Fig 1.
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.
Fig 2.
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).
Fig 3.
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.
Table 1.
Genome-wide association between ROH and DPR or SCS.
Fig 4.
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.
Table 2.
ROH associated with FPED and birth year of animals.
Table 3.
Summary of the most frequent haplotypic allele using 50 SNP window.
Fig 5.
Association between DPR and the most frequent haplotype using additive (A) and recessive model (B).
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.