Additional file 1 of Across-country genetic and genomic analyses of foot score traits in American and Australian Angus cattle
Creators: name: Alvarenga, Amanda B.
name: Retallick, Kelli J.
name: Garcia, Andre
name: Miller, Stephen P.
name: Byrne, Andrew
name: Oliveira, Hinayah R.
name: Brito, Luiz F.
Publisher: name: figshare
Year: 2023
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 1: Table S1. Descriptive analyses of the raw dataset of foot scores for American (US) and Australian (AU) Angus populations. The dataset provided presents the number of records, frequency of foot angle and claw set scores, number of animals, number of herds, number of contemporary groups, and date of birth of the animals. Table S2. Variance explained by the first ten principal components using different datasets to create the genomic relationship matrix. Variance explained by the 10 principal components using the four data subsets. Table S3. Estimates of the heritability for foot angle (FA) and claw set (CS) using the American (AU) and Australian (AU) Angus datasets analyzed with a single-trait model within each country dataset. Table S4. Genetic parameters (heritability, repeatability, and genetic correlation) for foot angle (FA) and claw set (CS) based on multi-country two-trait models (MC-TT) between the American (AU) and Australian (AU) Angus populations. Table S5. Genetic parameters (heritability, repeatability, and genetic correlation) for foot angle (FA) or claw set (CS) using genomic information based on a multi-country single-trait model (MC-ST) between American (US) and Australian (AU) Angus populations. Table S6. Genetic parameters for foot angle (FA) and claw set (CS) based on joint-country two-trait model (JC-TT). Table S7. Accuracy, bias, and dispersion of the genomic prediction: within-country two-trait (WC) and across-country two-trait (AC) model using Australian Angus (AU) as the estimation set. Predictive ability from a forward validation using the linear regression method, including bias, dispersion, and accuracy for a forward validation in the AU animals (2019–2020) and across-country evaluation.Table S8. Accuracy, bias, and dispersion of the genomic prediction: within-country two-trait (JC) and across-country two-trait (AC) model using American Angus (US) as the estimation set. Predictive ability from a forward validation using the linear regression method, including bias, dispersion, and accuracy for a forward validation in the US animals (2020) and across-country evaluation. Table S9. Accuracy, bias, and dispersion of the genomic prediction based on multi-country two-trait models (MC-TT). Predictive ability from a forward validation using the linear regression method, including bias, dispersion, and accuracy for a forward validation. Table S10. Accuracy, bias, and dispersion of the genomic prediction based on joint-country two-trait models (JC-TT). Predictive ability from a forward validation using the linear regression method, including bias, dispersion, and accuracy for a forward validation. Table S11. Accuracy, bias, and dispersion of the single-trait (ST) genomic prediction scenarios within-country (WC-ST), multi-country (MC-ST), and joint countries (JC-ST). Predictive ability from a forward validation using the linear regression method, including bias, dispersion, and accuracy in scenarios using genomic (ssGBLUP) or not (BLUP). Table S12. Predictive ability for all genomic prediction scenarios for the Australian Angus target population (AU) presented by validation year: for single-trait within-country (WC-ST), multi-country (MC-ST), and joint-country (JC-ST) models. Predictive ability from a forward validation using the linear regression method, including bias, dispersion, and accuracy in scenarios using genomic (ssGBLUP). Results are presented for each birth year validation group in the AU population. Table S13. Average individual accuracy for the genomic prediction scenarios for foot angle based on single-trait models (-ST). Table S14. Average individual accuracy for the genomic prediction scenarios for claw set based on single-trait models (-ST). Table S15. Pearson and Spearman correlations of genomic estimated breeding values (GEBV) of proven sires (with more than 50 progeny with phenotypic records and raised in either one of the countries) across scenarios for foot angle based on single-trait within-country (WC-ST), multi-country (MC-ST), and joint countries (JC-ST) models. Table S16. Pearson and Spearman correlations of genomic estimated breeding values (GEBV) of proven sires (with more than 50 progeny with phenotypic records and raised in either one of the countries) across scenarios for claw set based on single-trait within-country (WC-ST), multi-country (MC-ST), and joint countries (JC-ST) models. Table S17. Significant SNPs associated with foot angle, and the genes located within a 100-kb genomic region down- and up-stream based on multi-country single-trait models (MC-ST). The list of genes name, gene Ensembl identification, gene position, the identification of the significant SNP, the population in which the SNPs were identified (US or AU), and the log (p-value). Table S18. Gene ontology terms and pathways in which the annotated genes for foot angle are involved based on multi-country single-trait models (MC-ST). Table S19. Significant SNPs associated with claw set, and the genes located within a 100-kb genomic region down- and up-stream based on multi-country single-trait models (MC-ST). The list of genes name, gene Ensembl identification, gene position, the identification of the significant SNP, the population in which the SNP were identified (US or AU), and the log (p-value). Table S20. Gene ontology terms and pathways in which the annotated genes for claw set are involved based on a multi-country single-trait model (MC-ST). Table S21. Genetic parameters (heritability, repeatability, and genetic correlations) between dataset collected by technicians and farmers in the Australian Angus dataset: two-recorder-trait considering the covariance between FA and CS equal to zero (-ST).