Validation of loci and genes associated with fertility in Holstein cows using gene-set enrichment analysis-SNP and genotype-by-sequencing

Abstract

Abstract Background The financial strain fertility issues cause the dairy cattle industry is substantial, with over $7 billion in lost revenue accrued annually due to a relatively low cow conception rate (CCR; 30–43%) for US dairy cows. While CCR has been improving through genomic selection, identification of causal mutations would help improve the rate of genetic progress with genomic selection and provide a better understanding of infertility. The objectives of this study were to: (1) identify genes and gene-sets associated with CCR to the first breeding (CCR1) and the number of breedings required to conceive (TBRD) in Holstein cows and (2) identify putative functional variants associated with CCR1 and TBRD through a custom genotype-by-sequencing array. The study consisted of 1,032 cows (494 pregnant to first breeding, 472 pregnant to subsequent [2–20] services, and 66 that never conceived). Cows were artificially inseminated, and pregnancy was determined 35d later by rectal palpation of uterine contents. Gene-set enrichment analyses with SNP data (GSEA-SNP) were conducted for CCR1 and TBRD with a normalized enrichment score (NES) ≥ 3.0 required for significance. Leading edge genes (LEG) and positional candidate genes from this and 26 additional studies were used to validate 100 loci associated (P < 1 × 10− 5) with cow fertility using a custom sequencing genotyping array of putative functional variants (exons, promoters, splice sites, and conserved regions). Results GSEA-SNP identified 95 gene-sets (1,473 LEG) enriched for CCR1 and 67 gene sets enriched (1,438 LEG) for TBRD (NES ≥ 3). Thirty-four gene-sets were shared between CCR1 and TBRD along with 788 LEG. The association analysis for TBRD identified three loci: BTA1 at 83 Mb, BTA1 at 145 Mb, and BTA 20 at 46 Mb (P < 1 × 10− 5). The loci associated with TBRD contained candidate genes with functions relating to implantation and uterine receptivity. No loci were associated with CCR1, however a single locus on BTA1 at 146 Mb trended toward significance with an FDR of 0.04. Conclusions The validation of three loci associated with CCR and TBRD in Holsteins can be used to improve fertility through genomic selection and provide insight into understanding infertility.

Keywords

• Fertility
• GBS
• GSEA-SNP
• Holstein cattle
• Uterine receptivity