Manhattan plots of genome-wide association studies for EBVs of commercially important traits in pigs.

<p>The red lines indicate the significance threshold for moderately significant associations (p = 5×10⁻⁵). “Chromosome 0” harbors SNP markers that have not yet been mapped to the pig reference genome. The inserted quantile-quantile (QQ) plots show the observed versus expected log p-values. The straight line in the QQ plots indicates the distribution of SNP markers under the null hypothesis and the skew at the right edge indicate that these markers are stronger associated with the traits than it would be expected by chance. Please note that in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0055951#pone-0055951-g001" target="_blank">Figure 1A</a> there are appear to be associated SNPs on SSC 3, 11, and 14. The two associated SNPs on SSC 3 and 11 mapped to these chromosomes in the Sscrofa 9.2 assembly, but are no longer placed on any chromosome in the Sscrofa 10.2 assembly.</p

Top allelic association hits in the GWAS for QTL affecting commercially important traits.

a<p>p-values were calculated using χ2 tests in an allelic association study.</p>b<p>The positions of the associated SNPs on the latest version of the pig reference genome were determined by BLAST searches with the flanking sequences of the SNPs as provided by illumina with respect to the Sscrofa 10.2 assembly. Some of the flanking sequences did not give a significant BLAST hit with respect to this genome reference sequence.</p

Genotype-phenotype correlations.

<p>The animals were grouped according to genotype at the best associated SNPs of each of the four detected QTL. Animal numbers are indicated at the bottom. The call rates for these SNPs were >98.9%. For each of the four QTL the homozygous alternative genotype classes have different phenotypic distributions (p<0.05, Welch's t-test). (A) EBV pH1 distributions with respect to genotype at SNP ASGA0061594 on SSC 14. (B) EBV carcass length in boars with respect to genotype at SNP ASGA0010032 on SSC 2. (C) EBV rear view hind legs distributions in Swiss Large White boars with respect to genotype at SNP ALGA0058443 on SSC 10. (D) EBV rear view hind legs distributions in Swiss Large White boars with respect to genotype at SNP H3GA0045902 on SSC 16.</p