Regulatory sequences and transposable elements(TEs)account for a large proportion of the genomic sequences of species;however,their roles in gene transcription,especially tissue-specific expression,remain largely unkn...Regulatory sequences and transposable elements(TEs)account for a large proportion of the genomic sequences of species;however,their roles in gene transcription,especially tissue-specific expression,remain largely unknown.Pigs serve as an excellent animal model for studying genomic sequence biology due to the extensive diversity among their wild and domesticated populations.Here,we conducted an integrated analysis using H3K27ac ChIP-seq,H3K4me3 ChIP-seq,and RNA-seq data from 10 different tissues of seven fetuses and eight closely related adult pigs.We aimed to annotate the regulatory elements and TEs to elucidate their associations with histone modifications and mRNA expression across different tissues and developmental stages.Based on correlation analysis between mRNA expression and H3K27ac and H3K4me3 peak activity,results indicated that H3K27ac exhibited stronger associations with gene expression than H3K4me3.Furthermore,1.45%of TEs overlapped with either the H3K27ac or H3K4me3 peaks,with the majority displaying tissue-specific activity.Notably,a TE subfamily(LTR4C_SS),containing binding motifs for SIX1 and SIX4,showed specific enrichment in the H3K27ac peaks of the adult and fetal ovaries.RNA-seq analysis also revealed widespread expression of TEs in the exons or promoters of genes,including 4688 TE-containing transcripts with distinct development stage-specific and tissue-specific expression.Of note,1967 TE-containing transcripts were enriched in the testes.We identified a long terminal repeat(LTR),MLT1F1,acting as a testis-specific alternative promoter in SRPK2(a cell cycle-related protein kinase)in our pig dataset.This element was also conserved in humans and mice,suggesting either an ancient integration of TEs in genes specifically expressed in the testes or parallel evolutionary patterns.Collectively,our findings demonstrate that TEs are deeply embedded in the genome and exhibit important tissue-specific biological functions,particularly in the reproductive organs.展开更多
Fragrance pig is a famous miniature local breed in China,which is similar to human on the aspects of physical structure,anatomy,nutrition,metabolism and blood biochemical indicators. The internal organs of Congjiang f...Fragrance pig is a famous miniature local breed in China,which is similar to human on the aspects of physical structure,anatomy,nutrition,metabolism and blood biochemical indicators. The internal organs of Congjiang fragrance pig and Huanjiang fragrance pig with different month ages were weighed. The results showed that the proportion of stomach in body weight in Congjiang fragrance pig was higher than that in Min pig,Harbin white and Landrace,and the proportion of large intestine in body weight in Congjiang fragrance pig was also higher than that in ordinary pigs; the weights of heart,liver and kidney in 8- 10 months old Congjiang fragrance pig were similar to that in Chinese adults. This provided reference data for future in-depth development and utilization of fragrance pig.展开更多
Autoimmunity is believed to develop when genetically predisposed individuals undergo epigenetic modifcations in response to environmental factors. Recent advances in the understanding of epigenetic mechanisms suggest,...Autoimmunity is believed to develop when genetically predisposed individuals undergo epigenetic modifcations in response to environmental factors. Recent advances in the understanding of epigenetic mechanisms suggest, in autoimmune diseases, a multi-step process involving environmental factors (e.g. , drugs, stress) and endogenous factors (e.g. , cytokines, gender), both leading to the deregulation of the epigenetic machinery (DNA methylation, histone modifications, miRNA), that in turn specifically affects the immune system and/or the target organ(s). Such effect is reinforced in those patients with risk variants mapping to epigenetically-controlled regulators of immune cells. As a consequence, autoreactive lymphocytes and autoantibodies are produced leading to the development of the autoimmune disease. Potential new therapeutic strategies and biomarkers are also addressed.展开更多
Background:N6-methyladenosine(m^(6)A)and DNA 5-methylcytosine(5mC)methylation plays crucial roles in diverse biological processes,including skeletal muscle development and growth.Recent studies unveiled a potential li...Background:N6-methyladenosine(m^(6)A)and DNA 5-methylcytosine(5mC)methylation plays crucial roles in diverse biological processes,including skeletal muscle development and growth.Recent studies unveiled a potential link between these two systems,implicating the potential mechanism of coordinated transcriptional and post-transcrip-tional regulation in porcine prenatal myogenesis and postnatal skeletal muscle growth.Methods:Immunofluorescence and co-IP assays were carried out between the 5mC writers and m^(6)A writers to investigate the molecular basis underneath.Large-scale in-house transcriptomic data were compiled for applying weighted correlation network analysis(WGCNA)to identify the co-expression patterns of m^(6)A and 5mC regulators and their potential role in pig myogenesis.Whole-genome bisulfite sequencing(WGBS)and methylated RNA immu-noprecipitation sequencing(MeRIP-seq)were performed on the skeletal muscle samples from Landrace pigs at four postnatal growth stages(days 30,60,120 and 180).Results:Significantly correlated expression between 5mC writers and m^(6)A writers and co-occurrence of 5mC and m^(6)A modification were revealed from public datasets of C2C12 myoblasts.The protein-protein interactions between the DNA methylase and the m^(6)A methylase were observed in mouse myoblast cells.Further,by analyzing tran-scriptome data comprising 81 pig skeletal muscle samples across 27 developmental stages,we identified a 5mC/m^(6)A epigenetic module eigengene and decoded its potential functions in pre-or post-transcriptional regulation in postnatal skeletal muscle development and growth of pigs.Following integrative multi-omics analyses on the WGBS methylome data and MeRIP-seq data for both m^(6)A and gene expression profiles revealed a genome/transcriptome-wide correlated dynamics and co-occurrence of 5mC and m^(6)A modifications as a consequence of 5mC/m^(6)A crosstalk in the postnatal myogenesis progress of pigs.Last,we identified a group of myogenesis-related genes collaboratively regulated by both 5mC and m^(6)A modifications in postnatal skeletal muscle growth in pigs.Conclusions:Our study discloses a potential epigenetic mechanism in skeletal muscle development and provides a novel direction for animal breeding and drug development of related human muscle-related diseases.展开更多
Background: Fatness traits in animals are important for their growth, meat quality, reproductive performance, and immunity. The liver is the principal organ of the regulation of lipid metabolism, and this study used ...Background: Fatness traits in animals are important for their growth, meat quality, reproductive performance, and immunity. The liver is the principal organ of the regulation of lipid metabolism, and this study used massive parallelized high-throughput sequencing technologies to determine the porcine liver tissue transcriptome architecture of two full-sibling Songliao black pigs harboring extremely different phenotypes of backfat thickness. Results: The total number of reads produced for each sample was in the region of 53 million, and 8,226 novel transcripts were detected. Approximately 92 genes were differentially regulated in the liver tissue, while 31 spliced transcripts and 33 primary transcripts showed significantly differential expression between pigs with higher and lower backfat thickness. Genes that were differentially expressed were involved in the metabolism of various substances, smal molecule biochemistry, and molecular transport. Conclusions: Genes involved in the regulation of iipids could play an important role in lipid and fatty acid metabolism in the liver. These results could help us understand how liver metabolism affects the backfat thickness of pigs.展开更多
