The genetic antagonism between lean meat yield and meat quality dictates the need for precise selection in pigs. This study evaluated the impact of terminal sire lines (Duroc [D], Pietrain [P], and their F1 cross [PD]) on production traits and performed a genome-wide association study (GWAS) in a 1295 commercial population. Results revealed a clear genetic trade-off: D-sired progeny showed superior intramuscular fat (IMF) and meat color (p < 0.05), while P-sired progeny excelled in loin muscle area and leanness. PD-sired pigs generally showed intermediate performance and did not outperform the purebred terminal-sire groups for the major traits evaluated. GWAS replicated major known QTLs, including the VRTN locus for rib count (SSC7:97575068_A_G, p = 2.30e-39) and the BMP2 locus for carcass length (SSC17:15820953_G_A, p = 1.59e-09). Rib count was positively correlated with adjusted carcass straight length (r = 0.393, p = 5.80e-31), and combined genotype analysis of the VRTN and BMP2 loci revealed a joint effect on axial skeleton traits. Novel QTLs were discovered for drip loss (SSC13, SSC14) and myofiber perimeter (SSC1), with TUSC1 identified as a candidate gene. Our findings demonstrate that the PD cross does not mitigate the leanness-quality trade-off and highlight the VRTN and BMP2 loci, together with novel trait-associated markers, as potential targets for crossbred breeding programs.

This study aimed to identify genomic regions and candidate genes associated with body composition, and meat quality traits in Iberian pigs fattened in Montanera. A genome-wide association study (GWAS) was conducted on 528 pigs for 29 phenotypic traits using genomic data from the GGP Porcine HD Array. After quality control, 526 animals and 35,894 SNPs were retained for the association analysis. Despite the limitations of the genotyping chip used, which lacked coverage for Iberian-specific variants, the GWAS performed with GCTA software identified 165 SNPs significantly associated with 11 traits. Among these, 145 SNPs were clustered into 25 quantitative trait loci (QTL) regions. Five QTLs were identified for ham yield, containing genes such as KCNIP4, ZNF438, and PID1. Eight QTLs were associated with loin yield, with genes like PREX2, RSPO1, and PDE4B. One QTL was associated with shear force, and 16 QTLs were related to fatty acid composition. Genes linked to these traits included ELOVL6, associated with myristic and palmitic acids, and ADCY9 and ROBO1, associated with linoleic acid. Overall, these results provide novel genomic insights and markers that could enhance selection strategies in Iberian pig breeding programs, while highlighting the need for improved genomic tools tailored to local breeds.

Backfat thickness is a key carcass trait reflecting fat deposition in pigs, while semen quality represents a critical measure of boar reproductive performance in artificial insemination systems. Despite their economic importance, the genetic relationship between these traits remains largely unexplored. In this study, we applied the PLACO method under the composite null hypothesis to identify genes affectingadjusted backfat thickness at 100 kg (BFT_100), semen volume (SEMVOL), and sperm motility (SPMOT). The consistency and heterogeneity of pleiotropic gene effects were evaluated using Pearson correlation and Cochran's Q test, and protein-protein interaction (PPI) networks were constructed based on the STRING database. Generalized Summary-data-based Mendelian Randomization (GSMR) was employed to investigate potential genetic associations between BFT_100 and semen traits. We identified 99 significant pleiotropic genes (FDR < 0.05), including seven genes (PACSIN1, TTC26, PSMD13, PKHD1, VARS2, MDFI, MRPS10) associated with all three traits. Approximately 57.5% of genes exhibited positive correlations between traits, while 42.5% showed negative correlations. PPI analysis revealed that these genes formed interconnected networks enriched in energy metabolism and immune-related pathways. GSMR indicated a significant positive genetic effect of BFT_100 on SEMVOL (β = 19.09, P = 1.545 × 10-7) but a negative effect on SPMOT (β = -0.0051, P = 0.0138). These results reveal the complex genetic links between fat deposition and semen traits, highlight key pleiotropic genes, and suggest mechanisms by which adiposity may influence reproductive performance, providing valuable insights for molecular breeding and genetic improvement in pigs.

