Quantifying the Genetic Contribution of Donor Embryos in Chimaeric Animals Using Illumina Beadchips

Our research is aimed at accelerating genetic gain in the New Zealand dairy herd by genetically selecting and multiplying elite in vitroproduced bovine embryos.  Elite embryos on Day 5 of development are identified via embryo biopsy, whole genome amplification and genotyping using Illumina BovineLD BeadChips.  The remaining embryos are further subdivided and each portion aggregated with unrelated embryos with the aim of generating multiple germline chimaeras from each donor embryo, thus propagating the elite genetics.

To ascertain the level of chimaerism, the proportion of the elite embryo in each resulting animal must be determined.  In a preliminary experiment, we simulated chimaeric tissue by mixing two unrelated cell lines at different ratios, in triplicate and genotyped them on Illumina BovineLD BeadChips.  SNP theta values that represent the colour intensity scale between fluorescent dye-labelled Red AT alleles and Green GC alleles were used to measure the mixed cell samples against the two non-mixed samples. The analysis was performed in GenomeStudio on SNPs that were both homozygous AA for one cell line (theta value <0.05) and BB for the other cell line (theta value >0.95). There were 300 SNPs that fitted these criteria.  A regression analysis was performed on the mean theta values and the expected cell ratios producing a standard curve with a correlation of R²  = 0.9787. We used this method to estimate the level of donor embryo contribution in chimaeric tissue which may then be used to predict the germline contribution of an elite embryo in a chimaeric animal.