Swine

Repeatability estimates and genome-wide association studies accounted for additive and non-additive genetic effects in semen production traits in Duroc pig

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Abstract

The reproductive traits exhibited by males are among the essential factors in determining the production efficiency in pig breeding, and understanding the genetic architecture of these traits is imperative. Recently, non-additive quantitative trait loci (QTLs) for semen production traits were reported in cattle, and non-additive effects may contribute to semen production traits in pig populations. In this study, we estimated heritability and repeatability and performed genome-wide association studies (GWAS) that explicitly modeled both additive and non-additive genetic effects to detect QTLs associated with four semen production traits. A total of four traits including semen volume (VOL), sperm number (NUM), sperm concentration (CON), and proportion of morphologically abnormal sperm (PAS) were regarded as semen production traits and were used in this study. The dataset, which consisted of 13,788 records from 502 genotyped boars using a GGP Porcine HD array (70K), was evaluated to investigate the genetic effects on semen production traits. Following quality control, including the application of minor allele frequency (MAF) > 0.01 and Hardy-Weinberg equilibrium (HWE) test with P-value < 1à—10⁻⁴, a total of 44,158 single-nucleotide polymorphisms (SNPs) were retained for analysis. First, repeatability was quantified using single-trait repeatability animal models. An extended model partitioned repeatability into additive (A), dominance (D), epistasis (I; AA+AD+DD), and permanent environmental (pe) components. The contribution of dominance effect was consistently negligible across traits. Total repeatability ranged approximately from 0.38 to 0.51, with VOL showing 0.39 under the additive model (A=0.17, pe=0.22) and 0.38 under the A+D+I model (A=0.16, I=0.02, pe=0.20). CON remained stable at 0.41 (A=0.16, pe=0.25). In contrast, NUM and PAS exhibited higher levels of repeatability, driven by epistatic contributions. NUM reached 0.44 (A=0.21, I=0.19, pe=0.04) and PAS exhibited 0.50 (A=0.16, I=0.27, pe=0.07) under the A+D+I model. These results suggest that locus-by-locus interactions may contribute to these traits. Second, genome-wide association studies (GWAS) were conducted based on SNP data which accounted for additive, dominance and recessive effects. Significant associations were detected exclusively under non-additive models. For NUM, a recessive effect on chromosome 1 demonstrated the strongest significance (P = 8.0 à— 10⁻⁷), with the SNP (rs80957931) located within the PPP1R14C gene, previously implicated in sperm performance. For CON, two SNPs (rs81404444 and rs81341226) on chromosome 8 exhibited dominance effects (P = 1.4 à— 10⁻⁶), though no functionally relevant candidate genes were identified in the region. These results indicates that the non-additive effects model can improve the detection of semen production-related QTLs that remain invisible under GWAS with only additive effects. It demonstrates that non-additive effects contribute to the genetic architecture underlying male reproductive traits in pigs. This finding can serve as a motivation for the development of selection strategies that incorporate non-additive information in pig breeding.

Keywords: 2026

How to Cite:

Choi, Y., Suzuki, K., Yobuko, A., Terui, S., Ikufumi, Y. & Uemoto, Y., (2026) “Repeatability estimates and genome-wide association studies accounted for additive and non-additive genetic effects in semen production traits in Duroc pig”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2283802. doi: https://doi.org/10.31274/wcgalp.23513

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