The sensory quality of pork constitutes a complex phenotype that arises from the interplay between genetic factors and environmental conditions. As a local pig breed in China, Tibetan pigs (TPs) are known for their high-quality meat. However, their slow growth rate and low production efficiency limit their large-scale breeding. We have used Duroc as a hybrid sire to improve TP. Our study found that TPs have higher intramuscular fat content and higher levels of monounsaturated fatty acids. Duroc × Tibetan crossbred pigs (DZs) not only retain the paternal high productivity but also inherit the superior meat quality of the maternal parent. Transcriptome analysis identified IL6, GPX1, GPX3, AOX1, ALDH7A1, PTGS2, NFKBIA, ADIPOQ and PPARG as being involved in affecting meat quality. Metabolomic analysis found that betaine, carnosine, L-carnitine, and lysophosphatidylcholine were important components that affect meat quality. Joint analysis further reveals that the expression of ATF4, DGKB, GNMT, and ADSL genes is closely related to arachidonic acid, lysophosphatidylcholine, betaines, and hypoxanthine, ultimately affecting the quality of the meat. By comprehensively analyzing the carcass and meat quality traits, genes and metabolites affecting meat quality traits, this study provides new evidence for improving pork quality and guiding breeding strategies.

Sichuan Baoning vinegar, a renowned traditional vinegar in China, exhibits a higher lactic acid content compared to acetic acid. The microbiota plays a crucial role in shaping the unique flavor of vinegar, but the species-level succession of key microorganisms and metabolic pathways of major organic acids in this vinegar are still unclear. This study utilized metagenomic sequencing to elucidate microbial succession during fermentation and the functional roles of the microbial community, as well as explore the metabolic network of lactic acid and acetic acid. Our findings revealed that bacteria dominated the fermentation process, with Acetilactobacillus jinshanensis, Lactobacillus amylovorus, and Limosilactobacillus sp. emerging as the top three species. Notably, Acetilactobacillus jinshanensis, Limosilactobacillus sp., Lactobacillus amylovorus, and Limosilactobacillus pontis were key players in lactic acid production, while acetic acid synthesis might be primarily driven by Lactobacillus amylovorus, Limosilactobacillus sp., Lactobacillus acetotolerans, and Acetobacter pasteurianus. This study enhances our understanding of the key microorganisms and organic acids metabolism in vinegar, shedding light on the fermentation mechanism of cereal vinegar.

Background/Objectives: Fat deposition traits in pigs directly influence pork flavor, tenderness, and juiciness and are closely linked to overall pork quality. The Tibetan pig, an indigenous breed in China, not only possesses a high intramuscular fat content but also exhibits a unique fat metabolism pattern due to long-term adaptation to harsh environments. This makes it an excellent genetic and physiological model for investigating fat deposition characteristics. Adipose tissue from different body regions displays varying morphologies, cytokines, and adipokines. This study aimed to examine adipose tissue deposition characteristics in different parts of Tibetan pigs and provide additional data to explore the underlying mechanisms of differential fat deposition. Methods: Our research identified significant differences in the morphology and gene expression patterns between subcutaneous fat (abdominal fat [AF] and back fat [BF]) and intramuscular fat (IMF) in Tibetan pigs. Results: Histological observations revealed that subcutaneous fat cells were significantly larger in area and diameter compared to IMF cells. The transcriptomic analysis further identified differentially expressed genes (DEGs) between subcutaneous fat and IMF, with a total of 65 DEGs in BF vs. IMF and 347 DEGs in AF vs. IMF, including 25 DEGs common to both comparisons. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses indicated that these genes were significantly associated with lipid metabolism-related signaling pathways, such as the Wnt, mTOR, and PI3K-Akt signaling pathways. Several DEGs, including DDAH1, ADRA1B, SLCO3A1, and THBS3, may be linked to the differences in fat deposition in different parts of Tibetan pigs, thereby affecting meat quality and nutritional value. Conclusions: These findings provide new insights into the unique fat distribution and deposition characteristics of Tibetan pigs and establish a foundation for breeding strategies aimed at improving pork quality.

