The porcine endometrium undergoes dynamic cellular remodeling across the estrous cycle, yet epithelial heterogeneity and differentiation trajectories remain incompletely characterized. In this study, a single-cell transcriptomic atlas of the endometrial epithelium during the follicular and luteal phases in Meishan pigs was generated using high-resolution single-cell RNA sequencing. Canonical epithelial cell types were identified, including glandular epithelium (GE), secretory glandular epithelium (secretory GE), luminal epithelium (LE), ciliated epithelium, as well as an epithelial stem cell subpopulation marked by ALDH1A3 and LGR5 and a progenitor subpopulation marked by ALDH1A1. During the follicular phase, the epithelium was primarily composed of ALDH1A3+LGR5+ stem cells and ALDH1A1+ progenitor cells, whereas GE, secretory GE, and LE predominated during the luteal phase. Integrated trajectory inference and RNA velocity analyses suggested a continuous differentiation trajectory from ALDH1A3+LGR5+ stem cells through ALDH1A1+ progenitors toward GE. Gene expression patterns indicated that glandular epithelial formation was associated with activation of transcriptional regulatory programs and increased mitochondrial respiratory activity. In contrast, differentiation toward the secretory glandular epithelial lineage was characterized by early activation of stress-response pathways, secretion-related genes, and specific metabolic programs. Several transcription factors, including ZFP36L1, TRPS1, and KLF6, were associated with glandular differentiation, whereas MBD4, CREB3L4, ZNF524, SPDEF, USF1, XBP1, and MLX were predicted to contribute to glandular secretory function. These genes showed significant associations with sow reproductive traits in a phenome-wide association study. Overall, this study provides a single-cell framework for understanding epithelial dynamics in the porcine endometrium across the estrous cycle.

Respiratory diseases significantly impair pig growth performance by reducing average daily gain and feed conversion efficiency. Pneumonia lesion score (PLS) is a reliable phenotypic indicator for detecting respiratory issues in pig herds, including subclinical infections that often remain undiagnosed. In this study, PLS data was collected from 327 Large White pigs, and whole-genome resequencing (WGS) was performed. Lung tissue samples from pigs with extremely high and low PLS values were subjected to transcriptomic sequencing and Fixation Index (Fst) analysis. Additionally, a transcriptome-wide association study (TWAS) was conducted using FarmGTEx prediction models based on blood and lung tissues. By integrating Fst, Genome-Wide Association Study (GWAS), TWAS, and transcriptomic data, we identified key genomic regions and pathways associated with PLS variation, including immune regulation, inflammation, and metabolic adaptation. Candidate genes, RAB11FIP2 and SLC18A2 are implicated in immune modulation: RAB11FIP2 enhances TLR4 signaling and phagocytosis, whereas reduced SLC18A2 expression may compromise monoamine-mediated immune regulation. FBXL13 and ALPK2, identified via Fst and transcriptomic analysis, are linked to macrophage migration and Wnt/β-catenin signaling. Similarly, Genes like TRAF3IP1 and ASB1, highlighted by Fst and GWAS, contribute to ciliary transport, epithelial defense, and regulation of NF-κB and MAPK signaling. Moreover, GWAS and TWAS pinpointed RAMP1, as a novel candidate gene influencing immune modulation and airway responses through CGRP signaling, vascular tone regulation, and neuro-immune interactions, these findings have not been previously reported in PLS studies. Overall, this study provides novel insights into the genetic mechanisms underlying porcine lung lesions and offers a foundation for breeding strategies aimed at improving respiratory disease resistance and herd health.