With the improvement of people's living standards, public attention to pork quality has grown increasingly. This study aimed to identify the key genes affecting meat quality in pigs. Castrated Mashen (MS) pigs (n = 6) with an average body weight of 112.5kg (300days of age) and Duroc × (Landrace × Yorkshire) (DLY) pigs (n = 6) with an average body weight of 114.5kg (165days of age) were selected for slaughter. The longissimus dorsi muscle (LDM) was collected for meat quality traits determination and omics analyses. The results showed that MS pigs exhibited significantly superior meat color, intramuscular fat (IMF) content, marbling, shear force, and pH compared with DLY pigs (p < 0.05). A total of 1330 differentially expressed genes (DEGs), 94 differentially expressed lipids (DELs), and 185 differentially accumulated metabolites (DAMs) were screened between MS and DLY pigs (p < 0.05). Further weighted gene co-expression network analysis (WGCNA) revealed that glycerophospholipids (GP) and glycerolipids (GL) were key lipids affecting pork quality. Additionally, integration of lipidomic and metabolomic data identified "lipids-metabolites strong correlation pairs" influencing meat quality, such as the significant positive correlation between carnitine derivatives and various triglycerides (TG) (|r|> 0.8, p < 0.05). Furthermore, we conducted transcriptome-metabolome and transcriptome-lipidome correlation analyses based on expression abundance and functional annotations, and screened four key gene sets. Finally, after the intersection of these key genes, 19 core genes such as ALDOB, ASS1, CYP2A13, CYP2E1, DMGDH, PLCB1, and MAT1A may be related to pork quality. This study provides potential targets for further exploring the molecular mechanisms underlying pork quality by identifying several key genes linked to pork quality traits.

BackgroundSelective breeding has substantially improved productive and reproductive traits in pigs. Yet, these traits are biologically interconnected, and selection for one often affects others in unintended ways. While genome-wide association studies (GWAS) have uncovered many loci linked to these traits, they provide limited insight into causal mechanisms. Mendelian randomization (MR) provides a robust framework for inferring causality and identifying shared genetic determinants. Here, we integrated MR, colocalization, and functional genomics to investigate the biological links between growth, carcass composition, and reproduction in pigs.ResultsUsing average daily gain (ADG) as the exposure, MR revealed potentially significant causal effects (P < 0.05) of ADG on carcass composition traits, including backfat thickness (BFT: widehat{b}{ }_{xy} = 0.13) and loin muscle depth (LMDEP: widehat{b}{ }_{xy}= 0.35), suggesting a potential causal contribution of increased ADG to both fat deposition and muscle development. Additionally, ADG showed a negative causal association with age at first farrowing (AFF: widehat{b}{ }_{xy}= −3.24), indicating that faster growth promotes earlier sexual maturity and reproductive onset. In addition to the statistical evidence, gene annotation of instrumental variants (IVs) identified overlapping candidate genes, which may help explain the causal associations observed across the four exposure–outcome analyses. Among these, MC4R and CDH20 were supported by colocalization analysis, indicating shared genetic signals potentially linking growth, carcass composition, and reproductive traits. Integrative analysis supported the tissue-specific roles of these genes in regulating growth, carcass composition, and reproduction.ConclusionsOur findings suggest a shared genetic architecture and provide potential evidence of a causal influence of ADG on carcass composition and reproductive traits in pigs. This integrative framework supports the development of multi-trait breeding strategies that enhance productivity while managing inherent trade-offs in regulating complex traits.Supplementary InformationThe online version contains supplementary material available at 10.1186/s40104-026-01363-5.

Variations in both transcription and translation of genes play a pivotal role in shaping complex traits and disease phenotypes. However, systematic analyses of genetic variants regulating transcription and translation, as well as their contribution to the genetic architecture of complex traits, remain scarce. Here, by generating a multi-omics dataset consisting of 132 datasets (48 transcriptomic, 48 translational, 30 proteomic, and 6 WGS) across 16 tissues from two breeds, with 3 pigs per breed, we demonstrated widespread translational buffering/amplification across tissues and breeds, with translation efficiency (TE) contributing significantly to phenotypic variation. Through integrative analysis of transcriptional and translational profiles, population genetics, and dual-luciferase reporter assays, we developed a novel framework for prioritizing gene regulatory networks (GRNs) underlying complex traits. Using this framework, we identified 33 functional 5'UTR variants linked to pork production traits, modulating 14 target genes through changes in TE. RNA interference assays confirmed the involvement of AQP4 and MYO18B in myogenic differentiation. In particular, the AQP4 variant (chr6_111421187) likely alters TE by modifying RNA secondary structure, while MYO18B variants (chr14_43476491) affect TE via RNA-binding protein interactions. More broadly, our framework can serve as a paradigm for uncovering the genetic basis of complex traits, extending beyond traditional transcriptional regulation.