This experiment was conducted to explore the effects of different neutral detergent fiber (NDF) levels on nutrient apparent digestibility and intestinal microbiota composition and function in adult male forest musk deer (FMD) (Moschus berezovskii). A total of 18 adult male forest musk deer (FMD) (aged 4–10 years) with an initial average body weight of 7.09 ± 0.82 kg were selected and randomly divided into three groups with different NDF levels: L: 21.60%, M: 25.14%, and H: 28.47%. The FMD were used in a 50-day trial. The results showed that the apparent digestibility of NDF and acid detergent fiber (ADF) first increased and then decreased as NDF levels rose, with the M group showing the highest digestibility (p < 0.05). The H group exhibited significantly higher (p < 0.05) Chao1 and ACE indices compared to the L group. In addition, at the phylum level (the relative abundance > 0.5%), no significant differences were observed among the three groups, except for Mycoplasmatota, which showed higher (p < 0.05) relative abundance in the M group compared to the L group. At the genus level (the relative abundance > 1%), the three groups did not change (p > 0.05) significantly. In the KEGG function analysis, differentially expressed genes were primarily enriched in pathways related to organismal systems and human diseases. In the CAZy functional analysis, significant differences (p < 0.05) were observed in glycoside hydrolases (GHs) and carbohydrate-binding modules (CBMs), with the M group showing clear enrichment in fiber-degrading enzymes. Overall, the M group demonstrated superior NDF apparent digestibility and enhanced fiber degradation capacity. Therefore, a dietary NDF level of approximately 25% is recommended as optimal for adult male FMD.

The aim of this study is to investigate the physiological characteristics and regulatory mechanisms of porcine intramuscular fat (IMF), subcutaneous fat (take back fat (BF), for example), and visceral fat (take perienteric fat (PF), for example) to address the challenge of optimizing meat quality without excessive fat deposition. Many improved breed pigs have fast growth rates, high lean meat rates, and low subcutaneous fat deposits, but they also have low IMF content, resulting in poor meat quality. There is usually a positive correlation between intramuscular fat and subcutaneous fat deposits. This study selected eight-month-old female Tibetan pigs as experimental subjects. After slaughter, fat samples were collected. Histological differences in adipocyte morphology were observed via hematoxylin–eosin (HE) staining of tissue sections, and phenotypic characteristics of different adipose tissues were analyzed through fatty acid composition determination. Transcriptome sequencing and untargeted metabolomics were employed to perform pairwise comparisons between different fatty tissues to identify differentially expressed genes and metabolites. A siRNA interference model was constructed and combined with Oil Red O staining and lipid droplet optical density measurement to investigate the regulatory role of WNT16 in adipocyte differentiation. Comparative analysis of phenotypic and fatty acid composition differences in adipocytes from different locations revealed that IMF adipocytes have significantly smaller areas and diameters compared to other fat depots and contain higher levels of monounsaturated fatty acids. Integrated transcriptomic and metabolomic analyses identified differential expression of WNT16 and L-tyrosine, both of which are involved in the melanogenesis pathway. Functional validation showed that inhibiting WNT16 in porcine preadipocytes downregulated adipogenic regulators and reduced lipid droplet accumulation. This cross-level regulatory mechanism of “phenotype detection–multi-omics analysis–gene function research” highlighted WNT16 as a potential key regulator of site-specific fat deposition, providing new molecular targets for optimizing meat quality through nutritional regulation and genetic modification.

Adult male forest musk deer (Moschus berezovskii; FMD) possess high medicinal and economic value due to their musk secretion capacity. However, under farming conditions, a subset of individuals exhibit abnormal musk secretion or complete secretory failure, resulting in economic losses. This phenomenon is associated with lipid metabolism and gut microbiota alterations. We compared fecal steroid hormones, short-chain fatty acids (SCFAs), and bacterial communities between high-yielding and low-yielding FMD under identical captive conditions. Seven male FMD (2 6 years old) secreting normal musk comprised the high-yielding group (HFMD), while seven age-matched males secreting abnormal musk formed the low-yielding group (LFMD). Results showed significantly higher concentrations of testosterone (T), estradiol (E2), cortisol, and corticosterone (CORT) in HFMD versus LFMD group (p < 0.05). Conversely, SCFA levels showed an inverse pattern: butyrate and hexanoate concentrations were significantly higher in LFMD group (p < 0.05). Following multiple testing correction, the relative abundances of Fibrobacteres (p = 0.013; FDR = 0.170), Tenericutes (p = 0.013; FDR = 0.107), and Verrucomicrobia (p = 0.037; FDR = 0.223) were observed to be significantly higher in the HFMD group compared to the LFMD group. Furthermore, distinct microbial biomarkers were identified between the two groups. Certainly, ASV_849 (taxonomically classified as Ruminococcaceae UCG-014) exhibited significant correlations with multiple steroid hormones and SCFAs (p < 0.05; FDR = 0.246). Moreover, correlation analysis demonstrated positive associations between musk secretion and E2, T, cortisol, and CORT (p < 0.05), but negative correlations with hexanoate (p < 0.05). Butyrate and hexanoate were inversely correlated with T (p < 0.05). These findings reveal that the gut microbiota may regulate musk secretion through their metabolites (SCFAs), which not only play a key mediating role in microbe-host interactions but may also indirectly influence the process of musk secretion via their interplay with steroid metabolism. This study provides valuable insights into the captive care management of adult male FMD and strategies for enhancing musk secretion.

