Intramuscular fat (IMF) content plays an essential role in the evaluation of meat quality. To select pig breeds with different IMF content, developing a method to predict the IMF content in live pigs was greatly significant to reduce the cost and time of breeding. In the current study, real-time ultrasound images 5 cm off-midline across the third and fourth last thoracic ribs of 336 live pigs were collected using the B-model technique, and image feature parameters were extracted by computer image processing techniques. Furthermore, multiple linear regression (MLR) and two machine learning algorithms, support vector machine (SVM) and back-propagation artificial neural network (BPANN), were used to develop the prediction models of IMF content. The experimental pigs were divided into a training dataset (n = 266) for developing the prediction models and a validation dataset (n = 70) for estimating the accuracy of the models, and a test set (n = 67) for additional model performance evaluation. The results reveal that the coefficient of determination (R-2) of models ranges from 0.65 to 0.80 with a root-mean-square error (RMSE) range of 0.50 %-0.65 % in the training dataset. By contrast, the correlation coefficients (R) between the predicted IMF (PIMF) and the chemically measured IMF (CIMF) range from 0.72 to 0.82 with an RMSE <= 0.69 % for all the models in the validation and test dataset. Moreover, the results indicate that the individual ratio of absolute difference (ADIF) within 1 % between PIMF and CIMF is > 86.57 % for all the models. In addition, classification accuracy shows that the BPANN1 model has superior classification ability in both low and high IMF content groups compared to the other two types of models in the validation dataset, but not in the test dataset. The MLR models are superior to other models in the medium IMF content group. Overall, our research demonstrates that it is feasible to predict IMF content based on ultrasound images in live pigs and provides several alternative models for accurate determination of IMF content, which could accelerate the genetic improvement of IMF content, thereby improving the pork quality 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.

The introduction of single-cell RNA sequencing (scRNA-seq) technology has spurred additional advancements in analyzing the cellular composition of tissues. The longissimus dorsi (LD) in pigs serves as the primary skeletal muscle for studying meat quality in the pig industry. However, the single-cell profile of porcine LD is still in its infancy stage. In this study, we profiled the transcriptomes of 16,018 cells in the LD of a newborn Suhuai pig at single-cell resolution. Subsequently, we constructed a cellular atlas of the LD, identifying 11 distinct cell populations, including endothelial cells (24.39%), myotubes (18.82%), fibro-adipogenic progenitors (FAPs, 18.11%), satellite cells (16.74%), myoblasts (3.99%), myocytes (5.74%), Schwann cells (3.81%), smooth muscle cells (3.22%), dendritic cells (2.99%), pericytes (1.86%), and neutrophils (0.33%). CellChat was employed to deduce the cell–cell interactions by evaluating the gene expression of receptor–ligand pairs across different cell types. The results show that FAPs and pericytes are the primary signal contributors in LD. In addition, we delineated the developmental trajectory of myogenic cells and examined alterations in the expression of various marker genes and molecular events throughout various stages of differentiation. Moreover, we found that FAPs can be divided into three subclusters (NR2F2-FAPs, LPL-FAPs, and TNMD-FAPs) according to their biological functions, suggesting that the FAPs could be associated with the differentiation of tendon cell. Taken together, we constructed the cellular atlas and cell communication network in LD of a newborn Suhuai pig, and analyzed the developmental trajectory of myogenic cells and the heterogeneity of FAPs subpopulation cells. This enhances our comprehension of the molecular features involved in skeletal muscle development and the meat quality control in pigs.

Background: The Meishan pig, native to China, is renowned for its superior reproductive capabilities, including a high ovulation rate, substantial uterine capacity, and an impressively high rate of embryo implantation. The endometrium plays a pivotal role in facilitating embryo implantation and sustaining pregnancy. It is regulated by ovarian hormones and uterine prostaglandins and undergoes a complex series of coordinated processes across the estrous cycle, including proliferation, differentiation, shedding, and regeneration. A detailed examination of the intricate sow endometrial gene expression patterns during this cycle can yield valuable insights into creating ideal conditions for successful embryo implantation and early embryonic development. To gain a comprehensive understanding of the Meishan pig endometrial biological functions across the estrous cycle, we specifically used uterine tissues in the proliferative and secretory phases for single-cell transcriptomic sequencing. Results: The comprehensive transcriptional profile of uterine cells was elucidated throughout the estrous cycle in Meishan pigs. We identified 7 distinct cell types within the primary cell categories, with 4 subpopulations specifically discerned among the endometrial epithelial cells. Considerable variability was observed in the types and quantities of epithelial cell subpopulations spanning the proliferative and secretory phases of the estrous cycle. Significantly, SOX9-expressing epithelial cells were characterised as potential endometrial epithelial stem cells in Meishan pigs. NURP1 and HES1were identified as potential marker genes for these stem cells. Pseudotime analysis indicated that these SOX9-expressing epithelial cells can differentiate into glandular epithelial (GE) or luminal epithelial (LE) cells. We also observed that SOX9-expressing epithelial cells may differentiate into ciliated epithelial (CE) cells. There was a marked increase in the number of GE and CE cells during the secretory phase compared to the proliferative phase. GE cells are vital for processes such as glycolysis, amino acid biosynthesis, and N-glycan biosynthesis, all of which are crucial for supplying essential nutrients required for embryo implantation and early stages of embryonic development. Conclusions: We reveal the integrated transcriptional profile of uterine cells in sexually mature Meishan pigs and delineate the gene expression patterns within the uterine horns throughout the estrous cycle. These findings provide potential new diagnostic indicators for determining the estrous cycle in sows.

