title: The Relationship between Runs of Homozygosity and Inbreeding in Jersey Cattle under Selection.
abstract: Inbreeding is often an inevitable outcome of strong directional artificial selection but on average it reduces population fitness 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 regions affecting fitness. To examine the influence of genomic autozygosity on fitness, we used a genome-wide association test to evaluate potential negative correlations between ROH and daughter pregnancy rate (DPR) or somatic cell score (SCS) in US Jersey cattle. In addition, relationships between changes of local ROH and inbreeding coefficients (F) were assessed to locate genomic regions with increased inbreeding. Despite finding some decreases in fertility associated with incremental increases in F, most emerging local ROH 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.
authors.affiliation: Animal Genomics & Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, Maryland, United States of America; Department of Animal Science, Iowa State University, Ames, Iowa, United States of America.
authors.forename: Eui-Soo
authors.initials: ES
authors.lastname: Kim
authors.affiliation: Animal Genomics & Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, Maryland, United States of America.
authors.forename: Tad S
authors.initials: TS
authors.lastname: Sonstegard
authors.affiliation: Animal Genomics & Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, Maryland, United States of America.
authors.forename: Curtis P
authors.initials: CP
authors.lastname: Van Tassell
authors.affiliation: Animal Genomics & Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, Maryland, United States of America.
authors.forename: George
authors.initials: G
authors.lastname: Wiggans
authors.affiliation: Department of Animal Science, Iowa State University, Ames, Iowa, United States of America.
authors.forename: Max F
authors.initials: MF
authors.lastname: Rothschild
mesh_terms: D000483:Alleles; D000818:Animals; D002417:Cattle / Q000235:genetics*; D005260:Female; D005298:Fertility / Q000235:genetics; D016678:Genome; D055106:Genome-Wide Association Study; D006239:Haplotypes / Q000235:genetics; D006720:Homozygote; D007178:Inbreeding; D008297:Male; D008957:Models, Genetic; D010375:Pedigree; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D011247:Pregnancy; D025341:Principal Component Analysis