Development of a formula for scoring competence of bovine embryos to sustain pregnancy

TL;DR

Researchers developed a formula to measure the ability of bovine embryos to sustain pregnancy using gene expression data.

Contribution

A novel R function was created to calculate an embryo competence index based on eight key genes.

Findings

An R function was developed to compute an embryo competence index from gene expression data.

The formula uses eight biomarker genes previously identified as predictors of embryo competence.

The function enables quantitative analysis of embryonic competence for statistical experiments.

Abstract

Embryo transfer in cattle and other species is a key reproductive technology to improve genetic merit. However, pregnancy loss after embryo transfer is still a major barrier to optimal utilization of the technology. Furthermore, the lack of a method to objectively quantify embryonic competence hinders investigations aimed at improving the competence of an embryo. Based on the knowledge that bovine embryos have an inherent molecular signature that determines their ability for pregnancy establishment which can result in distinct gene expression profiles, we have previously integrated transcriptomic data from independent experiments to identify eight genes capable of predicting embryo competence for survival with high accuracy. In this study, we developed a function for the R software containing a mathematical formula based on the model coefficients to yield an embryonic competence index (ECI) according to the expression of those eight critical genes. Application of the function to a gene expression dataset generates a quantitative ECI value for each embryo that can be employed in statistical analyses when performing an experiment. The folder with the R project and required datasets can be found in https://zenodo.org/records/12515587.

•In cattle, pregnancy loss after embryo transfer diminishes reproductive efficiency.•There is no method to objectively quantify the embryo ability to sustain pregnancy.•Previously, we identified eight biomarker genes that predicted embryo competence.•Based on these genes, we developed a formula to calculate embryo competence index.•Here, we introduce an R function that yields the index in an expression dataset.

In cattle, pregnancy loss after embryo transfer diminishes reproductive efficiency.

There is no method to objectively quantify the embryo ability to sustain pregnancy.

Previously, we identified eight biomarker genes that predicted embryo competence.

Based on these genes, we developed a formula to calculate embryo competence index.

Here, we introduce an R function that yields the index in an expression dataset.

Figures