Uncovering Sub-Structure and Genomic Profiles in Across-Countries Subpopulations of Angus Cattle

Citation

Cardoso, D.F., Fernandes Júnior, G.A., Scalez, D.C.B., Alves, A.A.C., Magalhães, A.F.B., Bresolin, T., Ventura, R.V., Li, C., de Sena Oliveira, M.C., Porto-Neto, L.R., Carvalheiro, R., de Oliveira, H.N., Tonhati, H., Albuquerque, L.G. (2020). Uncovering Sub-Structure and Genomic Profiles in Across-Countries Subpopulations of Angus Cattle. Scientific Reports, [online] 10(1), http://dx.doi.org/10.1038/s41598-020-65565-1

Plain language summary

Angus is one of commonly used breeds in beef production in the world. Investigation on genomic profiles of Angus populations from different geographical areas will provide insights into adaptation mechanisms to different environments and reveal genomic regions associated with divergent selection for various traits. In this study, similarities and differences between genomic patterns of Angus subpopulations born and raised in Canada (N=382) and Brazil (N=566) were assessed based on 31,483 DNA markers (i.e. single nucleotide polymorphisms). The results showed the Canadian and Brazilian Angus populations had similar measures of genomic relationships, inbreeding coefficients, and linkage disequilibrium between DNA markers at varying genomic distances. Further genomic analyses revealed common selection signatures to both Angus populations at chromosomes 13 (63.77-65.25Mb) and 14 (22.81-23.57Mb), which are notably known regions affecting growth traits. However, subdivision of the Canadian and Brazilian Angus populations was detected on chromosomes 7 and 18. These chromosomal regions harbor known genes of reproductive performance, thermoregulation, and resistance to infectious diseases, indicating divergent selection of Canadian and Brazilian Angus in genomic regions associated with the adaptation to different environments. These findings will help understand population differentiation of Angus due to adaptive selection and will also offer strategies to develop genomic tools through joint genomic analyses of different Angus populations.

Abstract

Highlighting genomic profiles for geographically distinct subpopulations of the same breed may provide insights into adaptation mechanisms to different environments, reveal genomic regions divergently selected, and offer initial guidance to joint genomic analysis. Here, we characterized similarities and differences between the genomic patterns of Angus subpopulations, born and raised in Canada (N = 382) and Brazil (N = 566). Furthermore, we systematically scanned for selection signatures based on the detection of autozygosity islands common between the two subpopulations, and signals of divergent selection, via FST and varLD tests. The principal component analysis revealed a sub-structure with a close connection between the two subpopulations. The averages of genomic relationships, inbreeding coefficients, and linkage disequilibrium at varying genomic distances were rather similar across them, suggesting non-accentuated differences in overall genomic diversity. Autozygosity islands revealed selection signatures common to both subpopulations at chromosomes 13 (63.77–65.25 Mb) and 14 (22.81–23.57 Mb), which are notably known regions affecting growth traits. Nevertheless, further autozygosity islands along with FST and varLD tests unravel particular sites with accentuated population subdivision at BTAs 7 and 18 overlapping with known QTL and candidate genes of reproductive performance, thermoregulation, and resistance to infectious diseases. Our findings indicate overall genomic similarity between Angus subpopulations, with noticeable signals of divergent selection in genomic regions associated with the adaptation in different environments.

Publication date

2020-12-01

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