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Background  Fertility is considered an important economic trait in dairy cattle. Most studies have investigated cow fertility while bull fertility has received much less consideration. The main objective of this study was to perform a comprehensive genomic analysis in order to unravel the genomic architecture underlying sire fertility in Holstein dairy cattle. The analysis included the application of alternative genome-wide association mapping approaches and the subsequent use of diverse gene set enrichment tools.    Results  The association analyses identified at least eight genomic regions strongly associated with bull fertility. Most of these regions harbor genes, such as  KAT8 ,  CKB ,  TDRD9  and  IGF1R , with functions related to sperm biology, including sperm development, motility and sperm-egg interaction. Moreover, the gene set analyses revealed many significant functional terms, including fertilization, sperm motility, calcium channel regulation, and SNARE proteins. Most of these terms are directly implicated in sperm physiology and male fertility.    Conclusions  This study contributes to the identification of genetic variants and biological processes underlying sire fertility. These findings can provide opportunities for improving bull fertility via marker-assisted selection.    Electronic supplementary material  The online version of this article (doi:10.1186/s12863-016-0454-6) contains supplementary material, which is available to authorized users.

Unravelling the genomic architecture of bull fertility in Holstein cattle