Establishment and validation of porcine embryo genomic selection system through SCNT technique

Abstract

Embryo genomic selection (EGS) refers to the technique of performing genotyping and genomic prediction at the preimplantation stage. When combined with in vitro embryo production method, EGS enhances selection intensity and offers the potential to prevent the birth of offspring carrying genetic defects or an undesired sex. Given that the somatic cell nuclear transfer (SCNT) technique can copy the genetic information from donor pigs into early embryos, this study aims to establish and validate a complete porcine EGS workflow by integrating SCNT with genomic selection methodology. First, porcine SCNT embryos were constructed using donor cells collected from candidate pigs with known genotypes and phenotypes. Cell biopsy performed in SCNT embryos revealed that collecting approximately 9.5 trophectoderm (TE) cells from blastocysts had the least impact on subsequent development. Next, a whole-genome multiple displacement amplification protocol was optimized for TE biopsy cells to conduct 80 K single nucleotide polymorphism (SNP) array analysis. The SNP call rates ranged from 94.44% to 99.77%, with genotype concordance between SCNT embryos and their donor pigs mostly exceeding 95%. Finally, genomic estimated breeding values (GEBVs) for three production traits were calculated using the GBLUP and Bayesian methods, and strong positive correlations (r > 0.90) of GEBVs were observed for each embryo and its donor. This study establishes and validates a complete EGS workflow for pigs, including embryo biopsy, whole-genome amplification, SNP genotyping, and GEBV prediction. The workflow provides a technical foundation for applying EGS in pig breeding and has the potential to accelerate genetic improvement through early embryo selection. Additionally, the results demonstrate that SCNT can be used to replicate elite genetic resources for the pig farming industry.