Introduction Host genes regulate gut microbial composition, but the mechanisms by which they influence porcine fiber-degrading bacteria remain poorly understood. Additionally, the potential for integrating host genetics and microbiota data into genomic selection (GS) models for fiber digestibility in pigs has yet to be explored. Objectives This study aimed to identify host genes and gut microbes that impact fiber digestibility and to enhance the predictive accuracy of GS models for this trait. Methods This study sacrificed 360 pigs to measure fiber digestibility and collected genomic and colonic microbiota data via sequencing. Genome-wide association studies (GWAS), microbiota-wide association studies (MWAS), and microbial abundance GWAS (mGWAS) were performed to identify host genes and key microbes involved in fiber digestion, along with genes influencing the abundance of these microbes. The results were then integrated to optimize the GS model. Results Fiber apparent digestibility exhibited higher microbiability (0.31-0.33) than heritability (0.03-0.05). GWAS identified 50 SNPs associated with fiber digestibility, with the most significant loci on SSC17 explaining 0.96% and 0.97% of variance. Six novel QTLs and five candidate genes for fiber digestion were discovered. Combined MWAS and linear discriminant analysis effect size revealed 89 key microbes influencing fiber digestibility. Heritability of Christensenellaceae_R-7_group and UCG-002 was 0.312 and 0.104, respectively. mGWAS identified 201 SNPs, with the most significant loci each explaining 0.96% of the phenotypic variance. Four novel QTLs and six candidate genes for microbial abundance were identified. The GS model, integrating genomic and key microbial information data, achieved the highest genomic prediction accuracy (0.421 ± 0.002). Conclusion The Christensenellaceae_R-7_group and UCG-002, key players in host fiber digestion, are regulated by host genes, including GALNT7. The integration of host genetics and microbiota holds significant potential for GS in pigs for improved fiber digestibility.

Total rib number (TRN) and total teat number (TTN) are key anatomical and economic traits in pigs, linked to carcass yield and reproductive performance, respectively, and are genetically correlated. However, the shared genetic basis underlying these traits remains incompletely understood. This study aimed to dissect the genetic architecture of TRN and TTN and to identify pleiotropic genes affecting both traits. Single-population genome-wide association studies (GWASs), multi-population meta-analysis, and multi-trait meta-analysis were conducted using phenotypic and genotypic data from three pig populations: Yorkshire (YY, n = 413), Suhuai (SH, n = 655), and Landrace × Yorkshire (LY, n = 678). Significant genetic and phenotypic correlations were observed between TRN and TTN, with genetic correlations of 0.82 in YY, 0.46 in SH, and 0.35 in LY. Ten quantitative trait loci (QTLs) associated with TRN were identified, including novel loci on SSC2 (39.38-40.49 Mb), SSC3 (123.79-125.58 Mb), SSC6 (103.40-104.53 Mb), SSC12 (53.30-54.84 Mb), and SSC18 (45.29-46.91 Mb). For TTN, eight QTLs were detected, including three newly discovered regions on SSC13 (142.82-143.99 Mb), SSC14 (7.26-8.54 Mb), and SSC16 (10.19-12.18 Mb). Candidate genes were identified through functional annotation and phenome-wide association analysis. For TRN, the prioritised genes included GREB1, SMCHD1, HES7, VRTN, ABCD4, NTN1, and members of the HOX gene family, whereas for TTN, the identified genes included FRMD4A, STC1, GREB1, and ABCD4. Colocalisation analysis integrating GWAS and multi-tissue expression QTL data suggested shared genetic signals for several genes, including EMILIN2, PTGR2, PSEN1, and ABCD4 for TRN, and PTGR2 and ENSSSCG00000033037 for TTN. Notably, GREB1, PTGR2, and ABCD4 were identified as pleiotropic genes potentially regulating both traits. These results clarify the shared genetic architecture of rib and teat number and provide candidate genes for future functional validation and genetic improvement in pig breeding.

Pork tenderness is a critical determinant of meat quality and is primarily assessed by shear force measurement. In this study, the shear force of the longissimus dorsi muscle was measured in 413 Large White pigs. A genome-wide association study (GWAS) based on imputed data identified multiple loci significantly associated with shear force on chromosomes 5, 8, 13, and 14. Comparison with the PigQTLdb indicated that these four QTLs have not been previously reported. By integrating GWAS results with transcriptomic data from the pigGTEx database, analyses including colocalization, TWAS, and SMR were performed, leading to the identification of two candidate genes, GRM2 and NISCH. PheWAS results showed that NISCH was significantly correlated with palmitoleic acid content, consistent with the positive correlation between palmitoleic acid and shear force in this population. GRM2 was significantly associated with backfat thickness. These results suggest a potential genetic association between fatty acid metabolism and pork tenderness.

