Genotyping of Bovine Embryo Biopsies with a High Density Panel for use in Genomic Selection

Currently, super-ovulation and embryo transfer are routinely used in dairy cattle to generate larger numbers of males and females from elite cows. The process could be cheaper and more efficient if embryos could be genotyped from biopsies using the Illumina 50k Beadchip and only those with superior genomic evaluations implanted into recipients. However, embryo biopsies contain a very limited amount of DNA. Therefore, special DNA extraction and amplification procedures were developed to genotype these biopsies. After amplification and genotyping, the genotypes were processed with a tailor-made imputation program designed, in particular, to correct for allele drop-out. To date, 681 out of 709 embryo biopsies were successfully amplified and genotyped (96%). As of now, 56 calves were born from these embryos and were genotyped. The average percentage of inconsistencies between embryo and calf genotypes, and the average percentage of missing SNPs were 1.60% and 11.4%, respectively. These figures improved to 0.94% and 0.01% after imputation. Direct genomic values were calculated from all genotypes using Canadian genomic evaluation methods. The correlation between direct genomic values of calves and embryos was 0.975 before imputation and 0.991 after imputation, indicating a high concordance rate. Based on these results, embryo genotyping is possible and will rank embryos in nearly the same way as the resulting calves.