Enhancing gene expression studies in bovine embryos fertilized <i>in vitro</i>: Identifying stable reference genes across blastocysts with different developmental speeds

In vitro fertilization (IVF) is crucial for livestock reproduction; however, pregnancy rates after embryo transfer vary depending on the developmental speeds of the embryos. Although quantitative PCR (qPCR) is used to predict developmental potential, its reliability depends on the selection of appropriate reference genes (RGs) for normalization. To determine suitable RGs in bovine blastocysts with different developing speed, we evaluated the stability of eight candidate RGs (18S, ACTB, GAPDH, HMBS, PPIA, TBP, HPRT1, and SDHA) in early-, mid-, and late-developing IVF blastocysts (E-BL, M-BL, and L-BL, respectively) using RefFinder. Despite morphological similarities, E-BL, M-BL, and L-BL exhibited different biological features, including significantly lower pregnancy rates in L-BL than in the other groups, and less abundant transcript levels of five candidate RGs in L-BL than in E-BL. RefFinder revealed that ACTB was the most stable RG, whereas TBP was the least stable. To emphasize the critical importance of selecting stable RGs, we analyzed the expression of key developmental markers including those of the inner cell mass (ICM; OCT4, SOX2) and trophectoderm (TE; CDX2, GATA3, IFNτ), using various RGs for normalization. For ICM markers, normalization with ACTB showed results consistent with pregnancy rates, whereas moderately stable (18S) and less stable (TBP) RGs yielded contradictory outcomes. Normalization with unstable RGs produced inconsistent TE marker expression patterns (CDX2, GATA3) and overestimated (IFNτ) results across groups, compared with the results of ACTB. These results demonstrate that selecting inappropriate RGs for qPCR normalization can lead to misinterpretation, highlighting the necessity of proper RG evaluation to ensure accurate results in bovine embryo research.