As a key index of reproductive performance in pigs, gestation length (GL) exerts a direct influence on litter size and the survival rate of piglets. Phenotypic variability in GL has been observed across Large White pig populations. To elucidate the genetic mechanisms underlying GL, this study analyzed 22,783 reproductive records from 9,057 pigs across five Large White populations. We employed a combination of diverse analytical strategies, encompassing genome-wide association studies (GWAS), GWAS meta-analysis, Bayesian fine-mapping (BFM), transcriptome-wide association studies (TWAS), phenome-wide association studies (PheWAS), and epigenetic profiling. GWAS and meta-analysis identified multiple novel GL-associated genomic regions on Sus scrofa chromosomes (SSC) 2, 7, 9, and 14. BFM refined the confidence intervals of these quantitative trait loci (QTLs), narrowing them to 10,460,892–10,737,692 bp and 31,384,086–31,384,333 bp on SSC7:, to 127,322,114–128,205,369 bp on SSC9:, and to 24,640,681–25,479,574 bp on SSC12:. TWAS revealed significant GL-related gene expression changes in relevant tissues, identifying GNAZ and SLC5A4—both located within the fine-mapped QTL on SSC14 (48.25–49.02 Mb)—as key regulators of GL. PheWAS further validated the association of GNAZ and SLC5A4 with GL, while epigenetic profiling showed active chromatin states and broad promoter activity at the GNAZ locus, supporting its regulatory potential. Through multi-omics integration, this study pinpoints GNAZ and SLC5A4 as core functional candidate genes regulating GL in Large White pigs. These results yield new perspectives on the genetic underpinnings governing porcine GL and supply valuable genetic materials for enhancing reproductive performance in swine breeding initiatives.

Litter size is an important economic trait in the swine industry, and increasing the number of piglets born is a key objective in pig breeding. The Erhualian pig, known for its exceptional prolificacy, has been reported to harbor a quantitative trait locus (QTL) for litter size on porcine chromosome 12 (SSC12). Through fine mapping of this QTL, RPS6KB1 was identified as a promising candidate gene associated with litter size in Erhualian pigs. Immunohistochemical analysis demonstrated that the p70S6K protein is predominantly expressed in the theca cells of Erhualian pig ovaries. Functional analyses revealed that p70S6K regulates androgen synthesis via the LH-responsive PI3K/Akt/mTOR/HSD3B1 signaling pathway and promotes follicular angiogenesis by activating the PI3K/Akt/mTOR/S6/HIF-1α/VEGFA axis. A single nucleotide polymorphism (rs325845933) located in the 3' untranslated region (3'UTR) of RPS6KB1 was identified, which binds to ssc-miR-7135-5p and modulates RPS6KB1 expression. Association analysis showed that rs325845933 is significantly associated with litter size in Erhualian, American Large White, and Canadian Large White pigs. These results suggest that rs325845933 is a putative functional variant affecting prolificacy and may serve as a valuable molecular marker for improving litter size in pig breeding programs.

Teat number is a crucial economic trait in pigs. It directly affects the ability of sows to lactate, which in turn influences the survival and health of piglets. The teat number of French Large White pigs is close to 16, while the teat number of American Large White and Landrace pigs is about 14. In order to improve the teat number of American Landrace and Large White pigs through molecular approaches and precise breeding techniques, we genotyped 2,131 American Landrace and 4,564 American Large White with teat number phenotype using a 50 K SNP chip. Then, the SNP-chip data was imputed to the level of whole-genome sequencing (iWGS). Based on iWGS data, we conducted GWAS to identify novel, significant SNPs associated with teat number and to incorporate them into genomic selection. In Landrace pigs, significant SNPs for TTN mapped to SSC2, SSC7, SSC8, and SSC14; the SSC8 and SSC14 effects are novel. LTN mapped to SSC7, RTN to SSC7 and SSC8. The lead SSC7 SNP explained 2.60