Background:Previous studies have shown that exogenous short-chain fatty acids(SCFAs)introduction attenuated the body fat deposition in conventional mice and pigs.However,limited studies have evaluated the effects of e...Background:Previous studies have shown that exogenous short-chain fatty acids(SCFAs)introduction attenuated the body fat deposition in conventional mice and pigs.However,limited studies have evaluated the effects of exogenously introduced SCFAs on the lipid and glucose metabolism independently of the gut microbiota.This study was to investigate the effects of exogenous introduction of SCFAs on the lipid and glucose metabolism in a germ-free(GF)pig model.Methods:Twelve hysterectomy-derived newborn pigs were reared in six sterile isolators.All pigs were hand-fed with sterile milk powder for 21 d,then the sterile feed was introduced to pigs for another 21 d.In the second 21-d period,six pigs were orally administrated with 25 mL/kg sterile saline per day and considered as the GF group,while the other six pigs were orally administrated with 25 mL/kg SCFAs mixture(acetic,propionic,and butyric acids,45,15,and 11 mmol/L,respectively)per day and regarded as FA group.Results:Orally administrated with SCFAs tended to increase the adiponectin concentration in serum,enhance the CPT-1 activity in longissimus dorsi,and upregulate the ANGPTL4 mRNA expression level in colon(P<0.10).Meanwhile,the mRNA abundances of ACC,FAS,and SREBP-1C in liver and CD36 in longissimus dorsi of the FA group were decreased(P<0.05)compared with those in the GF group.Besides,the mRNA expression of PGC-1αin liver and LPL in longissimus dorsi tended to(P<0.10)upregulate and downregulate respectively in the FA group.Moreover,oral administration of SCFAs tended to increase the protein level of GPR43(P<0.10)and decrease the protein level of ACC(P<0.10)in liver.Also,oral administration of SCFAs upregulated the p-AMPK/AMPK ratio and the mRNA expressions of GLUT-2 and GYS2 in liver(P<0.05).In addition,the metabolic pathway associated with the biosynthesis of unsaturated fatty acids was most significantly promoted(P<0.05)by oral administration of SCFAs.Conclusions:Exogenous introduction of SCFAs might attenuate the fat deposition and to some extent improve the glucose control in the pig model,which occurred independently of the gut microbiota.展开更多
Background:Early-weaning of piglets is often accompanied by severe disorders,especially diarrhea.The gut microbiota and its metabolites play a critical role in the maintenance of the physiologic and metabolic homeosta...Background:Early-weaning of piglets is often accompanied by severe disorders,especially diarrhea.The gut microbiota and its metabolites play a critical role in the maintenance of the physiologic and metabolic homeostasis of the host.Our previous studies have demonstrated that oral administration of Lactobacillus frumenti improves epithelial barrier functions and confers diarrhea resistance in early-weaned piglets.However,the metabolic response to L.frumenti administration remains unclear.Then,we conducted simultaneous serum and hepatic metabolomic analyses in early-weaned piglets administered by L.frumenti or phosphatebuffered saline(PBS).Results:A total of 1006-day-old crossbred piglets(Landrace×Yorkshire)were randomly divided into two groups and piglets received PBS(sterile,2 m L)or L.frumenti(suspension in PBS,10~8 CFU/m L,2 m L)by oral administration once per day from 6 to 20 days of age.Piglets were weaned at 21 days of age.Serum and liver samples for metabolomic analyses were collected at 26 days of age.Principal components analysis(PCA)showed that L.frumenti altered metabolism in serum and liver.Numerous correlations(P<0.05)were identified among the serum and liver metabolites that were affected by L.frumenti.Concentrations of guanosine monophosphate(GMP),inosine monophosphate(IMP),and uric acid were higher in serum of L.frumenti administration piglets.Pathway analysis indicated that L.frumenti regulated fatty acid and amino acid metabolism in serum and liver.Concentrations of fatty acidβ-oxidation related metabolites in serum(such as3-hydroxybutyrylcarnitine,C4-OH)and liver(such as acetylcarnitine)were increased after L.frumenti administration.Conclusions:Our findings suggest that L.frumenti regulates lipid metabolism and amino acid metabolism in the liver of early-weaned piglets,where it promotes fatty acidβ-oxidation and energy production.High serum concentrations of nucleotide intermediates,which may be an alternative strategy to reduce the incidence of diarrhea in early-weaned piglets,were further detected.These findings broaden our understanding of the relationships between the gut microbiota and nutrient metabolism in the early-weaned piglets.展开更多
Background:Over the past years,antibiotic growth promoter had been restricted in animal husbandry production in many countries because of antimicrobial resistance and foodborne antibiotic residues.However,the problems...Background:Over the past years,antibiotic growth promoter had been restricted in animal husbandry production in many countries because of antimicrobial resistance and foodborne antibiotic residues.However,the problems of poor intestinal health and low growth efficiency of piglets have not been solved completely in an antibiotic-free diet,and it is urgent to explore alternatives to antimicrobial growth promoters.Methods:Here,a total of 532 weaned pigs were assigned to one of 4 treatments,the low amino acid(AA)level diet(d 1 to d 14 is 1.35%,d 15 to d 42 is 1.25%)(Low AA),the low AA level diet supplementation with a carvacrol-thymol blend(50 mg carvacrol and 50 mg thymol/kg of diet)(CB)(Low AA+CB),the high AA level diet(d 1 to d 14 is 1.50%,d 15 to d 42 is 1.40%)(High AA),and the high AA level diet supplementation with a CB(High AA+CB),respectively.Then we measured growth performance and intestinal health indicators of weaned pigs.Results:Results showed that high AA level significantly reduced plasma urea nitrogen,plasma Interleukin-6(IL-6)and fecal lipocalin-2 contents(P<0.05),significantly increased the relative abundance of fecal Lactobacillus and Enterococcus,and had a trend to increase the fecal secretory immunoglobulin A(sIgA)and mucin 2(MUC 2)contents(P<0.05)in piglets,thereby alleviating the diarrhea of piglets and reducing the feed conversion ratio(FCR)of piglets during d 1~14 after weaning.Dietary supplementation with CB significantly increased the activity of plasma antioxidant enzymes T-SOD and GSH-px(P<0.05),while significantly reduced plasma malondialdehyde(MDA),plasma interleukin-1β(IL-1β),plasma endotoxin and D-lactic acid contents(P<0.05).Meanwhile,CB significantly decreased fecal lipocalin-2 contents and the abundance of fecal Escherichia coli(P<0.05).Thus,we hypothesis that dietary supplementation with CB significantly increased the average daily gain(ADG)of piglets(P<0.05)during d 1~14 after weaning through promoting intestinal health.Conclusion:These results suggest that high AA level and dietary supplementation with CB improved the growth performance of weaned pigs in an antibiotic-free diet by improving AA metabolism and intestinal antioxidant capacity.展开更多
In an attempt to generate g.A746G substitution in the BMPR-IB gene,we unexpectedly obtained BMPR-IB homozygous knockout piglets(BMPR-IB^(-/-))and heterogeneous knockout piglets with one copy of the A746G mutation(BMPR...In an attempt to generate g.A746G substitution in the BMPR-IB gene,we unexpectedly obtained BMPR-IB homozygous knockout piglets(BMPR-IB^(-/-))and heterogeneous knockout piglets with one copy of the A746G mutation(BMPR-IB-/746G)via CRISPR/Cas9 editing.Polymerase chain reaction(PCR)and sequencing revealed complex genomic rearrangements in the target region.All BMPR-IBdisrupted piglets showed an inability to stand and walk normally.Both BMPR-IB^(-/-)and BMPR-IB-/746G piglets exhibited severe skeletal dysplasia characterized by distorted and truncated forearms(ulna,radius)and disordered carpal,metacarpal,and phalangeal bones in the forelimbs.The piglets displayed more severe deformities in the hindlimbs by visual inspection,including fibular hemimelia,enlarged tarsal bone,and disordered toe joint bones.Limb deformities were more profound in BMPR-IB^(-/-)piglets than in the BMPR-IB-/746G piglets.Proteomic analysis identified 139 differentially expressed proteins(DEPs)in the hindlimb fibula of BMPR-IB-/746G piglets compared to the wild-type(WT)controls.Most DEPs are involved in skeletal or embryonic development and/or the TGF-βpathway and tumor progression.Gene Ontology(GO)and protein domain enrichment analysis suggested alterations in these processes.Of the top 50 DEPs,a large proportion,e.g.,C1QA,MYO1H,SRSF1,P3H1,GJA1,TCOF1,RBM10,SPP2,MMP13,and PHAX,were significantly associated with skeletal development.Our study provides novel findings on the role of BMPR-IB in mammalian limb development.展开更多
In winter, the confined pig house of northern China is severe. The environment variables are nonlinear, time-varying and coupled, which seriously affect the health of pigs and the qualities of the meat. In order to so...In winter, the confined pig house of northern China is severe. The environment variables are nonlinear, time-varying and coupled, which seriously affect the health of pigs and the qualities of the meat. In order to solve the problem multi-variables coupling, a multi-variables decoupled fuzzy logic control method was proposed. Two fuzzy logic controllers were designed based on fuzzy logic theory. The fans, heaters and humidifiers were used to control temperature, humidity and ammonia. The reductions of temperature and humidity caused by ventilating were compensated by heaters and humidifiers respectively which realized the multivariables decoupling. The proposed methods were validated through theoretical, experimental and simulation analysis. The results suggested that the methods were able to regulate the confined pig house environment effectively. In addition, comparing to the manual regulation, the proposed methods could reduce 19% power consumption as well.展开更多