Introduction: Intramuscular fat content (IFC) and meat color are vital indicators of pork quality.Methods: A significant positive correlation between IFC and redness of meat color (CIE a* value) indicates that these two traits are likely to be regulated by shared molecular pathways.To identify candidate genes, hub genes, and signaling pathways that regulate these two traits, we measured the IFC and CIE a* value in 147 hybrid pigs, and selected individuls with extreme phenotypes for transcriptome analysis.Results: The results revealed 485 and 394 overlapping differentially expressed genes (DEGs), using the DESeq2, limma, and edgeR packages, affecting the IFC and CIE a* value, respectively. Weighted gene co-expression network analysis (WGCNA) identified four modules significantly correlated with the IFC and CIE a* value. Moreover, we integrated functional enrichment analysis results based on DEGs, GSEA, and WGCNA conditions to identify candidate genes, and identified 47 and 53 candidate genes affecting the IFC and CIE a* value, respectively. The protein protein interaction (PPI) network analysis of candidate genes showed that 5 and 13 hub genes affect the IFC and CIE a* value, respectively. These genes mainly participate in various pathways related to lipid metabolism and redox reactions. Notably, four crucial hub genes (MYC, SOX9, CEBPB, and PPAGRC1A) were shared for these two traits.Discussion and conclusion: After functional annotation of these four hub genes, we hypothesized that the SOX9/CEBPB/PPARGC1A axis could co-regulate lipid metabolism and the myoglobin redox response. Further research on these hub genes, especially the SOX9/CEBPB/PPARGC1A axis, will help to understand the molecular mechanism of the co-regulation of the IFC and CIE a* value, which will provide a theoretical basis for improving pork quality.

This work aimed to identify markers and candidate genes underlying porcine digestive traits. In total, 331 pigs were genotyped by 80 K Chip data or 50 K Chip data. For apparent neutral detergent fiber digestibility, a total of 19 and 21 candidate single nucleotide polymorphisms (SNP) were respectively identified using a genome-wide efficient mixed-model association algorithm and linkage-disequilibrium adjusted kinship. Among them, three quantitative trait locus (QTL) regions were identified. For apparent acid detergent fiber digestibility, a total of 16 and 17 SNPs were identified by these two methods, respectively. Of these, three QTL regions were also identified. Moreover, two candidate genes (MST1 and LATS1), which are functionally related to intestinal homeostasis and health, were detected near these significant SNPs. Taken together, our results could provide a basis for deeper research on digestive traits in pigs.

