101 Selecting bovine embryos using genomics tools: sex determination and genetic merit assessment in developing cattle embryos

Genomic selection promises a rapid rate of genetic gain, and advanced genomic tools are being used to select elite animals at younger ages of their life for breeding programmes. The generation interval can further be shortened if the selection is made at the embryonic stage itself, leading to more genetic gain per year. By identifying elite animals early, breeders can accelerate genetic progress, improve breeding efficiency, and reduce the environmental impact of cattle farming. This approach leads to more sustainable livestock production, increased profits for farmers, and a higher-quality cattle population overall. The present study is envisaged to understand the possibility of utilising genomic technologies for early-stage sex determination and genetic merit assessment of cattle embryos. Standard in vitro embryo production (IVEP) protocol of the laboratory was used to produce bovine embryos. Trophoblast cells (10–15 cells) were collected from 17 bovine embryos at the expanded blastocyst stage, following the IETS grading pattern. The embryos were produced through pooled culture, and the biopsy procedures were conducted on Day 7 after IVF. The biopsies were performed using the RI Saturn 5 laser system (CooperSurgical). The DNA extraction was performed on 11 biopsied samples using the REPLI-g kit (Qiagen), with an average yield of 537 ng/µL, quantified using a Qubit 4 Fluorometer (ThermoFisher Scientific). Three samples with high DNA concentration (880 ng/µL, 650 ng/µL, and 650 ng/µL) and intact agarose gel bands were selected for genotyping. Microarray genotyping performed using INDUSCHIP2 (51253 SNPs) on the Illumina platform revealed an average call rate of 91%. Sex determination analysis using digital droplet polymerase chain reaction revealed varying percentages of X and Y chromosomes in the embryos (Embryo1 X% 39.1, Y% 60.94; Embryo2 X% 97.8, Y% 2.23; Embryo3 X% 37.3, Y% 62.65) confirming the identification of both male and female embryos. The occurrence of sex mosaicism in one of the embryos could indeed be attributed to the zona biopsied during the procedure. Zona contamination can potentially lead to mixed or mosaic results during sex determination analysis. Although genomic breeding value was not estimated in this study, the high genotyping call rates of these embryos hold potential for genomic breeding value analysis. These findings demonstrate the successful extraction of DNA from embryonic biopsy samples and early-stage sex determination in bovine embryos using digital polymerase chain reaction results coupled with SNP genotyping marker analysis. The study highlights the prospects of using embryonic genomic selection to enhance genetic gain and optimize breeding strategies in cattle breeding programmes.