Search bioRxiv⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.1101/2025.08.01.668164

Genetic parameters and genome-wide association analysis of service sire effect on litter size and its relationship with boar semen quality in three terminal sire lines

Chen, C.-Y.·Lourenco, D.·Kleve-Feld, M.·Bhatnagar, A.·Holl, J.
View original source ↗Export metadata ↓

Abstract

This study aimed to estimate the genetic parameters for service sire effects on the number born alive (NBA) and its relationship with semen quality traits. Data of 6,416, 23,188, and 48,890 litter size records collected between 2020 and 2024 from three purebred terminal sire lines were analyzed. The number of sows was 3,071, 11,819, and 24,089, with 197, 554, and 891 service sires for the three respective lines. There were 1,424,858, 4,344,630, and 2,146,583 animals in the pedigree of which 67,990, 259,250, and 365,392 were genotyped and imputed up to 50K SNPs. The service sire and dam effects were modeled as additive genetic effects, considering a covariance structure among them, given by the relationship matrix. The model also included fixed effects of contemporary group and parity group with random permanent environmental effects for service sire and dam. Genetic parameters were estimated using the AIREML option in the BLUPF90+ software, and GEBVs were generated by ssGBLUP with the algorithm for proven and young (APY). Heritability for the service sire effect ranged from 0.01 to 0.03, and the heritability for the dam effect ranged from 0.09 to 0.15, with genetic correlations ranging from -0.20 to 0.37. A single-step genome-wide association study (ssGWAS) was also performed, and no strong signals were detected for service sire effects on NBA. Sperm motility (MOT) and total abnormal morphology (ABN_MOR) GEBVs from the three lines were estimated based on about 57,500 to 608,996 ejaculates recorded using the computer-assisted semen analysis (CASA) system from 1,698 to 29,095 boars collected from 2013 to 2025. Heritability estimates ranged from 0.10 to 0.12 for motility and from 0.17 to 0.28 for total abnormal morphology. The correlations between service sire GEBV for NBA and semen quality were low but in the favorable direction. Results suggest that although paternal genetic contributions to litter size were small compared to maternal genetic contributions, selecting on service sire effects on litter size in addition to semen quality traits will improve overall reproductive success.

Source connections

Explore related subjects

geneticsPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Chen, C.-Y., Lourenco, D., Kleve-Feld, M., Bhatnagar, A., Holl, J.. 2025-08-06. Genetic parameters and genome-wide association analysis of service sire effect on litter size and its relationship with boar semen quality in three terminal sire lines. https://doi.org/10.1101/2025.08.01.668164

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

OPA1 controls mitochondrial dysfunction-driven liver fibrosis in MASLD

Progressive hepatic fibrosis is the principal determinant of morbidity and mortality in metabolic dysfunction-associated steatotic liver disease and steatohepatitis (MASLD/MASH). Mitochondrial dysfunction is a hallmark of MASH, and the release of mitochondrial damage-associated molecular patterns (mito-DAMPs) from injured hepatocytes can promote fibrosis. However, how mitochondrial dynamics and quality control shape the fibrotic response in MASLD/MASH remains unclear. Here, through large-scale genomic analyses of mitochondrial genes governing mitophagy, fusion and fission in human MASLD, with a power-equivalent sample size of approximately 700,000 individuals, we identify a strong association between hepatic fibrosis and the mitochondrial fusion factor dynamin-like GTPase optic atrophy 1 (OPA1). OPA1 transcripts and protein abundance in the liver epithelium were progressively dysregulated with advancing fibrosis. In mice, hepatocyte-specific OPA1 loss alone was sufficient to induce hepatic stellate cell activation and fibrosis in zone 3, promoted the release of mito-DAMPs into the circulation and exacerbated fibrosis in experimental MASH. These findings identify OPA1 as a central regulator of the hepatic fibrotic response and connect defective mitochondrial homeostasis to mito-DAMP release, hepatic stellate cell activation and fibrosis in MASLD.

genetics↗
bioRxiv2026

Mechanism-selective deep mutational scanning distinguishes ERCC2 disease phenotypes

Pathogenic ERCC2 variants cause xeroderma pigmentosum (XP), trichothiodystrophy (TTD) or both, yet variant effect scores are usually interpreted only as measures of pathogenicity rather than of which disease mechanism is disrupted. XPD, the ERCC2-encoded TFIIH subunit, functions in both nucleotide excision repair and transcription. Using yeast complementation deep mutational scanning, we measured the effects of nearly all XPD amino acid substitutions. The assay was mechanism-selective: it preferentially reported transcription-associated function, with pronounced intolerance at the p44 interface, whereas many substitutions affecting DNA binding and helicase activity retained near-wild-type fitness. Accordingly, TTD variants had much lower fitness than XP variants. Computational predictors discriminated pathogenic from benign variants similarly across phenotypes, but the DMS distinguished XP from TTD variants better than all 73 predictors tested. Phenotype-specific ACMG/AMP calibration provided evidence in both directions for TTD but mainly pathogenic evidence for XP. Thus, the selectivity of functional assays, often viewed as a limitation, can reveal disease mechanisms and support phenotype-aware variant interpretation.

genetics↗
bioRxiv2026

Temporal control of mitochondrial mutagenesis reveals the fate of mtDNA mutations with age

Mutations in the mitochondrial genome (mtDNA) play a critical role in the aging process and a wide variety of age-related diseases. However, it remains unclear when the mutations that drive physiological decline arise. To answer this question, we generated a new mouse model in which mitochondrial mutagenesis can be confined to a defined window of time. Surprisingly, we found that mutations that arise during the first two months of life are sufficient to drive a wide variety of age-related pathologies, and that the severity of this pathology is broadly regulated by distinct, tissue-specific selective pressures that control the fate of mtDNA mutations with age. Further, we found that selection against deleterious variants can be modulated by manipulation of mitochondrial fusion in vitro and in vivo. These observations raise the possibility that in some tissues, the pace of aging is pre-determined by events that occur early in life and that interventions targeting mitochondrial fusion may be able to slow down or reverse the expansion of these pathogenic variants. These results carry far-reaching implications for strategies aimed at preventing or delaying age-related decline.

genetics↗