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The Relationship between Runs of Homozygosity and Inbreeding in Jersey Cattle under Selection.

Kim ES, Sonstegard TS, Van Tassell CP, Wiggans G, Rothschild MF - PLoS ONE (2015)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

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.

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.

No MeSH data available.


Related in: MedlinePlus

Association between DPR and the most frequent haplotype using additive (A) and recessive model (B).Each bar demonstrates the association of DPR and haplotype that is defined by the 50-SNP window. Association of DPR and the most frequent haplotype (A) or homozygous status of the most frequent haplotype (B) represents an additive or recessive effect. Genome-wide significance level is shown on each plot.
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pone.0129967.g005: Association between DPR and the most frequent haplotype using additive (A) and recessive model (B).Each bar demonstrates the association of DPR and haplotype that is defined by the 50-SNP window. Association of DPR and the most frequent haplotype (A) or homozygous status of the most frequent haplotype (B) represents an additive or recessive effect. Genome-wide significance level is shown on each plot.

Mentions: When testing the association between ROH and fertility, we found that many regions with high or moderate levels of ROH were associated with fertility positively, suggesting that the genetic effect of most ROH appears to be unrelated to decreasing DPR. In Fig 5A, the significance for the regression showing the additive effect of the most frequent effect on DPR is shown, and in Fig 5B the significance of HH is seen. It was expected that results of the recessive model largely overlapped with regions harboring significant associations of ROH-DPR and correlation of associations from two models was considerably high (r = 0.8). Additionally, even the results from additive genetic model agreed for the regions that were associated with DPR using the recessive genetic model, in addition to the other region influencing fertility additively. In all, our results suggest that associations between ROH and DPR are concordant with the results from either the additive or recessive effects model using the most frequent haplotype, implying that ROH-DPR associations could be interpreted as quantitative trait loci as well as evidence of inbreeding depression due to increased homozygosity.


The Relationship between Runs of Homozygosity and Inbreeding in Jersey Cattle under Selection.

Kim ES, Sonstegard TS, Van Tassell CP, Wiggans G, Rothschild MF - PLoS ONE (2015)

Association between DPR and the most frequent haplotype using additive (A) and recessive model (B).Each bar demonstrates the association of DPR and haplotype that is defined by the 50-SNP window. Association of DPR and the most frequent haplotype (A) or homozygous status of the most frequent haplotype (B) represents an additive or recessive effect. Genome-wide significance level is shown on each plot.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4496098&req=5

pone.0129967.g005: Association between DPR and the most frequent haplotype using additive (A) and recessive model (B).Each bar demonstrates the association of DPR and haplotype that is defined by the 50-SNP window. Association of DPR and the most frequent haplotype (A) or homozygous status of the most frequent haplotype (B) represents an additive or recessive effect. Genome-wide significance level is shown on each plot.
Mentions: When testing the association between ROH and fertility, we found that many regions with high or moderate levels of ROH were associated with fertility positively, suggesting that the genetic effect of most ROH appears to be unrelated to decreasing DPR. In Fig 5A, the significance for the regression showing the additive effect of the most frequent effect on DPR is shown, and in Fig 5B the significance of HH is seen. It was expected that results of the recessive model largely overlapped with regions harboring significant associations of ROH-DPR and correlation of associations from two models was considerably high (r = 0.8). Additionally, even the results from additive genetic model agreed for the regions that were associated with DPR using the recessive genetic model, in addition to the other region influencing fertility additively. In all, our results suggest that associations between ROH and DPR are concordant with the results from either the additive or recessive effects model using the most frequent haplotype, implying that ROH-DPR associations could be interpreted as quantitative trait loci as well as evidence of inbreeding depression due to increased homozygosity.

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

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.

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.

No MeSH data available.


Related in: MedlinePlus