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Location: Animal Genomics and Improvement Laboratory

Title: The relationship between runs of homozygosity and inbreeding in Jersey cattle under selection

item KIM, EUI-SOO - Iowa State University
item Sonstegard, Tad
item Van Tassell, Curtis - Curt
item Wiggans, George
item ROTHSCHILD, MAX - Iowa State University

Submitted to: PLoS One
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/14/2015
Publication Date: 7/8/2015
Citation: Kim, E., Sonstegard, T.S., Van Tassell, C.P., Wiggans, G.R., Rothschild, M. 2015. The relationship between runs of homozygosity and inbreeding in Jersey cattle under selection. PLoS One. 10(7):e0129967.

Interpretive Summary: Inbreeding in cattle is often associated with decreases in fertility and overall animal fitness. In this study, we examined if the levels of genomic homozygosity were associated with fertility as measured by daughter pregnancy rate (DPR) and/or resistance to bacterial infection of the udder as measured by somatic cell score (SCS). Both of these phenotypic traits are measured by producers, and resultant breed calculations are used for making breeding decisions for genetic improvement of these traits with the index of net merit. The genomic homozygosity was determined using SNP data from the Illumina Bovine50K SNP chip. Our analysis found no significant association between homozygosity of specific genomic regions and the traits of DPR and SCS. However, it was noted that many of the homozygous regions are associated with increased production, as would be expected for selection based on traits with additive effects. Continued monitoring of Jersey breed diversity using SNP associations to these traits should continue in the future, if inbreeding levels should rise in future generations.

Technical Abstract: Inbreeding is often an inevitable outcome of strong directional artificial selection but it reduces fitness in a population with increased frequency of recessive deleterious alleles. Runs of homozygosity (ROH) representing genomic autozygosity that occur from mating between selected and genomically related individuals may be able to reveal the region(s) affecting fitness. A negative correlation between autozygosity and daughter pregnancy rate (DPR) or somatic cell score (SCS) provides evidence of inbreeding depression in dairy cattle. To examine the influence of genomic autozygosity on fitness, a genome-wide association test was performed between traits and ROH in Jersey cattle. In addition, relationships between changes of local ROH and inbreeding coefficient (F) were assessed to evaluate genomic regions which appear to have influenced increased inbreeding. Despite decreases in fertility associated with incremental increases in inbreeding coefficients, most emerging local ROH with increasing F were not significantly associated with DPR or SCS. Furthermore, the analyses of ROH could be approximated with the most frequent haplotype(s), including the associations of ROH and F or traits. The analysis of the most frequent haplotype revealed that associations of ROH and fertility could be accounted for by the additive genetic effect on the trait. Thus, we suggest that a change of autozygosity is more likely to demonstrate footprints of selected haplotypes for production rather than highlight the possible increased local autozygosity of a recessive detrimental allele resulting from the mating between closely related animals in Jersey cattle.