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

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

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

Additional file 1: of Genome-wide copy number variant analysis reveals variants associated with 10 diverse production traits in Holstein cattle

Figure S1. Box plot for dPTA distribution of the 2 feed intake-related phenotypes of RFI and DMI. (PDF 90 kb

Additional file 2: of Genome-wide copy number variant analysis reveals variants associated with 10 diverse production traits in Holstein cattle

Table S1. Primer information for CNV validation. Table S2. Characteristics of CNV and their overlapped genes. Table S3. Gene ontology (GO) of genes that overlap with CNV. Table S4. CNV-based GWAS results for the 10 phenotypes of interest among Holstein cattle. Table S5. qPCR validation of the significant CNV. (XLSX 96 kb

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

Average genome-wide and refined haplotype sequence read depth from exome capture.

1<p>Each group contains only the individuals that are heterozygous for HH2, HH3, or BH1, except for</p>2<p>L1 Dominette 01449.</p>3<p>UMD3.1 genome coordinates defining the refined haplotype boundaries are presented in the RESULTS.</p

Comparison of BH1 animal status to candidate SV marker genotype calls to identify putative causative mutation for BH1.

1<p>Columns represent the 20 candidate SV markers genotyped to compare concordance with BH1 animal status.</p>2<p>UMD 3.1 genome coordinates on Chr 7.</p>3<p>Ref. Allele is designated as “A” and represents the base call in the genome assembly and Alt. Allele is designated as “B” and represents the variant discovered by exome sequence data. “./.” indicates that no genotype was called. “DEL” equals deletion.</p>4<p>SV genotyped animals were grouped based on refined BH1 status as determined by BovineSNP50 genotypes; “Overall” represents summary of all animals together.</p>5<p>Brown Swiss animals with no BovineSNP50 genotypes.</p

Comparison of HH3 animal status to candidate SV marker genotype calls to identify putative causative mutation for HH3.

1<p>Columns represent the 14 candidate SV markers genotyped to compare concordance with HH3 animal status.</p>2<p>UMD 3.1 genome coordinates on Chr 8.</p>3<p>Ref. Allele is designated as “A” and represents the base call in the genome assembly and Alt. Allele is designated as “B” and represents the variant discovered by exome sequence data. “./.” indicates that no genotype was called. “DEL” equals deletion.</p>4<p>SV genotyped animals were grouped based on refined HH3 status as determined by BovineSNP50 genotypes; “Overall” represents summary of all animals together.</p>5<p>Holstein animals homozygous for sub-segments of refined HH3 based on BovineSNP50 genotypes.</p