Genome Wide Association Study of Nellore Bulls Fertility at in vitro Embryo Production

Discrepancies on fertility among bulls recorded at in vitro embryo production make it difficult to predict the percentage of blastocysts generated, causing negative impact in the application of such biotechnology. Combined information from laboratory databases and modern genomic screening tools, based in genome wide association approaches, should allow the identification of chromosome regions associated with high fertility bulls for in vitro procedures. The present study used the percentage of blastocysts generated in five different laboratories as phenotype. SNP profiles of 87 Nellore bulls were determined using 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 sample exclusion minor allele frequency < 0.02, call rate < 0.98, correlated SNP with r² > 0.995, significant deviations from Hardy-Weinberg equilibrium (HWE) with p < 10^-5 and samples with call rate < 0.90. Statistical methodology GRAMMAR was used to test phenotype / genotype association. Candidate SNP were choosen based on 0.1^th percentile of the P values of the statistical test and used to prune genomic coordinates from public genomic QTL data base (Cattle QTLdb). Candidate SNP presented concordance with several reproductive QTL highlighting those related to live sperm after thawing (# 9919 and # 9918), sperm abnormality cytoplasmic droplet (# 9921) and  sperm motility (# 9920 and # 9927).