Follistatin(FST) is an important regulator of skeletal muscle growth and adipose deposition through its ability to bind to several members of the transforming growth factor-β(TGF-β) superfamily, and thus may be a go...Follistatin(FST) is an important regulator of skeletal muscle growth and adipose deposition through its ability to bind to several members of the transforming growth factor-β(TGF-β) superfamily, and thus may be a good candidate for future animal breeding programs. However, the molecular mechanisms underlying the phenotypic changes have yet to be clarified in pig. We generated transgenic(TG) pigs that express human FST specifically in skeletal muscle tissues and characterized the phenotypic changes compared with the same tissues in wild-type pigs. The TG pigs showed increased skeletal muscle growth, decreased adipose deposition, and improved metabolism status(P<0.05). Transcriptome analysis detected important roles of the PIK3–AKT signaling pathway, calcium-mediated signaling pathway, and amino acid metabolism pathway in FST-induced skeletal muscle hypertrophy, and depot-specific oxidative metabolism changes in psoas major muscle. Furthermore, the lipid metabolism-related process was changed in adipose tissue in the TG pigs. Gene set enrichment analysis revealed that genes related to lipid synthesis, lipid catabolism, and lipid storage were down-regulated(P<0.01) in the TG pigs for subcutaneous fat, whereas genes related to lipid catabolism were significantly up-regulated(P<0.05) in the TG pigs for retroperitoneal fat compared with their expression levels in wild-type pigs. In liver, genes related to the TGF-β signaling pathway were over-represented in the TG pigs, which is consistent with the inhibitory role of FST in regulating TGF-β signaling. Together, these results provide new insights into the molecular mechanisms underlying the phenotypic changes in pig.展开更多
[ Objective] To study the effects of different oligosaccharides on immunity and production performance of piglets.[ Method] A total of 75 Yorkshire x Rongchang piglets were assigned into five groups, 15 in each group....[ Objective] To study the effects of different oligosaccharides on immunity and production performance of piglets.[ Method] A total of 75 Yorkshire x Rongchang piglets were assigned into five groups, 15 in each group. Isomalto-oligosaccharide ( IMO), fructo-oligosaccharide ( FOS), mannan-oligosacchadde (MOS), and mixed oligosacchadde were supplemented to basal diet (7.5 g/kg), respectively. The control group was also set. The experimental period lasted for 53 d. The clinic symptoms and diarrhea were observed. All piglets were weighed once a week. Feed intake was also recorded. Blood was collected via precaval vein for determination of immunology indexes at the age of 30 and 60 d, respectively. [ Result] The IMO and FOS enhanced cellular immunity of 30-day-old piglets significantly (P 〈 0.05), and the IMO also enhanced their humoral immunity. The MOS enhanced cellular immunity and humoral immunity of 60-day-old piglets significantly (P 〈 0.05). It also improved production performance largest, and its diarrhea rate was the lowest. [ Conclusion] Different oligosaccharides have various effects on immunity and production performance of oiolets.展开更多
Imprinted genes play significant roles in the regulation of fetal growth, development, function of the placenta and postnatal behavior in mammals, but little is known in pigs. In order to investigate the imprinting st...Imprinted genes play significant roles in the regulation of fetal growth, development, function of the placenta and postnatal behavior in mammals, but little is known in pigs. In order to investigate the imprinting status of porcine retro-transposon like 1 (RTL1) and type 3 iodothyronine deiodinase (DIO3) genes, DNA or RNA samples of the parents and F1 animals, generated with reciprocal crosses between Large White and Meishan breeds, were isolated, and analyzed by reverse transcription polymerase chain reaction restriction fragment length polymorphism (RT-PCR-RFLP). The results demonstrated that the RTL1 gene was paternally expressed in 10 tissues, such as the skeletal muscle, heart, spleen, liver, kidney, lung, stomach, fat, small intestine and brain, and D103 gene exhibited paternal expression in the skeletal muscle, heart, spleen, lung, stomach, and brain, in 2-month-old pigs. The association of RTL1 and DI03 with carcass traits was further analyzed in the F2 population of Large White×Meishan pigs. The statistical results showed that the R TL1 A1101G polymorphism (EU781029) was significantly associated with lean meat percentage (LMP) and fat meat percentage (FMP) (P〈0.05), while the D103 A744C polymorphism (AY533208) was not significantly associated with any carcass traits. These results indicate that the imprinting status of RTL1 and DIO3 is well kept across the mammalian species, and porcine RTL1 may have important roles in muscle growth and fat deposition.展开更多
DNA methyltransferases(Dnmts)comprise a family of proteins which involved in the establishment and maintenance of DNA methylation patterns.In pig,the molecular characterization and tissue expression profile of Dnmt ...DNA methyltransferases(Dnmts)comprise a family of proteins which involved in the establishment and maintenance of DNA methylation patterns.In pig,the molecular characterization and tissue expression profile of Dnmt gene family are not clear.To solve this problem,reverse transcriptase PCR and rapid amplification of c DNA ends were used to clone the sequences of the porcine Dnmt2 and Dnmt3b genes.Furthermore,the m RNA expression profiles of Dnmt1,Dnmt2,Dnmt3a and Dnmt3b genes from 54 adult tissues and 2 entire fetuses of Rongchang pig were analyzed by quantitative real-time PCR(q RT-PCR).As a result,the lengths of porcine Dnmt2 and Dnmt3b gene c DNAs were 1 227 and 2 559 bp with cytosine-C5specific DNA methylase domain,respectively.The four Dnmt genes were highly expressed in longissimus dorsi muscle(P〈0.01).Dnmt1 is highly expressed in heart(P〈0.01)and Dnmt 2 shows its preference in liver and seminal vesicle tissue(P〈0.01).Dnmt3a and Dnmt3b are highly expressed in the two fetus stages(P〈0.01).All these results suggested that each gene has its specific expression profile,and deeper study is required to dig more details between the methylation level and Dnmt family m RNA expressions in different tissues.展开更多
Background:Short tandem repeats(STRs)were recently found to have significant impacts on gene expression and diseases in humans,but their roles on gene expression and complex traits in pigs remain unexplored.This study...Background:Short tandem repeats(STRs)were recently found to have significant impacts on gene expression and diseases in humans,but their roles on gene expression and complex traits in pigs remain unexplored.This study investigates the effects of STRs on gene expression in liver tissues based on the whole-genome sequences and RNA-Seq data of a discovery cohort of 260 F6 individuals and a validation population of 296 F7 individuals from a heterogeneous population generated from crosses among eight pig breeds.Results:We identified 5203 and 5868 significantly expression STRs(eSTRs,FDR<1%)in the F6 and F7 populations,respectively,most of which could be reciprocally validated(π1=0.92).The eSTRs explained 27.5%of the cisheritability of gene expression traits on average.We further identified 235 and 298 fine-mapped STRs through the Bayesian fine-mapping approach in the F6 and F7 pigs,respectively,which were significantly enriched in intron,ATAC peak,compartment A and H3K4me3 regions.We identified 20 fine-mapped STRs located in 100 kb windows upstream and downstream of published complex trait-associated SNPs,which colocalized with epigenetic markers such as H3K27ac and ATAC peaks.These included eSTR of the CLPB,PGLS,PSMD6 and DHDH genes,which are linked with genome-wide association study(GWAS)SNPs for blood-related traits,leg conformation,growth-related traits,and meat quality traits,respectively.Conclusions:This study provides insights into the effects of STRs on gene expression traits.The identified eSTRs are valuable resources for prioritizing causal STRs for complex traits in pigs.展开更多
