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Fig. 2 | Genetics Selection Evolution

Fig. 2

From: Whole-genome sequencing of cryopreserved resources from French Large White pigs at two distinct sampling times reveals strong signatures of convergent and divergent selection between the dam and sire lines

Fig. 2

Signature of divergent selection around the IGF2 gene. Top: Summary of the genome scan for selection on chromosome 2. P values of the time-LWD (blue), time-LWS (green) and hapFLK (red) tests are plotted in log10 scale (y axis) for HQSNPs as a function of the genomic position (x axis). Opposite signs are used for time-LWD and time-LWS on the one hand and hapFLK on the other hand, i.e. low p values correspond to highly negative points for time-LWD and time-LWS and to highly positive points for hapFLK. Significant p values are shown in darker color for the three tests. For time-LWD and time-LWS, SNPs ranked as significant by the local score approach (see “Methods” for further details) may be hidden by non-significant SNPs with higher individual p values, so significant regions for the local score were also highlighted by small triangle marks below the plot. Bottom: focus on the signature of selection detected in both LWD and LWS from 1.22 to 1.53 Mb (SSC2:1 region). The left panel shows the values of the three statistics plus FLK (in purple) for all available variants (AV set) in the region, together with genes included in the region (genes without gene name are reported with their Ensembl ID). The right panel shows the haplotype diversity in this region, estimated using hapFLK with 10 haplotype clusters (for a single EM run). For a given genomic position, each color corresponds to a different haplotype cluster and the height of the color band in a given population (represented by one of the panels) gives the frequency of the cluster in this population

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