Identification of loci associated with fertility traits in United States of America Holstein heifers

Justine M. Galliou

The dairy industry faces economic losses due to subfertility, as the current heifer conception rate (HCR) is approximately 61%. A lack of knowledge of the genetics underlying the complex physiological processes involved in fertility limits the ability to make accurate selection decisions. The objectives of this study were to identify loci, positional candidate genes, transcription factor binding sites (TFBS), and biological networks associated with HCR in U.S. Holstein heifers. Heifers were bred via artificial insemination (AI), and pregnancy was determined at day 35 post insemination via ultrasound. Two genome-wide association analyses (GWAA) were performed. One focused on heifer conception rate at first service (HCR1) comparing heifers that conceived at the first AI and maintained the pregnancy until day 35 to those that conceived at subsequent AIs or that did not conceive. The other GWAA explored the loci associated with the times bred to achieve a pregnancy (TBRD) in heifers that conceived at the first, second, third, or later (fourth to seventh) AI services. Genes and TFBS associated with positional candidate genes were used in the Ingenuity Pathway Analysis (IPA). The GWAA for HCR1 identified 146 loci in the additive model, 317 loci in the dominant model, and 9 loci in the recessive model. The GWAA for TBRD identified 246, 579, and 16 loci associated with the additive, dominant and recessive models, respectively. There were 302 SNPs shared between phenotypes, as well as 56 loci validated in previous studies using independent cattle populations. Eleven canonical pathways, 207 master regulators and 11 upstream regulators were identified as associated with HCR1 and TBRD through IPA. These results give insight into the genomic architecture underlying heifer conception rate. The positional candidate genes, pathways, and regulators identified by this study had functions relating to implantation and placentation. Loci associated with multiple phenotypes and validated in independent populations are good candidates for genomic selection and further analysis to identify causal mutations to better understand the mechanisms of infertility. This study provides the foundation for improving fertility through genomic selection and elucidating the mechanisms associated with infertility in cattle.

Identification of loci associated with fertility traits in United States of America Holstein heifers

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