Fine mapping genetic variants associated with age at puberty and sow fertility using Sowpro90 genotyping array

Authors: WIJESENA, H - University Of Nebraska; KACHMAN, S - University Of Nebraska; Lents, Clay; RIETHOVEN, J - University Of Nebraska; TRENHAILE-GRANNEMANN, M - University Of Nebraska; SAFRANSKI, T - University Of Missouri; SPANGLER, M - University Of Nebraska; CIOBANU, D - University Of Nebraska

Submitted to: Journal of Animal Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/31/2020
Publication Date: 9/4/2020
Citation: Wijesena, H.R., Kachman, S.D., Lents, C.A., Riethoven, J.J., Trenhaile-Grannemann, M.D., Safranski, T.J., Spangler, M.L., Ciobanu, D.C. 2020. Fine mapping genetic variants associated with age at puberty and sow fertility using Sowpro90 genotyping array. Journal of Animal Science. 98(10):1-12. https://doi.org/10.1093/jas/skaa293.
DOI: https://doi.org/10.1093/jas/skaa293

Interpretive Summary: Improving reproductive traits of sows, such as litter size and reproductive longevity, via traditional breeding and genetic approaches is challenging for pork producers because reproductive traits are lowly heritable and expressed late in life. With the aim of improving accuracy of genomic prediction for sow reproductive and fertility traits, ARS scientists at Clay Center, Nebraska, in collaboration with researchers from the University of Nebraska developed a custom genotyping array called SowPro90 that contains novel single nucleotide polymorphisms (SNP) predicted to affect the level of gene expression or cause loss of gene function. Researchers used the SowPro90 to determine if SNP located in genomic regions controlling age at puberty are also related to litter size and reproductive longevity. They discovered several SNP associated with all three of the traits and further confirmed the genetic association with litter size in sows from commercial swine production. Results from this study provide producers with critical information about genetic markers on the commercially available SowPro90 genotyping platform that are useful for selecting replacement sows and improving reproductive traits.

Technical Abstract: Sow fertility traits, such as litter size and the number of lifetime parities produced (reproductive longevity), are economically important. Selection for these traits is difficult because they are lowly heritable and expressed late in life. Age at puberty (AP) is an early indicator of reproductive longevity. Here, we utilized a custom Affymetrix single-nucleotide polymorphisms (SNPs) array (SowPro90) enriched with positional candidate genetic variants for AP and a haplotype-based genome-wide association study to fine map the genetic sources associated with AP and other fertility traits in research (University of Nebraska-Lincoln [UNL]) and commercial sow populations. Five major quantitative trait loci (QTL) located on four Sus scrofa chromosomes (SSC2, SSC7, SSC14, and SSC18) were discovered for AP in the UNL population. Negative correlations (r = -0.96 to -0.10; P < 0.0001) were observed at each QTL between genomic estimated breeding values for AP and reproductive longevity measured as lifetime number of parities (LTNP). Some of the SNPs discovered in the major QTL regions for AP were located in candidate genes with fertility-associated gene ontologies (e.g., P2RX3, NR2F2, OAS1, and PTPN11). These SNPs showed significant (P < 0.05) or suggestive (P < 0.15) associations with AP, reproductive longevity, and litter size traits in the UNL population and litter size traits in the commercial sows. For example, in the UNL population, when the number of favorable alleles of an SNP located in the 3' untranslated region of PTPN11 (SSC14) increased, AP decreased (P < 0.0001), while LTNP increased (P < 0.10). Additionally, a suggestive difference in the observed NR2F2 isoforms usage was hypothesized to be the source of the QTL for puberty onset mapped on SSC7. It will be beneficial to further characterize these candidate SNPs and genes to understand their impact on protein sequence and function, gene expression, splicing process, and how these changes affect the phenotypic variation of fertility traits.