Low level of drip loss (DL) is an important quality characteristic of meat with high economic value. However, the key genes and regulatory networks contributing to DL in pork remain largely unknown. To accurately identify the key genes affecting DL in muscles postmortem, 12 Duroc x (Landrace x Yorkshire) pigs with extremely high (n = 6, H group) and low (n = 6, L group) DL at both 24 and 48 h postmortem were selected for transcriptome sequencing. The analysis of differentially expressed genes and weighted gene co-expression network analysis (WGCNA) were performed to find the overlapping genes using the transcriptome data, and functional enrichment and protein-protein interaction (PPI) network analysis were conducted using the overlapping genes. Moreover, we used machine learning to identify the key genes and regulatory networks related to DL based on the interactive genes of the PPI network. Finally, nine potential key genes (IRS1, ESR1, HSPA6, INSR, SPOP, MSTN, LGALS4, MYLK2, and FRMD4B) mainly associated with the MAPK signaling pathway, the insulin signaling pathway, and the calcium signaling pathway were identified, and a single-gene set enrichment analysis (GSEA) was performed to further annotate the functions of these potential key genes. The GSEA results showed that these genes are mainly related to ubiquitin-mediated proteolysis and oxidative reactions. Taken together, our results indicate that the potential key genes influencing DL are mainly related to insulin signaling mediated differences in glycolysis and ubiquitin-mediated changes in muscle structure and improve the understanding of gene expression and regulation related to DL and contribute to future molecular breeding for improving pork quality. This study contributes to elucidating the molecular mechanism of drip loss in pork and provides potential promising genes for the genetic improvement of drip loss. A low level of drip loss (DL) is critical for the economic value of pork. However, the genetic basis underlying DL remains unclear. In this study, pigs with extremely high and low DL at both 24 and 48 h postmortem were selected, and total RNA from longissimus dorsi (LD) muscles was extracted for transcriptome sequencing. Subsequently, a variety of analytical methods, were integrated to identify the potential key genes and pathways affecting DL. As a result, nine potential key genes (IRS1, ESR1, HSPA6, INSR, SPOP, MSTN, LGALS4, MYLK2, and FRMD4B) mainly associated with the MAPK signaling pathway, insulin signaling pathway, and calcium signaling pathway, were identified, and these genes are primarily related to ubiquitin-mediated proteolysis and oxidation reactions. This study contributes new evidence for elucidating the molecular mechanism of DL and provides potential target genes for precise genetic improvement of DL.

Muscle satellite cells (MuSCs) are crucial for muscle development and regeneration. The primary pig MuSCs (pMuSCs) is an ideal in vitro cell model for studying the pig’s muscle development and differentiation. However, the long-term in vitro culture of pMuSCs results in the gradual loss of their stemness, thereby limiting their application. To address this conundrum and maintain the normal function of pMuSCs during in vitro passaging, we generated an immortalized pMuSCs (SV40 T-pMuSCs) by stably expressing SV40 T-antigen (SV40 T) using a lentiviral-based vector system. The SV40 T-pMuSCs can be stably sub-cultured for over 40 generations in vitro. An evaluation of SV40 T-pMuSCs was conducted through immunofluorescence staining, quantitative real-time PCR, EdU assay, and SA-β-gal activity. Their proliferation capacity was similar to that of primary pMuSCs at passage 1, and while their differentiation potential was slightly decreased. SiRNA-mediated interference of SV40 T-antigen expression restored the differentiation capability of SV40 T-pMuSCs. Taken together, our results provide a valuable tool for studying pig skeletal muscle development and differentiation.

Meat color is an attractive trait that influences consumers' purchase decisions at the point of sale. To decipher the genetic basis of meat color traits, we performed a genome-wide association study based on low-coverage whole-genome sequencing. In total, 669 (Pietrain × Duroc) × (Landrace × Yorkshire) pigs were genotyped using low-coverage whole-genome sequencing. Single nucleotide polymorphism (SNP) calling and genotype imputation were performed using the BaseVar + STITCH channel. Six individuals with an average depth of 12.05× whole-genome resequencing were randomly selected to assess the accuracy of imputation. Heritability evaluation and genome-wide association study for meat color traits were conducted. Functional enrichment analysis of the candidate genes from genome-wide association study and integration analysis with our previous transcriptome data were conducted. The imputation accuracy parameters, allele frequency R2 , concordance rate, and dosage R2 were 0.959, 0.952, and 0.933, respectively. The heritability values of a*45 min , b*45 min , L*45 min , C*, and H0 were 0.19, 0.11, 0.06, 0.16, and 0.26, respectively. In total, 3884 significant SNPs and 15 QTL, corresponding to 382 genes, were associated with meat color traits. Functional enrichment analysis revealed that 10 genes were the potential candidates for regulating meat color. Moreover, integration analysis revealed that DMRT2, EFNA5, FGF10, and COL11A2 were the most promising candidates affecting meat color. In summary, this study provides new insights into the molecular basis of meat color traits, and provides a new theoretical basis for the molecular breeding of meat color traits in pigs.

