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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

Comparisons of ROH-DPR, ROH-SCS and ROH-FPED.On each chromosome, red (upper), orange (middle) and blue (lower) bar display the significant associations of ROH-SCS, ROH-FPED, and ROH-DPR, respectively. The chromosome number is shown on the left side of each chromosome. Horizontal scale on top and bottom indicates genomic position (Mb) on a chromosome.
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pone.0129967.g004: Comparisons of ROH-DPR, ROH-SCS and ROH-FPED.On each chromosome, red (upper), orange (middle) and blue (lower) bar display the significant associations of ROH-SCS, ROH-FPED, and ROH-DPR, respectively. The chromosome number is shown on the left side of each chromosome. Horizontal scale on top and bottom indicates genomic position (Mb) on a chromosome.

Mentions: When comparing the regions significantly associated with traits or F, ROH that affected the change of inbreeding coefficient did not greatly influence the traits known to be influenced by inbreeding depression in most genomic regions (Fig 4). However, the association of ROH and DPR appeared to be related to local autozygosity that has increased with overall inbreeding at six regions. To assess the correlation further, a genome-wide correlation coefficient was calculated between the associations. Overall, moderate correlations were found between the results from genome-wide associations of ROH and traits, birth year, and inbreeding coefficient using regression coefficients (S2 Table). The effects of ROH-FPED associations and ROH-DPR associations were correlated negatively (-0.24). The association between birth year and ROH, which reflects the consistent change of ROH during the past few decades, was correlated with the effect of associations of ROH-SCS (0.43) or ROH-DPR (-0.28), respectively.


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)

Comparisons of ROH-DPR, ROH-SCS and ROH-FPED.On each chromosome, red (upper), orange (middle) and blue (lower) bar display the significant associations of ROH-SCS, ROH-FPED, and ROH-DPR, respectively. The chromosome number is shown on the left side of each chromosome. Horizontal scale on top and bottom indicates genomic position (Mb) on a chromosome.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0129967.g004: Comparisons of ROH-DPR, ROH-SCS and ROH-FPED.On each chromosome, red (upper), orange (middle) and blue (lower) bar display the significant associations of ROH-SCS, ROH-FPED, and ROH-DPR, respectively. The chromosome number is shown on the left side of each chromosome. Horizontal scale on top and bottom indicates genomic position (Mb) on a chromosome.
Mentions: When comparing the regions significantly associated with traits or F, ROH that affected the change of inbreeding coefficient did not greatly influence the traits known to be influenced by inbreeding depression in most genomic regions (Fig 4). However, the association of ROH and DPR appeared to be related to local autozygosity that has increased with overall inbreeding at six regions. To assess the correlation further, a genome-wide correlation coefficient was calculated between the associations. Overall, moderate correlations were found between the results from genome-wide associations of ROH and traits, birth year, and inbreeding coefficient using regression coefficients (S2 Table). The effects of ROH-FPED associations and ROH-DPR associations were correlated negatively (-0.24). The association between birth year and ROH, which reflects the consistent change of ROH during the past few decades, was correlated with the effect of associations of ROH-SCS (0.43) or ROH-DPR (-0.28), respectively.

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