Genome-Wide Selection Signatures and Human-Mediated Introgression Events in Bos taurus indicus-influenced Composite Beef Cattle

Seyed Milad Vahedi; Siavash Salek Ardestani; Kian Pahlevan Afshari; Seyed Mohammad Ghoreishifar; Sima Moghaddaszadeh-Ahrabi; Mohammad Hossein Banabazi; Luiz Fernando Brito

doi:10.3389/fgene.2022.844653

Genome-Wide Selection Signatures and Human-Mediated Introgression Events in Bos taurus indicus-influenced Composite Beef Cattle

Front Genet. 2022 May 30:13:844653. doi: 10.3389/fgene.2022.844653. eCollection 2022.

Authors

Seyed Milad Vahedi¹, Siavash Salek Ardestani², Kian Pahlevan Afshari³, Seyed Mohammad Ghoreishifar⁴, Sima Moghaddaszadeh-Ahrabi⁵, Mohammad Hossein Banabazi⁶, Luiz Fernando Brito⁷

Affiliations

¹ Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada.
² Department of Animal Science, Science and Research Branch, Islamic Azad University, Tehran, Iran.
³ Department of Animal Sciences, Islamic Azad University, Varamin-Pishva Branch, Varamin, Iran.
⁴ Department of Animal Science, University College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran.
⁵ Department of Animal Science, Faculty of Agriculture and Natural Resources, Islamic Azad University, Tabriz Branch, Tabriz, Iran.
⁶ Department of Animal Breeding and Genetics (HGEN), Centre for Veterinary Medicine and Animal Science (VHC), Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden.
⁷ Department of Animal Sciences, Purdue University, West Lafayette, IN, United States.

Abstract

Genetic introgression from interbreeding hybridization of European Bos taurus taurus (EBT) and Indian Bos taurus indicus (IBI) cattle breeds have been widely used to combine the climatic resilience of the IBI cattle and the higher productivity of EBT when forming new composite beef cattle (CB) populations. The subsequent breeding strategies have shifted their initial genomic compositions. To uncover population structure, signatures of selection, and potential introgression events in CB populations, high-density genotypes [containing 492,954 single nucleotide polymorphisms (SNPs) after the quality control] of 486 individuals from 15 cattle breeds, including EBT, IBI, and CB populations, along with two Bos grunniens genotypes as outgroup were used in this study. Then, in-depth population genetics analyses were performed for three CB breeds of Beefmaster, Brangus, and Santa Gertrudis. Neighbor-joining, principal components, and admixture analyses confirmed the historical introgression of EBT and IBI haplotypes into CB breeds. The f_dM statistics revealed that only 12.9% of CB populations' genetic components are of IBI origin. The results of signatures of selection analysis indicated different patterns of selection signals in the three CB breeds with primary pressure on pathways involved in protein processing and stress response in Beefmaster, cell proliferation regulation and immune response in Brangus, and amino acids and glucose metabolisms in Santa Gertrudis. An average of >90% of genomic regions underlying selection signatures were of EBT origin in the studied CB populations. Investigating the CB breeds' genome allows the estimation of EBT and IBI ancestral proportions and the locations within the genome where either taurine or indicine origin alleles are under selective pressure. Such findings highlight various opportunities to control the selection process more efficiently and explore complementarity at the genomic level in CB populations.

Keywords: composite beef cattle; indicine; introgression; population genetics; recent selection signatures; taurine.