The size and angle of the vulva are economically important traits in pig production. Gilts with small or upward-tilted vulva are typically culled directly. Selective breeding aimed at improving vulva traits can enhance the retention rate of replacement gilts. This study aimed to systematically explore the key quantitative trait loci (QTL) and genes influencing vulva traits in Large White pigs using genome-wide association studies (GWAS) and meta-analysis techniques. Data on vulva length (VL), vulva width (VW), and vulva angle scores (VAS) were collected from 2,197 Large White gilts across three distinct populations (313 from PIC, 1,169 from Topigs, and 715 from Canada), with genotyping performed using a 50K single-nucleotide polymorphism (SNP) array. The SNP-chip data were imputed to the whole-genome sequencing (iWGS) level. This study used iWGS data to conduct GWAS, identifying a genomic region (SSC5: 103.04-103.34 Mb) significantly associated with VAS in both the Topigs and Canadian Large White pig populations. The significance of this region was further strengthened through multi-population meta-analysis. The most significant SNP (rs3470833446), identified on chromosome 14 and associated with VW in PIC Large White pigs, explained 16.98% of the phenotypic variation (PVE). Multi-population meta-analysis identified novel significant SNPs associated with VL on SSC4, VW on SSC1, SSC4, and SSC6, and VAS on SSC2 and SSC5. Furthermore, a significant potential pleiotropic QTL (SSC4: 36.42-41.24 Mb) regulating both VL and VW was identified. Bayes fine mapping was employed to determine the confidence intervals for these novel QTLs, with the most refined confidence interval narrowed down to 30 kb (SSC4: 38.73-38.76 Mb for VW, and SSC5: 103.20-103.23 Mb for VAS). Based on the biological functions of the genes, the following were identified as novel regulatory candidate genes for vulva traits: VIP, NAV3, and ESR1. These findings reveal potential key genes and genetic mechanisms influencing vulva traits in pigs, providing a crucial molecular genetic basis for improving pig breeding and reproductive performance.

Drip loss (DL) is a crucial trait for evaluating muscle quality in pigs. In this study, Chinese Suhuai pigs with DL records were genotyped using the Neogen GGP Porcine 80 K single-nucleotide polymorphism (SNP) array to identify quantitative trait locus (QTL) affecting DL and dissect candidate genes for this trait. The SNP-chip data was imputed to the level of whole-genome sequence (iWGS). Through genome-wide association studies (GWAS) based on iWGS data, significant SNPs were detected on Sus scrofa chromosomes (SSC) 4, SSC13, and SSC14 for DL, involving 37 candidate genes such as AACS, CRB4, and OXSM. Notably, 3 QTL regions (SSC4, SSC13, and SSC14) were newly identified in this study, which were SSC4: 65.2 to 66.1 Mb, SSC13:12.46 to 12.48 Mb and SSC14: 20.7 to 20.9 Mb respectively. Additionally, RNA sequencing (RNA-seq) was conducted on muscle tissues from individual pigs with extremely high and low genomic estimated breeding values of DL, identifying 21 differentially expressed genes (DEGs). Integrating these DEGs with quantitative trait transcriptome (QTT) analysis results from our Suhuai pig muscle tissue transcriptome data pinpointed 6 DEGs strongly linked to DL: GALNT15, TBC1D1, MLLT11, PPARGC1A, NREP, and CNTFR. Integration of candidate genes identified by GWAS with the results of QTT analysis revealed that the expression of GWAS-identified genes NCOA2, HPF1, and CLCN3 was significantly correlated with DL. Functional enrichment analysis, combining the 37 candidate genes identified by GWAS and the 6 DEGs co-identified by RNA-seq and QTT analyses, suggested that GALNT15, TBC1D1, PPARGC1A, AACS, CBR4, and OXSM genes may be functionally related to pork DL, thereby positioning them as important candidate genes. These genes (NCOA2, HPF1, CLCN3, PPARGC1A, TBC1D1, GALNT15, CBR4, AACS, and OXSM) were newly identified candidate genes for DL. This research provides a foundation for improving meat quality traits through marker-assisted or genomic selection in pig breeding programs.