【Objective】The purposes of this study were to analyze the variation of teat number, to explore the quantitative trait locus (QTL) and candidate genes related to teat number, and to provide important molecular markers for the breeding of pig teat number.【Method】This study accurately measured left, right, total teat number of 709 Suhuai pigs (335 fattening pigs and 374 breeding pigs). Fattening pigs were selected for 80K chip genotyping and the heritability and genomic estimated breeding value (GEBV) of left, right and total teat number were calculated by chip data. Based on the rank of GEBV and phenotype of teat number, the top 10% individuals and the bottom 10% individuals were selected for Fixation Index (FST) analysis to detect highly differentiated loci. Then, the loci associated with teat number were identified by genome wide association analysis (GWAS) and loci which were highly differentiated and significantly associated with teat number were selected as candidate loci. Genes located near candidate loci and related to teat number after functional annotation were selected as candidate genes. Finally, the association analyses between the most significant candidate loci on each chromosome and teat number of 709 Suhuai pigs were performed to verify the significance of the above loci.【Result】The variation coefficients of left, right and total teat number of Suhuai fattening pigs were 10.20%, 9.26% and 8.50%, respectively, and the heritability were 0.212, 0.257 and 0.312, respectively. Based on FST and GWAS analyses, a total of 20 candidate loci on Sus scorfa chromosomes (SSC) 7, 13, 16 and 18 for teat number were identified and these candidate loci could explain 5.49%-8.03% of the phenotypic variance. Among them, locus rs80894106 on SSC7 associated with total teat number was consistent with the reported candidate locus of total teat number based on Large white and Duroc pig populations, but candidate loci rs81444134 (26.51 Mb, SSC13) and rs81233299 (8.13 Mb, SSC18) of left teat number were newly discovered loci related to teat number. Interestingly, candidate loci of left, right and total teat number were mainly concentrated in the 6.36-10.66 Mb interval on SSC16; Linkage disequilibrium (LD) analysis found that candidate loci in 7.47-8.27 Mb interval fit into a 795 kb haplotype block, and this haplotype block was a newly discovered candidate area that affected teat number; rs337606862 (7.47 Mb) in the haplotype block was the most significantly SNP associated with the left and total teat number, and three loci in the haplotype block were all located on the intron of cadherin 18 (CDH18) gene; CDH18 gene encoded type II cadherin, and cadherin was related to the identification, sorting, proliferation, apoptosis of cells in developing tissue and the occurrence of breast cancer. Thus, CDH18 might be a new candidate gene that affected pig teat number. In addition, the most significant loci rs81444134, rs80894106, rs337606862 and rs81233299 on 4 chromosomes were genotyped in 709 Suhuai pigs in this study. After association analysis, these loci were significantly associated with teat number, and could be used as potential molecular markers for the selection of teat number.【Conclusion】In this study, 20 loci significantly related to teat number were identified in Suhuai pig population by genome analysis. Among them, 26.51 Mb on SSC13 and 8.13 Mb on SSC18 were new candidate QTLs for teat number. The 7.47-8.27 Mb on SSC16 was also a newly discovered candidate QTL for teat number, and CDH18 gene in this interval might be a new candidate gene that affected the formation of pig teat.

Zearalenone (ZEA) is a prevalent mycotoxin functions as an endocrine disrupter to the reproductive systems of farm animals, especially in pigs. To evaluate the effect and the underlying molecular changes that occurred when the porcine germline stem cells were exposed to ZEA, prospermatogonia (ProSGs) were enriched and treated with a gradient concentration (0-10 & mu;M) of ZEA for 2-8 days. Our results showed that the ZEA treatment inhibited the proliferation of ProSGs in a dose-dependent manner with a critical concentration at 1 & mu;M. Transcriptome analysis revealed that the differentially expressed genes mainly concentrated on the molecular function of positive regulation of response to stimulus, and the most enriching pathway is cytokine-cytokine receptor interaction. ZEA exposure decreased a buck of cytokine/chemokine expression involved in the inflammatory response and stem cells maintenance/self-renewal, moreover, some energy expenditure and anti-apoptosis genes were also down-regulated, while the up-regulated genes were mainly connected with the innate immunity. These data demonstrate that ZEA induces multiply cellular damage and may eventually do harm to the health and fertility of animals.

