GENOMIC ASSOCIATIONS FOR SPONTANEOUS ABORTION IN HOLSTEIN CATTLE RECEIVING EMBRYO TRANSFER OR ARTIFICIAL INSEMINATION
Creators: name: Suarez, Emaly Michelle
Publisher: name: Washington State University
Year: 2024
Subjects: Artificial Insemination
Cattle
Dairy
Embryo Transfer
Genomic Selection
Spontaneous Abortion

description: Spontaneous abortion (SA) has been a consistent issue within the dairy industry, often resulting in increased culling and economic losses. To improve the ability of Holstein dairy cattle to conceive and maintain a full-term pregnancy, three studies were undertaken. The objective of the first study was to identify loci and positional candidate genes associated with spontaneous abortion in US Holstein heifers bred by artificial insemination (AI) or as embryo transfer (ET) recipients from an Idaho dairy using genome-wide association analysis (GWAA). Heifers bred by AI (n = 1,414) and those receiving ET (n = 864) were identified using producer records for those that maintained their pregnancy &gt; 260 days to those that aborted between days 42 and 260 of gestation. The GWAA compared 1,351 AI bred Holstein heifers that maintained pregnancy to 63 AI bred Holstein heifers that experienced spontaneous abortion and 591 Holstein heifers that were ET recipients that maintained their pregnancy to 273 ET Holstein heifer recipients that experience abortion. The GWAA identified 216 loci and 413 positional candidate genes associated (FDR &lt; 0.05) with SA in heifers bred by AI and no loci associated with SA in heifers that were embryo transfer recipients. The objective of the second study was to identify loci and positional candidate genes associated with SA in Holstein primiparous cows bred by AI or as ET recipients from the same Idaho dairy from the first study. This study compared 679 cows bred by AI that maintained their pregnancy to
description: 69 cows bred by AI that aborted and 236 ET recipient cows that maintained their pregnancy to 41 ET recipient cows that aborted. The GWAA for this study identified 86 loci and 168 positional candidate genes associated (FDR &lt; 0.05) with SA in primiparous cows bred by AI and four loci and 17 positional candidate genes associated (FDR &lt; 0.05) with SA in ET recipients. The third study objective was to identify gene sets and leading-edge genes enriched for SA in US Holstein heifers and primiparous cows receiving ET or AI using a gene-set enrichment analysis-single nucleotide polymorphism (GSEA-SNP) of the cattle from the first two studies. The GSEA-SNP identified four gene sets (NES ≥ 3.0) enriched for SA in heifers bred by AI, one gene set (NES ≥ 3.0) enriched for SA in primiparous cows bred by AI, eight gene sets (NES ≥ 3.0) enriched for SA in heifers receiving ET, and one gene set enriched (NES ≥ 3.0) for SA in primiparous cows receiving ET. Heifers bred with AI had 272 leading-edge genes enriched for SA, heifers receiving ET had 99 leading-edge genes enriched for SA, primiparous cows bred with AI had 33 leading-edge genes enriched for SA, and primiparous cows receiving ET had eight leading-edge genes enriched for SA. These studies identified loci, genes, and gene-sets associated with spontaneous abortion that could be beneficial for utilization in genomic selection.