The mechanistic underlying the favorable meat quality of Tibetan pigs has not been fully elucidated. This study integrated flavor chemistry, histomorphology, and proteomics to explore the structural and molecular features of their meat. Longissimus dorsi samples from Tibetan and Duroc pigs (n = 6 each biological replicates) were quantitatively analyzed for amino acid profiling, histological assessment, and proteomic characteristic. Statistical approaches included weighted correlation network analysis, t-tests, and functional enrichment. Tibetan pork contained 34 mg/100g more total free amino acids, notably sweet-tasting Ala (+49.2%) and Thr (+32.2%). Muscle fiber density was >250% higher and diameter > 30% smaller, indicating finer texture. Proteomics revealed 149 upregulated proteins, including 57 mitochondrial differentially expressed proteins (DEPs)—11 of which belonged to electron transport chain complexes (e.g., NDUFAB1, COX2). The significant enrichment of oxidative phosphorylation pathways may be associated with mitochondrial efficient energy metabolism under hypoxic in Tibetan pigs, potentially linking to the breed’s unique meat characteristics. Ala levels showed strong correlations with metabolic and structural protein modules. The finer fibers and mitochondrial protein profile of Tibetan pigs contribute to higher amino acid content and meat quality. This structural–metabolic–flavor axis supports both hypoxia adaptation and high meat quality. Given the central role of mitochondrial electron transport chain (ETC) proteins in energy metabolism and Ala in flavor presentation, their synergistic action provides a molecular bridge between hypoxia adaptation and meat quality. Therefore, this study suggests that ETC and Ala may serve as key biomarkers for meat quality differences, offering new perspectives for meat quality research.

Congenital developmental abnormalities in piglets, such as intersex and aproctia, adversely affect survival rates, growth performance, and genetic breeding efficiency in pig populations. To elucidate their genetic basis, we performed a genome-wide association study (GWAS) on 1030 Large White pigs. We combined 50 K SNP chip data with SWIM-based genotype imputation to enhance the resolution of genetic variation detection, followed by MLM analysis. Our results identified 53 significant SNPs, with 52 associated with intersex and 1 with aproctia. Key candidate genes included MAD1L1, ID4, EFNA5, and PPP1R16B for intersex and ARNT2 for aproctia. Functional enrichment analysis highlighted pathways related to gonadal development (e.g., progesterone-mediated oocyte maturation) and embryonic morphogenesis. Collectively, the identification of these SNPs and candidate genes advances our understanding of the genetic architecture of intersex and aproctia in piglets. These findings provide actionable insights for optimizing genetic breeding strategies and improving health management in Large White pig production, with potential implications for reducing economic losses caused by congenital disorders.

