Posterior mean estimates (standard errors within brackets) for proportion of genetic variance for milk, fat and protein yield, and fertility captured from the GBLUP model fitting jointly: pedigree and common and rare variants, using 3311 Holstein sires.

<p>Posterior mean estimates (standard errors within brackets) for proportion of genetic variance for milk, fat and protein yield, and fertility captured from the GBLUP model fitting jointly: pedigree and common and rare variants, using 3311 Holstein sires.</p

Observed vs expected less common alleles transmitted in 38 sire-son duos(left) and confidence interval of unrelated duos at different MAF (right) in the Bos Taurus autosome 1 (BTA1).

<p>Almost 35% of sequence variants had MAF<0.01 (green dashed line in left plot), however 50% of these variants were not observed in the expected proportions in the parent offspring duos (red solid line in left plot). The proportion of transmitted alleles to the progeny was modeled according to the MAF (right plot). Green lines represent each of the duos, and the solid green line is the local weighted regression for the 38 duos. Red shadow represent the confident interval for the same regression when 10 pairs of unrelated animals were evaluated, with the red solid line being the local weighted regression. The dashed black line represents the expected theoretical proportion of transmission for the less frequent allele from sire to son under random mating. At MAF<0.10 we observed that observed proportions of transmission deviated from the theory, which implies that up to 50% of the uncommon and rare variants (at MAF<0.01) are sequencing errors.</p

Genetic variance estimates from genomic markers () or pedigree () and their respective standard error (s.e.) for milk, fat and protein yield, and fertility captured from GBLUP models using 3311 Holstein sires.

<p>Narrow sense heritability from pedigree is provided, and the proportion of missing heritability from markers was calculated as .</p

Number of variants detected by number of parent-offspring duos.

<p>Boxplot for the occurrence of variants with MAF<0.01 detected from 38 sire-son duos (blue). The boxplots in red show how many of them were present in transcript regions. Each boxplot is constructed from 50 replicates of random samples of a given number of duos (from 1 to 38). Solid lines are the corresponding quadratic regression for the number of rare variants discovered in the Australian Holstein population according the number of duos used. The regression equation for the total number of rare variants (y) according to the number of duos (x) was y = 108432+80557x-926x². The regression equation equivalent for the number of rare variants in transcript regions was y = 653+775x-6.7x². This means that we would need 44 duos for detecting most of the rare variants along the genome, which number is projected to be 1,860,826. Among these 23,000 are expected to be present in transcript regions, and 58 parent offspring duos would be necessary to detect them.</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

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

Effects of 28 lead SNPs on the individual traits (signed values with |t|>1 are shown).

<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

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