Pork cutting is a very important processing in promoting economic appreciation across the swine business chain. The goal of this research is to determine the proportion and weight of meat cuts, as well as to analyze t...Pork cutting is a very important processing in promoting economic appreciation across the swine business chain. The goal of this research is to determine the proportion and weight of meat cuts, as well as to analyze the effects of carcass weight, sex and breed composition on meat cuts. Simultaneously, we investigate the correlation between meat cuts, carcass traits and meat quality traits. To assess 17 meat cut traits, 12 carcass traits and 6 meat quality traits, we sample 2 012 pigs from four breeds, including Landrace(LD), Yorkshire(YK), Landrace Yorkshire(LY), and Duroc Landrace Yorkshire(DLY). The results showed that carcass weight, sex and breed composition have significant effects on the weight and proportion of most meat cuts. The proportion of cuts for muscle and bone decrease as carcass weight grows, whereas the proportion of cuts for fat increases. Moreover, the thickness of four-point backfat was significantly increasing(P<0.001) with increase of carcass weights, indicating that large amount of intaking energy in the late finishing stage was used for fat deposition. Besides, the proportion of Shoulder cut(SC) and Back fat(BF) in barrows was significantly higher(P<0.001) than that in sows, whereas the Leg cut(LC) showed the opposite trend. The Loin(LO) proportion and Loin muscle area(LMA) of barrows were significantly lower(P<0.001), but the proportion of fat areas in the image(PFAI) and visual marbling score(VMS) were significantly higher(P<0.001) than those of sows, respectively. In terms of breeds, LD had the longest straight carcass length, significantly longer(P<0.001) than the other three breeds, which partially explains why LD had the largest proportion of the Middle cut(MC). Moreover, the proportion of SC in DLY was the highest. Last but not least, the correlations between the proportions of most meat cuts, and also between meat cuts and meat quality or carcass traits were low or not significant(P>0.05). The effects of carcass weight, sex and breed composition on the meat cuts, meat quality and carcass traits are breed and growth stage dependent. It also reflects the asynchrony of the growth curve between different sexes. Our results laid an important foundation for breeding pig carcass cuts and composition.展开更多
Background:A comprehensive landscape of chromatin states for multiple mammalian tissues is essential for elucidating the molecular mechanism underlying regulatory variants on complex traits.However,the genome-wide chr...Background:A comprehensive landscape of chromatin states for multiple mammalian tissues is essential for elucidating the molecular mechanism underlying regulatory variants on complex traits.However,the genome-wide chromatin accessibility has been only reported in limited tissue types in pigs.Results:Here we report a genome-wide landscape of chromatin accessibility of 20 tissues in two female pigs at ages of 6 months using ATAC-seq,and identified 557,273 merged peaks,which greatly expanded the pig regulatory ele-ment repository.We revealed tissue-specific regulatory elements which were associated with tissue-relevant biologi-cal functions.We identified both positive and negative significant correlations between the regulatory elements and gene transcripts,which showed distinct distributions in terms of their strength and distances from corresponding genes.We investigated the presence of transposable elements(TEs)in open chromatin regions across all tissues,these included identifications of porcine endogenous retroviruses(PERVs)exhibiting high accessibility in liver and homology of porcine specific virus sequences to universally accessible transposable elements.Furthermore,we prior-itized a potential causal variant for polyunsaturated fatty acid in the muscle.Conclusions:Our data provides a novel multi-tissues accessible chromatin landscape that serve as an important resource for interpreting regulatory sequences in tissue-specific and conserved biological functions,as well as regula-tory variants of loci associated with complex traits in pigs.展开更多
Pasteurella multocida is a leading cause of respiratory disorders in pigs.This study was designed to understand the genotypical and antimicrobial resistant characteristics of P.multocida from pigs in China.To achieve ...Pasteurella multocida is a leading cause of respiratory disorders in pigs.This study was designed to understand the genotypical and antimicrobial resistant characteristics of P.multocida from pigs in China.To achieve this,we briefly investigated 158 P.multocida isolates from pigs with respiratory disorders in China between 2019 and 2020.Genotyping through multiplex PCR assays assigned these 158 isolates into capsular genotypes A(60.13%,95/158),D(35.44%,56/158),F(4.43%,7/158),and/or lipopolysaccharide(LPS)genotypes L3(28.48%,45/158)and L6(66.46%,105/158).In addition,eight isolates(5.06%,8/158)were found to be nontypable using the LPS genotyping method.When combining the capsular genotypes and the LPS genotypes,D:L6(34.81%,55/158)and A:L6(31.65%,50/158)were the predominant genotypes,followed by A:L3(24.05%,38/158).PCR detection of virulence factor-encoding genes showed that over 80%of the isolates were positive for exbB,tonB,exbD,ompH,ptfA,fimA,sodA,sodC,fur,ompA,oma87,plpB,hsf-2,nanH and hgbB,suggesting the presence of these genes were broad characteristics of P.multocida.We also found approximately 63.92%(101/158),51.27%(81/158),8.86%(14/158),7.59%(12/158),3.16%(5/158),0.63%(1/158),and 0.63%(1/158)of the isolates grew well in media with the presence of colistin(4μg/mL),tetracycline(16μg/mL),tigecycline(1μg/mL),ampicillin(32μg/mL),chloramphenicol(32μg/mL),cefepime(16μg/mL),and ciprofloxacin(1μg/mL),respectively.This study contributes to the understanding of genotypes and antimicrobial resistance profile of P.multocida currently circulation in pigs of China.展开更多
Homeobox A10(Hoxa10) gene is one of the most important candidate genes associated with the reproductive performance of humans and mice. Overexpression of Hoxa10 in mouse endometrium can increase litter size. Moreover,...Homeobox A10(Hoxa10) gene is one of the most important candidate genes associated with the reproductive performance of humans and mice. Overexpression of Hoxa10 in mouse endometrium can increase litter size. Moreover, Hoxa10 plays a key role in regulating the embryo implantation of sows. This study aimed to generate transgenic pigs using Hoxa10 via somatic cell nuclear transfer(SCNT). We established seven Hoxa10-transgenic cell lines, and two of the cell lines were selected as nuclear donors for the transfer. A total of 1 270 cloned embryos were generated and transferred to five surrogate mothers(Landrace×Yorkshire). Eight cloned male piglets were produced including one with cryptorchidism. Six transgenic piglets grew up healthy and produced 56 offspring. Finally, we obtained six transgenic male pigs and 26 transgenic positive offspring that can be used to further study the regulatory mechanism of Hoxa10 on the reproductive performance of pigs.展开更多
基金supported by the National Natural Science Foundation of China(32160781)。
文摘Regulatory sequences and transposable elements(TEs)account for a large proportion of the genomic sequences of species;however,their roles in gene transcription,especially tissue-specific expression,remain largely unknown.Pigs serve as an excellent animal model for studying genomic sequence biology due to the extensive diversity among their wild and domesticated populations.Here,we conducted an integrated analysis using H3K27ac ChIP-seq,H3K4me3 ChIP-seq,and RNA-seq data from 10 different tissues of seven fetuses and eight closely related adult pigs.We aimed to annotate the regulatory elements and TEs to elucidate their associations with histone modifications and mRNA expression across different tissues and developmental stages.Based on correlation analysis between mRNA expression and H3K27ac and H3K4me3 peak activity,results indicated that H3K27ac exhibited stronger associations with gene expression than H3K4me3.Furthermore,1.45%of TEs overlapped with either the H3K27ac or H3K4me3 peaks,with the majority displaying tissue-specific activity.Notably,a TE subfamily(LTR4C_SS),containing binding motifs for SIX1 and SIX4,showed specific enrichment in the H3K27ac peaks of the adult and fetal ovaries.RNA-seq analysis also revealed widespread expression of TEs in the exons or promoters of genes,including 4688 TE-containing transcripts with distinct development stage-specific and tissue-specific expression.Of note,1967 TE-containing transcripts were enriched in the testes.We identified a long terminal repeat(LTR),MLT1F1,acting as a testis-specific alternative promoter in SRPK2(a cell cycle-related protein kinase)in our pig dataset.This element was also conserved in humans and mice,suggesting either an ancient integration of TEs in genes specifically expressed in the testes or parallel evolutionary patterns.Collectively,our findings demonstrate that TEs are deeply embedded in the genome and exhibit important tissue-specific biological functions,particularly in the reproductive organs.