To evaluate the tolerance of a high-fiber diet in Erhualian pigs (Er-HL), the present investigation systematically investigated the ramifications of varying wheat bran fiber levels, specified as total dietary fiber (TDF) values of 14.07%, 16.32%, 17.99%, and 18.85%, on growth performance, fiber digestibility and gut microbiota in Er-HL, large Large White pigs (L-LW, the same physiological stage as the Er-HL) and small Large White pigs (S-LW, the same body weight as the Er-HL). Our results revealed that fiber levels exerted no discernable impact on growth performance (average daily feed intake (ADFI), and average daily gain (ADG)) of Er-HL (p > 0.05). Conversely, L-LW exhibited a decrease in ADFI and ADG with increasing fiber levels (p < 0.05). Notably, the apparent total tract digestibility (ATTD) of various fiber components, including neutral detergent fiber (NDF), acid detergent fiber (ADF), hemicellulose, TDF and insoluble dietary fiber (IDF), in Er-HL were significantly higher than those in S-LW and L-LW irrespective of diets (p < 0.05). The ATTD of cellulose and hemicellulose in Er-HL significantly decreased with increasing fiber levels (p < 0.05), yet remained statistically indifferent when comparing the 7%-wheat-bran-replaced diet (7% WRB, TDF 16.32%) to the basal diet (TDF 14.07%) (p > 0.05). The cecal microbiota of Er-HL had higher richness estimators (Chao1 and ACE) than those of S-LW and L-LW irrespective of diets (p < 0.01). Breed serves as a pivotal determinant in shaping swine gut microbiota. Thirteen genera were selected as the key bacteria related to high fiber digestibility of Er-HL. Further functional examination of these key genera elucidated an enrichment of pathways pertinent to carbohydrate metabolism in Er-HL samples compared with S-LW and L-LW samples. In summary, Er-HL exhibited high-fiber tolerance both in terms of growth performance and fiber digestibility compared with Large White pigs. Specifically, the ATTD of NDF, ADF, hemicellulose, IDF and TDF were significantly higher in Er-HL compared with L-LW and S-LW, irrespective of diets. Fiber level exerted no discernable impact on growth performance (ADFI, ADG) and the ATTD of fiber (NDF, ADF, IDF and TDF) in Er-HL. The optimum fiber level of the Er-HL was identified as 7% WRB (TDF 16.32%). Thirteen genera were ascertained to significantly contribute to high fiber digestibility of Er-HL, correlating with an enhancement of carbohydrate metabolism pathways.

The number of ribs (NR) and carcass length (CL) are important economic traits in pig breeding programs. Pigs with a higher NR and longer CL produce greater pork yields. In the present study, Suhuai pigs with NR and CL phenotypes were genotyped using the Neogen® GGP Porcine 80 K SNP array to identify the QTL affecting NR and CL and dissect the candidate genes for the two traits. The SNP-chip data was imputed to the whole-genome sequence (iWGS) to increase the probability of identifying causal variants. Through genome-wide association studies (GWAS) based on both chip and iWGS data, significant SNPs were detected on Sus scrofa chromosome (SSC) 1, SSC4 and SSC7 for NR and on SSC5, SSC16 and SSC17 for CL. Moreover, two SNPs (H3GA0022644 and WU_10.2_7_103460706) on SSC7 detected in chip-based GWAS were significantly associated with both NR and CL. Through Bayes fine mapping, one reported QTL for NR on SSC7 and two reported QTL for CL on SSC17 were verified, and two new QTL (SSC1: 14.05-15.84 Mb and SSC4: 64.83-66.59 Mb) affecting NR and two new QTL (SSC5: 58.31-59.84 Mb and SSC16: 22.98-23.43 Mb) affecting CL were detected. According to the biological functions of genes, MTHFD1L on SSC1 and SULF1 on SSC4 are novel functional candidate genes for NR, and EMP1 on SSC5 and EGFLAM on SSC16 are novel functional candidate genes for CL. Overall, our findings provide a basis for identifying new causal genes and mutations affecting NR and CL.

Previous study have found that 7% bran replacement basal diet can significantly improve the redness value of longissimus dorsi muscle of Erhualian pigs and improve their meat quality， but its potential physiological and molecular regulatory mechanisms remain unknown. The aim of the study was to identify the candidate metabolites of dietary fiber affecting meat quality traits of Erhualian pigs using non-targeted metabolomics technology and explore the potential physiological and molecular regulatory mechanism of dietary fiber affecting the meat quality using in vitro myotubes derived from Erhualian pigs. In this study， differential plasma metabolites between basal diet group and 7% bran replacement basal diet group were detected using non-targeted metabolomics technology in Erhualian pigs， then the correlation between differential plasma metabolites and meat quality phenotype data were analyzed to identify dietary fiber candidate metabolites affecting the meat quality traits of Erhualian pigs. Then the candidate metabolite was used to treat Erhualian pig myotubes in vitro to study its effect on the transformation of muscle fiber types. A total of 9 different metabolites were identified between the basal diet group and the 7% bran replacement basal diet group， of which 4 different metabolites had higher level in the basal diet group and 5 different metabolites had higher level in the 7% bran replacement basal diet group. KEGG pathway analysis showed that plasma differential metabolites of Erhualian pigs were mainly involved in melanin generation pathway， ABC transporter pathway and tyrosine and tryptophan biosynthesis pathway etc. The plasma metabolite heptadecanoic acid was found to be positively correlated with the 24-hour redness value (a 24 h ) of longissimus dorsi muscle of Erhualian pigs by correlation analysis with the meat quality phenotype data obtained in previous studies. The results of in vitro cell experiments showed that the expression level of type I muscle fiber type marker gene MyHC I was increased by heptadecanoic acid treatment in Erhualian pig myotube cells. Appropriate dietary fiber supplementation changed the plasma metabolome of Erhualian pigs， and heptadecanoic acid may improve the flesh color of longissimus dorsi muscle of Erhualian pigs by increasing the expression of MyHC I gene and thus improved the quality of pork.

