Potential functional variants in AHR signaling pathways are associated with age at puberty in swine

Authors: Nonneman, Danny - Dan; Lents, Clay; Rempel, Lea; Rohrer, Gary

Submitted to: Animal Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/7/2021
Publication Date: 3/5/2021
Citation: Nonneman, D.J., Lents, C.A., Rempel, L.A., Rohrer, G.A. 2021. Potential functional variants in AHR signaling pathways are associated with age at puberty in swine. Animal Genetics. 52(3):284-291. Article 13051. https://doi.org/10.1111/age.13051.
DOI: https://doi.org/10.1111/age.13051

Interpretive Summary: Reproductive failure accounts for about a third of sow removals and most of these removals are animals in lower parities. Gilts that reach puberty earlier tend to stay in the herd longer and be more productive. Genetic improvement of reproductive traits in pigs has been challenging because these traits are sex-limited, have low heritabilities, are not expressed until later in the animal’s life and are not routinely measured in industry settings. Selecting on causal genetic variants that affect these traits would greatly accelerate genetic progress. This study tested for genetic associations of protein-coding variants in candidate genes identified in genome-wide association studies. Ten amino acid changes or variants in six candidate genes were found to be associated with age at puberty. These variants may be causative mutations that influence age at puberty in gilts and possibly sow lifetime productivity.

Technical Abstract: Puberty in female pigs is defined as age at first estrus and gilts that have an earlier age at puberty are more likely to have greater lifetime productivity. Because age at puberty is predictive for sow longevity and lifetime productivity, but not routinely measured in commercial herds, it would be beneficial to use genomic or marker-assisted selection to improve these traits. A GWAS at the US Meat Animal Research Center (USMARC) identified several loci associated with age at puberty in pigs. Candidate genes in these regions were scanned for potential functional variants using sequence information from the USMARC swine population founder animals and public databases. In total, 135 variants (SNP and insertion/deletions) in 39 genes were genotyped in 1284 phenotyped animals from a validation population sired by Landrace and Yorkshire industry semen using the Agena MassArray system. Twelve variants in eight genes were associated with age at puberty (P < 0.005) with estimated additive SNP effects ranging from 1.6 to 5.3 days. Nine of these variants were non-synonymous coding changes in AHR, CYP1A2, OR2M4, SDCCAG8, TBC1D1 and ZNF608, two variants were deletions of one and four codons in aryl hydrocarbon receptor, AHR, and the most significant SNP was near an acceptor splice site in the acetyl-CoA carboxylase alpha, ACACA. Several of the loci identified have a physiological and a genetic role in sexual maturation in humans and other animals and are involved in AHR-mediated pathways. Further functional validation of these variants could identify causative mutations that influence age at puberty in gilts and possibly sow lifetime productivity.