文摘Fragrance pig is a famous miniature local breed in China,which is similar to human on the aspects of physical structure,anatomy,nutrition,metabolism and blood biochemical indicators. The internal organs of Congjiang fragrance pig and Huanjiang fragrance pig with different month ages were weighed. The results showed that the proportion of stomach in body weight in Congjiang fragrance pig was higher than that in Min pig,Harbin white and Landrace,and the proportion of large intestine in body weight in Congjiang fragrance pig was also higher than that in ordinary pigs; the weights of heart,liver and kidney in 8- 10 months old Congjiang fragrance pig were similar to that in Chinese adults. This provided reference data for future in-depth development and utilization of fragrance pig.
基金Supported by The"Région Bretagne",the"Association Franaise Gougerot-Sjgren et des Syndromes Secs"the"Institut Franais pour la Recherche Odontologique"+1 种基金the Innovative Medicines Initiative Joint Undertaking under grant agreement n°115565,resources of which are composed of financial contribution from the European Union’s Seventh Framework Programme(FP7/2007-2013)EFPIA companies’ in-kind contribution
文摘Autoimmunity is believed to develop when genetically predisposed individuals undergo epigenetic modifcations in response to environmental factors. Recent advances in the understanding of epigenetic mechanisms suggest, in autoimmune diseases, a multi-step process involving environmental factors (e.g. , drugs, stress) and endogenous factors (e.g. , cytokines, gender), both leading to the deregulation of the epigenetic machinery (DNA methylation, histone modifications, miRNA), that in turn specifically affects the immune system and/or the target organ(s). Such effect is reinforced in those patients with risk variants mapping to epigenetically-controlled regulators of immune cells. As a consequence, autoreactive lymphocytes and autoantibodies are produced leading to the development of the autoimmune disease. Potential new therapeutic strategies and biomarkers are also addressed.
基金supported by the Agricultural Science and Technology Innovation Program and The Elite Young Scientists Program of CAAS.ZT was supported by the National Natural Science Foundation of China(31830090)the Basic and Applied Basic Research Foundation of Guangdong province(2019B1515120059)+1 种基金the Shenzhen Dapeng New District Special Fund for Industry Development(KY20180114)the Agricultural Science and Technology Innovation Program(CAAS-ZDRW202006).
文摘Background:N6-methyladenosine(m^(6)A)and DNA 5-methylcytosine(5mC)methylation plays crucial roles in diverse biological processes,including skeletal muscle development and growth.Recent studies unveiled a potential link between these two systems,implicating the potential mechanism of coordinated transcriptional and post-transcrip-tional regulation in porcine prenatal myogenesis and postnatal skeletal muscle growth.Methods:Immunofluorescence and co-IP assays were carried out between the 5mC writers and m^(6)A writers to investigate the molecular basis underneath.Large-scale in-house transcriptomic data were compiled for applying weighted correlation network analysis(WGCNA)to identify the co-expression patterns of m^(6)A and 5mC regulators and their potential role in pig myogenesis.Whole-genome bisulfite sequencing(WGBS)and methylated RNA immu-noprecipitation sequencing(MeRIP-seq)were performed on the skeletal muscle samples from Landrace pigs at four postnatal growth stages(days 30,60,120 and 180).Results:Significantly correlated expression between 5mC writers and m^(6)A writers and co-occurrence of 5mC and m^(6)A modification were revealed from public datasets of C2C12 myoblasts.The protein-protein interactions between the DNA methylase and the m^(6)A methylase were observed in mouse myoblast cells.Further,by analyzing tran-scriptome data comprising 81 pig skeletal muscle samples across 27 developmental stages,we identified a 5mC/m^(6)A epigenetic module eigengene and decoded its potential functions in pre-or post-transcriptional regulation in postnatal skeletal muscle development and growth of pigs.Following integrative multi-omics analyses on the WGBS methylome data and MeRIP-seq data for both m^(6)A and gene expression profiles revealed a genome/transcriptome-wide correlated dynamics and co-occurrence of 5mC and m^(6)A modifications as a consequence of 5mC/m^(6)A crosstalk in the postnatal myogenesis progress of pigs.Last,we identified a group of myogenesis-related genes collaboratively regulated by both 5mC and m^(6)A modifications in postnatal skeletal muscle growth in pigs.Conclusions:Our study discloses a potential epigenetic mechanism in skeletal muscle development and provides a novel direction for animal breeding and drug development of related human muscle-related diseases.
基金financially supported by the innovation research team for modern agricultural industry and technology in Beijing
文摘Background: Fatness traits in animals are important for their growth, meat quality, reproductive performance, and immunity. The liver is the principal organ of the regulation of lipid metabolism, and this study used massive parallelized high-throughput sequencing technologies to determine the porcine liver tissue transcriptome architecture of two full-sibling Songliao black pigs harboring extremely different phenotypes of backfat thickness. Results: The total number of reads produced for each sample was in the region of 53 million, and 8,226 novel transcripts were detected. Approximately 92 genes were differentially regulated in the liver tissue, while 31 spliced transcripts and 33 primary transcripts showed significantly differential expression between pigs with higher and lower backfat thickness. Genes that were differentially expressed were involved in the metabolism of various substances, smal molecule biochemistry, and molecular transport. Conclusions: Genes involved in the regulation of iipids could play an important role in lipid and fatty acid metabolism in the liver. These results could help us understand how liver metabolism affects the backfat thickness of pigs.
基金study was supported by National Natural Science Foundation of China(31730091)the National Key Research and Development Program of China(2017YFD0500503).
