Reproduction

Investigation of genomic regions associated with embryonic loss in biopsied Holstein Friesian embryos from elite matings

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Abstract

Hereditary defects can cause embryonic developmental failure in cattle. Genomic analyses may facilitate early detection of carrier animals and enable informed mating to prevent the spread of recessive deleterious alleles. In Holstein Friesian cattle, several haplotypes associated with fertility traits have been identified, but their direct relationship to embryonic development remains unclear. This study aimed to investigate genomic regions associated with fertility and to assess their relationship with haplotypes that may affect embryo developmental competence to term. Accordingly, genotype frequencies and deviations from Hardy-Weinberg equilibrium (HWE) were analyzed and compared between parental and embryonic generations to identify molecular DNA signatures that were over- or under-represented in embryos relative to the parental generation and thus suggested to be associated with embryo developmental competence to term. A dataset of 2,110 biopsied Holstein Friesian embryos from elite matings, 911 embryos in vivo-derived (IVD) and 1,199 in vitro-produced (IVP) was analyzed. Single-nucleotide polymorphism (SNP) genotyping data (~50K), available for embryos and parents, were used to examine selected genomic regions (865 SNP markers) previously identified in the literature as potentially relevant to fertility and fetal viability. After quality control and application of methodological criteria, 65 autosomal SNP markers were selected for deeper analysis. Markers were retained if: frequency of Q-genotypes (aa) among parental animals ≤10, frequency of Q-genotypes among embryos >0, and minor allele frequency (MAF) among parents >5%. The final dataset included 1,674 embryos and 715 parental animals. Statistical analyses focused on deviations from HWE, genotype frequency distributions, and frequency differences between IVD and IVP embryos. Deviation from HWE and genotype proportions (Q-genotypes) were compared across generations and embryo production methods. The analyses revealed significant deviations (p-value<0.05) from HWE for 55 out of 65 SNP markers in embryos. The frequency for Q-genotypes in parents was on average 0.7%, whereas in the embryos they were overrepresented (1.9%). While HWE was maintained among parents, it was disrupted in the embryos, primarily due to an excess of homozygous Q-genotypes. This over-representation was higher in IVP embryos than in IVD embryos, with IVP embryos showing increased frequencies of Q-genotypes (2.00% vs. 1.75%) and stronger deviations from HWE (38 vs. 23 SNP markers). Over-representation of certain haplotypes in the embryo generation relative to their parental generation may indicate an effect of these on embryo and/or fetal developmental competence to term, following an autosomal recessive inheritance pattern. In conclusion, a higher frequency of homozygous Q-genotypes was observed in embryos compared to what was expected on the basis of their parents implicating effects on developmental competence; a phenomenon not previously described in this context. While the present study focused on specific genomic regions, future research will extend to additional regions to further explain the genetic mechanisms underlying embryonic loss.

Keywords: 2026

How to Cite:

Rienesl, L., Hoffmann, L., Diederich, M., Meier, S., Grothmann, H., Tholen, E., Held-Hoelker, E., Hoelker, M. & Große-Brinkhaus, C., (2026) “Investigation of genomic regions associated with embryonic loss in biopsied Holstein Friesian embryos from elite matings”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2286340. doi: https://doi.org/10.31274/wcgalp.23938

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