ABSTRACT Although metagenomic investigations into microbial fiber-degrading capabilities are currently prevalent, there is a notable gap in research concerning the regulatory mechanisms underpinning host-microbiota interactions that confer tolerance to high-fiber diets in pigs. In this study, 28 Meishan (MS) and 28 Large White (LW) pigs were subjected to feeding experiments involving various fiber levels. Subsequently, multi-omics was employed to investigate the influence of host-microbiota interactions on the fiber degradation of pigs. MS exhibited superior fiber digestibility compared with LW, particularly evident when fed a high-fiber diet. In MS, positive interactions among Treponema bryantii , Treponema sp., Rikenellaceae bacterium, and Bacteroidales bacterium WCE2004 facilitated the degradation of both cellulose and pectin. The reduced polymerization of polysaccharides and oligosaccharides observed in MS provides compelling evidence for their superior microbial fiber-degrading capability. The concentrations of propionate and butyrate retained in cecal lumen of MS was unchanged, whereas it was significantly increased in LW, indicating a strong absorption of short-chain fatty acids (SCFAs) in MS intestines. Correlation analysis using RNA-seq data revealed distinct patterns in LW and MS. In LW, microbial profiles along with GPR183 and GPR174 exhibited negative correlations with butyrate and propionate, respectively. Conversely, in MS, GPR174 and SLC2A4 were positively correlated with butyrate. Our findings underscore the dynamic collaboration among microbial species in degrading cellulose and pectin, coupled with the synergistic effects of SCFA transport-related genes, as crucial underpinnings for the heightened fiber digestibility observed in MS. These discoveries offer fresh perspectives into the intricate mechanisms governing host-microbiota interactions that influence fiber digestion in pigs. IMPORTANCE Studies on porcine intestinal microbiota have been widely conducted, and some microbial taxa with fiber degradation functions have been identified. However, the mechanisms of division among gut microbes in the degradation of complex fiber components are still unclear. In addition, the regulation of fiber digestion by host through absorption of short-chain fatty acids (SCFAs) needs to be further investigated. Our study used apparent total tract digestibility of dietary fiber to assess the utilization efficiency of dietary fiber between Meishan and Large White pigs. Subsequently, through metagenome sequencing and determination of fiber-degrading products, we found that in Meishan pigs, positive interactions among Treponema bryantii , Treponema sp . , Rikenellaceae bacterium, and Bacteroidales bacterium WCE2004 facilitated the degradation of both cellulose and pectin. RNA-seq analysis elucidated breed-specific genes associated with SCFA absorption in cecum. By integrating multi-omics data, we constructed a framework outlining host-microbiota interactions that control dietary fiber utilization in pigs. Our data provide novel insights into host-microbiota interactions regulating fiber degradation and lay some theoretical foundations for improving the utilization efficiency of high-fiber cereal feed in pigs through targeted modulation of gut microbial function.

Understanding the molecular and cellular mechanisms underlying complex traits in pigs is crucial for enhancing genetic gain via artificial selection and utilizing pigs as models for human disease and biology.Here,we conducted comprehensive genome-wide association studies(GWAS) followed by a cross-breed meta-analysis for 232 complex traits and a within-breed met a-analysis for 12 traits,using 28.3 million imputed sequence variants in 70 328 animals across 14 pig breeds.We identified 6878 quantitative trait loci(QTL) for 139 complex traits.Leveraging the Pig Genotype-Tissue Expression resource,we systematically investigated the biological context and regulatory me chanisms behind these trait-QTLs,ultimately prioritizing 14 829 variant-gene-tissue-trait regulatory circuits.For instance,rs344053754 regulates UGT2B31 expression in the liver and intestines,potentially by modulating enhancer activity,ultimately influencing litter weight at weaning in pigs.Furthermore,we observed conservation of certain genetic and regulatory mechanisms underlying complex traits between humans and pigs.Overall,our cross-breed meta-GWAS in pigs provides invaluable resources and novel insights into the genetic regulatory and evolutionary mechanisms of complex traits in mammals.

The number of teats is a critical reproductive trait in sows, exerting a direct impact on the survival rate of weaned piglets. Existing studies on selection signals associated with teat numbers in different strains of Large White pigs are scarce. We performed selection signal detection on three distinct strains of Large White pigs with 16 or more nipples: the French CG (Choice Genetics), the French Cooperl, and the Dutch Topigs. Our goal was to identify pivotal candidate genes contributing to the higher nipple count in Large White pigs. A comprehensive analysis, including CLR (Composite Likelihood Ratio), iHS (integrated haplotype score), and nSL (number of segregating sites by length) methods, alongside XP-EHH (Cross-population Extended Haplotype Homozygosity), was undertaken to identify genetic positive selection signatures in Large White pigs. Through our analysis, we identified six key candidate genes in the CG Large White pigs: DPP6, COL22A1, TRPC7, PROX1, ROR2, and ABCG1. In the Cooperl Large White pigs, the key candidate genes were PPARA, TRPC7, and NR3C1. In the Topigs Large White pigs, the key candidate genes were DOCK1, PCM1, and MRTFA. Among the aforementioned genes, PCM1 and DOCK1 have been identified as correlated with the number of teats in pigs, while TRPC7, DOCK1, and MRTFA have shown a significant link with teat number based on PheWAS (Phenome-wide association study) analysis. Our findings show that multiple genes associated with teat development in Large White pigs have experienced significant selection pressure throughout the breeding program. These results deepen our understanding of the progress in breeding Large White pigs and provide a valuable framework for their continued selection.

