Identification of genomic regions associated with characters correlated with the ferlitizing capacity of Holstein bulls

The sustainability of dairy farms is at risk due to the decline in the reproductive efficiency of cows with high rates of milk production throughout the world. The cow component of fertility has been included in the genetic improvement programs as a selection goal. However, male fertility has been considered to a lesser extent. Early identification of infertile or subfertile bulls is of large economic importance for artificial insemination (AI) centres, which could be achieved by the identification of molecular makers defining subfertility and genotyping of bulls at birth. The objective of this study was to identify single nucleotide polymorphisms (SNPs) significantly associated to the phenotypic evaluation of bull fertility and semen quality parameters and analyse the genomic base of genetic correlations between seminal quality and male fertility. Phenotypes included were from 715 animals with male fertility measured as success at AI (EAI); 431 bulls with records of post-thawing motility (PTM), individual motility (IM), mass motility (MM), concentration (CON), number of spermatozoa (NSPZ) and volume (VOL); and 199 bulls with data of rate of sperm DNA fragmentation at 0 and 6 hours (SDF 0-6). Genotypes of the Illumina BovineSNP50 bead chip of 754 bulls having one or more of the phenotypes have been used in the study. SNPs were edited on their minor allele frequency (greater than 0.0001) and call rate (greater than 0.95). Analysis of association based on a linear mixed model that considers the effect of each SNP to be tested for association and an additive polygenic effect was used to estimate the effect of markers for each of the examined traits. The Benjamini and Hochberg method to control FDR at 10 per cent was used to determine the SNPs with relevant signals for each trait. Overall, 52 SNPs providing significant signals for all the traits analysed were discovered. The SNPs associated with EAI, PTM, SDF0 and SDF6 are in or near (within a 1Mb window) genes with biological functions involved in reproduction, such as CD3E gene (CD3E), caspase 4 gen (CASP4), platelet-derived growth factor D gene (PDGFD) and spermatid perinuclear RNA-binding protein gene (STRBP) that participates in the gamete generation in spermatogenesis process. Despite the observed genetic correlations between seminal quality traits and male fertility, these phenotypes did not show significantly associated SNPs in common. However, blocks of moderate linkage disequilibrium between them were defined. From a subnetwork interaction analysis, regulatory interaction or participation in the same process or pathway was found for genes associated with significant SNPs for different phenotypes, which demonstrates that existing relationship among traits. A test for pleiotropic effects between significant SNPs associated with seminal quality and male fertility phenotypes showed only three pleiotropic SNP associated with individual motility, mass motility and sperm DNA fragmentation. More genomic and phenotypic data is necessary to analyse with more detail and confirm the genomic relationship between seminal quality traits and male fertility to improve the fertility in dairy cattle and facilitate identify viable male in Artificial Insemination Centres