Effect of Artificial Selection on Runs of Homozygosity in U.S. Holstein Cattle

Abstract

The intensive selection programs for milk made possible by mass artificial insemination increased the similarity among the genomes of North American (NA) Holsteins tremendously since the 1960s. This migration of elite alleles has caused certain regions of the genome to have runs of homozygosity (ROH) occasionally spanning millions of continuous base pairs at a specific locus. In this study, genome signatures of artificial selection in NA Holsteins born between 1953 and 2008 were identified by comparing changes in ROH between three distinct groups under different selective pressure for milk production. The ROH regions were also used to estimate the inbreeding coefficients. The comparisons of genomic autozygosity between groups selected or unselected since 1964 for milk production revealed significant differences with respect to overall ROH frequency and distribution. These results indicate selection has increased overall autozygosity across the genome, whereas the autozygosity in an unselected line has not changed significantly across most of the chromosomes. In addition, ROH distribution was more variable across the genomes of selected animals in comparison to a more even ROH distribution for unselected animals. Further analysis of genome-wide autozygosity changes and the association between traits and haplotypes identified more than 40 genomic regions under selection on several chromosomes (Chr) including Chr 2, 7, 16 and 20. Many of these selection signatures corresponded to quantitative trait loci for milk, fat, and protein yield previously found in contemporary Holsteins.

Genomic inbreeding estimation in small populations: evaluation of runs of homozygosity in three local dairy cattle breeds

“…The maximum size of ROH was 112.65 Mb and was found on BTA8 in Cinisara breed. Kim et al (2013) . The comparison of ROH is not straightforward since different studies used different criteria in particular for the minimum length of ROH and the minimum number of SNPs involved in ROH.…”

Inferring Individual Inbreeding and Demographic History from Segments of Identity by Descent inFicedulaFlycatcher Genome Sequences

“…Although the frequency and genomic distribution of ROH has been characterized in humans (McQuillan et al 2008(McQuillan et al , 2012Auton et al 2009;Nalls et al 2009;Kirin et al 2010;Nothnagel et al 2010;Polašek et al 2010;Pemberton et al 2012) and commercial livestock or closely related species (Pollinger et al 2011;Purfield et al 2012;Ferenčaković et al 2013;Kim et al 2013;MacLeod et al 2013), we know little about ROH in natural populations of nonmodel organisms where demographic histories and genomic characteristics often differ substantially from humans and livestock. The rapidly increasing availability of genome assemblies and resequencing data in nonmodel organisms now makes it possible to study ROH at a very high resolution in any species.…”

Evaluating signatures of selection through variation in linkage disequilibrium among different cattle breeds

“…The changes in genetic aspects of behavioural control for new adaptations, from survive to thrive, and using available resources have also been detected under positive selection in several populations (Randhawa et al, 2016). Kim et al (2013) found that several of the regions that had differing levels of ROH across populations were associated with economically important traits including milk, fat and protein yield. The same approach was utilized in this study to detect signatures of selection in common and different across populations.…”

“…Due to this the usefulness of F ST to determine regions that are different within a breed is reduced, therefore alternative methods have been used (Howard et al, 2015). One such alternative method to characterize the genomic differences across populations is to compute the average or a specific region's ROH (runs of homozygosity) frequency (Ferenčaković et al, 2013;Kim et al, 2013).…”