Limits...
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

Genome-wide associations of ROH and F.Associations of ROH-FPED (-log10p) are plotted against each SNP locus across the genome (A). The y axis (B) represent the effect (slope) of ROH-FPED association and a dotted line indicates the effect = 0 (B). Genome-wide suggestive level is–log10p = 4.3, and the significant threshold (–log10p = 5.4) is shown with dotted line (A). PCA based adjusted associations between ROH and FPED (C) and its effect (D) are plotted. A dotted line displays genome-wide significance level (C).
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4496098&req=5

pone.0129967.g002: Genome-wide associations of ROH and F.Associations of ROH-FPED (-log10p) are plotted against each SNP locus across the genome (A). The y axis (B) represent the effect (slope) of ROH-FPED association and a dotted line indicates the effect = 0 (B). Genome-wide suggestive level is–log10p = 4.3, and the significant threshold (–log10p = 5.4) is shown with dotted line (A). PCA based adjusted associations between ROH and FPED (C) and its effect (D) are plotted. A dotted line displays genome-wide significance level (C).

Mentions: The existence of substantial amounts of variation in the levels of ROH leads us to examine that particular genomic regions were more likely to contribute to changes of the inbreeding coefficient. Associations of ROH and pedigree-based inbreeding coefficients (ROH-FPED associations) were assessed to identify genomic regions accounting for FPED increases. This analysis revealed ROH levels had increased at 60 or more regions (≥1 Mb, genome-wide threshold p≥0.01) with increasing FPED during the last five decades (Fig 2A; Fig 2B; S1 Table). Despite weak statistical evidence, the levels of ROH in most regions (>99%) have increased concomitant with inbreeding coefficient (FPED), whereas ROH of a few genomic regions decreased as inbreeding increased but with weak statistical significance (Fig 2B). Notably, autozygosity in the major histocompatibility complex region (MHC, 25–30 Mb) on BTA 23 has increased as levels of inbreeding elevation, which may affect immune response to infectious disease like somatic cell score (SCS) that is an indicative parameter of mastitis in cattle.


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)

Genome-wide associations of ROH and F.Associations of ROH-FPED (-log10p) are plotted against each SNP locus across the genome (A). The y axis (B) represent the effect (slope) of ROH-FPED association and a dotted line indicates the effect = 0 (B). Genome-wide suggestive level is–log10p = 4.3, and the significant threshold (–log10p = 5.4) is shown with dotted line (A). PCA based adjusted associations between ROH and FPED (C) and its effect (D) are plotted. A dotted line displays genome-wide significance level (C).
© Copyright Policy
Related In: Results  -  Collection

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

pone.0129967.g002: Genome-wide associations of ROH and F.Associations of ROH-FPED (-log10p) are plotted against each SNP locus across the genome (A). The y axis (B) represent the effect (slope) of ROH-FPED association and a dotted line indicates the effect = 0 (B). Genome-wide suggestive level is–log10p = 4.3, and the significant threshold (–log10p = 5.4) is shown with dotted line (A). PCA based adjusted associations between ROH and FPED (C) and its effect (D) are plotted. A dotted line displays genome-wide significance level (C).
Mentions: The existence of substantial amounts of variation in the levels of ROH leads us to examine that particular genomic regions were more likely to contribute to changes of the inbreeding coefficient. Associations of ROH and pedigree-based inbreeding coefficients (ROH-FPED associations) were assessed to identify genomic regions accounting for FPED increases. This analysis revealed ROH levels had increased at 60 or more regions (≥1 Mb, genome-wide threshold p≥0.01) with increasing FPED during the last five decades (Fig 2A; Fig 2B; S1 Table). Despite weak statistical evidence, the levels of ROH in most regions (>99%) have increased concomitant with inbreeding coefficient (FPED), whereas ROH of a few genomic regions decreased as inbreeding increased but with weak statistical significance (Fig 2B). Notably, autozygosity in the major histocompatibility complex region (MHC, 25–30 Mb) on BTA 23 has increased as levels of inbreeding elevation, which may affect immune response to infectious disease like somatic cell score (SCS) that is an indicative parameter of mastitis in cattle.

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