Simulation parameters.

a<p>Expressed as percentage of total variance; numbers in parentheses are the range for 100 replicates.</p

Adjusted allele effects from different formulas.

<p>Adjusted positive (A) and negative (B) allele effects based on allele frequency using linear and nonlinear formulas with δ = 0.4 as well as using arcsin and square root formulas comparing to unweighted genomic selection (δ = 0).</p

Standard deviation of true breeding value by generation based on a heavy-tailed QTL distribution.

<p>True breeding values (BVs) for a simulated population were based on unweighted (δ = 0) or weighted (various δ) genomic selection and calculated using on true marker effects. Linear (A) and nonlinear (B) formulas were used to weight allele frequency.</p

Ratio of adjusted to unadjusted genetic progress by generation for a normal QTL distribution.

<p>The ratio was calculated as the genetic progress for a simulated population based on adjusted genomic breeding value using various δ in the linear (A) and nonlinear (B) adjustment formula divided by genetic progress based on genomic breeding value from unweighted selection.</p

The correlation between official and FMA (favorable minor allele) evaluation using linear and nonlinear formulas, as well as Correlation of the difference between FMA using linear weighting and official evaluation with GFI (genomic future inbreeding) and EFI (expected future inbreeding).

<p>δ = 0.4 was used for FMA selection.</p

Standard deviation of true breeding value by generation based on a normal QTL distribution.

<p>True breeding values (BVs) for a simulated population were based on unweighted (δ = 0) or weighted (various δ) genomic selection and calculated using on true marker effects. Linear (A) and nonlinear (B) formulas were used to weight allele frequency.</p

Mean inbreeding coefficients in the final generation calculated using different allele frequencies for simulated populations using 2 QTL distributions.

a<p>Mean of diagonal elements of genomic relationship matrix calculated using an allele frequency of 0.5.</p>b<p>Mean of diagonal elements of genomic relationship matrix calculated using true allele frequency in the base population.</p>c<p>Inbreeding based on pedigree information.</p

Ratio of adjusted to unadjusted genetic progress by generation for 2 QTL distributions.

<p>The ratio was calculated as the genetic progress for a simulated population based on adjusted genomic breeding value from the Jannink <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0088510#pone.0088510-Jannink1" target="_blank">[5]</a> formula divided by genetic progress based on genomic breeding value from unweighted selection. A QTL distribution with normally distributed allele effects and a heavy-tailed QTL distribution were tested.</p

Size and location of marker additive and dominance effects for milk yield of Holsteins and Jerseys.

<p>Holstein additive (A) and dominance (B) effects and Jersey additive (C) and dominance (D) effects were estimated with a model that included additive and dominance (values) effects.</p

Holstein and Jersey likelihood statistics (−2 log likelihood, <i>P</i>-value of <i>χ</i>²test^b using likelihood ratio) for milk, fat, and protein yields, productive life (PL), daughter pregnancy rate (DPR), somatic cell score (SCS), fat percent (fat%) and protein percent (protein%) using three different models.

a<p>MA = only additive effects included; MAD = additive and dominance (values) effects included; and MAD2 = additive and dominance (deviations) effects included.</p>b<p></p