The in vitro effect of omentin-1 on the global proteome of granulosa cells from normal weight Large White and fat Meishan pigs.

Growth traits in pigs are governed by complex polygenic architectures, with most associated loci residing in non-coding regions that exert substantial influence on economically relevant phenotypes. However, the molecular mechanisms underlying these regulatory elements remain poorly characterized. In this study, a non-coding mutation-designated as NR2C2 recognition motif sequence variation (NRMSV), located 2083 bp upstream of the HMGA1 gene-was identified as a functional modulator of growth traits in a three-generation Eurasian hybrid pig population. NR2C2 is a nuclear receptor implicated in skeletal development and metabolic regulation, while HMGA1 is a key determinant of body size across mammalian species. In embryonic fibroblasts, where NR2C2 is abundantly expressed, the mutant NRMSV suppressed transcriptional activity, functioning as a silencer. In contrast, in bone marrow mesenchymal stem cells, characterized by low NR2C2 expression, the same allele acted as a robust transcriptional enhancer. Knockdown of NR2C2 in embryonic fibroblasts abrogated this repression and restored enhancer activity, confirming the context-dependent, bidirectional regulatory effect of NRMSV on HMGA1 expression. These findings establish the NR2C2-NRMSV-HMGA1 pathway as a novel regulatory mechanism underpinning phenotypic variation in pig growth traits, offering mechanistic insights into mammalian developmental regulation and informing targeted genomic selection for improved productivity in porcine breeding programs.

Hematological traits are essential indicators of an animal's immune status and overall health, reflecting both physiological and pathological conditions. The complete blood count (CBC), a commonly used clinical test, evaluates the concentrations, proportions, and characteristics of various blood cell parameters, providing insights into an animal's current health status. CBC phenotypes are dynamic, influenced not only by health status but also by factors such as physiology, nutrition, environmental conditions, age, and genetic makeup. Previous studies have estimated heritability for specific blood parameters and genome-wide association studies have identified loci associated with CBC phenotypes. While some loci seem to have similar effects across age and breeds and even across species, other loci seem to have a more breed and/or age-specific effect. This study extends previous research by conducting genome-wide association studies (GWAS) of 24 hematological traits measured in the same pig cohort at two ages (25 and 46 days). The GWAS included 1884 pigs at 25 days and 1615 pigs at 46 days, with 1499 pigs sampled at both time points. This analysis identified 57 QTLs for complete blood count (CBC) traits, including 11 lead SNPs associated with more than one trait. All animals were (Landrace × Yorkshire) × Duroc crossbred pigs. Thirty QTLs overlapped with previously reported CBC QTLs in different pig breeds, providing further evidence for shared regulatory regions for CBC traits across pig breeds. Genes in 29 QTLs were associated with comparable CBC phenotypes in humans.

Iris pigmentation is a heritable trait with a complex genetic architecture. While the genetic basis of iris pigmentation has been extensively studied in humans, little is known about iris pigmentation in pigs. Iris pigmentation in pigs varies from different shades of brown or pale irises to heterochromia manifesting either as different colors between both irises (heterochromia iridum) or multiple colors within a single iris (heterochromia iridis). This study investigates the genetics of iris pigmentation variability in the Swiss Landrace and Swiss Large White pig breeds. Iris pigmentation was phenotyped in 837 Swiss Landrace and 328 Swiss Large White pigs of which the majority also had array-derived genotypes. A high prevalence of heterochromia iridum (18.6%) was observed in the Swiss Landrace breed. Heritability estimates for iris pigmentation were high in both breeds (h2 = 57.6-64.4%). Iris pigmentation was not genetically correlated with production traits. Genome-wide association analysis identified several loci associated with iris pigmentation (P < 10-5), including regions near functional candidate genes such as TYR, ALX4 and DCT. The strongest association was detected near the KITLG gene, which was identified as a candidate gene for iris pigmentation in a previous study on Italian Large White pigs. Fine-mapping identified a highly significantly associated (P = 2.0 × 10-12) missense variant in KITLG (5_94084790_G > A, rs342599807, p.R124K) as a potential causal variant for pale and heterochromatic iris pigmentation in Swiss pigs. Our findings provide new insights into the genetic architecture of iris pigmentation in pigs and indicate that KITLG plays a key role. The identification of a putative causal missense variant offers a foundation for further functional studies aiming to better understand pigmentation traits in pigs.

