60 Holstein and 72 Sarabi cattle were analyzed to identify these selection signatures. Quality control and data filtering were performed using PLINK_1.9 software. The genetic group was identified using three complementary methods: principal component analysis (PCA) with PLINK 1.9, discriminant analysis of principal components (DAPC) implemented in the adegenet package in R, and Admixture analysis conducted with Admixture version 1.23. Subsequently, FST, XP-EHH, and Rsb statistics were used to identify selection signatures. The chromosomal positions of the selected regions were aligned with the bovine genome data (ARS-UCD1.2 Bos Taurus) from the Ensembl Biomart database. Genetic analyses revealed the presence of two distinct genetic groups with different origins. In this study, 16 genomic regions were identified using the FST method, and 18 regions were determined using XP-EHH and Rsb methods, covering approximately 17.5 and 24 Mbp of the bovine genome, respectively. Based on gene ontology analyses, these regions contained coding genes related to key biological processes such as immune response, muscle growth, reproduction, and milk production. Several genes, including MYO1A, STAT6, and PRKAA1, were associated with traits such as carcass quality, fertility, and metabolic processes. The analysis of identified QTLs confirmed the presence of economically important traits, such as growth rate, disease resistance, meat quality, and milk composition. Regions on  Bos taurus autosome (BTA) 6 and 10 were identified as key areas for immune-related genes, while milk production traits were observed on regions of BTA 5, 7, and 20. Overall, these findings provide valuable insights into the genetic basis of important economic traits in cattle and can contribute to future breeding programs aimed at improving productivity and disease resistance.

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References

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Available Online from 13 July 2025

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