Gestation length (GL) is a critical indicator of reproductive performance in sows and is closely associated with other reproductive traits, such as total number born (TNB) and number born alive (NBA). Despite its importance, the genetic mechanisms underlying GL and its impact on reproductive traits remain poorly understood. In this study, we investigated the relationship between GL and reproductive traits using 7013 farrowing records and conducted an imputed whole-genome sequence-based genome-wide association study (GWAS) for GL in first-parity sows, involving 3005 French Large White sows. Our findings revealed that the heritability of GL ranged from 0.22 to 0.26. Both excessively short and long GLs were associated with negative impacts on TNB, NBA, and other reproductive traits. A total of 64 SNPs exceeded the significance threshold, leading to the identification of two novel quantitative trait loci (QTLs) on chromosome 5 (QTL-1: 15.29–15.39 Mb and QTL-2: 12.86–12.94 Mb) and three promising candidate genes: TROAP, RFX4, and ADCY6. Gene ontology and KEGG pathway enrichment analyses revealed that these candidate genes are enriched in key biological processes, including ovarian steroidogenesis, the GnRH signaling pathway, and the regulation of cAMP biosynthesis, all of which are crucial for gestation and pregnancy maintenance. These findings improve our understanding of the genetic architecture of GL in sows and offer valuable genetic markers for enhancing reproductive efficiency in breeding programs.

Background: Backfat thickness (BFT) is a vital economic trait in pigs, reflecting subcutaneous fat levels that affect meat quality and production efficiency. As a complex trait shaped by multiple genetic factors, BFT has been studied using genome-wide association studies (GWAS) and linkage analyses to locate fat-related quantitative trait loci (QTLs), but pinpointing causal variants and genes is hindered by linkage disequilibrium and limited regulatory data. This study aimed to dissect the QTLs affecting BFT on Sus scrofa chromosome 1 (SSC1), elucidating regulatory variants, effector genes, and the cell types involved. Results: Using whole-genome genotyping data from 3,578 pigs and phenotypic data for five BFT traits, we identified a 630.6 kb QTL on SSC1 significantly associated with these traits via GWAS and fine-mapping, pinpointing 34 candidate causal variants. Using deep convolutional neural networks to predict regulatory activity from sequence data integrated with detailed pig epigenetic profiles, we identified five SNPs potentially affecting enhancer activity in specific tissues. Notably, rs342950505 (SSC1:161,123,588) influences weak enhancer activity across multiple tissues, including the brain. High-throughput chromosome conformation capture (Hi-C) analysis identified that rs342950505 interacts with eight genes. Chromatin state annotations confirmed enhancer activity at this QTL in the cerebellum. Leveraging these insights, single-cell ATAC-seq revealed a chromatin accessibility peak encompassing rs342950505 that regulates PMAIP1 expression in inhibitory neurons via enhancer-mediated mechanisms, with an adjacent peak modulating CCBE1 expression in neuroblasts and granule cells. Transcriptome-wide association studies (TWAS) confirmed PMAIP1’s role in the hypothalamus, and Mendelian randomization (MR) validated PMAIP1 and CCBE1 as key brain expression quantitative trait locus (eQTL) effectors. We propose that the variant rs342950505, located within a regulatory peak, modulates PMAIP1 expression in inhibitory neurons, potentially influencing energy homeostasis via hypothalamic regulation. Similarly, CCBE1 may contribute to this process. Conclusions: Our results, through systematic dissection of pleiotropic BFT-associated loci, provide a framework to elucidate regulatory mechanisms of complex traits, offering insights into polygenic control through lipid metabolism and neural signaling pathways.

Porcine models are increasingly recognized for their similarities to humans and have been utilized in disease modeling and organ grafting research. While extensive metabolomics studies have been conducted in swine, primarily focusing on conventional cohorts or specific animal models, the composition and functions of fecal metabolites in pigs across different age groups—particularly in the elderly—remain inadequately understood. In this study, an untargeted metabolomics approach was employed to analyze the fecal metabolomes of pigs at three distinct age stages: young (one year), middle-aged (four years), and elderly (eight years). The objective was to elucidate age-associated changes in metabolite composition and functionality under standardized rearing conditions. The untargeted metabolomic analysis revealed a diverse array of age-related metabolites. Notably, L-methionine sulfoxide levels were found to increase with age, whereas cytidine-5-monophosphate levels exhibited a gradual decline throughout the aging process. These metabolites demonstrated alterations across various biological pathways, including energy metabolism, pyrimidine metabolism, lipid metabolism, and amino acid metabolism. Collectively, the identified key metabolites, such as L-methionine sulfoxide and Cholecalciferol, may serve as potential biomarkers of senescence, providing valuable insights into the mechanistic understanding of aging in pigs.

