Additional file 2 of 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
Creators: name: Boitard, Simon
name: Liaubet, Laurence
name: Paris, Cyriel
name: Fève, Katia
name: Dehais, Patrice
name: Bouquet, Alban
name: Riquet, Juliette
name: Mercat, Marie-José
Publisher: name: figshare
Year: 2023
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 2: Figure S1. MDS analysis of the genetic diversity observed in French LW pigs. High-quality SNPs (HQSNP set) with a MAF greater than 0.1 were considered. Figure S2. Summary of the genome-wide scan for recent selection in French LW pigs, chromosomes 1 to 9. Each panel of the figure shows the results of the three tests for selection for a different autosome. P values of the time-LWD (blue), time-LWS (green) and hapFLK (red) tests are plotted in log10 scale (y axis) according to 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 these tests were also highlighted by small triangle marks below the p value plot. Figure S3. Summary of the genome-wide scan for recent selection in French LW pigs, chromosomes 10 to 18. See Figure S2 for details. Figure S4. Top 20 significant GO terms for Biological Processes and association between these terms and groups of selection signature categories. See Fig. 5 for details. Figure S5. Top 20 significant KEGG terms and association between these terms and groups of selection signature categories. See Fig. 5 for details. Table S1. Determination of candidate genes in several selection signatures. This table reports all the genes that (i) can be considered as good candidate genes within their region (based on criteria described below) and (ii) are associated to one of the enriched biological functions listed in Table 3 (or more generally whose biological function is consistent with selection objectives in LW). For a given region of interest, genes that represent even better candidates than those selected based on condition (ii) are also included. Column ‘Nb. genes’ gives the number of genes in a region, and column ‘Gene ID’ lists the candidate genes. Column ‘Local peak’ indicates whether the most relevant test statistic for the region shows a local peak within or close to the gene (see Additional file 4 for summary plots of the four test statistics in all candidate regions); this column takes value NA when no or a single gene is observed in a region. Column ‘Diff. expr.’ indicates whether the gene was found differentially expressed between LWS and LWD in [40]; this column takes value ‘no data’ for genes that were not included in this study. Column ‘Causal variant’ indicates whether a causal variant under selection is known for this gene, or if a small number of potential candidate variants have been identified in our study (these candidates may be functional or not, see the text for more details). Based on all these observations, column ‘Overall evidence’ quantifies the evidence for each candidate gene to be the one under selection in a given region.