Number of records, mean, standard deviation (SD), heritability estimate (h²) of each trait for the genotyped animals and their 5-generation ancestors.¹

1<p> = similar summary statistics for 19 of the above traits can be found in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004198#pgen.1004198-Bolormaa2" target="_blank">[8]</a>.</p

Number of significant SNPs (<i>P</i><10⁻⁵) in reference population that were also significant in the validation population.

<p>%-same = percentage of SNPs, which have an effect in the same direction in both validation and reference sets.</p

The positions of the best SNPs (5×10⁻⁷) that are highly correlated with each group of linear index.

<p>The positions of the best SNPs (5×10⁻⁷) that are highly correlated with each group of linear index.</p

The accuracy of imputation (R²) obtained from Beagle of the genotyped data.¹

1<p> = this table is sourced from <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004198#pgen.1004198-Bolormaa2" target="_blank">[8]</a>;</p>2<p> = Angus (AA), Brahman (BB), Belmont Red (BR), Hereford (HH), recent Brahman crosses (BX), Murray Grey (MG), Santa Gertrudis (SG), Shorthorn (SS) and Tropical Composites (TC); AAMG = genotypes of AA and MG animals were imputed together.</p

A: The −log₁₀(<i>P</i>-values) of single SNP regressions for 4 traits and multi-trait chi-squared statistic on a region of BTA 5; B: The −log₁₀(<i>P</i>-values) of single SNP regressions for 4 traits when SNP_i along with 28 lead SNPs were simultaneously fitted in the GWAS model.

<p>A: The −log₁₀(<i>P</i>-values) of single SNP regressions for 4 traits and multi-trait chi-squared statistic on a region of BTA 5; B: The −log₁₀(<i>P</i>-values) of single SNP regressions for 4 traits when SNP_i along with 28 lead SNPs were simultaneously fitted in the GWAS model.</p

Total number of significant SNPs (<i>P</i><10⁻⁵), their FDR (%), and number of significant SNP on each chromosome (which is in parenthesis) for the 28 linear indexes corresponding to the 28 lead SNPs.

1<p> = Group of the lead SNPs that were clustered together as shown on <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004198#pgen-1004198-g007" target="_blank">Figure 7</a>.</p>2<p> = This SNP order refers SNPs, which are given on <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004198#pgen-1004198-t004" target="_blank">Table 4</a>.</p>3<p> = 28 linear indexes corresponding to the 28 lead SNPs.</p>4<p> = Total number of significant SNPs which are significantly (<i>P</i><10⁻⁵) associated with each of linear indexes.</p>5<p> = only presented if number of significant SNPs on each chromosome (<i>P</i><10⁻⁵) is more than four. Chromosome number is in parentheses.</p

The number of genotypes used by each breed within each platform.¹

1<p> = Columns 6–8 are sourced from <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004198#pgen.1004198-Bolormaa2" target="_blank">[8]</a>.</p>2<p> = number of HD (high density SNP chip) and 50 K genotypes used for imputation as reference animals;</p>3<p> = number of animals with HD, 50 K, 7 K, and 10 K genotypes used in this study; Bt = <i>Bos taurus</i>; Bi = <i>Bos indicus</i>; Bt×Bi = composite breed.</p

Correlations between pairs of the SNP effects on 32 traits.

<p>A: Correlations on BTA7 from 93 Mb to 99 Mb. Three blocks of SNPs with high correlations within a block and low correlation between blocks are shown in blue. B: Correlations on BTA 14 near 25 Mb. The blue line shows the SNPs closest to the <i>PLAG1</i> gene.</p

Description of the 28 lead SNPs and their <i>P</i> values in the genome wide association studies (GWAS).

1<p> = Group of the lead SNPs that were clustered together as shown on <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004198#pgen-1004198-g007" target="_blank">Figure 7</a>.</p>2<p> = <i>Bos taurus</i> chromosome number.</p>3<p> = 28 linear indexes corresponding to the 28 lead SNPs.</p

Number of SNPs and their false discovery rates (%) at <i>P</i><5×10⁻⁷ for each trait before and after fitting the 28 leading SNPs in the model.

<p>*  = empty cells are not available.</p