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Background  Due to ethical reasons, surgical castration of young male piglets in their first week of life without anesthesia will be banned in Germany from 2021. Breeding against boar taint is already implemented in sire breeds of breeding organizations but in recent years a low demand made this trait economically less important.  The objective of this study was to estimate heritabilities and genetic relationships between boar taint compounds androstenone and skatole and maternal/paternal reproduction traits in 4′924 Landrace (LR) and 4′299 Large White (LW) animals from nucleus populations. Additionally, genome wide association analysis (GWAS) was performed per trait and breed to detect SNP marker with possible pleiotropic effects that are associated with boar taint and fertility.    Results  Estimated heritabilities (h 2 ) were 0.48 (±0.08) for LR (0.39 ± 0.07 for LW) for androstenone and 0.52 (±0.08) for LR (0.32 ± 0.07 for LW) for skatole. Heritabilities for reproduction did not differ between breeds except age at first insemination (LR: h 2  = 0.27 (±0.05), LW: h 2  = 0.34 (±0.05)). Estimates of genetic correlation (r g ) between boar taint and fertility were different in LR and LW breeds. In LR an unfavorable r g  of 0.31 (±0.15) was observed between androstenone and number of piglets born alive, whereas this r g  in LW (− 0.15 (±0.16)) had an opposite sign. A similar breed-specific difference is observed between skatole and sperm count. Within LR, the r g  of 0.08 (±0.13) indicates no relationship between the traits, whereas the r g  of − 0.37 (±0.14) in LW points to an unfavorable relationship. In LR GWAS identified QTL regions on SSC5 (21.1–22.3 Mb) for androstenone and on SSC6 (5.5–7.5 Mb) and SSC14 (141.1–141.6 Mb) for skatole. For LW, one marker was found on SSC17 at 48.1 Mb for androstenone and one QTL on SSC14 between 140.5 Mb and 141.6 Mb for skatole.    Conclusion  Knowledge about such genetic correlations could help to balance conventional breeding programs with boar taint in maternal breeds. QTL regions with unfavorable pleiotropic effects on boar taint and fertility could have deleterious consequences in genomic selection programs. Constraining the weighting of these QTL in the genomic selection formulae may be a useful strategy to avoid physiological imbalances.

Genomic background and genetic relationships between boar taint and fertility traits in German Landrace and Large White