Optimization of Preimplantation Genome Profiling Supports Genomic Selection in Cattle

Preimplantation embryo genomic selection (eGS) enables selection prior to implantation and could accelerate genetic gain in cattle. A major hurdle is the limited DNA from embryo biopsies, requiring efficient whole-genome amplification (WGA) for accurate genomic analyses. However, alternative WGA methods and genotyping strategies have not been systematically compared in cattle. This study evaluated different methods for WGA (multiple displacement amplification (MDA) or multiple annealing and looping-based amplification cycles (MALBAC)) and for genotyping (single nucleotide polymorphism array (SNP-array), genotyping by targeted sequencing (GBTS), or whole-genome sequencing (WGS)) using 3-, 6-, and 9-cell bovine samples. MDA consistently outperformed MALBAC across various performance metrics, including amplification length, call rates, genome coverage (93.43–94.40% vs. 53.01–67.08%), and genotyping concordance (0.89–0.98 vs. 0.75–0.92). GBTS achieved the highest call rates, while SNP-array and GBTS showed excellent concordance and low error rates. WGS provided genome-wide data for precise aneuploidy detection. We further validated the workflow in trophectoderm biopsies and arrested embryos, generating reliable data for genomic evaluation, sex determination, and aneuploidy screening. MDA from ≥6 cells combined with GBTS or SNP-array showed a favorable balance of efficiency and accuracy for bovine eGS. This framework may facilitate the application of eGS in cattle breeding by enhancing selection intensity and accelerating genetic improvement.