Achieving food independence is one of the key elements necessary to ensure the country’s food security. In the Ryazan region, the annual steady growth in livestock production continues, largely due to the growth of the pig population. This became possible due to the launch of new pig breeding feedlots. The purpose of the work was to substantiate the choice of a pig breed for the production of high–quality pork and meat delicacies in the Ryazan region. According to the research results, the relative increase in pigs from birth to the age of seven months indicated the most intensive growth in the fi rst month of life. Suckling piglets increased their live weight by 5.7–6.2 times in the fi rst month of life compared to their birth weight. In the following months of life the growth rate of pigs decreased from 140.3–144.1 % to 20.0–20.7 % at the end of fattening. During the entire rearing period, the relative growth rate of the experimental pigs was in the range of 194.5–194.7 %. Pigs of the 1st experimental group (Duroc breed) had the best indicators of meat productivity. The maximum live weight was 107 kg, the slaughter weight was 84.2 kg, which was by 8.3 % more than in the control group (Large White breed). The maximum values were obtained for the slaughter yield 78.7 %, carcass weight 74.1 kg, carcass length 110 cm, fat thickness 2.0 cm and the area of the “muscle eye” 38.4 cm2. The muscle tissue content in the half-carcasses of pigs of Duroc and Yorkshire breeds was relatively high, ranging from 57.2–57.5 % and was 0.9 and 0.6 abs.% higher than in herdmates Large White breed, respectively. Thus, the young pigs of Duroc and Yorkshire breeds showed higher fattening and meat qualities compared to their herdmates of Large White breed.

The study analyzed ten reproductive traits in three major commercial breeds-Yorkshire, Landrace, and Duroc-raised under uniform management. Genetic parameters were estimated using a repeatability animal model in ASReml, genome-wide association studies (GWAS) were performed with 46,358 post-QC SNPs using GCTA, and genomic prediction was evaluated with GBLUP. Heritability estimates were low to moderate, with gestation length (GL) highest (0.33-0.41). GWAS identified significant loci across breeds: in Yorkshire, 37 genome-wide significant SNPs across 17 SSCs for seven traits; in Landrace, 16 SNPs for TNB and one for NBW; and in Duroc, 31 SNPs across 12 SSCs (predominantly for TNB). Among these SNPs, CNC10042060, CNC10160995, and CNCB10003799 were consistently associated with TNB in both Yorkshire and Duroc pigs. Additionally, five SNPs, CNC10012965, CNC10042060, CNC10120451, CNCB10003799, and CNCB10007759, showed significant associations with NBW in Yorkshire and Landrace pigs. Candidate genes mapped within ±1 Mb of significant SNPs were enriched for biologically plausible pathways. Genomic prediction accuracies ranged from low to high depending on trait and breed, such as reaching 0.68 for GL in 39 Yorkshire and 0.59 in Landrace. These results delineate shared and breed-specific genetic architectures, provide actionable markers and candidate genes, and can accelerate genetic gains in commercial breeding programs.