文摘Background:Previous studies have shown that exogenous short-chain fatty acids(SCFAs)introduction attenuated the body fat deposition in conventional mice and pigs.However,limited studies have evaluated the effects of exogenously introduced SCFAs on the lipid and glucose metabolism independently of the gut microbiota.This study was to investigate the effects of exogenous introduction of SCFAs on the lipid and glucose metabolism in a germ-free(GF)pig model.Methods:Twelve hysterectomy-derived newborn pigs were reared in six sterile isolators.All pigs were hand-fed with sterile milk powder for 21 d,then the sterile feed was introduced to pigs for another 21 d.In the second 21-d period,six pigs were orally administrated with 25 mL/kg sterile saline per day and considered as the GF group,while the other six pigs were orally administrated with 25 mL/kg SCFAs mixture(acetic,propionic,and butyric acids,45,15,and 11 mmol/L,respectively)per day and regarded as FA group.Results:Orally administrated with SCFAs tended to increase the adiponectin concentration in serum,enhance the CPT-1 activity in longissimus dorsi,and upregulate the ANGPTL4 mRNA expression level in colon(P<0.10).Meanwhile,the mRNA abundances of ACC,FAS,and SREBP-1C in liver and CD36 in longissimus dorsi of the FA group were decreased(P<0.05)compared with those in the GF group.Besides,the mRNA expression of PGC-1αin liver and LPL in longissimus dorsi tended to(P<0.10)upregulate and downregulate respectively in the FA group.Moreover,oral administration of SCFAs tended to increase the protein level of GPR43(P<0.10)and decrease the protein level of ACC(P<0.10)in liver.Also,oral administration of SCFAs upregulated the p-AMPK/AMPK ratio and the mRNA expressions of GLUT-2 and GYS2 in liver(P<0.05).In addition,the metabolic pathway associated with the biosynthesis of unsaturated fatty acids was most significantly promoted(P<0.05)by oral administration of SCFAs.Conclusions:Exogenous introduction of SCFAs might attenuate the fat deposition and to some extent improve the glucose control in the pig model,which occurred independently of the gut microbiota.
基金supported by the National Key Research and Development Program of China(2017YFD0500503 and 2018YFD0500404)the Natural Science Foundation of China(31730090)Hubei Provincial Natural Science Foundation of China(2018CFA020).
文摘Background:Early-weaning of piglets is often accompanied by severe disorders,especially diarrhea.The gut microbiota and its metabolites play a critical role in the maintenance of the physiologic and metabolic homeostasis of the host.Our previous studies have demonstrated that oral administration of Lactobacillus frumenti improves epithelial barrier functions and confers diarrhea resistance in early-weaned piglets.However,the metabolic response to L.frumenti administration remains unclear.Then,we conducted simultaneous serum and hepatic metabolomic analyses in early-weaned piglets administered by L.frumenti or phosphatebuffered saline(PBS).Results:A total of 1006-day-old crossbred piglets(Landrace×Yorkshire)were randomly divided into two groups and piglets received PBS(sterile,2 m L)or L.frumenti(suspension in PBS,10~8 CFU/m L,2 m L)by oral administration once per day from 6 to 20 days of age.Piglets were weaned at 21 days of age.Serum and liver samples for metabolomic analyses were collected at 26 days of age.Principal components analysis(PCA)showed that L.frumenti altered metabolism in serum and liver.Numerous correlations(P<0.05)were identified among the serum and liver metabolites that were affected by L.frumenti.Concentrations of guanosine monophosphate(GMP),inosine monophosphate(IMP),and uric acid were higher in serum of L.frumenti administration piglets.Pathway analysis indicated that L.frumenti regulated fatty acid and amino acid metabolism in serum and liver.Concentrations of fatty acidβ-oxidation related metabolites in serum(such as3-hydroxybutyrylcarnitine,C4-OH)and liver(such as acetylcarnitine)were increased after L.frumenti administration.Conclusions:Our findings suggest that L.frumenti regulates lipid metabolism and amino acid metabolism in the liver of early-weaned piglets,where it promotes fatty acidβ-oxidation and energy production.High serum concentrations of nucleotide intermediates,which may be an alternative strategy to reduce the incidence of diarrhea in early-weaned piglets,were further detected.These findings broaden our understanding of the relationships between the gut microbiota and nutrient metabolism in the early-weaned piglets.
基金supported by Hubei Province Science and Technology Innovation Major Project(2019ABA081,2021BBA083)China Agriculture Research System of MOF and MARA.
文摘Background:Over the past years,antibiotic growth promoter had been restricted in animal husbandry production in many countries because of antimicrobial resistance and foodborne antibiotic residues.However,the problems of poor intestinal health and low growth efficiency of piglets have not been solved completely in an antibiotic-free diet,and it is urgent to explore alternatives to antimicrobial growth promoters.Methods:Here,a total of 532 weaned pigs were assigned to one of 4 treatments,the low amino acid(AA)level diet(d 1 to d 14 is 1.35%,d 15 to d 42 is 1.25%)(Low AA),the low AA level diet supplementation with a carvacrol-thymol blend(50 mg carvacrol and 50 mg thymol/kg of diet)(CB)(Low AA+CB),the high AA level diet(d 1 to d 14 is 1.50%,d 15 to d 42 is 1.40%)(High AA),and the high AA level diet supplementation with a CB(High AA+CB),respectively.Then we measured growth performance and intestinal health indicators of weaned pigs.Results:Results showed that high AA level significantly reduced plasma urea nitrogen,plasma Interleukin-6(IL-6)and fecal lipocalin-2 contents(P<0.05),significantly increased the relative abundance of fecal Lactobacillus and Enterococcus,and had a trend to increase the fecal secretory immunoglobulin A(sIgA)and mucin 2(MUC 2)contents(P<0.05)in piglets,thereby alleviating the diarrhea of piglets and reducing the feed conversion ratio(FCR)of piglets during d 1~14 after weaning.Dietary supplementation with CB significantly increased the activity of plasma antioxidant enzymes T-SOD and GSH-px(P<0.05),while significantly reduced plasma malondialdehyde(MDA),plasma interleukin-1β(IL-1β),plasma endotoxin and D-lactic acid contents(P<0.05).Meanwhile,CB significantly decreased fecal lipocalin-2 contents and the abundance of fecal Escherichia coli(P<0.05).Thus,we hypothesis that dietary supplementation with CB significantly increased the average daily gain(ADG)of piglets(P<0.05)during d 1~14 after weaning through promoting intestinal health.Conclusion:These results suggest that high AA level and dietary supplementation with CB improved the growth performance of weaned pigs in an antibiotic-free diet by improving AA metabolism and intestinal antioxidant capacity.
基金supported by the National Natural Science Foundation of China(31560304)National Key Research Programs of China(2016ZX08006-003)。
文摘In an attempt to generate g.A746G substitution in the BMPR-IB gene,we unexpectedly obtained BMPR-IB homozygous knockout piglets(BMPR-IB^(-/-))and heterogeneous knockout piglets with one copy of the A746G mutation(BMPR-IB-/746G)via CRISPR/Cas9 editing.Polymerase chain reaction(PCR)and sequencing revealed complex genomic rearrangements in the target region.All BMPR-IBdisrupted piglets showed an inability to stand and walk normally.Both BMPR-IB^(-/-)and BMPR-IB-/746G piglets exhibited severe skeletal dysplasia characterized by distorted and truncated forearms(ulna,radius)and disordered carpal,metacarpal,and phalangeal bones in the forelimbs.The piglets displayed more severe deformities in the hindlimbs by visual inspection,including fibular hemimelia,enlarged tarsal bone,and disordered toe joint bones.Limb deformities were more profound in BMPR-IB^(-/-)piglets than in the BMPR-IB-/746G piglets.Proteomic analysis identified 139 differentially expressed proteins(DEPs)in the hindlimb fibula of BMPR-IB-/746G piglets compared to the wild-type(WT)controls.Most DEPs are involved in skeletal or embryonic development and/or the TGF-βpathway and tumor progression.Gene Ontology(GO)and protein domain enrichment analysis suggested alterations in these processes.Of the top 50 DEPs,a large proportion,e.g.,C1QA,MYO1H,SRSF1,P3H1,GJA1,TCOF1,RBM10,SPP2,MMP13,and PHAX,were significantly associated with skeletal development.Our study provides novel findings on the role of BMPR-IB in mammalian limb development.
