IDENTIFICATION OF GENOMIC REGIONS ASSOCIATED WITH EMBRYONIC LOSS IN AMERICAN HOLSTEIN CATTLE

Victoria Kelson

doi:10.7273/000007060

The objective of the following studies was to identify loci and gene sets in Holsteins associated with conception to the first service (CR1) or number of times bred to a successful pregnancy (TBRD) to study embryonic loss. Heifers from one dairy in Idaho were bred by artificial insemination (AI, n = 2829) or were embryo transfer recipients (ET, n = 2086) for conception rate to the first service, and for times bred to successful pregnancy heifers bred by AI (n = 2754) or ET (n = 1566) recipients. A genome wide association analysis (GWAA) and a gene set enrichment analysis using single nucleotide polymorphisms (GSEA-SNP) were performed. Three unique loci, containing four positional candidate genes, were associated (p < 1 × 10−5) with heifer CR1 for ET recipients, while the GSEA-SNP identified four gene sets (NES ≥3) and sixty-two leading edge genes (LEGs) enriched for HCR1. No loci were associated with HCR1 bred by AI, one gene set and twelve LEGs were enriched for HCR1 with the GSEA-SNP. Eight loci on BTA4, 6, 10, 14, 26, and 27 associated with eight positional candidate genes associated with TBRD in AI bred heifers. The GSEA-SNP identified one gene set, and one leading edge gene as enriched for TBRD in AI bred heifers. In heifers that were ET recipients four loci, two on BTA15, and one each on BTA17 and BTA27 were associated with TBRD and contained 11 positional candidate genes. Two gene sets containing 41 leading edge genes were enriched for TBRD in ET recipients. Many of the positional candidate and leading edge genes have functions related to embryonic loss in humans or cattle. Analyses focused on primiparous cows included conception rate to the first service (CCR1) that received AI (n = 882) or ET (n = 353) breeding services, and the number of times bred to a successful pregnancy (TBRD) for AI services (n = 1851). A genome-wide association analysis and gene set enrichment analysis using SNP data for each phenotype and group was completed. Two unique loci, containing five positional candidate genes, were associated with CCR1 AI services, while the GSEA-SNP identified one gene set (NES ≥3) containing eighteen LEGs. Five unique loci were associated with CCR1 ET services; however, no gene sets were associated. The TBRD phenotype was associated with five unique loci, and two gene sets containing eight LEGs. These studies identified loci as potential genomic selection markers for AI and ET to incorporate into indices that could help producers select for higher reproductive efficiency based on reproductive technology. Many genes identified had direct roles in fertility and are crucial to embryonic development. Further research on the causative mutations at these loci will provide more information on the role of the positional candidate and LEGs in fertility and embryonic loss in Holstein heifers and primiparous cattle.

IDENTIFICATION OF GENOMIC REGIONS ASSOCIATED WITH EMBRYONIC LOSS IN AMERICAN HOLSTEIN CATTLE

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