Identification of Gene and Gene Sets Enriched for Heifer Conception Rate in US Holstein Heifers

Heifer conception rates remain low in the dairy industry. The objective of this study was to identify genes and the biological pathways associated with heifer conception in Holstein dairy heifers. Breeding and health records were analyzed from a commercial dairy heifer raising facility in Southern Idaho. All heifers were bred by artificial insemination (AI) at observed estrus, and pregnancy was determined at day 35 after AI via palpation. A total of 497 heifers were classified as highly fertile (HF; conceived on their first AI service), and 429 heifers did not conceive until after fourth AI service or were culled due to failure to conceive and were classified subfertile (SF). Genotyping of heifers was conducted using the Illumina BovineHD BeadChip. Quality control consisted of removing animals with <90% of genotypes and removing markers with less than a 90% call rate, a minor allele frequency <1%, or if they failed Hardy-Weinberg Equilibrium testing. Based on those criteria, 466 HF and 368 SF heifers and 590,904 SNPs remained for the analysis. A genome-wide associated analysis (GWAA) was conducted using an additive model of the Efficient Mixed-Model Association expedited (EMMAX) statistical test with a genomic relationship matrix. The GWAA identified 147 QTLs (P< 5.5 x 10^-5) that were moderately associated and 26 QTLs (P< 5.5 x 10^-7) that were strongly associated with heifer fertility. The most significant SNP within 8 kb of each of 19,723 genes was used in a gene-set enrichment SNP analysis (GSEA-SNP) with the GenGen software package and gene sets from Gene Ontology (n=3147), Kyoto Encyclopedia of Genes and Genomes (n=186), Reactome (n=674), Biocarta (n=217) and Panther (n=165). The significance for each gene set was calculated using the null distribution generated from 10,000 phenotype based permutations using GenABEL. The GSEA-SNP identified seven gene sets associated (Normalized Enrichment Score > 3.0) with heifer conception rate and 195 leading edge genes. These results provide insight into the interaction and mechanism of genes important in heifer conception rate. Acknowledgement: This project was supported by Agriculture and Food Research Initiative Competitive Grant no. 2013-68004-20365 from the USDA National Institute of Food and Agriculture.