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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

Principal component analysis of Jersey cattle using ROH (A) and SNP genotypes (B).Principal component 1 (PC1, x axis) and principal component 2 (PC2, y axis) are plotted. Three groups that are classified based on inbreeding coefficient (FPED) are indicated with three different colors. Blue, red, and black circles represent individuals with FPED<0.03, FPED = 0.03–0.10, and FPED>0.10, respectively.
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pone.0129967.g001: Principal component analysis of Jersey cattle using ROH (A) and SNP genotypes (B).Principal component 1 (PC1, x axis) and principal component 2 (PC2, y axis) are plotted. Three groups that are classified based on inbreeding coefficient (FPED) are indicated with three different colors. Blue, red, and black circles represent individuals with FPED<0.03, FPED = 0.03–0.10, and FPED>0.10, respectively.

Mentions: Although obvious sub-populations were not separated, ROH based PCA showed that the levels of inbreeding coefficients could be roughly separated by PC1 (Fig 1A), which agreed with the trends of changes of inbreeding coefficients in the Jersey population. Using principal components based on ROH, the correlation of PC1 and FPED was high (r = 0.68), whereas correlations of FPED and PC2-PC5 did not exceed 0.1. Based on SNP genotypes, sub groups were not clearly separated by two principal components PC1 and PC2 (Fig 1B).


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)

Principal component analysis of Jersey cattle using ROH (A) and SNP genotypes (B).Principal component 1 (PC1, x axis) and principal component 2 (PC2, y axis) are plotted. Three groups that are classified based on inbreeding coefficient (FPED) are indicated with three different colors. Blue, red, and black circles represent individuals with FPED<0.03, FPED = 0.03–0.10, and FPED>0.10, respectively.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0129967.g001: Principal component analysis of Jersey cattle using ROH (A) and SNP genotypes (B).Principal component 1 (PC1, x axis) and principal component 2 (PC2, y axis) are plotted. Three groups that are classified based on inbreeding coefficient (FPED) are indicated with three different colors. Blue, red, and black circles represent individuals with FPED<0.03, FPED = 0.03–0.10, and FPED>0.10, respectively.
Mentions: Although obvious sub-populations were not separated, ROH based PCA showed that the levels of inbreeding coefficients could be roughly separated by PC1 (Fig 1A), which agreed with the trends of changes of inbreeding coefficients in the Jersey population. Using principal components based on ROH, the correlation of PC1 and FPED was high (r = 0.68), whereas correlations of FPED and PC2-PC5 did not exceed 0.1. Based on SNP genotypes, sub groups were not clearly separated by two principal components PC1 and PC2 (Fig 1B).

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