Improving accuracy of direct and maternal genetic effects in genomic evaluations using pooled boar semen: a simulation study1

Abstract

Pooling semen of multiple boars is commonly used in swine production systems. Compared with single boar systems, this technique changes family structure creating maternal half-sib families. The aim of this simulation study was to investigate how pooling semen affects the accuracy of estimating direct and maternal effects for individual piglet birth weight, in purebred pigs. Different scenarios of pooling semen were simulated by allowing the same female to mate from 1 to 6 boars, per insemination, whereas litter size was kept constant (N = 12). In each pooled boar scenario, genomic information was used to construct either the genomic relationship matrix (G) or to reconstruct pedigree in addition to G. Genotypes were generated for 60,000 SNPs evenly distributed across 18 autosomes. From the 5 simulated generations, only animals from generations 3 to 5 were genotyped (N = 36,000). Direct and maternal true breeding values (TBV) were computed as the sum of the effects of the 1,080 QTLs. Phenotypes were constructed as the sum of direct TBV, maternal TBV, an overall mean of 1.25 kg, and a residual effect. The simulated heritabilities for direct and maternal effects were 0.056 and 0.19, respectively, and the genetic correlation between both effects was −0.25. All simulations were replicated 5 times. Variance components and direct and maternal heritability were estimated using average information REML. Predictions were computed via pedigree-based BLUP and single-step genomic BLUP (ssGBLUP). Genotyped littermates in the last generation were used for validation. Prediction accuracies were calculated as correlations between EBV and TBV for direct (accdirect) and maternal (accmat) effects. When boars were known, accdirect were 0.21 (1 boar) and 0.26 (6 boars) for BLUP, whereas for ssGBLUP, they were 0.38 (1 boar) and 0.43 (6 boars). When boars were unknown, accdirect was lower in BLUP but similar in ssGBLUP. For the scenario with known boars, accmat was 0.58 and 0.63 for 1 and 6 boars, respectively, under ssGBLUP. For unknown boars, accmat was 0.63 for 2 boars and 0.62 for 6 boars in ssGBLUP. In general, accdirect and accmat were lower in the single-boar scenario compared with pooled semen scenarios, indicating that a half-sib structure is more adequate to estimate direct and maternal effects. Using pooled semen from multiple boars can help us to improve accuracy of predicting maternal and direct effects when maternal half-sib families are larger than 2.

Simulation studies to optimize genomic selection in honey bees

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The efficiency of multi-generation selection on maternal traits, with implications for reindeer

“…The increased FS family size always benefits the selection of MGE. Although rarely available within the same generation, maternal half-sibs are naturally more desirable than paternal half-sibs (Maiorano et al 2019) in increasing the accuracy of MGE predictions. In animal breeding studies is often found to be negative (Bradford 1972, Koch 1972, Robinson 1972, Bijma 2006).…”

“…A general (analytical) method is desirable because the alternative, stochastic simulation, would give answers only to specific situations. Simulation have been used for example by Lourenco et al (2013) to study the effect of genetic evaluation method and Maiorano et al (2019) to study selection when using pooled semen. Where available, maternal half-sibs are expected to be efficient in predicting MGE (Willham 1963, Noble et al 2014, Maiorano et al 2019).…”

“…Simulation have been used for example by Lourenco et al (2013) to study the effect of genetic evaluation method and Maiorano et al (2019) to study selection when using pooled semen. Where available, maternal half-sibs are expected to be efficient in predicting MGE (Willham 1963, Noble et al 2014, Maiorano et al 2019). Wray and Hill (1989) introduced an analytical method for approximating the use of multi-generation pedigree information for predicting the response to selection (often now called pseudo-BLUP).…”