Comparison of selection signatures among five meat sheep breeds

Abstract

Selection over the years has led to changes in the animal and plant genomes. Haplotypic blocks throughout the sheep genome are continuously under natural and artificial selection and may contain favorable mutations that cause genome-wide signatures. The present study aimed to compare selection signatures among five meat sheep breeds that were included Charmoise, Mouton Charollais, Lacaune meat, Suffolk, and Texel. selection signatures were identified using the XP-EHH and iHS. Genomic regions under selection in each breed, relative to others, were detected based on XP-EHH scores between each breed and the others, as well as iHS scores within each breed, with thresholds set at the top 0.99. The results of this study showed that the comparison of selection signatures among sheep breeds revealed specific genes under selection in each breed. In Charmoise sheep, the genes HOXD3, MAP3K20, RAPGEF4, SP3, LPGAT1, DNAH8, KIF6, and ABCD3 were identified in selected regions. In Mouton Charollais, the genes DGKB, ADGRB3, and PITPNC1 were detected. In Lacaune meat sheep, the genes ANO4, GRID2, and DBF4B were found. In Suffolk sheep, the genes PTK2B, FNIP1, EYA4, UBASH3B, and SPPL2B were identified. Gene ontology analysis indicated that these genes were associated with cellular pathways. In addition, the results of the QTL report showed that selection in Charmoise sheep primarily targeted carcass traits compared to other breeds. In Mouton Charolais, selection was more focused on body weight, muscle development, and bone density. In Lacaune meat sheep, selection was primarily associated with daily weight gain, body weight, carcass traits, and bone density. In Suffolk sheep, selection targeted carcass weight and muscle density. Finally, in Texel sheep, selection was focused on carcass weight, bone traits, daily weight gain, and bone density. These findings suggest that, despite all breeding programs were focused on meat production in breeds, the direction and type of traits under selection varied among them. Additionally, even for shared traits, the specific selected genomic regions differed across breeds.