ROH associated with FPED and birth year of animals.

<p>¹ Region is defined by the common regions of genome-wide ROH-FPED associations and significant associations of birth year and ROH.</p><p>² Genome-wide associations of ROH and FPED <b>(-log</b>_<b>10</b><b>p)</b>.</p><p>³ Effect (slope) and position of the most significant association of ROH and FPED.</p><p>⁴<i>F</i>_<i>L</i> = Level of ROH at the locus with the most significant association.</p><p>ROH associated with FPED and birth year of animals.</p

ROH-DPR associations.

<p>A) Significance of ROH-DPR association B) Effect of ROH-DPR association. A dotted line shows genome-wide significant threshold (adjusted 1% level, A). The positive or negative effect of daughter pregnancy rate (DPR) and ROH, which are defined by the slope of regression is plotted across the genome (B). Negative effect represents the region with decreased the levels of DPR by increased levels of ROH.</p

Summary of the most frequent haplotypic allele using 50 SNP window.

<p>¹ Allele 1 to 5 was assigned by the descending order of haplotype frequency.</p><p>² Mean of expected frequency/homozygosity and standard deviation without inbreeding.</p><p>³ Mean of expected homozygosity.</p><p>⁴ Mean of observed homozygosity.</p><p>⁵ Percentage of observed homozygosity in homozygosity of all haplotypes.</p><p>Summary of the most frequent haplotypic allele using 50 SNP window.</p

Genome-wide association between ROH and DPR or SCS.

<p>¹DPR = daughter pregnancy rate; SCS = somatic cell score.</p><p>²Regions was defined by genome-wide suggestive level of ROH-trait associations.</p><p>³Maximum association in the region.</p><p>⁴<i>F</i>_<i>L</i>⁼ ROH of a SNP locus.</p><p>⁵**1%, *5%, genome-wide thresholds of association between ROH and FPED without considering stratification. The value shows-log₁₀(p-value).</p><p>Genome-wide association between ROH and DPR or SCS.</p

Association between DPR and the most frequent haplotype using additive (A) and recessive model (B).

<p>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.</p

Comparison of genomic locations for GWAS, signature of selection, and ROH results.

<p>Each bar in red (upper), orange (middle), and blue (lower) represents SNP:BC-MFEC associations (adjusted p<0.05), |iHS|>3.0, and ROH>0.3, respectively.</p

Genome-wide plot of standardized |iHS|.

<p>Each dot represents |iHS| of a SNP that is located at the center of an extended haplotype (10 Mb) plotted against its genome coordinate on UMD 3.1. Dotted line is |iHS| = 3.</p

Genomic regions encompassing significant |iHS| scores.

<p>¹ Region represents location between the first and the last core SNP with |iHS|>3.</p><p>² The UMD 3.1 genome coordinate of SNP with the highest |iHS| score in the designated signature region.</p><p>³ The number of core haplotype SNPs with |iHS|>3 in the designated signature region.</p><p>Genomic regions encompassing significant |iHS| scores.</p

Positional candidate genes related to immunological pathways.

<p>¹Gene ID (Chromosomal location).</p><p>²Annotation in KEGG pathway [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0119380#pone.0119380.ref034" target="_blank">34</a>].</p><p>Positional candidate genes related to immunological pathways.</p

Manhattan plot of BovineSNP50 marker association tests with transformed mean FEC.

<p>Each dot indicates significance level (–log₁₀p) of an association for BovineSNP50 marker relative to its UMD 3.1 genome coordinate. Suggestive and significance thresholds are described in the Materials and Methods.</p