This study evaluated the influence of sire genetic merit for residual feed intake (RFI) on carcass and ham quality traits in heavy pigs raised under the restricted feeding conditions typical of Protected Designation of Origin dry-cured ham production. A total of 417 purebred C21 Goland pigs, offspring of 23 sires, were randomly assigned to ad libitum, restricted medium-protein, or restricted low-protein dietary treatments. Sire breeding values (EBV) for RFI were estimated using RFI records of ad libitum-fed progeny between 96 and 161 kg body weight. Sires were classified into three RFI groups: low EBV (LRFI), medium EBV (MRFI), and high EBV (HRFI). Effects of RFI sire groups were estimated on traits recorded on the restricted-fed progeny. Progeny of LRFI sires exhibited differences in carcass traits, including a significantly higher carcass weight gain (+0.03 kg/day, corresponding to +7.3%; p< 0.01) and increased green ham yield (+1.3%, p < 0.05), compared to those of HRFI sires. LRFI progeny showed no differences in ham fat depth, but exhibited improved subcutaneous fat quality, including higher saturation (increased stearic acid, reduced linoleic acid and polyunsaturated fatty acids) and lower iodine number, as well as firmer subcutaneous fat. No variation in ham weight loss during dry-curing was observed across RFI sire groups. These findings suggest that selection for improved RFI does not significantly compromise carcass and dry-cured ham quality in restricted-fed heavy pigs. Incorporating RFI into selection objectives for sire lines could therefore provide a viable strategy for balancing production efficiency and product quality in heavy pig systems. These findings apply to restricted-fed heavy pigs of the population studied, and potential genotype × feeding regime interactions may limit direct extrapolation to other genetic backgrounds or production systems.

Meat quality traits are typically regulated by multiple genes, each contributing a small effect. In this study, to pinpoint candidate genes involved in meat quality traits, we performed transcriptome profiles of porcine longissimus dorsi (LD) muscle and applied machine learning (ML) models to analyze RNA-seq data. We also carried out Gene Set Enrichment Analysis (ssGSEA), Weighted gene co-expression network analysis (WGCNA) and functional validation of putative target genes to better support the biological relevance of our findings. In this study, LD muscle samples were collected from 142 Huoshou Black (HSH) pigs and 191 Anqing Six-end-white (AQLB) pigs. Based on results of the estimated breeding values (EBV) analysis, of meat quality traits, we selected 101 HSH pigs and 99 AQLB pigs for transcriptomic analysis. Using an integrative analytical framework that combined ssGSEA and WGCNA, we identified 197 candidate genes 197 candidate genes. These genes were significantly associated with various metabolic pathways, including fatty-acid elongation and metabolism, amino-acid catabolism, protein turnover, and biosynthetic processes. To further refine the identification of key regulatory genes, we systematically evaluated ten ML models, ultimately selecting XGBoost, Random Forest, and Lasso Regression for subsequent analysis. This approach pinpointed CYSLTR1 and LPCAT2 as the key regulatory genes. To investigate the functional roles of CYSLTR1 and LPCAT2 in intramuscular fat (IMF) deposition, we established a porcine intramuscular adipocyte model via siRNA-mediated knockdown of either CYSLTR1 or LPCAT2. RNA-Seq analysis identified 339 differentially expressed genes (DEGs) in the siLPCAT2 group and 2,376 DEGs in the siCYSLTR1 group relative to the control. Heatmap analysis indicated that genes involved in triacylglycerol (TAG) biosynthesis were upregulated in the siCYSLTR1 group, but downregulated in the siLPCAT2 group. KEGG pathway enrichment analysis further demonstrated that LPCAT2-associated DEGs were predominantly enriched in the MAPK signaling pathway, mTOR signaling pathway, biosynthesis of unsaturated fatty acids, and glycerolipid metabolism—pathways closely linked to cell proliferation, nutrient sensing, and lipid remodeling. In contrast, CYSLTR1-associated DEGs were significantly enriched in lipid metabolism, atherosclerosis, and adipocytokine signaling pathways—processes directly implicated in adipocyte differentiation, lipid storage, and inflammatory crosstalk within adipose tissue. Collectively, these findings elucidate distinct yet complementary regulatory roles for CYSLTR1 and LPCAT2 in intramuscular adipogenesis and provide mechanistic support for targeting these genes to modulate IMF content and improve pork quality traits. In conclusion, CYSLTR1 and LPCAT2 were identified as pivotal regulatory genes governing IMF deposition. Functional enrichment and pathway analyses revealed that both genes exert their effects on IMF accumulation through the coordinated regulation of lipid metabolism–associated pathways—including fatty acid synthesis, triglyceride assembly, and phospholipid remodeling. These findings offer mechanistically grounded evidence and actionable biological insights for improving pork quality traits, particularly marbling and tenderness.

An InDel in the Promoter of Ribosomal Protein S27-like Gene Regulates Skeletal Muscle Growth in Pigs

IGF2 in livestock: boosting productivity and enhancing meat quality.

