PSXIII-B-11 Identification of Haplotypes Associated with Fetal Loss in Dairy Cattle

Abstract Fetal loss occurs in 4 to 13% of dairy cattle worldwide with a subsequent $487 to $1900 economic loss per pregnancy. Previous studies have identified SNPs associated with fetal loss, but few have investigated haplotypes (DNA that segregates to offspring together) associated with fetal loss. The objective of this study was to identify haplotypes associated with fetal loss in Holstein heifers and cows that conceived to the first insemination. This study consisted of 529 Holstein heifers (470 maintained pregnancies to term while 59 experienced fetal loss) and 517 Holstein cows (490 maintained pregnancies to term while 28 suffered fetal loss). Cattle with fetal loss (cases) were genotyped using the Neogen BovineGGP50 BeadChip (SNPs = 43,938) and cattle that calved at term (controls) were genotyped with the Illumina BovineHD BeadChip (SNPs = 777,962). Cases were imputed to HD density using BEAGLE (4.1). Cases and controls were combined to identify 62,819 haplotypes. Haplotype association tests were run for three populations (heifers, cows, and combined) with a chi-squared Bonferroni (BF) corrected significance of p < 0.05. The haplotype analyses identified 121, 47, and 102 haplotypes associated with fetal loss in heifer, cow and combined populations, respectively. Of these, 37 haplotypes were shared between the heifer and cow populations, 39 between cows and the combined, 76 between the heifers and combined, and 37 across all analyses. Loci identified in the haplotype analyses were compared to loci associated (BF p < 0.05) with fetal loss in a SNP by SNP genome wide association analyses. There were 22 loci shared in heifers, 10 in cows and 21 in the combined population. The use of haplotypes, identified an additional 150 loci associated with fetal loss that can be further characterized for their value in selecting cattle that are less prone to late term abortions.