Genetic variation in the regulation of gene expression contributes substantially to phenotypic variation. Understanding how variation in DNA sequences and epigentic modifications leads to gene expression variation remains a challenging task. In hybrid animals where cellular environments are homogeneous, differences between the expression of paternal and maternal alleles must be due to cis sequence or epigenic differences. Therefore, hybrid mapping is a powerful approach to efficiently identify and characterize genes under regulation through mechanisms in cis . In this study, using reciprocal crosses of the phenotypically divergent Duroc and Lulai pig breeds, we performed a comprehensive multi-omic characterization of regulatory variation across brain, liver, muscle, and placenta in four developmental stages. We produced one of the largest multi-omic datasets to date in pigs, including 16 whole genome sequenced genomes, 48 whole genome bisulfite sequencing, 168 ATAC-Seq and 168 RNA-Seq samples. We developed a novel read count-based method to reliably assess allele-specific methylation, chromatin accessibility, and RNA expression. We showed that tissue specificity was much stronger than developmental stage specificity in all of DNA methylation, chromatin accessibility, and gene expression. We identified 573 genes showing allele specific expression, including those influenced by parent-of-origin as well as allele genotype effects. By integrating methylation, chromatin accessibility, and gene expression data, many of these allele specific expression can be explained by allele specific methylation and/or chromatin accessibility. This study provides one of the most comprehensive characterizations of regulatory variation across multiple tissues and developmental stages in pigs and offers new opportunity of genetic improvement for this important food animal species.### Competing Interest StatementThe authors have declared no competing interest.

The pig bone weight trait holds significant economic importance in southern China. To expedite the selection of the pig bone weight trait in pig breeding, we conducted molecular genetic research on these specific traits. These traits encompass the bone weight of the scapula (SW), front leg bone weight (including humerus and ulna) (FLBW), hind leg bone weight (including femur and tibia) (HLBW), and spine bone weight (SBW). Up until now, the genetic structure related to these traits has not been thoroughly explored, primarily due to challenges associated with obtaining the phenotype data. In this study, we utilized genome-wide association studies (GWAS) to discern single nucleotide polymorphisms (SNPs) and genes associated with four bone weight traits within a population comprising 571 Duroc × (Landrace × Yorkshire) hybrid pigs (DLY). In the analyses, we employed a mixed linear model, and for the correction of multiple tests, both the false discovery rate and Bonferroni methods were utilized. Following functional annotation, candidate genes were identified based on their proximity to the candidate sites and their association with the bone weight traits. This study represents the inaugural application of GWAS for the identification of SNPs associated with individual bone weight in DLY pigs. Our analysis unveiled 26 SNPs and identified 12 promising candidate genes (OPRM1, SLC44A5, WASHC4, NOPCHAP1, RHOT1, GLP1R, TGFB3, PLCB1, TLR4, KCNJ2, ABCA6, and ABCA9) associated with the four bone weight traits. Furthermore, our findings on the genetic mechanisms influencing pig bone weight offer valuable insights as a reference for the genetic enhancement of pig bone traits.

The study determined the impacts of dietary fermented residues’ (FBR) inclusion on growth, nutrient utilization, carcass characteristics, and meat properties in fattening pigs. Seventy-two robust pigs were randomly assigned to two experimental groups (Duroc × Landrace × Yorkshire, thirty-six pigs each). Each group was subjected to a 52-day trial, during which they received either a corn–soybean meal-based diet or diet enhanced with a 10% addition of FBR. Consequently, adding 10% FBR caused a significant decrease in the digestive utilization of crude dietary components in fattening pigs (p < 0.05) but showed no significant impact on the growth performance. Additionally, FBR inclusion increased the marbling scores (p < 0.05) and total antioxidant functions (p < 0.05) of muscle tissues, indicating improved meat quality. Gender affected backfat depth, with barrows showing thicker backfat depth. In conclusion, dietary supplementation with 10% FBR in finishing pigs influenced the meat quality by improving the marbling score and antioxidant performance while reducing digestibility without compromising growth performance.