From genomes to phenomes: Multi-omics dissection of positive and balancing selection in Jinhua pig.

Pigs are one of the most important livestock species for providing meat products in the world. Deciphering the genetic architecture of feed efficiency-related traits is beneficial to improve the genetic progress of these traits and save the total cost of pork production. However, the genetic architecture of feed efficiency-related traits remains unclear. To address this problem, we collected 1301 genotyped Yorkshire pigs with three feed efficiency-related traits, including days at 100 kg (DAYS_100), backfat thickness at 100 kg (BFT_100), and feed conversion ratio from 30 to 100 kg (FCR_30_100), to explore the genetic parameters and genetic basis of these traits. The heritability of DAYS_100, BFT_100, and FCR_30_100 was 0.25 ± 0.04, 0.40 ± 0.05, and 0.23 ± 0.04, respectively. Additionally, BFT_100 and DAYS_100 had a weak negative genetic correlation (-0.01 ± 0.12), while trait FCR_30_100 showed a positive genetic correlation with DAYS_100 (0.51 ± 0.11) and BFT_100 (0.28 ± 0.12). A genome-wide association study identified 7, 5, and 4 SNPs independently associated with BFT_100, DAYS_100, and FCR_30_100, respectively. Further analysis found that the candidate gene ETV4 was significantly associated with DAYS_100 and the candidate gene ENSSSCG00000045751 was associated with FCR_30_100. The functional annotation of candidate genes was enriched in the bile acid metabolic process and protein ubiquitination terms. This study discovered 16 quantitative trait loci associated with feed efficiency-related traits, providing a comprehensive insight for understanding the genetic basis of feed efficiency-related traits in pigs. The candidate genes, such as ETV4 gene in DAYS_100, CAMK1D gene for BFT_100, and ENSSSCG00000045751 gene for FCR_30_100, could be used for further investigation.

Reproductive efficiency is a fundamental determinant of productivity in pig breeding programs. However, the role of the X chromosome in shaping the genetic basis of reproductive traits remains underexplored. To address this problem, Genome-Wide Association Studies were conducted to explore the genetic basis of reproductive traits in Yorkshire pigs. We collected data from 2659 Yorkshire sows, focusing on four reproductive traits across the first three parties. Statistical analyses included principal component analysis, estimation of genetic parameters, and mixed linear model association to identify SNPs and candidate genes. Heritability estimates (h2) ranged from 0.037 (TLWT_BA_P1) to 0.215 (TNB_P3). Genome-wide association analysis identified 23 significant SNPs and candidate genes, including several putatively significant X-linked genes; however, only a single X-linked locus was significantly associated with one trait. These findings demonstrate that, for 9 of the 12 parities, the proportion of total heritability attributable to X-linked variation was 0-2.7%. For the remaining three parities, the corresponding proportions were 8.4%, 21.5%, and 50.9%, while autosomes accounted for most of the genetic variation. In all but one trait, heritability estimated from X-linked GRMs was not significantly different from zero, highlighting the importance of incorporating X-linked information into genomic selection strategies for improving reproductive efficiency in pigs.

This study aimed to characterize the site-specific variation in skin traits of Shenxian pigs and to identify key genetic loci regulating skin thickness. A total of 50 Shenxian pigs were selected, and skin samples were collected from nine different anatomical sites. Total skin thickness was precisely measured, and collagen content was determined for each site. Based on literature review and database screening, TAF11 was identified as a candidate gene. Genotyping of the g.35543837 locus was performed using Sanger sequencing and KASP, followed by association analysis between different genotypes and skin thickness traits. The results showed significant site-specific variations in skin thickness (1.26-7.20 mm) and collagen content (7.01-24.54 g/100 g) in Shenxian pigs. Association analysis revealed that the TAF11 g.35543837 C > G variant was significantly associated with increased skin thickness, with the effect being particularly evident in gilt. Individuals with the CG genotype exhibited greater skin thickness at multiple anatomical sites compared with those carrying the CC genotype. This study preliminarily identified a potential locus associated with skin thickness in Shenxian pigs within the TAF11 gene. The sex-dependent effect observed at this locus provides a new clue for understanding the genetic basis of this complex trait and offers valuable information for the genetic improvement of skin-related traits in Shenxian pigs.