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

• Published in: Scientific reports Vol. 10; no. 1; p. 8770
• Main Authors: Cardoso, Diercles Francisco, Fernandes Júnior, Gerardo Alves, Scalez, Daiane Cristina Becker, Alves, Anderson Antonio Carvalho, Magalhães, Ana Fabrícia Braga, Bresolin, Tiago, Ventura, Ricardo Vieira, Li, Changxi, de Sena Oliveira, Márcia Cristina, Porto-Neto, Laercio Ribeiro, Carvalheiro, Roberto, de Oliveira, Henrique Nunes, Tonhati, Humberto, Albuquerque, Lucia Galvão
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 29-05-2020; Nature Publishing Group
• Subjects: 631/1647/2217/457; 631/1647/2217/748; 631/181/457/649; 631/208/1348; Agriculture; Animal sciences; Animals; Beef; Body Temperature Regulation - genetics; Brazil; Breeding; Canada; Cattle; Cattle - classification; Cattle - genetics; Chromosomes; Disease Resistance - genetics; Divergence; Genetic Markers; Genome; Genomic analysis; Genomics; Humanities and Social Sciences; Inbreeding; Infectious diseases; Islands; Linkage Disequilibrium; multidisciplinary; Population; Principal components analysis; Quantitative trait loci; Reproduction; Reproduction - genetics; Science; Science (multidisciplinary); Species Specificity; Subpopulations; Thermoregulation; Zoology; Brazil; Canada
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-020-65565-1

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 F
ST
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 F
ST
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.