Sequencing & Pangenomes

Optimizing whole-genome amplification and genotyping methods for low-input cells: Towards efficient preimplantation embryo genomic selection in cattle

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Abstract

Preimplantation embryo genomic selection (eGS) holds substantial potential to accelerate genetic improvement in cattle by enabling selection prior to implantation. However, the limited DNA yield from embryo biopsies necessitates whole-genome amplification (WGA) for downstream analyses. The performance of common WGA techniques, multiple displacement amplification (MDA) and multiple annealing and looping-based amplification cycles (MALBAC), remains understudied in bovine systems. This study systematically evaluated the impacts of initial cell count (3, 6, and 9 cells), WGA method, and genotyping platform, SNP-array, genotyping by targeted sequencing (GBTS), and whole-genome sequencing (WGS), on genomic profiling accuracy in low-input bovine cells. Results demonstrate that MDA outperformed MALBAC across key metrics, exhibiting superior amplification length, call rates, genome coverage ( >93% vs. à¢â€°Â¥6 cells coupled with GBTS or SNP-array as the optimal workflow, balancing efficiency and accuracy. These findings provide a robust technical framework for implementing eGS in cattle, enhancing selection intensity, reducing costs and accelerating genetic improvement.

Keywords: 2026

How to Cite:

Yan, S., Si, J., Zeng, S. & Zhang, Y., (2026) “Optimizing whole-genome amplification and genotyping methods for low-input cells: Towards efficient preimplantation embryo genomic selection in cattle”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2286181. doi: https://doi.org/10.31274/wcgalp.23873

Rights: 1