This study aimed to prepare a complex of montmorillonite (MMT) intercalated with porcine glucagon-like peptide (pGLP-2) and evaluate its therapeutic effects in weaning piglets challenged with lipopolysaccharide (LPS). Forty-eight 28-day-old weaning pigs with an average body weight (BW) of 8.47 kg were divided into two groups: a control group fed a basal diet and an MMT/pGLP-2 group fed a basal diet supplemented with 0.5‰ MMT/pGLP-2 complex. At the end of the experiment, 12 piglets from each group were intraperitoneally administered LPS (100 g/kg BW) or saline. The results demonstrated that at pH 3.4, 98.67% of pGLP-2 was adsorbed onto MMT. At pH 9.0 and 7.5, the desorption rates of pGLP-2 were approximately 40% and 26%, respectively, which were significantly greater than those at pH 5.0 or 2.0 (less than 1%). Desorption reached equilibrium within 0.5 h. The interlayer spacing of MMT increased from 1.28 nm to 1.49 nm after pGLP-2 adsorption. Compared to the control diet, the MMT/pGLP-2-supplemented diet significantly (P < 0.05) enhanced maltase, lactase, and Na+-K+-ATPase activities in the jejunum and ileum and sucrose activity in the jejunum. The lengths and weights of the jejunum and ileum were significantly greater in the MMT/pGLP-2 group (P > 0.05). No significant differences (P > 0.05) were observed in body weight, average daily gain, average daily feed intake, or feed-to-gain ratio among the groups. Under LPS challenge, piglets supplemented with MMT/pGLP-2 exhibited significant increases (P < 0.05) in maltase, sucrose, and Na+-K+-ATPase activities in the jejunum and ileum and lactase activity in the jejunum compared to those in piglets administered saline. These findings suggest that the MMT/pGLP-2 complex, prepared under acidic conditions and releasing pGLP-2 under basic conditions, can mitigate intestinal injury from LPS and restore intestinal function, making it a potential feed additive for piglets.

Hybrid mapping is a powerful approach to efficiently identify and characterize genes regulated through mechanisms in cis. In this study, using reciprocal crosses of the phenotypically divergent Duroc and Lulai pig breeds, we perform a comprehensive multi-omic characterization of regulatory variation across the brain, liver, muscle, and placenta through four developmental stages. We produce one of the largest multi-omic datasets in pigs to date, including 16 whole genome sequenced individuals, as well as 48 whole genome bisulfite sequencing, 168 ATAC-Seq and 168 RNA-Seq samples. We develop a read count-based method to reliably assess allele-specific methylation, chromatin accessibility, and RNA expression. We show that tissue specificity was much stronger than developmental stage specificity in all of DNA methylation, chromatin accessibility, and gene expression. We identify 573 genes showing allele specific expression, including those influenced by parent-of-origin as well as allele genotype effects. We integrate methylation, chromatin accessibility, and gene expression data to show that allele specific expression can be explained in great part by allele specific methylation and/or chromatin accessibility. This study provides a comprehensive characterization of regulatory variation across multiple tissues and developmental stages in pigs.

The present study sought to assess the effects of manganese complexes with lysine and glutamic acid (Mn-LG) as manganese (Mn) sources on growth performance, trace element deposition, antioxidant capacity, and metacarpal strength in weaned piglets. The study involved 288 healthy Duroc x Landrace x Yorkshire piglets that were weaned at 25 to 28 d of age and weighed 8.66 +/- 0.96 kg. These piglets were randomly divided into six groups: a control group (Mn-LG-0, receiving a basal diet without Mn supplementation), a Mn sulfate group (basal diet supplemented with 40 mgkg(-1) diet of Mn, Mn-S-40 group), and four Mn-LG groups (Mn-LG-20, Mn-LG-40, Mn-LG-60, Mn-LG-80, supplemented with 20, 40, 60, and 80 mgkg(-1) Mn from Mn-LG in the basal diet). Grouping began at weaning on the 0th day of the experiment. The corn-soybean-based basal diet during the early (days 0 to 14) and late (days 15 to 42) phases of the experiment contained 20.88 and 30.12 mgkg(-1) Mn, respectively. Blood samples were collected on days 14 and 42, and pigs were sacrificed for sample collection on day 42. The results indicated no significant differences in average daily gain, average daily feed intake, or feed-to-gain ratio among the groups (P > 0.05). The diarrhea rates of all Mn-LG groups and the Mn-S-40 group were significantly lower in the 0 to 14 d and during the entire experimental period than in the Mn-LG-0 group (P < 0.001). The Mn-LG-40 group exhibited a significant increase in liver Mn concentration and serum Mn superoxide dismutase (Mn-SOD) activity on day 42 (P < 0.01), as well as a significant decrease in fecal Mn concentration (P < 0.05), compared to those of the Mn-S-40 group. Significant differences (P < 0.05) were detected in the serum, liver, and fecal Mn concentrations, as well as in the serum and liver Mn-SOD activity, across the different Mn-LG groups. The serum and fecal Mn concentrations and serum Mn-SOD activity increased linearly or quadratically (P < 0.01) with increasing Mn-LG supplementation. No significant differences (P > 0.05) were found in kidney, heart, or metacarpal bone Mn concentrations or in bone strength indices. In summary, compared with the Mn-LG-0 diet, dietary supplementation with Mn-LG enhanced serum Mn deposition and Mn-SOD activity and decreased the incidence of diarrhea. Additionally, the fecal Mn concentration was lower in the Mn-LG group than in the inorganic group at equivalent dosages. This research explored the effects of a manganese complex containing lysine and glutamic acid (Mn-LG) on various health parameters in weaned piglets. Utilizing samples of 288 piglets, the study investigated how Mn-LG supplementation influences growth performance, Mn deposition and emission, antioxidant capacity, and metacarpal strength. Key findings include an increase in serum Mn levels and Mn superoxide dismutase (Mn-SOD) activity, a reduction in diarrhea incidence, and no significant effects in bone strength indices in piglets receiving Mn-LG. Additionally, the fecal Mn concentration was notably lower in the Mn-LG group than in the group receiving inorganic Mn at equivalent dosages.

