The low heritability and moderate repeatability of semen production traits in beef and dairy bulls suggest that nonadditive genetic effects, such as dominance and epistatic effects, play an important role in semen production and should therefore be considered in genetic improvement programs. In this study, the repeatability of semen production traits in Japanese Black bulls (JB) as beef bulls and Holstein bulls (HOL) as dairy bulls was evaluated by considering additive and nonadditive genetic effects using the Illumina BovineSNP50 BeadChip. We also evaluated the advantage of using more complete models that include nonadditive genetic effects by comparing the rank of genotyped animals and the phenotype prediction ability of each model. In total, 65,463 records for 615 genotyped JB and 48,653 records for 845 genotyped HOL were used to estimate additive and nonadditive (dominance and epistatic) variance components for semen volume (VOL), sperm concentration (CON), sperm motility (MOT), MOT after freeze-thawing (aMOT), and sperm number (NUM). In the model including both additive and nonadditive genetic effects, the broad-sense heritability (0.17 to 0.43) was more than twice as high as the narrow-sense heritability (0.04 to 0.11) for all traits and breeds, and the differences between the broad-sense heritability and repeatability were very small for VOL, NUM, and CON in both breeds. A large proportion of permanent environmental variance was explained by epistatic variance. The epistatic variance as a proportion of total phenotypic variance was 0.07 to 0.33 for all traits and breeds. In addition, heterozygosity showed significant positive relationships with NUM, MOT, and aMOT in JB and NUM in HOL, when the heterozygosity rate was included as a covariate. In a comparison of models, the inclusion of nonadditive genetic effects resulted in a re-ranking of the top genotyped bulls for the additive effects. Adjusting for nonadditive genetic effects could be expected to produce a more accurate breeding value, even if the models have similar fitting. However, including nonadditive genetic effects did not improve the ability of any model to predict phenotypic values for any trait or breed compared with the predictive ability of a model that includes only additive effects. Consequently, although nonadditive genetic effects, especially epistatic effects, play an important role in semen production traits, they do not improve prediction accuracy in beef and dairy bulls.
Keywords: broad-sense heritability; dominance effects; epistatic effects; genetic parameter estimates; heterozygosity rate.
Improving reproductive efficiency is a key objective in the beef and dairy cattle industries, and bull fertility is an important determinant of the reproductive performance of cows. The heritability of semen production traits is generally low; however, their repeatability is moderate. This difference between repeatability and heritability suggests that nonadditive genetic effects, such as dominance and epistatic genetic effects, could have an important role in semen production traits in bulls. Here, we estimated repeatability for semen production traits in beef and dairy bulls by considering additive and nonadditive genetic effects. Our results suggest that the contribution of nonadditive genetic effects to differences between repeatability and heritability was very high. Nonadditive genetic effects, especially epistatic effects, played important roles in semen production traits in beef and dairy bulls. However, we found that the inclusion of nonadditive genetic effects in a predictive model does not improve phenotypic prediction accuracy; further studies are needed to improve the predictive ability when using nonadditive genetic effects.
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