Vulva morphologies represent significant traits in pig production. Recent studies suggest that vulva size can be predictive of the reproductive performance of gilts. This study aimed to analyse the genetic parameters of vulva traits, including vulva length, vulva width, and vulva angle score (VAS), as well as litter traits, including total number born, number born alive, number stillborn, and piglet survival rate, across three Large White pig strains (PIC, Topigs, and Canadian). We estimated the correlations between vulva traits and litter performance, as well as the reasons for culling gilts. In this study, single-trait and multitrait models were employed to estimate the heritability and genetic correlations between vulva and litter traits. The heritabilities of vulva traits ranged from 0.167 to 0.426, whereas the heritability of litter traits ranged from 0.013 to 0.147. The VAS in Topigs Large White pigs exhibited the highest heritability. The genetic correlation coefficients between vulva length and width in PIC and Topigs Large White pigs were significantly positively correlated, ranged from 0.585 to 0.767. No significant correlation was found between vulva and litter traits. Subsequently, we scored the vulva traits according to previously reported studies, linear relationship analysis between vulva score and reasons for culling gilts revealed that gilts with larger vulva widths had a lower risk of culling. The average vulva width score of the gilts that were culled due to prolonged oestrus was significantly lower (2.75) compared to that of gilts with normal oestrus (2.90). In the population of gilts aged 220-230 days, the gilts with higher vulva angle scores had a lower risk of culling due to vulva inflammation with purulent discharge. The results suggest that selecting vulva traits in replacement gilts is an effective strategy to reduce gilt culling rates. (c) 2025 The Author(s). Published by Elsevier B.V. on behalf of The animal Consortium. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

17β-Estradiol (E2), secreted by granulosa cells (GCs), is essential for ovarian development and female fertility. However, its action mechanism and synthetic regulation remain elusive. Here, functional analysis showed that E2, highly synthesized in dominant follicles, effectively inhibited GC apoptosis. RNA-seq revealed that the impact of E2 was at a transcriptome-wide scale, and 1326 estrogen responsive elements (EREs) were identified in the promoter of 72.8 % (653/897) of the differentially expressed genes. ChIP assays showed that estrogen receptor β (ERβ) mediated the regulation of E2 on transcriptome in a transcription factor activity-dependent manner. Furthermore, a novel anti-apoptotic feedback regulatory loop, E2/ERβ/CYP19A1, was identified. Specifically, E2 activates ERβ, which induces CYP19A1 transcription by directly binding to its promoter. Notably, ESR2 c.949G > A, a missense SNV associated with sow reproductive traits, affects cumulus expansion and oocyte maturation, with A being the favourable allele. Mechanistically, it causes p.V317M substitution, which locates in the ligand binding domain of ERβ and influences its sensitivity to E2. Our findings highlight the critical role of ERβ in mediating the feedback regulation and anti-apoptotic function of E2 in GCs, and its feasibility as a candidate causal gene for sow fertility, providing valuable clues for steroid hormone regulation and female fertility improvement.

