Genome-wide association analyses identify single nucleotide polymorphisms associated with in vitro embryo cleavage...

Reproductive success is an essential component of profitable and sustainable dairy operations. Although selection for production traits such as milk yield has led to a decline in fertility in dairy cattle, strategies including assisted reproductive technologies such as in vitro fertilization and embryo transfer, as well as genomic selection for fertility traits, are being implemented to help mitigate this loss. Previous studies have identified genetic markers associated with fertility traits such as daughter pregnancy rate, conception rate, and interval to first conception. However, genetic markers associated with in vitro embryo development have yet to be explored. Therefore, this study aimed to identify genetic markers associated with in vitro embryo cleavage and blastocyst rates with the future goal of creating an index to select bulls with superior abilities to produce embryos in vitro. Rigorous in vitro fertilization trials identified Holstein bulls with divergent abilities to produce embryos that successfully cleave and develop into blastocysts in vitro. A total of 40 bulls with embryo cleavage and blastocyst rate phenotypes were whole-genome sequenced. Sequencing was performed on an Illumina platform with PE150 reads followed by cleaning, mapping to ARS-UCD1.2, variant calling with GATK HaplotypeCaller, and quality control following the 1000 Bulls Genomes Project best practices. Genome-wide association analyses identified 819 and 442 SNPs associated with embryo cleavage and blastocyst rates, respectively. Significant regions on chromosomes 15, 18, 21, 22, and 23 were in linkage disequilibrium with QTL previously associated with reproductive traits in cattle. Further, a region on chromosome 28 with the most significant variant associated with cleavage rate contained several synonymous variants in EGLN1, which is a critical component of the hypoxia inducible pathway. An additional region on chromosome 18 associated with cleavage rate contained a missense variant in SMG9, a gene involved in the nonsense-mediated mRNA decay pathway. A region on chromosome 21 associated with blastocyst rate also contained variants in regulatory regions downstream from AEN, a gene required for efficient DNA fragmentation during the p53-dependent apoptosis pathway. In summary, this study identified a preliminary collection of genomic regions associated with embryo cleavage and blastocyst rates in vitro that contain relevant genes and other QTL associated with reproductive traits in cattle. These regions, after validation, could contribute to a selection index for identification of bulls with genetic predispositions to produce a greater number of embryos in vitro for use in assisted reproduction techniques.