Dynamics of genomic architecture during composite breed development in cattle

Authors: PAIM, TIAGO - University Of Brasilia; Hay, El Hamidi; Wilson, Carrie - Welsh; THOMAS, MILT - Colorado State University; Kuehn, Larry; PAVIA, SAMUEL - Embrapa; MCMANUS, CONCEPTA - University Of Brasilia; Blackburn, Harvey

Submitted to: Animal Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/19/2019
Publication Date: 1/21/2020
Citation: Paim, T., Hay, E.A., Wilson, C.S., Thomas, M., Kuehn, L.A., Pavia, S.R., McManus, C., Blackburn, H.D. 2020. Dynamics of genomic architecture during composite breed development in cattle. Animal Genetics. 51(2):224-234. https://doi.org/10.1111/age.12907.
DOI: https://doi.org/10.1111/age.12907

Interpretive Summary: Hybridization is an important tool for conserving genetic diversity across life forms and increasing productivity among agronomic species. Cattle breeding routinely uses hybridization between the subspecies (B. taurus and B. indicus) to form new breeds like Brangus, which creates a unique opportunity to evaluate the hybridization process across generations of newly formed populations. Using high dense genotyping, we follow the evolution of the hybrid and evaluated its emerging significant genetic structure. We observed an uneven distribution of the founder contributions on various chromosomes and/or specific genomic regions. Therefore, evolutionary events (such as drift, selection and complementarity) are likely shaping the genetic architecture of hybrids promoting this differential composition in the subspecies and the emergence of a uniquely different population. These results can be used by breed associations to better plan strategic breeding goals and marketing strategies.

Technical Abstract: Livestock breeds and threatened species face similar challenges of reduced genetic variation, increased inbreeding and potentially inbreeding depression due genetic drift and selection. Hybridization is useful in extreme cases for conservation biology to perform genetic rescue of highly inbred populations. In livestock, hybridization for formation of new breeds has been used to increase environmental adaptation and productivity. In this study, we used, as proof of concept, Brangus cattle breed, an indicine/taurine hybrid, through the first nine generations after the hybrid was formed. The objective was to understand how the hybridization process and subsequent generations of the new population alters allelic combinations among chromosomes. Furthermore, we explored the genomic regions with deviations from the expected subspecies composition and related these regions to traits under selection. After five generations of inter se mating, a new genetic profile for the breed was identified, showing how complementarity, genetic drift and selection form new genetic groups. We observed that Brangus had 70.38% taurine composition, differing from the expected breed composition of 62.5%. Moreover, some chromosome regions showed different subspecies composition when compared with the whole genome. Sex chromosomes were predominantly taurine. Therefore, we highlighted how complementarity and selection can act on favorable haplotypes coming from the founder breeds and how this contributes to shape the genetic architecture of the new hybrid. Understanding and evaluating the hybridization process at the genomic level can be a powerful tool for livestock and conservation biology.