Additional file 2 of Combining genetic markers, on-farm information and infrared data for the in-line prediction of blood biomarkers of metabolic disorders in Holstein cattle
Creators: name: Mota, Lucio F. M.
name: Giannuzzi, Diana
name: Pegolo, Sara
name: Toledo-Alvarado, Hugo
name: Schiavon, Stefano
name: Gallo, Luigi
name: Trevisi, Erminio
name: Arazi, Alon
name: Katz, Gil
name: Rosa, Guilherme J. M.
name: Cecchinato, Alessio
Publisher: name: figshare
Year: 2024
Subjects: subject: Medicine
subject: Physiology
subject: FOS: Biological sciences
subject: Environmental Sciences not elsewhere classified
subject: Chemical Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified

description: Additional file 2: Fig. S1. Relative difference (%) in predictive ability for 5-fold random cross-validation scenarios using Elastic-net for Model 2 (M2; milk NIR data and on-farm data) and Model 3 (M3; milk NIR data, on-farm and genomic information) against Model 1, which considers only the NIR infrared data. Data are shown as mean ± SD (red error bar line). Glu – glucose; Cholest – cholesterol; NEFA – non-esterified fatty acids; BHB – β-hydroxybutyrate; Crea – creatinine; AST – aspartate aminotransferase; GGT – γ-glutamyl transferase; BILt – total bilirubin; ALB – albumin; ALP – alkaline phosphatase; PON – paraoxonase; CuCp – ceruloplasmin; Glob – globulins; PROTt – total proteins; Hapto – haptoglobin; MPO – myeloperoxidase; ROMt – total reactive oxygen metabolites; AOPP – advanced oxidation protein products; FRAP – ferric reducing antioxidant power; SHp – total thiol groups; Ca – calcium; P – phosphorus; Mg – magnesium; K – potassium; Na – sodium; Cl – chlorine; Zn – zinc. Fig. S2. Relative gain in predictive ability Pearson correlation, considering three thresholds based on marker significance (-log10(P-value)) higher than 2.0, 2.5, and 3.0 against fitting all 61k SNPs, including standard errors, assessed for energy-related (a) and liver function and hepatic damage (b) blood metabolites. Data are shown as mean ± SD (black error bar line). Glu – glucose; Cholest – cholesterol; NEFA – non-esterified fatty acids; BHB – β-hydroxybutyrate; Crea – creatinine; AST – aspartate aminotransferase; GGT – γ-glutamyl transferase; BILt – total bilirubin; ALB – albumin; ALP – alkaline phosphatase; PON – paraoxonase. Fig. S3. Relative gain in predictive ability Pearson correlation, considering three thresholds based on marker significance (-log10(P-value)) higher than 2.0, 2.5 and 3.0 against fitting all 61k SNPs, including standard errors, assessed for inflammation/innate immunity response (a) and oxidative stress blood metabolites (b). Data are shown as mean ± SD (black error bar line). CuCp – ceruloplasmin; PROTt – total proteins; Glob – globulins; Hapto – haptoglobin; MPO – myeloperoxidase; ROMt – total reactive oxygen metabolites; AOPP – advanced oxidation protein products; FRAP – ferric reducing antioxidant power; SHp – total thiol groups. Fig. S4. Relative gain in predictive ability Pearson correlation, considering three thresholds based on marker significance (higher than 2.0, 2.5 and 3.0 against fitting all 61k SNPs, including standard errors, assessed for blood minerals. Data are shown as mean ± SD (black error bar line). Ca – calcium; P – phosphorus; Mg – magnesium; Na – sodium; K – potassium; Cl – chlorine; Zn – zinc. Fig. S5. Manhattan plot for the average value of markers significance (-log10(P-value)) across the 5-fold cross-validation for energy-related metabolites. Glu – glucose; Cholest – cholesterol; NEFA – non-esterified fatty acids; BHB – β-hydroxybutyrate; Crea – creatinine. Fig. S6. Manhattan plot for the average value of markers significance (-log10(P-value)) across the 5-fold cross-validation for blood metabolites related to inflammation/innate immunity response. CuCp – ceruloplasmin; PROTt – total proteins; Glob – globulins; Hapto – haptoglobin; MPO – myeloperoxidase. Fig. S7. Manhattan plot for the average value of markers significance (-log10(P-value)) across the 5-fold cross-validation for blood metabolites related to liver function and hepatic damage. AST – aspartate aminotransferase; GGT – γ-glutamyl transferase; BILt – total bilirubin; ALB – albumin; ALP – alkaline phosphatase; PON – paraoxonase. Fig. S8. Manhattan plot for the average value of markers significance (-log10(P-value)) across the 5-fold cross-validation for oxidative stress blood metabolites. ROMt – total reactive oxygen metabolites; AOPP – advanced oxidation protein products; FRAP – ferric reducing antioxidant power; SHp – total thiol groups. Fig. S9. Manhattan plot for the average value of markers significance (-log10(P-value)) across the 5-fold cross-validation for blood minerals. Ca – calcium; P – phosphorus; Mg – magnesium; K – potassium; Na – sodium; Cl – chlorine; Zn – zinc.