Additional file 1 of Marker effect p-values for single-step GWAS with the algorithm for proven and young in large genotyped populations
Creators: name: Leite, Natália Galoro
name: Bermann, Matias
name: Tsuruta, Shogo
name: Misztal, Ignacy
name: Lourenco, Daniela
Publisher: name: figshare
Year: 2024
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 1: Figure S1. Manhattan plots for all p-value computing methods with a reduced data set in replicate 2. Single-step genome-wide association study for post-weaning weight with p-values obtained from a data set of 50K genotyped animals with (A) $${\mathbf{G}}^\mathbf{-1}$$ G - 1 and $${\mathbf{C}}^{{\mathbf{u}}_\mathbf{2}{\mathbf{u}}_\mathbf{2}}$$ C u 2 u 2 (Exact_Ginv), (B) $${\mathbf{G}}_{\mathbf{A}\mathbf{P}\mathbf{Y}}^\mathbf{-1}$$ G A P Y - 1 and $${\mathbf{C}}^{{{\mathbf{u}}_{\mathbf{2}_{\mathbf{C}}}}{\mathbf{u}}_{\mathbf{2}_{\mathbf{C}}}}$$ C u 2 C u 2 C (Exact_GinvAPY), and (C) $${\mathbf{G}}_{\mathbf{A}\mathbf{P}\mathbf{Y}}^\mathbf{-1}$$ G A P Y - 1 and $${\mathbf{C}}^{{{\mathbf{u}}_{\mathbf{2}_{\mathbf{C}}}}{\mathbf{u}}_{{\mathbf{2}_{\mathbf{C}}}_{{\varvec{a}}{\varvec{p}}{\varvec{p}}{\varvec{r}}{\varvec{o}}{\varvec{x}}}}}$$ C u 2 C u 2 C a p p r o x (Approx_GinvAPY) in replicate 2; SNPs highlighted in green represent the three most significant SNP in the two peaks found with Exact_Ginv (benchmark). Figure S2. Manhattan plots for all p-value computing methods with a reduced data set in replicate 3. Single-step genome-wide association study for post-weaning weight with p-values obtained from a data set of 50K genotyped animals with (A) $${\mathbf{G}}^\mathbf{-1}$$ G - 1 and $${\mathbf{C}}^{{\mathbf{u}}_\mathbf{2}{\mathbf{u}}_\mathbf{2}}$$ C u 2 u 2 (Exact_Ginv), (B) $${\mathbf{G}}_{\mathbf{A}\mathbf{P}\mathbf{Y}}^\mathbf{-1}$$ G A P Y - 1 and $${\mathbf{C}}^{{{\mathbf{u}}_{\mathbf{2}_{\mathbf{C}}}}{\mathbf{u}}_{\mathbf{2}_{\mathbf{C}}}}$$ C u 2 C u 2 C (Exact_GinvAPY), and (C) $${\mathbf{G}}_{\mathbf{A}\mathbf{P}\mathbf{Y}}^\mathbf{-1}$$ G A P Y - 1 and $${\mathbf{C}}^{{{\mathbf{u}}_{\mathbf{2}_{\mathbf{C}}}}{\mathbf{u}}_{{\mathbf{2}_{\mathbf{C}}}_{{\varvec{a}}{\varvec{p}}{\varvec{p}}{\varvec{r}}{\varvec{o}}{\varvec{x}}}}}$$ C u 2 C u 2 C a p p r o x (Approx_GinvAPY) in replicate 3; SNPs highlighted in green represent the three most significant SNP in the two peaks found with Exact_Ginv (benchmark). Figure S3. QQ plots for all p-value computing methods with a reduced data set in replicate 2. QQ plots for p-values obtained from a data set of 50K genotyped animals with (A) $${\mathbf{G}}^\mathbf{-1}$$ G - 1 and $${\mathbf{C}}^{{\mathbf{u}}_\mathbf{2}{\mathbf{u}}_\mathbf{2}}$$ C u 2 u 2 (Exact_Ginv), (B) $${\mathbf{G}}_{\mathbf{A}\mathbf{P}\mathbf{Y}}^\mathbf{-1}$$ G A P Y - 1 and $${\mathbf{C}}^{{{\mathbf{u}}_{\mathbf{2}_{\mathbf{C}}}}{\mathbf{u}}_{\mathbf{2}_{\mathbf{C}}}}$$ C u 2 C u 2 C (Exact_GinvAPY), and (C) $${\mathbf{G}}_{\mathbf{A}\mathbf{P}\mathbf{Y}}^\mathbf{-1}$$ G A P Y - 1 and $${\mathbf{C}}^{{{\mathbf{u}}_{\mathbf{2}_{\mathbf{C}}}}{\mathbf{u}}_{{\mathbf{2}_{\mathbf{C}}}_{{\varvec{a}}{\varvec{p}}{\varvec{p}}{\varvec{r}}{\varvec{o}}{\varvec{x}}}}}$$ C u 2 C u 2 C a p p r o x (Approx_GinvAPY) in replicate 2. Figure S4. QQ plots for all p-value computing methods with a reduced data set in replicate 3. QQ plots for p-values obtained from a data set of 50K genotyped animals with (A) $${\mathbf{G}}^\mathbf{-1}$$ G - 1 and $${\mathbf{C}}^{{\mathbf{u}}_\mathbf{2}{\mathbf{u}}_\mathbf{2}}$$ C u 2 u 2 (Exact_Ginv), (B) $${\mathbf{G}}_{\mathbf{A}\mathbf{P}\mathbf{Y}}^\mathbf{-1}$$ G A P Y - 1 and $${\mathbf{C}}^{{{\mathbf{u}}_{\mathbf{2}_{\mathbf{C}}}}{\mathbf{u}}_{\mathbf{2}_{\mathbf{C}}}}$$ C u 2 C u 2 C (Exact_GinvAPY), and (C) $${\mathbf{G}}_{\mathbf{A}\mathbf{P}\mathbf{Y}}^\mathbf{-1}$$ G A P Y - 1 and $${\mathbf{C}}^{{{\mathbf{u}}_{\mathbf{2}_{\mathbf{C}}}}{\mathbf{u}}_{{\mathbf{2}_{\mathbf{C}}}_{{\varvec{a}}{\varvec{p}}{\varvec{p}}{\varvec{r}}{\varvec{o}}{\varvec{x}}}}}$$ C u 2 C u 2 C a p p r o x (Approx_GinvAPY) in replicate 3.