MOESM3 of Signatures of selection and environmental adaptation across the goat genome post-domestication
Creators: name: Bertolini, Francesca
name: Servin, Bertrand
name: Talenti, Andrea
name: Rochat, Estelle
name: Kim, Eui
name: Oget, Claire
name: Palhière, Isabelle
name: Crisà, Alessandra
name: Catillo, Gennaro
name: Steri, Roberto
name: Amills, Marcel
name: Colli, Licia
name: Marras, Gabriele
name: Milanesi, Marco
name: Nicolazzi, Ezequiel
name: Rosen, Benjamin
name: Tassell, Curtis
name: Guldbrandtsen, Bernt
name: Sonstegard, Tad
name: Tosser-Klopp, Gwenola
name: Stella, Alessandra
name: Rothschild, Max
name: Joost, Stéphane
name: Crepaldi, Paola
Publisher: name: figshare
Year: 2018
Subjects: subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: FOS: Biological sciences
subject: Genetics
subject: Biotechnology
subject: Evolutionary Biology
subject: Immunology
subject: FOS: Clinical medicine
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: Computational Biology

description: Additional file 3: Table S1. Environmental variables considered for the landscape genomic analysis. Table S2. FLK and hapFLK windows for the sub-continental groups after filtering steps. Overlapping or partially overlapping regions across the different geographical subdivisions are reported with the same letter as used for the population group (from a to m). Table S3. Selective sweeps of early adaptation. The bold values indicate overlap or partial overlap between comparisons. Table S4 Common regions between ROH and XP-EHH and/or FST analyses for the group of “fiber-producing” goat breeds and genes within these regions. Table S5. Common regions between ROH and XP-EHH and/or FST analyses for the group of “meat-producing” goat breeds and genes within these regions. Table S6. Common regions between ROH and XP-EHH and/or FST analyses for the group of “milk-producing” goat breeds and genes within these regions. Table S7. Top four regions detected for the coat color groups (Black, White and Red), indicated comparisons between the groups and genes located nearby these regions. Table S8. Results of the most significant associations involving the 57 filtered SNPs. For each SNP: SNP probe, genotype, genomic coordinate, associated environmental variable (“Env”) and scores and statistical test output values (“Gscore”, “WaldScore”, “Efron”, “AIC”, “Beta_0” and “Beta_1”) are reported. Table S9. List of genes located nearby (± 100 kb) the 57 filtered SNPs obtained by the landscape genomics analysis. Table S10. GO term biological processes. Table S11. MAF (minor allele frequency) and major allele of the 13 SNPs shared by Dry and Temperate/Continental groups. Table S12. Samβada significant results for the SNPs of the FST analyses. For each SNP probe: chromosome and position are reported, as well as Environment, G score, Wald Score, AIC, Abs_Beta1 and the Köppen group in which the SNP was detected by the FST analyses. Table S13. List of genes located nearby (± 100 kb) of the 65 SNPs selected with the FST approach and confirmed by Samβada. The * symbol indicates the SNPs with the highest value (&gt; 0.999) also in landscape genomic analysis