This study aimed to analyze the effects of different levels of wheat bran replacing basal diet on blood routine， blood biochemistry， serum immunoglobulin， and large intestinal mucosal secretory immunoglobulin A （SIgA） of Meishan pigs， using Large White pigs as the control. Then further studied the mechanism of dietary fiber affecting the immune indicators of Meishan pigs from the perspective of host intestinal genes and microorganisms. In this study， 28 Meishan pigs （initial body weight was 67.08±1.53 kg） and 28 Large White pigs （initial body weight was 81.04±1.64 kg， at the same physiological stage as Meishan pigs） were randomly divided into 4 treatment groups with 7 replications in each group for 1 per duplicate. During the pre-feeding period of 7 days， all pigs were fed the basal diet， and during the main trial period of 28 days， they were fed with the basal diet （Basal）， 7%， 10.5%， and 14% wheat bran substituted in the basal diet （7% WBR， 10.5%WBR and 14% WBR）， respectively. During the trial period， all pigs had free access to food and water. At the end of the experiment， all pigs were slaughtered， and blood samples were collected for the determination of blood routine， blood biochemical， and serum immunoglobulin indicators. Cecal and colonic mucosal samples were collected for SIgA determination， and colonic mucosal were collected to perform RNA-seq. Colonic contents were collected for metagenomic sequencing. The results showed that: 1) With the increasing of wheat bran replacing basal diet level， the number of eosinophils and basophils， and percentage of eosinophils decreased in Meishan pigs （linear， P ＜ 0.01）， and the serum globulin level of Meishan pigs in the 14% WBR group were significantly higher than that of Large White pigs （P ＜ 0.05）. 2) With the increasing of wheat bran replacing basal diet level， the serum immunoglobulin M （IgM） and immunoglobulin G （IgG） of Meishan pigs increased （linear， P ＜ 0.01）， and the serum IgM of Large White pigs increased （linear， P ＜ 0.01）. The serum IgG concentration of Meishan pigs in the 14% WBR group was significantly higher than that of Large White pigs （P ＜ 0.01）. In addition， compared with the Basal group， the concentration of colonic mucosal SIgA of Meishan pigs in the 14% WBR group was significantly increased （P ＜ 0.01）， but there was no significant change between the 14% WBR group and the Basal group in Large White pigs. 3). To elucidate the mechanism of increased colonic mucosal SIgA concentration of Meishan pigs in the 14% WBR group， on the one hand， the colonic mucosa of Meishan pigs in the Basal group and the 14% WBR group were selected to perform RNA-seq. A total of 38 differentially expressed genes were identified， and the functional items enriched by GO and the signal pathway enriched by KEGG are mainly related to the immune system. The expression of CD4 molecule （CD4） and C-C chemokine receptor 9 （CCR9） regulating intestinal SIgA production was significantly increased in the 14% WBR group （P ＜ 0.01）. On the other hand， the colonic contents of Meishan pigs in the Basal group and the 14% WBR group were selected to perform metagenomic sequencing. The results of LEFSe analysis showed that 14% WBR group was significantly enriched to 2 family-level microorganisms， 1 genus-level microorganism， and 5 species-level microorganisms. Correlation analysis revealed that there was no direct interaction between species-level different microorganisms and host mucosal genes regulating the production of intestinal SIgA （P ＞ 0.05）， but Sutterella sp.， Clostridium sp. CAG:138， Clostridium sp. CAG:762 and Nitrospira sp. were significantly positively correlated with serum IgG. Moreover， Clostridium sp. CAG:138 and Nitrospira sp. were significantly positively correlated with colonic mucosal SIgA. Finally， KEGG functional analysis found that the relative abundance of the Intestinal immune network for IgA production in the 14% WBR group was significantly higher than that of the Basal group （P ＜ 0.05）. In summary， replacing part of the basal diet with wheat bran could reduce the inflammatory level， enhance humoral immunity and promote the health of the colon of Meishan pigs， and the beneficial effect of 14% wheat bran replaced basal diet on Meishan pigs is better than that on Large White pigs. In addition， this study also found that the effects of dietary fiber on colonic mucosal SIgA of Meishan pigs may be through up-regulating the expression of CD4 and CCR9 genes in the colonic mucosa， affecting the composition of intestinal microorganisms， enhancing the functional pathway of Intestinal immune network produced by IgA， improving intestinal barrier function and promoting body health.