IntroductionPlant carbon black (PCB) is a new feed additive for zearalenone adsorption in China. However, information regarding whether PCB can effectively absorb deoxynivalenol (DON) is limited.MethodsTo explore this research gap, the present study examined the adsorption effectiveness of DON by PCB using a phosphate buffer, artificial gastric juice, and artificial intestinal juice. In a 21-day in vivo trial, 48 male piglets were randomly assigned to four treatment groups: (1) uncontaminated basal diet (CTR), (2) basal diet supplemented with 1 mg/kg PCB(PCB), (3) 2.3 mg/kg DON-contaminated diet (DON), and (4) 2.3 mg/kg DON-contaminated diet supplemented with 0.1% PCB (DON+PCB).ResultsWhen DON concentration was 1 µg/mL, the adsorption rate of PCB on DON in phosphate buffer systems (pH 2.0 and 6.0) and the artificial gastric and intestinal juices were 100%, 100%, 71.46%, and 77.20%, respectively. In the in vivo trial, the DON group significantly increased the DON+deepoxy-deoxynivalenol (DOM-1) content in serum as well as the inflammation cytokine proteins (interleukin-6, interleukin-8, and tumor necrosis factor-α) and mRNA expression of interleukin-6 and longchain acyl-CoA synthetase 4 in the jejunum and ileum. It decreased the villus height, goblet cells, mucosal thickness, and mRNA expression of Claudin-1 compared to the CTR group. In addition, DON decreased the Shannon and Simpson indices; reduced the relative abundances of Firmicutes, Lactobacillus, Candidatus_Saccharimonas, and Ruminococcus; and increased the relative abundances of Terrisporobacter and Clostridium_sensu_stricto_1 in the cecal content.DiscussionIn conclusion, these results suggest that PCB showed high adsorption efficacy on DON in vitro, and exhibit the protective effects against various intestinal toxicity manifestations in DON-challenged piglets.

Body conformation is the most direct production index, which can fully reflect pig growth status and is closely related to critical economic traits. In this study, we conducted a genome-wide association study (GWAS) on body conformation traits in a population of 1518 Duroc × (Landrace × Yorkshire) commercial pigs. These traits included body length (BL), body height (BH), chest circumference (CC), abdominal circumference (AC), and waist circumference (WC). Both the mixed linear model (MLM) and fixed and random model circulating probability unification (FarmCPU) approaches were employed for the analysis. Our findings revealed 60 significant single nucleotide polymorphisms (SNPs) associated with these body conformation traits in the crossbred pig population. Specifically, sixteen SNPs were significantly associated with BL, three SNPs with BH, thirteen SNPs with CC, twelve SNPs with AC, and sixteen SNPs with WC. Moreover, we identified several promising candidate genes located within the genomic regions associated with body conformation traits. These candidate genes include INTS10, KIRREL3, SOX21, BMP2, MAP4K3, SOD3, FAM160B1, ATL2, SPRED2, SEC16B, and RASAL2. Furthermore, our analysis revealed a novel significant quantitative trait locus (QTL) on SSC7 specifically associated with waist circumference, spanning an 84 kb interval. Overall, the identification of these significant SNPs and potential candidate genes in crossbred commercial pigs enhances our understanding of the genetic basis underlying body conformation traits. Additionally, these findings provide valuable genetic resources for pig breeding programs.

