Genomic variants associated with oocyte and embryo production in dairy Gir cattle

The combined use of in vitro fertilization and genomics contribute to increasing productive potential and genetic gain in dairy cattle. The aim of this study is to deepen the understanding of the genomic architecture of the dairy Gir breed by identifying variants associated with the number of oocytes and embryos. This study is a continuation of a previous family analysis study conducted in the dairy Gir, in which a region on chromosome 7 (BTA7) was associated with the number of oocytes and embryos. In the current study, a genomic variant call file (VCF) of 12 sires with positive Predicted Transmission Ability (PTA) for milk production was investigated. These bulls are widely used in dairy herds to produce Gir daughters, whose oocyte and embryo data were collected. This region on BTA 7 was analyzed using the online tool EnsemblVEP and four variants were classified as lead SNPs. Two lead SNPs were single-nucleotide substitutions and both caused the inclusion of a premature stop codon in XRCC4 and HAPLN1 genes. A third lead SNP regards the deletion of five sequential thymines in an intergenic region. The fourth lead SNP involves the deletion of one nucleotide in EDIL3 gene, causing frameshift. In conclusion, these lead SNPs may have a positive or negative impact on the production of oocytes and in vitro embryos in the dairy Gir, which can be verified through subsequent association studies. Therefore, it is extremely important to verify how genetic improvement and breeding programs can increase gains for the reproductive traits.