Additional file 1 of Using pre-selected variants from large-scale whole-genome sequence data for single-step genomic predictions in pigs
Creators: name: Jang, Sungbong
name: Ros-Freixedes, Roger
name: Hickey, John M.
name: Chen, Ching-Yi
name: Holl, Justin
name: Herring, William O.
name: Misztal, Ignacy
name: Lourenco, Daniela
Publisher: name: figshare
Year: 2024
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 1: Table S1. Combination of selected variants for each model. ADFI: average daily feed intake; ADG: average daily gain; BF: backfat thickness; LDP: loin depth; TNB: total number of piglets born; NSB: number of stillborn; RET: return to oestrus seven days after weaning; WWT: litter weaning weight; Top40k: Top40k preselected genotype panel; ChipPlusSign: ChipPlusSign preselected genotype panel. Table S2. Number of animals and SNPs for the pre-selected SNP panels in the maternal lines. ML1: maternal line 1; ML2: maternal line 2; Top40k: Top40k preselected genotype panel; *ChipPlusSign: ChipPlusSign preselected genotype panel. Table S3. Number of animals and SNPs for the pre-selected SNP panels in the terminal lines. TL1: terminal line 1; TL2: terminal line 2; TL3: terminal line 3; TL4: terminal line 4; Top40k: Top40k preselected genotype panel; ChipPlusSign: ChipPlusSign preselected genotype panel. Table S4. Number of training and test animals for each model in the two maternal and four terminal lines. ADFI: average daily feed intake; ADG: average daily gain; BF: backfat thickness; LDP: loin depth; TNB: total number of piglets born; NSB: number of stillborn; RET: return to oestrus seven days after weaning; WWT: litter weaning weight; ADGX: ADG recorded in crossbred; BFX: BF recorded in crossbred; LDPX: LDP recorded in crossbred. Table S5. Prediction accuracy of the maternal lines using ssGBLUP. ML1: maternal line 1; ML2: maternal line 2; ADFI: average daily feed intake; ADG: average daily gain; BF: backfat thickness; LDP: loin depth; TNB: total number of piglets born; NSB: number of stillborn; RET: return to oestrus seven days after weaning; WWT: litter weaning weight; standard errors are presented in parenthesis. Table S6. Accuracy gain and reduction (%) compared to Chip data in the maternal lines. ML1: maternal line 1; ML2: maternal line 2; ADFI: average daily feed intake; ADG: average daily gain; BF: backfat thickness; LDP: loin depth; TNB: total number of piglets born; NSB: number of stillborn; RET: return to oestrus seven days after weaning; WWT: litter weaning weight. Table S7. Prediction accuracy of the terminal lines using ssGBLUP. TL1: terminal line 1; TL2: terminal line 2; TL3: terminal line 3; TL4: terminal line 4; ADFI: average daily feed intake; ADG: average daily gain; BF: backfat thickness; LDP: loin depth; ADGX: ADG recorded in crossbred; BFX: BF recorded in crossbred; LDPX: LDP recorded in crossbred; standard errors are presented in parenthesis. Table S8. Accuracy gain and reduction (%) compared to Chip data in the terminal lines. TL1: terminal line 1; TL2: terminal line 2; TL3: terminal line 3; TL4: terminal line 4; ADFI: average daily feed intake; ADG: average daily gain; BF: backfat thickness; LDP: loin depth; ADGX: ADG recorded in crossbred; BFX: BF recorded in crossbred; LDPX: LDP recorded in crossbred. Table S9. Slope (b1) of the regression of dEBV on GEBV for the maternal lines using ssGBLUP. ML1: maternal line 1; ML2: maternal line 2; ADFI: average daily feed intake; ADG: average daily gain; BF: backfat thickness; LDP: loin depth; TNB: total number of piglets born; NSB: number of stillborn; RET: return to oestrus seven days after weaning; WWT: litter weaning weight; Standard errors are presented in parenthesis. Table S10. Slope (b1) of the regression of dEBV on GEBV for the terminal lines using ssGBLUP. TL1: terminal line 1; TL2: terminal line 2; TL3: terminal line 3; TL4: terminal line 4; ADFI: average daily feed intake; ADG: average daily gain; BF: backfat thickness; LDP: loin depth; ADGX: ADG recorded in crossbred; BFX: BF recorded in crossbred; LDPX: LDP recorded in crossbred; Standard errors are presented in parenthesis. Table S11. Slope (b1) of the regression of dEBV on GEBV for WssGBLUP compared to ssGBLUP. ML1: maternal line 1; ML2: maternal line 2; TL1: terminal line 1; TL4: terminal line 4; ADFI: average daily feed intake; ADG: average daily gain; BF: backfat thickness; LDP: loin depth; Top40k: top40k preselected genotype panel; Top40k weighted: top40k using BayesR weighting; ChipPlusSign: ChipPlusSign preselected genotype panel; ChipPlusSign weighted: ChipPlusSign using BayesR weighting; Standard errors are presented in parenthesis