Eurasian pigs have undergone lineage admixture throughout history. It has been confirmed that the genes of indigenous pig breeds in China have been introduced into Western commercial pigs, providing genetic materials for breeding Western pigs. Pigs in Taihu Lake region (TL), such as the Meishan pig and Erhualian pig, serve as typical representatives of indigenous pig breeds in China due to their high reproductive performances. These pigs have also been imported into European countries in 1970 and 1980 s. They have played a positive role in improving the reproductive performances in European commercial pigs such as French Large White pigs (FLW). However, it is currently unclear if the lineage of TL pigs have been introgressed into the Danish Large White pigs (DLW), which are also known for their high reproductive performances in European pigs. To systematically identify genomic regions in which TL pigs have introgressed into DLW pigs and their physiological functions, we collected the re-sequencing data from 304 Eurasian pigs, to identify shared haplotypes between DLW and TL pigs. The findings revealed the presence of introgressed genomic regions from TL pigs in the genome of DLW pigs indeed. The genes annotated within these regions were found to be mainly enriched in neurodevelopmental pathways. Furthermore, we found that the 115 kb region located in SSC16 exhibited highly shared haplotypes between TL and DLW pigs. The major haplotype of TL pigs in this region could significantly improve reproductive performances in various pig populations. Around this genomic region, NDUFS4 gene was highly expressed and showed differential expression in multiple reproductive tissues between extremely high and low farrowing Erhualian pigs. This suggested that NDUFS4 gene could be an important candidate causal gene responsible for affecting the reproductive performances of DLW pigs. Our study has furthered our knowledge of the pattern of introgression from TL into DLW pigs and the potential effects on the fertility of DLW pigs.

旨在体外获得纯度较高的苏淮猪背最长肌纤维/脂肪形成祖细胞(fibro/adipogenic progenitors,FAPs),并评价其在体外传代过程中成脂能力与基因表达模式的变化.本研究取1日龄苏淮公猪背最长肌,消化获得悬浮混合细胞,利用抗表面特异抗原血小板衍生生长因子受体α(PDGFRα)抗体通过免疫荧光评价4种不同差速贴壁时间分离的FAPs细胞的纯度,确定最佳差速贴壁时间.然后比较不同代数FAPs细胞(P1、P3和P5代)的体外成脂分化能力,并利用RNA-Seq比较不同代数FAPs细胞的基因表达模式,鉴别差异表达基因、KEGG通路与GO功能分类.研究结果表明,差速贴壁30 min分离的苏淮猪背最长肌FAPs细胞的纯度较高.对不同代数FAPs成脂能力评价发现,随着体外传代次数的增加,其成脂能力显著下降.利用RNA-Seq发现P3和P5代FAPs细胞的基因表达模式相近,P3和P5代分别与P1代FAPs细胞相比,鉴定到2 336个共有的差异表达基因,其中差异上调基因1 102个,差异下调基因1 234个,KEGG和GO分析表明共有的差异上调基因主要富集在PI3K-AKT-FoxO、PI3K-AKT-HIF-1和cGMP-PKG等通路,共有的差异下调基因主要富集在DNA复制和修复等通路,其中可抑制细胞增殖与成脂分化的IRS1、FOXO3、CCNG2、EGFR、FGF1基因表达上调,可促进细胞增殖的CSF1R和SIPA1L2基因表达下调.P3与P5相比发现,差异上调基因主要富集在NOD-like、MAPK和非典型 Wnt信号等通路;差异下调基因主要富集在VEGF、PPAR、Notch以及IL-17等信号通路,其中可抑制细胞成脂分化的TNFAIP3、AREG、FGF1、FGF9基因表达上调,可促进成脂分化的PPARγ、C/EBPα、LCN2基因下调.本研究结果表明,差速贴壁30 min能够得到纯度较高的猪FAPs细胞,FAPs细胞在体外培养过程中成脂分化能力不断下降,其基因表达模式发生了较大变化,主要表现为可促进细胞增殖和成脂分化的信号通路及其相关基因表达水平下降,本研究结果可为开发能维持猪FAPs细胞体外成脂能力的培养基配方提供参考.