The number of ribs (NRs) and the carcass length (CL) are important economic traits. The traits are usually measured after slaughter. To improve the prediction performance of genomic selection (GS) for NRs and CL, one strategy is to integrate the significant loci identified from whole-genome sequencing (WGS) data by genome-wide association study (GWAS) into the genomic prediction (GP) model. This study investigated the GP of different genomic best linear unbiased prediction (GBLUP) and Bayesian models using chip genotype data, imputed WGS (iWGS) data and modeling significant single-nucleotide polymorphisms (SNPs) in different ways for the GP of NRs and CL in the Suhuai pig population. The prediction accuracy, bias and running time of 15 different GP models were evaluated by 10-fold cross-validation. The prediction accuracy of GBLUP using chip data for NRs and CL was 0.314 ± 0.022 and 0.194 ± 0.040, respectively. For NRs, based on the iWGS data, treating the most significant SNP as fixed effects in the GBLUP model had the highest predictive performance, with a prediction accuracy of 0.528 ± 0.023. For CL, based on the chip data, the model that added all the significant SNPs identified by imputed data by GWAS into the multi-trait GBLUP as the second random additive effect was the highest predictive performance, with a prediction accuracy of 0.305 ± 0.027. This study provides insights into optimizing GP models for small populations with phenotypes that are difficult to measure.

Milk is an essential source of nutrition for preweaning piglets. Therefore, in the breeding process, sows were expected to have sufficient teats to suckle their piglets. However, in Danish Landrace and Large White pigs, the number of piglets born currently exceeds the number of teats, making it urgent to select and breed for an increased teat number. In this study, the samples of 491 Danish Landrace pigs and 1,047 Danish Large White pigs with teat number phenotype were used to perform genome-wide association studies to identify SNPs associated with total teat number (TTN) based on SNP-chip data and data imputed to the level of whole-genome sequencing (iWGS), respectively. In Landrace pigs, the most significant SNP on SSC10 explains 5.14% of the phenotypic variance, while in Large White pigs, the most significant SNP on SSC7 explains 4.46% of the phenotypic variance. Additionally, linkage disequilibrium and linkage analysis (LDLA) were used to refine the regions of QTLs on SSC10 to 2.89 to 5.43 Mb in Danish Landrace pigs and to 96.00 to 97.95 Mb on SSC7 in Danish Large White pigs, respectively. To maximize the utility of information from 2 populations, meta-analysis was conducted across multiple populations. A total of 12 protein-coding genes were identified within the candidate QTL regions determined by LDLA and meta-analysis. To supplement the candidate gene set, transcriptome-wide association studies (TWAS) based on embryo and placenta tissues identified 7 protein-coding genes associated with TTN in Landrace and Large White pigs. Phenome-wide association studies (PheWAS) query was conducted for all the above genes, revealing that nearly all of them are associated with teat number traits. Additionally, some genes showed strong associations with carcass traits, suggesting a potential association between teat number and carcass traits. Through functional annotation and integrated analysis, BRINP3, LIN52, ABCD4, and UBE3B were determined as the functional candidate genes regulating TTN. These findings lay the foundation for identifying the genetic loci regulating teat number in Danish pigs, as well as for their molecular breeding.

Teat number is an important economic trait in pigs, affecting piglet health and survival. While numerous GWAS have identified candidate genes for teat number in Duroc, Landrace, and Large White pigs, the causal genes remain unclear, largely due to a lack of transcriptional and epigenetic studies on mammary placodes in 26-day-old pig embryos, a critical stage for teat formation. Erhualian and Bamaxiang pigs, derived from Chinese wild boars, serve as ideal models for studying genetic variation in teat number, with Erhualian averaging nearly 20 teats and Bamaxiang around 10. This study collected mammary placodes from these breeds at embryonic day 26 and performed ATAC-seq and RNA-seq to explore chromatin accessibility and gene expression. Results indicate widespread chromatin accessibility across mammary placodes. Of the 30,806 open chromatin regions (OCRs) identified, only 30 showed breed-specific differences, suggesting conserved accessibility patterns across breeds. OCRs are enriched in intergenic and promoter regions, and significantly overlap with QTL intervals for teat number. RNA-seq revealed 4432 differentially expressed genes between the two breeds, including WTN10B and WNT6, indicating breed-specific gene expression patterns. Combining ATAC-seq and RNA-seq results identified three protein-coding genes (ENSSSCG00000031037, ENSSSCG00000032042, and ENSSSCG00000039180) near 48.80 Mb on SSC14 that are associated with teat number according to pheWAS and GWAS data. FISH analysis confirmed that ENSSSCG00000031037 is specifically expressed in epithelial cells of mammary placodes, and this region is under stronger selection in Erhualian pigs, suggesting its role in the breed's higher teat number. In conclusion, this study integrates ATAC-seq and RNA-seq to construct a chromatin accessibility and gene expression map of pig mammary placodes. It identifies ENSSSCG00000031037, ENSSSCG00000032042, and ENSSSCG00000039180 as key candidate genes driving teat number differences, providing insights for understanding QTL intervals and identifying causal genes linked to teat number in pigs.

