Genomic Breed Composition of Selection Signatures in Brangus Beef Cattle.

Tiago Do Prado Paim,Carrie Wilson,Harvey Blackburn,Samuel R Paiva,Concepta Mcmanus,Milt G Thomas,El Hamidi A Hay,Larry A Kuehn

doi:10.3389/fgene.2020.00710

Abstract

Cattle breeding routinely uses crossbreeding between subspecies (Bos taurus taurus and Bos taurus indicus) to form composite breeds, such as Brangus. These composite breeds provide an opportunity to identify recent selection signatures formed in the new population and evaluate the genomic composition of these regions of the genome. Using high-density genotyping, we first identified runs of homozygosity (ROH) and calculated genomic inbreeding. Then, we evaluated the genomic composition of the regions identified as selected (selective sweeps) using a chromosome painting approach. The genomic inbreeding increased at approximately 1% per generation after composite breed formation, showing the need of inbreeding control even in composite breeds. Three selected regions in Brangus were also identified as Angus selection signatures. Two regions (chromosomes 14 and 21) were identified as signatures of selection in Brangus and both founder breeds. Five of the 10 homozygous regions in Brangus were predominantly Angus in origin (probability >80%), and the other five regions had a mixed origin but always with Brahman contributing less than 50%. Therefore, genetic events, such as drift, selection, and complementarity, are likely shaping the genetic composition of founder breeds in specific genomic regions. Such findings highlight a variety of opportunities to better control the selection process and explore heterosis and complementarity at the genomic level in composite breeds.

Highlights

Breeding methods that exploit heterosis are common in livestock production
A genomic inbreeding coefficient based on runs of homozygosity (ROH) (FROH) was calculated on each animal according to McQuillan et al (2008) with the equation where LROHj is the length of ROHj, and Ltotal is the total size of the autosomes
The runs of homozygosity (ROH) were categorized into four classes according to the expected number of prior generations to a common ancestor (>10, >5, >3, and

Summary

Introduction

Breeding methods that exploit heterosis are common in livestock production. The challenge for adopting terminal crossbreeding systems is consistent genetic composition of replacement heifers from the maternal breed (Lightner and Williams, 2018). Composite breeds ( referred to as synthetic breeds) allow for consistency in heterosis retention and heifer replacement. Brangus, developed in the United States, are an example of a composite breed, defined as 62.5%. Angus and 37.5% Brahman (International Brangus Breeders Association). The breed represents the complementarity between the tropically adapted Bos taurus indicus and the temperate high-valued carcass of Bos taurus taurus cattle (Gregory and Cundiff, 1980; Buzanskas et al, 2017). Brangus registration by the International Brangus Breeders Association started in 1949

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