The high-fertility Meishan pig is currently categorized into medium sized (MMS) and small sized (SMS) based on body size. To identify causal genes responsible for the variation in body size within the two categories, we sequenced individuals representing the entire consanguinity of the existing Meishan pig. This enabled us to conduct genome selective signal analysis. Our findings revealed the genomes of MMS and SMS are stratified, with selective sweep regions formed by differential genomic intervals between the two categories enriched in multiple pig body size related quantitative trait loci (QTLs). Furthermore, the missense mutation c.575T > C of candidate causal gene NR6A1, accounting for the variation in lumbar vertebrae number in pigs, was positively selected in MMS only, leading to an increase in body length of MMS at 6 months of age. To precisely identify causal genes accounting for body size variation through multi-omics, we collected femoral cartilage and liver transcription data from MMS and SMS respectively, and re-sequencing data from pig breeds exhibiting varying body sizes. We found that two selected regions where the RSAD2-CMPK2 and COL3A1 genes are located, respectively, showed different haplotypes in pig breeds of varying body size, and was associated with body or carcass length in hybridized Suhuai pig. Additionally, the above three hub genes, were significantly greater expressed in SMS femoral cartilage and liver tissues compared to MMS. These three genes could strengthen the pathways related to bone resorption and metabolism in SMS, potentially hindering bone and skeletal development and resulting in a smaller body size in SMS. These findings provide valuable insights into the genetic mechanism of body size variation in Meishan pig population.

Abstract Integrating the single‐nucleotide polymorphisms (SNPs) significantly affecting target traits from imputed whole‐genome sequencing (iWGS) data into the genomic prediction (GP) model is an economic, efficient, and feasible strategy to improve prediction accuracy. The objective was to dissect the genetic architecture of intramuscular fat content (IFC) by genome wide association studies (GWAS) and to investigate the accuracy of GP based on pedigree‐based BLUP (PBLUP) model, genomic best linear unbiased prediction (GBLUP) models and Bayesian mixture (BayesMix) models under different strategies. A total of 482 Suhuai pigs were genotyped using an 80 K SNP chip. Furthermore, 30 key samples were selected for resequencing and were used as a reference panel to impute the 80 K chip data to the WGS dataset. The 80 K data and iWGS data were used to perform GWAS and test GP accuracies under different scenarios. GWAS results revealed that there were four major regions affecting IFC. Two important functional candidate genes were found in the two most significant regions, including protein kinase C epsilon (PRKCE) and myosin light chain 2 (MYL2). The results of the predictions showed that the PBLUP model had the lowest reliability (0.096 ± 0.032). The reliability (0.229 ± 0.035) was improved by replacing pedigree information with 80 K chip data. Compared with using 80 K SNPs alone, pruning iWGS SNPs with the R‐squared cutoff of linkage disequilibrium (0.55) led to a slight improvement (0.006), adding significant iWGS SNPs led to an improvement of reliability by 0.050 when using a one‐component GBLUP, a further increase of 0.033 when using a two‐component GBLUP model. For BayesMix models, compared with using 80 K SNPs alone, adding additional significant iWGS SNPs into one‐ or two‐component BayesMix models led to improvements of reliabilities for IFC by 0.040 and 0.089, respectively. Our results may facilitate further identification of causal genes for IFC and may be beneficial for the improvement of IFC in pig breeding programs.

红灯笼猪是优质的江苏省地方畜禽资源.为探明红灯笼猪种质特异性,解析其种质特性背后的关键基因位点,本试验选取了包括红灯笼猪、米猪和淮猪在内的45个欧亚猪种1 228头猪的基因组数据,通过邻接系统发育树、遗传距离、遗传分化系数、祖先血统组成K分析(K pos-tulated ancestral populations)以及位点特异性分枝长度(locus-specific branch length,LSBL)分析等进行整合分析.结果显示:红灯笼猪在邻接系统发育树分析中独立成簇,没有与其他猪种交叉.在遗传距离和遗传分化系数分析中,红灯笼猪与其他猪种,包括淮猪和米猪,都保持较远的遗传距离和遗传分化,这种差异甚至超过了梅山和二花脸等现有确认的地方猪种间差异.此外,在祖先血统组成分析中,红灯笼猪在K=39时,形成了独立的祖先血统组成,此时的二花脸和米猪仍共享同一个祖先血统,表明红灯笼猪进化路线特异.最后通过将红灯笼猪、米猪和淮猪进行LSBL分析,结果发现相关位点所注释到的基因主要富集在生长代谢、抗病性和神经发育等功能上,表明红灯笼猪在种质形成过程中,相关性状受到选择.本试验确定了红灯笼猪的品种独立性,初步解析了红灯笼猪种质的遗传机制,为进一步保护和利用这一珍贵猪种奠定了理论基础.