Base editing is an efficient and precise gene-editing technique, by which a single base can be changed without introducing double-strand breaks, and it is currently widely used in studies of various species. In this study, we used hA3A-BE3-Y130F to simultaneously introduce premature stop codons (TAG, TGA, and TAA) into three tumor suppressor genes, TP53, PTEN, and APC, in large white porcine fetal fibroblasts (PFFs). Among the isolated 290 single-cell colonies, 232 (80%) had premature stop codons in all the three genes. C−to−T conversion was found in 98.6%, 92.8%, and 87.2% of these cell colonies for TP53, PTEN, and APC, respectively. High frequencies of bystander C−to−T edits were observed within the editing window (positions 3–8), and there were nine (3.01%) clones with the designed simultaneous three-gene C−to−T conversion without bystander conversion. C−to−T conversion outside the editing window was found in 9.0%, 14.1%, and 26.2% of the 290 cell colonies for TP53, PTEN, and APC, respectively. Low-frequency C−to−G or C−to−A transversion occurred in APC. The mRNA levels of the three genes showed significant declines in triple-gene-mutant (Tri-Mut) cells as expected. No PTEN and a significantly lower (p < 0.05) APC protein expression were detected in Tri-Mut cells. Interestingly, the premature stop codon introduced into the TP53 gene did not eliminate the expression of its full-length protein in the Tri-Mut cells, suggesting that stop codon read-through occurred. Tri-Mut cells showed a significantly higher (p < 0.05) proliferation rate than WT cells. Furthermore, we identified 1418 differentially expressed genes (DEGs) between the Tri-Mut and WT groups, which were mainly involved in functions such as tumor progression, cell cycle, and DNA repair. This study indicates that hA3A-BE3-Y130F can be a powerful tool to create diverse knockout cell models without double-strand breaks (DSBs), with further possibilities to produce porcine models with various purposes.

Porcine metabolomics research has been extensively conducted, primarily focusing on conventional cohorts or animal models. However, the composition and functions of fecal metabolites in pigs at various ages, particularly in the elderly, remain poorly understood. In the present study, an untargeted metabolomics approach was employed to analyze the fecal metabolomes of pigs at three distinct age stages, with the aim of elucidating age-associated changes in metabolite composition and functionality under standardized rearing conditions. Through the untargeted metabolomic analysis of fecal samples from young (one year), middle-aged (four years), and elderly (eight years) pig cohorts, a variety of age-related metabolites were identified. For example, L-methionine sulfoxide was observed to increase with age, while cytidine-5-monophosphate exhibited a concomitant gradual decrease during the aging process. These metabolites were found to undergo alterations across multiple biological pathways, including energy metabolism, pyrimidine metabolism, lipid metabolism, and amino acid metabolism. Furthermore, the age-dependent metabolic changes were associated with known senescence biomarkers, offering new insights into the mechanistic understanding of aging in pigs.

Background: Labour dystocia (LAD) in sows is a common reproductive disorder that reduces piglet survival rates and increases the number of stillbirths, causing substantial economic losses to pig farms. However, the genetic basis of LAD remains elusive. Herein, we performed a single-breed genome-wide association study (GWAS) for LAD using imputed whole-genome sequence data from 3263 sows (487 Landrace and 2776 Yorkshire). Results: In this study, analysis of the reproductive traits showed that the total number of piglets born and the number of piglets born alive were 1.43–2.85 and 1.60–2.94 higher, respectively, in sows with natural labour than in those with LAD. We identified 250 and 12 SNPs associated with LAD in primiparous and multiparous sows, respectively. Furthermore, in primiparous Yorkshire sows, two major QTL were fine-mapped to a 498.44 kb interval (23.18–23.68 Mb) on SSC2 and a 779.85 kb interval (43.34–44.12 Mb) on SSC9. Further analysis revealed that the two significant SNPs (2_23340612 and 9_44119733) within these QTL regions were located within regulatory regions across multiple pig breeds and tissues. The potentially regulatory SNP (2_23340612) is located within the binding sites of 27 transcription factors, that are primarily involved in oxytocin signalling, muscle contraction, and the development of female genitalia and embryo. The other potentially regulatory SNP (9_44119733) is located within the binding sites of eight transcription factors, among which three transcription factors (ZNF274, HMGA1, and CTCF) are predicted to interact with six candidate genes ( APOA1 , APOC3 , APOA4 , APOA5 , BUD13 , and ZPR1 ). Finally, eight promising candidate genes ( APOA1 , APOC3 , APOA4 , APOA5 , BUD13 , ZPR1 , ACAN , and HAPLN3 ) were identified to be associated with LAD. Functional enrichment analysis indicated that the candidate genes were enriched in pathways related to lipid metabolism, extracellular matrix organization, cell adhesion and response to estrogen. Conclusions: The LAD is a prominent reproductive disorder trait that negatively impacts the reproductive efficiency of sows. This study identified potentially regulatory SNPs (2_23340612 and 9_44119733) and eight promising genes ( APOA1 , APOC3 , APOA4 , APOA5 , BUD13 , ZPR1 , ACAN , HAPLN3 ) associated with LAD. To our knowledge, this is the first whole-genome-sequence-based GWAS with large-scale reproductive data to identify genetic markers and candidate genes of LAD of sows.