基金Supported by the 13th Five-year National Key R&D Program(2016YFD0700204-02)the"Young Talents"Project of Northeast Agricultural University(17QC20,17QC19)the Earmarked Fund for China Agriculture Research System(CARS-35)
文摘In winter, the confined pig house of northern China is severe. The environment variables are nonlinear, time-varying and coupled, which seriously affect the health of pigs and the qualities of the meat. In order to solve the problem multi-variables coupling, a multi-variables decoupled fuzzy logic control method was proposed. Two fuzzy logic controllers were designed based on fuzzy logic theory. The fans, heaters and humidifiers were used to control temperature, humidity and ammonia. The reductions of temperature and humidity caused by ventilating were compensated by heaters and humidifiers respectively which realized the multivariables decoupling. The proposed methods were validated through theoretical, experimental and simulation analysis. The results suggested that the methods were able to regulate the confined pig house environment effectively. In addition, comparing to the manual regulation, the proposed methods could reduce 19% power consumption as well.
基金supported by grants from the National Key R&D Program of China(2020YFA0509500)the National Natural Science Foundation of China(U19A2036,32102512,31872335,and 31802044)+1 种基金the National Special Foundation for Transgenic Species of China(2014ZX0800605B)the Sichuan Science and Technology Program,China(2021YFYZ0009 and 2021YFYZ0030)。
文摘Follistatin(FST) is an important regulator of skeletal muscle growth and adipose deposition through its ability to bind to several members of the transforming growth factor-β(TGF-β) superfamily, and thus may be a good candidate for future animal breeding programs. However, the molecular mechanisms underlying the phenotypic changes have yet to be clarified in pig. We generated transgenic(TG) pigs that express human FST specifically in skeletal muscle tissues and characterized the phenotypic changes compared with the same tissues in wild-type pigs. The TG pigs showed increased skeletal muscle growth, decreased adipose deposition, and improved metabolism status(P<0.05). Transcriptome analysis detected important roles of the PIK3–AKT signaling pathway, calcium-mediated signaling pathway, and amino acid metabolism pathway in FST-induced skeletal muscle hypertrophy, and depot-specific oxidative metabolism changes in psoas major muscle. Furthermore, the lipid metabolism-related process was changed in adipose tissue in the TG pigs. Gene set enrichment analysis revealed that genes related to lipid synthesis, lipid catabolism, and lipid storage were down-regulated(P<0.01) in the TG pigs for subcutaneous fat, whereas genes related to lipid catabolism were significantly up-regulated(P<0.05) in the TG pigs for retroperitoneal fat compared with their expression levels in wild-type pigs. In liver, genes related to the TGF-β signaling pathway were over-represented in the TG pigs, which is consistent with the inhibitory role of FST in regulating TGF-β signaling. Together, these results provide new insights into the molecular mechanisms underlying the phenotypic changes in pig.
基金funded by the Technology Programme Project of Zhongshan City (China) (20073A159)the Open Project of the Key Laboratory of Animal Nutrition and Feed of Yunnan Province
文摘[ Objective] To study the effects of different oligosaccharides on immunity and production performance of piglets.[ Method] A total of 75 Yorkshire x Rongchang piglets were assigned into five groups, 15 in each group. Isomalto-oligosaccharide ( IMO), fructo-oligosaccharide ( FOS), mannan-oligosacchadde (MOS), and mixed oligosacchadde were supplemented to basal diet (7.5 g/kg), respectively. The control group was also set. The experimental period lasted for 53 d. The clinic symptoms and diarrhea were observed. All piglets were weighed once a week. Feed intake was also recorded. Blood was collected via precaval vein for determination of immunology indexes at the age of 30 and 60 d, respectively. [ Result] The IMO and FOS enhanced cellular immunity of 30-day-old piglets significantly (P 〈 0.05), and the IMO also enhanced their humoral immunity. The MOS enhanced cellular immunity and humoral immunity of 60-day-old piglets significantly (P 〈 0.05). It also improved production performance largest, and its diarrhea rate was the lowest. [ Conclusion] Different oligosaccharides have various effects on immunity and production performance of oiolets.
基金supported by the National Natural Sci-ence Foundation of China (30571331)the China Postdoctoral Science Foundation (2005038161)
文摘Imprinted genes play significant roles in the regulation of fetal growth, development, function of the placenta and postnatal behavior in mammals, but little is known in pigs. In order to investigate the imprinting status of porcine retro-transposon like 1 (RTL1) and type 3 iodothyronine deiodinase (DIO3) genes, DNA or RNA samples of the parents and F1 animals, generated with reciprocal crosses between Large White and Meishan breeds, were isolated, and analyzed by reverse transcription polymerase chain reaction restriction fragment length polymorphism (RT-PCR-RFLP). The results demonstrated that the RTL1 gene was paternally expressed in 10 tissues, such as the skeletal muscle, heart, spleen, liver, kidney, lung, stomach, fat, small intestine and brain, and D103 gene exhibited paternal expression in the skeletal muscle, heart, spleen, lung, stomach, and brain, in 2-month-old pigs. The association of RTL1 and DI03 with carcass traits was further analyzed in the F2 population of Large White×Meishan pigs. The statistical results showed that the R TL1 A1101G polymorphism (EU781029) was significantly associated with lean meat percentage (LMP) and fat meat percentage (FMP) (P〈0.05), while the D103 A744C polymorphism (AY533208) was not significantly associated with any carcass traits. These results indicate that the imprinting status of RTL1 and DIO3 is well kept across the mammalian species, and porcine RTL1 may have important roles in muscle growth and fat deposition.
基金supported by the grants from the Specialized Doctor Research Fund of Southwestern University of China (2013Bsr8)the Youth Fund of Rongchang Campus of Southwest University, China (20700429)+2 种基金the Chongqing Fund of Application and Development, China (cstc2013yykf C80003)the Chongqing Fund of Basic Research, China (15428, 14440)the National Biological Breeding Capacity Building and Industrialization Projects, China (2014-2573)
文摘DNA methyltransferases(Dnmts)comprise a family of proteins which involved in the establishment and maintenance of DNA methylation patterns.In pig,the molecular characterization and tissue expression profile of Dnmt gene family are not clear.To solve this problem,reverse transcriptase PCR and rapid amplification of c DNA ends were used to clone the sequences of the porcine Dnmt2 and Dnmt3b genes.Furthermore,the m RNA expression profiles of Dnmt1,Dnmt2,Dnmt3a and Dnmt3b genes from 54 adult tissues and 2 entire fetuses of Rongchang pig were analyzed by quantitative real-time PCR(q RT-PCR).As a result,the lengths of porcine Dnmt2 and Dnmt3b gene c DNAs were 1 227 and 2 559 bp with cytosine-C5specific DNA methylase domain,respectively.The four Dnmt genes were highly expressed in longissimus dorsi muscle(P〈0.01).Dnmt1 is highly expressed in heart(P〈0.01)and Dnmt 2 shows its preference in liver and seminal vesicle tissue(P〈0.01).Dnmt3a and Dnmt3b are highly expressed in the two fetus stages(P〈0.01).All these results suggested that each gene has its specific expression profile,and deeper study is required to dig more details between the methylation level and Dnmt family m RNA expressions in different tissues.
