Supplemental Material for Falker-Gieske et al., 2019

Supplementary Table 1 contains the coefficients of determination (R²) for each variant on QTL harboring chromosomes where calculation was possible. Supplementary Table 2 containts the complete list of clusters identified in the GWAS with additional supporting information for cluster assignment. GRMs from F2 60k genotypes (File_S1.zip) were created by a "leave one chromsome out" approach using the program "Genome-wide Complex Trait Analysis (GCTA) version 1.91.4 beta3".GWAS was conducted with imputed sequence level F2 genotypes (Supplementary File_S2.zip) for each chromosome using the GRM where the respective chromosome was left out(GRM command: gcta64 --bfile SG_F2_chip_wo_chrNO --autosome --maf 0.01 --make-grm --out SG_F2_chip_wo_chrNO --thread-num 10 --autosome-num 18 ; GWAS command: gcta64 --mlma --covar Kiel_Hoh_cross.covar --bfile F2_beagle4.0_ped_ChrNO --grm SG_F2_chip_wo_chrNO --pheno TRAIT.pheno --out TRAIT_chrNO --maf 0.01 --thread-num 10; replace NO with the respective chromosome number and TRAIT with the respective trait to be analyzed) Phenotype files located in Supplementary File_S2.zip for the traits ADG, BFT, MFR, and CRCL were used in the GWAS. Crosses were used as covariates in the GWAS and provided as a gcta compatible covar file in Supplemental File_S4.zip. SNP locations can be found in the bim files of the genotype data (Supplementary File_S1.zip and Supplementary File_S2.zip). Population structure information is provided in form of a Beagle 4.0 compatible pedigree file (Supplementary File_S3.zip). Raw sequencing data will be made publicly available in the NCBI Sequence Read Archive (SRA). File_S5 contains the 60k chip genotype data in variant call file (VCF) format. Genomic positions have been lifted to genome assembly Sus scrofa 11.1 (GCA_000003025.6) and annotated with dbSNP build 150. gcta compatible covar files for the conditional association analyses with top variants are provided in File_S6.