Genome Wide Association Study and Functional Enrichment Analysis of Spermatic Cryotolerance in Nellore Cattle

The artificial insemination industry is highly affected by losses in production due to the reduction in semen quality after freezing procedures. Predicting response to freezing would allow AI centers to identify bulls with low spermatic cryotolerance earlier and to optimize the concentration of spermatozoa contained in a straw. Genome wide association approach was performed in order to identify gene groups related to sperm cryotolerance in Nellore cattle using following phenotypes: (1) difference between fresh and post-thaw semen motility, and (2) difference between fresh and post thermal resistance test semen motility. SNP profiles of 125 Nellore bulls were determined using a high density SNP chip (BovineHD Illumina^®). Genotype calling was based on a GenCall Score > 0.7. Initial data cleanup was performed in order to remove poorly performing and non autosomal probes from the analysis, considering as criteria for SNP or samples exclusion minor allele frequencies < 0.02, call rates < 0.98, highly correlated SNP with r² > 0.995, significant deviations from Hardy-Weinberg equilibrium (HWE) with p < 10^-5 and samples with call rate < 0.90. The statistical methodology GRAMMAR was used to test the phenotype / genotype association and functional enrichment analysis was performed using DAVID software. These analyses pointed out to external stimulus regulatory genes (enrichment score (ES) = 3.11, p < 10^-4), protease inhibitors (ES = 2.41, p < 10^-4), and calcium channels and carrier proteins (ES = 2.01, p < 10^-4), as the most associated gene groups for the evaluated traits.