The number of teats is a crucial reproductive trait with significant economic implications on maternal capacity and litter size. Consequently, improving this trait is essential to facilitate genetic selection for increased litter size. In this study, we performed a genome-wide association study (GWAS) of the number of teats in a three-way crossbred commercial Duroc × (Landrace × Yorkshire) (DLY) pig population comprising 1518 animals genotyped with the 50K BeadChip. Our analysis identified crucial quantitative trait loci (QTL) for the number of teats, containing the ABCD4 and VRTN genes on porcine chromosome 7. Our results establish SNP variants of ABCD4 and VRTN as new molecular markers for improving the number of teats in DLY pigs. Furthermore, the most significant noteworthy single nucleotide polymorphism (SNP) (7_97568284) was identified within the ABCD4 gene, exhibiting a significant association with the total teat number traits. This SNP accounted for a substantial proportion of the genetic variance, explaining 6.64% of the observed variation. These findings reveal a novel gene on SSC7 for the number of teats and provide a deeper understanding of the genetic mechanisms underlying reproductive traits.

Genetic mapping to identify genes and alleles associated with or causing economically important quantitative trait variation in livestock animals such as pigs is a major goal in animal genetic improvement. Despite recent advances in high-throughput genotyping technologies, the resolution of genetic mapping in pigs remains poor due in part to the low density of genotyped variant sites. In this study, we overcame this limitation by developing a reference haplotype panel for pigs based on 2259 whole genome-sequenced animals representing 44 pig breeds. We evaluated software combinations and breed composition to optimize the imputation procedure and achieved an average concordance rate in excess of 96%, a non-reference concordance rate of 88%, and an r2 of 0.85. We demonstrated in two case studies that genotype imputation using this resource can dramatically improve the resolution of genetic mapping. A public web server has been developed to allow the pig genetics community to fully utilize this resource. We expect this resource to facilitate genetic mapping and accelerate genetic improvement in pigs.

Pigeons (Columba livia) are among a select few avian species that have developed a specialized reproductive mode wherein the parents produce a 'milk' in their crop to feed newborn squabs. Nonetheless, the transcriptomic dynamics and role in the rapid transition of core crop functions during 'lactation' remain largely unexplored. Here, we generated a de novo pigeon genome assembly to construct a high resolution spatio-temporal transcriptomic landscape of the crop epithelium across the entire breeding stage. This multi-omics analysis identified a set of 'lactation'-related genes involved in lipid and protein metabolism, which contribute to the rapid functional transitions in the crop. Analysis of in situ high-throughput chromatin conformation capture (Hi-C) sequencing revealed extensive reorganization of promoter-enhancer interactions linked to the dynamic expression of these 'lactation'-related genes between stages. Moreover, their expression is spatially localized in specific epithelial layers, and can be correlated with phenotypic changes in the crop. These results illustrate the preferential de novo synthesis of 'milk' lipids and proteins in the crop, and provides candidate enhancer loci for further investigation of the regulatory elements controlling pigeon 'lactation'.

Internal organ weight is an essential indicator of growth status as it reflects the level of growth and development in pigs. However, the associated genetic architecture has not been well explored because phenotypes are difficult to obtain. Herein, we performed single-trait and multi-trait genome-wide association studies (GWASs) to map the genetic markers and genes associated with six internal organ weight traits (including heart weight, liver weight, spleen weight, lung weight, kidney weight, and stomach weight) in 1518 three-way crossbred commercial pigs. In summation, single-trait GWASs identified a total of 24 significant single- nucleotide polymorphisms (SNPs) and 5 promising candidate genes, namely, TPK1, POU6F2, PBX3, UNC5C, and BMPR1B, as being associated with the six internal organ weight traits analyzed. Multi-trait GWAS identified four SNPs with polymorphisms localized on the APK1, ANO6, and UNC5C genes and improved the statistical efficacy of single-trait GWASs. Furthermore, our study was the first to use GWASs to identify SNPs associated with stomach weight in pigs. In conclusion, our exploration of the genetic architecture of internal organ weights helps us better understand growth traits, and the key SNPs identified could play a potential role in animal breeding programs.