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

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

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

Summary of genomic regions with ROH>0.4.

<p>¹Regions representing homozygosity >0.4, where homozygosity was calculated using ROH status of each SNP in a ≥100 SNP window.</p><p>²Number of SNP associated with BC-MFEC in this genomic region,</p><p>* suggestive.</p><p>³Maximum change of ROH in the region between ancestors born before 1991 and animals born in 2004–7.</p><p>Summary of genomic regions with ROH>0.4.</p

Runs of homozygosity (ROH) in each chromosome.

<p>The levels of ROH (y-axis) are plotted against the SNP genome coordinate on UMD 3.1 (x-axis).</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 plots of scrotal circumference variance explained by SNP windows in Nellore cattle.

<p>Pseudo-phenotypes were based on dEBVs corrected for age (SC_A) and corrected for age and weight at yearling (SC_AW). Each dot represents a 1 Mb SNP window. Horizontal dashed lines represent adopted thresholds (SC_A = 0.40% and SC_Aw = 0.42%). Arrows indicate signals shared between the two models. Histograms represent the distribution of phenotypic variance explained by SNP windows, and the dotted vertical line marks the adopted thresholds.</p

Detected major loci explaining variance in scrotal circumference in Nellore cattle.

a<p>MAF =  Minor allele frequency.</p>b<p> =  Average percentage of phenotypic variance explained by overlapping 1 Mb SNP windows.</p

Regional plots of scrotal circumference variance explained by SNP windows in Nellore cattle.

<p>Pseudo-phenotypes were based on dEBVs corrected for age (SC_A) and corrected for age and weight at yearling (SC_AW). Clear common signals between SC_A and SC_Aw were found on chromosomes A) 6, B) 10, C) 14 and D) 21. Vertical black dashed lines delimit the regions where the highest variance explained were found. Linkage disequilibrium structure for these regions (bottom) is portrayed as a heatmap of r² values between SNPs.</p