基金supported by National Natural Science Foundation of China(31790413)supported by National Natural Science Foundation of China(31760657)。
文摘Background:Short tandem repeats(STRs)were recently found to have significant impacts on gene expression and diseases in humans,but their roles on gene expression and complex traits in pigs remain unexplored.This study investigates the effects of STRs on gene expression in liver tissues based on the whole-genome sequences and RNA-Seq data of a discovery cohort of 260 F6 individuals and a validation population of 296 F7 individuals from a heterogeneous population generated from crosses among eight pig breeds.Results:We identified 5203 and 5868 significantly expression STRs(eSTRs,FDR<1%)in the F6 and F7 populations,respectively,most of which could be reciprocally validated(π1=0.92).The eSTRs explained 27.5%of the cisheritability of gene expression traits on average.We further identified 235 and 298 fine-mapped STRs through the Bayesian fine-mapping approach in the F6 and F7 pigs,respectively,which were significantly enriched in intron,ATAC peak,compartment A and H3K4me3 regions.We identified 20 fine-mapped STRs located in 100 kb windows upstream and downstream of published complex trait-associated SNPs,which colocalized with epigenetic markers such as H3K27ac and ATAC peaks.These included eSTR of the CLPB,PGLS,PSMD6 and DHDH genes,which are linked with genome-wide association study(GWAS)SNPs for blood-related traits,leg conformation,growth-related traits,and meat quality traits,respectively.Conclusions:This study provides insights into the effects of STRs on gene expression traits.The identified eSTRs are valuable resources for prioritizing causal STRs for complex traits in pigs.
基金the National Natural Science Foundation of China (32160782) for their financial support。
文摘Pork cutting is a very important processing in promoting economic appreciation across the swine business chain. The goal of this research is to determine the proportion and weight of meat cuts, as well as to analyze the effects of carcass weight, sex and breed composition on meat cuts. Simultaneously, we investigate the correlation between meat cuts, carcass traits and meat quality traits. To assess 17 meat cut traits, 12 carcass traits and 6 meat quality traits, we sample 2 012 pigs from four breeds, including Landrace(LD), Yorkshire(YK), Landrace Yorkshire(LY), and Duroc Landrace Yorkshire(DLY). The results showed that carcass weight, sex and breed composition have significant effects on the weight and proportion of most meat cuts. The proportion of cuts for muscle and bone decrease as carcass weight grows, whereas the proportion of cuts for fat increases. Moreover, the thickness of four-point backfat was significantly increasing(P<0.001) with increase of carcass weights, indicating that large amount of intaking energy in the late finishing stage was used for fat deposition. Besides, the proportion of Shoulder cut(SC) and Back fat(BF) in barrows was significantly higher(P<0.001) than that in sows, whereas the Leg cut(LC) showed the opposite trend. The Loin(LO) proportion and Loin muscle area(LMA) of barrows were significantly lower(P<0.001), but the proportion of fat areas in the image(PFAI) and visual marbling score(VMS) were significantly higher(P<0.001) than those of sows, respectively. In terms of breeds, LD had the longest straight carcass length, significantly longer(P<0.001) than the other three breeds, which partially explains why LD had the largest proportion of the Middle cut(MC). Moreover, the proportion of SC in DLY was the highest. Last but not least, the correlations between the proportions of most meat cuts, and also between meat cuts and meat quality or carcass traits were low or not significant(P>0.05). The effects of carcass weight, sex and breed composition on the meat cuts, meat quality and carcass traits are breed and growth stage dependent. It also reflects the asynchrony of the growth curve between different sexes. Our results laid an important foundation for breeding pig carcass cuts and composition.
基金supported by National Key Research and Development Program of China(2021YFF1000601).
文摘Background:A comprehensive landscape of chromatin states for multiple mammalian tissues is essential for elucidating the molecular mechanism underlying regulatory variants on complex traits.However,the genome-wide chromatin accessibility has been only reported in limited tissue types in pigs.Results:Here we report a genome-wide landscape of chromatin accessibility of 20 tissues in two female pigs at ages of 6 months using ATAC-seq,and identified 557,273 merged peaks,which greatly expanded the pig regulatory ele-ment repository.We revealed tissue-specific regulatory elements which were associated with tissue-relevant biologi-cal functions.We identified both positive and negative significant correlations between the regulatory elements and gene transcripts,which showed distinct distributions in terms of their strength and distances from corresponding genes.We investigated the presence of transposable elements(TEs)in open chromatin regions across all tissues,these included identifications of porcine endogenous retroviruses(PERVs)exhibiting high accessibility in liver and homology of porcine specific virus sequences to universally accessible transposable elements.Furthermore,we prior-itized a potential causal variant for polyunsaturated fatty acid in the muscle.Conclusions:Our data provides a novel multi-tissues accessible chromatin landscape that serve as an important resource for interpreting regulatory sequences in tissue-specific and conserved biological functions,as well as regula-tory variants of loci associated with complex traits in pigs.
基金This work was supported in part by the China Postdoctoral Foundation(grant 2020 T130232)the Key Laboratory of Livestock Disease Prevention of Guangdong Province and the Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province,Ministry of Agriculture and Rural Affairs,China(grant YDWS1901)Hubei Provincial Key R&D program.The funder had no role in the study design,data collection,data analysis,data interpretation,or writing of the manuscript.
文摘Pasteurella multocida is a leading cause of respiratory disorders in pigs.This study was designed to understand the genotypical and antimicrobial resistant characteristics of P.multocida from pigs in China.To achieve this,we briefly investigated 158 P.multocida isolates from pigs with respiratory disorders in China between 2019 and 2020.Genotyping through multiplex PCR assays assigned these 158 isolates into capsular genotypes A(60.13%,95/158),D(35.44%,56/158),F(4.43%,7/158),and/or lipopolysaccharide(LPS)genotypes L3(28.48%,45/158)and L6(66.46%,105/158).In addition,eight isolates(5.06%,8/158)were found to be nontypable using the LPS genotyping method.When combining the capsular genotypes and the LPS genotypes,D:L6(34.81%,55/158)and A:L6(31.65%,50/158)were the predominant genotypes,followed by A:L3(24.05%,38/158).PCR detection of virulence factor-encoding genes showed that over 80%of the isolates were positive for exbB,tonB,exbD,ompH,ptfA,fimA,sodA,sodC,fur,ompA,oma87,plpB,hsf-2,nanH and hgbB,suggesting the presence of these genes were broad characteristics of P.multocida.We also found approximately 63.92%(101/158),51.27%(81/158),8.86%(14/158),7.59%(12/158),3.16%(5/158),0.63%(1/158),and 0.63%(1/158)of the isolates grew well in media with the presence of colistin(4μg/mL),tetracycline(16μg/mL),tigecycline(1μg/mL),ampicillin(32μg/mL),chloramphenicol(32μg/mL),cefepime(16μg/mL),and ciprofloxacin(1μg/mL),respectively.This study contributes to the understanding of genotypes and antimicrobial resistance profile of P.multocida currently circulation in pigs of China.
基金supported by the National Major Special Project on New Varieties Cultivation for Transgenic Organisms,China(2014ZX08006-005 and 2014ZX0800950B)
文摘Homeobox A10(Hoxa10) gene is one of the most important candidate genes associated with the reproductive performance of humans and mice. Overexpression of Hoxa10 in mouse endometrium can increase litter size. Moreover, Hoxa10 plays a key role in regulating the embryo implantation of sows. This study aimed to generate transgenic pigs using Hoxa10 via somatic cell nuclear transfer(SCNT). We established seven Hoxa10-transgenic cell lines, and two of the cell lines were selected as nuclear donors for the transfer. A total of 1 270 cloned embryos were generated and transferred to five surrogate mothers(Landrace×Yorkshire). Eight cloned male piglets were produced including one with cryptorchidism. Six transgenic piglets grew up healthy and produced 56 offspring. Finally, we obtained six transgenic male pigs and 26 transgenic positive offspring that can be used to further study the regulatory mechanism of Hoxa10 on the reproductive performance of pigs.