The carcass backfat thickness (BFT) provides a valuable indication of fat deposition and carcass leanness, which are essential for the determination of carcass grading and pricing. Identifying genetic loci and crucial genes related to BFT using integrated multi-omics methods offers significant contributions to the genetic advancement of pig. In the present study, 418 Chinese Suhuai pigs were slaughtered, and carcass BFT were subsequently measure. We conducted a genome-wide association study (GWAS) based on SNP chip data and imputed whole-genome sequencing data (iWGS), respectively. Significant quantitative trait loci (QTL) correlated with carcass BFT were identified on Sus scrofa chromosome (SSC) 2, SSC4, and SSC14, with the most significant single-nucleotide polymorphisms (SNPs) explaining 6.58 %-9.91 % of the phenotypic variance. Bayesian fine mapping validated two previously reported quantitative trait loci (QTLs), narrowing the most refined confidence interval to 3 kb (SSC2, 37.337-37.340 Mb and SSC4, 75.407-77.006 Mb), while identifying two novel QTLs (SSC14, 137.086-138.863 Mb and SSC4, 95.237-96.894 Mb) associated with carcass BFT. Furthermore, transcriptome analysis identified 322 differentially expressed genes (DEGs) and several critical regulatory pathways related to lipid and energy metabolism, including fatty acid and pyruvate metabolism. The integration of genomic and transcriptomic data identified three pivotal candidate genes, S100A12, XKR4 and PENK, which are typically associated with BFT. Transcriptome-wide association study (TWAS) and Phenome-wide association study (PheWAS) provided further evidence that these three genes were significantly associated with BFT and fatty acid composition. This study uncovers novel insights into the important genes and molecular markers related to carcass BFT in pig.

BACKGROUND:After long-term artificial selection and lineage mixing, the Danish Landrace pig (DLR), has developed characteristics such as a long body length, high lean meat rate, rapid growth rate, high litter size, and a longer gestation period, with an average gestation length of 117 days. However, the genes responsible for these desirable traits remain partly unknown. According to the breeding history of DLR pigs, it has undergone introgression from British Large White pigs (BLW), selection for high lean meat rate and long body length within the population, and a rapid improvement in reproductive performance since 1992. Research on Danish Duroc and Large White pigs has detected that the lineage of pigs in Taihu Lake region (TL) has introgressed into these two breeds. Therefore, we performed resequencing and chip scanning on 106 TL pigs and 557 DLR pigs, and downloaded 163 resequencing data from Eurasian pigs for shared haplotype analysis, selective sweep analysis, and GWAS. RESULTS:The results indicate that 12 important genes, including CREB3L2, PRKAB2, HIF1A, IGF1, have introgressed from BLW into DLR pigs. These genes enhance lean meat percentage by participating in thermogenesis, oxidative phosphorylation and HIF-1 signaling pathways. In the DLR pig population, 13 shared selected genes were identified across three selective sweep methods. These genes including HBM, RHBDF1, POLR3K, ZNF484, were found to be associated with growth rate, body length, lean meat percentage, and reproductive performance by pheWAS analysis. Interestingly, reproductive performance is primarily related to gestational trait. GWAS for gestational trait in DLR pig population revealed 13 significant genes which also under selection in selective sweeps. These genes include INSYN1, NPTN, NEO1, ZDHHC21. Our study clarifies that the lineage of TL pigs has also introgressed into DLR pigs, with NDUFS4 being an important introgressed gene influencing reproductive performance. Moreover, compared to the low-fertility American Landrace pigs, HTR7, RPP30, ANKRD1, ARHGAP42, and CNTN5 may be important genes selected for enhancing litter size within the DLR pigs. CONCLUSIONS:Our research deepens the understanding of the breeding history of DLR pigs, preliminarily identifies genes associated with the characteristics of high lean meat percentage, long body length, and high fertility in DLR pigs, and also finds that the high litter size of DLR pigs may be related to gestation length.