Estimation of the Genetic Components of (Co)variance and Preliminary Genome-Wide Association Study for Reproductive Efficiency in Retinta Beef Cattle

SIMPLE SUMMARY: Fertility is one of the most important traits for productivity in extensive beef production systems, since it has a major effect on the number of calves born and, as a result, the quantity of weaned calves produced per year. However, it is difficult to improve this trait under extensive conditions, mainly due to the lack of reliable and easy-to-obtain selection criteria. In this study, fertility was analyzed using reproductive efficiency, which was calculated as the deviation between the optimal and real parity number of females at each age. We demonstrated a high h(2) value (0.30) using a classic repeatability model and a random regression model (ranging from 0.24 to 0.51), which suggests that the latter model can be recommended to improve fertility in beef breeds raised under extensive environmental conditions such as the Retinta. In addition, we performed the first GWAS analysis looking for SNP genetic markers associated with this character in cattle, which showed five markers significantly associated with the trait located on BTA4 and BTA28. Finally, the functional analysis revealed the presence of five candidate genes located within these regions, which were previously shown to be related to fertility in cattle and mice models. ABSTRACT: In this study, we analyzed the variation of reproductive efficiency, estimated as the deviation between the optimal and real parity number of females at each stage of the cow’s life, in 12,554 cows belonging to the Retinta Spanish cattle breed, using classical repeatability and random regression models. The results of the analyses using repeatability model and the random regression model suggest that reproductive efficiency is not homogeneous throughout the cow’s life. The h(2) estimate for this model was 0.30, while for the random regression model it increased across the parities, from 0.24 at the first calving to 0.51 at calving number 9. Additionally, we performed a preliminary genome-wide association study for this trait in a population of 252 Retinta cows genotyped using the Axiom Bovine Genotyping v3 Array. The results showed 5 SNPs significantly associated with reproductive efficiency, located in two genomic regions (BTA4 and BTA28). The functional analysis revealed the presence of 5 candidate genes located within these regions, which were previously involved in different aspects related to fertility in cattle and mice models. This new information could give us a better understanding of the genetic architecture of reproductive traits in this species, as well as allow us to accurately select more fertile cows.