Genetically modified pigs:Emerging animal models for hereditary hearing loss

Hereditary hearing loss(HHL),a genetic disorder that impairs auditory function,significantly affects quality of life and incurs substantial economic losses for society.To investigate the underlying causes of HHL and evaluate therapeutic outcomes,appropriate animal models are necessary.Pigs have been extensively used as valuable large animal models in biomedical research.In this review,we highlight the advantages of pig models in terms of ear anatomy,inner ear morphology,and electrophysiological characteristics,as well as recent advancements in the development of distinct genetically modified porcine models of hearing loss.Additionally,we discuss the prospects,challenges,and recommendations regarding the use pig models in HHL research.Overall,this review provides insights and perspectives for future studies on HHL using porcine models.

Associations of genome-wide structural variations with phenotypic differences in cross-bred Eurasian pigs

Background During approximately 10,000 years of domestication and selection,a large number of structural variations(SVs)have emerged in the genome of pig breeds,profoundly influencing their phenotypes and the ability to adapt to the local environment.SVs(≥50 bp)are widely distributed in the genome,mainly in the form of insertion(INS),mobile element insertion(MEI),deletion(DEL),duplication(DUP),inversion(INV),and translocation(TRA).While studies have investigated the SVs in pig genomes,genome-wide association studies(GWAS)-based on SVs have been rarely conducted.Results Here,we obtained a high-quality SV map containing 123,151 SVs from 15 Large White and 15 Min pigs through integrating the power of several SV tools,with 53.95%of the SVs being reported for the first time.These high-quality SVs were used to recover the population genetic structure,confirming the accuracy of genotyping.Potential functional SV loci were then identified based on positional effects and breed stratification.Finally,GWAS were performed for 36 traits by genotyping the screened potential causal loci in the F2 population according to their corresponding genomic positions.We identified a large number of loci involved in 8 carcass traits and 6 skeletal traits on chromosome 7,with FKBP5 containing the most significant SV locus for almost all traits.In addition,we found several significant loci in intramuscular fat,abdominal circumference,heart weight,and liver weight,etc.Conclusions We constructed a high-quality SV map using high-coverage sequencing data and then analyzed them by performing GWAS for 25 carcass traits,7 skeletal traits,and 4 meat quality traits to determine that SVs may affect body size between European and Chinese pig breeds.

Excess dietary Lys reduces feed intake, stimulates jejunal CCK secretion and alters essential and non‑essential blood AA profile in pigs

Background Commercial diets are frequently formulated to meet or exceed nutrient levels including those of lim-iting essential amino acids(AA)covering potential individual variations within the herd.However,the provision of dietary excess of AA,such as Lys,may lead to reduced appetite and growth in pigs.The mechanisms modulat-ing these responses have not been extensively investigated.This study evaluated the effect of Lys dietary excesses on performance and satiety biomarkers in post weaning pigs.Methods Twenty-four pigs aged 21 d and weighing 6.81±0.12kg(mean±SEM)were individually housed and offered 1 of 4 dietary treatments for 3weeks:a diet containing a standardized ileal digestible Lys reaching 100%(T0),120%(T1),150%(T2)or 200%(T3)of the NRC(2012)requirements.At the end of the experiment,blood samples from the cephalic vein of the T0 and T3 groups were obtained for AA analysis.In addition,primary intestinal cultures from T0 pigs were used,following their humane killing,to evaluate the effect of Lys on gut hormone secretion and AA sensors gene expression under ex vivo conditions.Results Feed intake was linearly reduced(P<0.001)and the weight gain to feed ratio reduced(P<0.10)with increased dietary levels of Lys during the third-and first-week post weaning,respectively.Cholecystokinin con-centration(P<0.05)and the metabotropic glutamate receptor 1 and the solute carrier family 7 member 2(P<0.10)gene expression was enhanced in proximal jejunum tissues incubated with Lys at 20mmol/L when compared to the control(Lys 0mmol/L).Plasma Lys and Glu(P<0.05)concentration increased in the T3 compared to T0 pigs.In contrast,plasma levels of His,Val,Thr,Leu(P<0.05)and Gln(P<0.10)were lower in T3 than T0 pigs.Conclusion The present results confirm that excess dietary Lys inhibits hunger in pigs.Moreover,the results provide evidence of pre-and post-absorptive mechanisms modulating these responses.Lys dietary excesses should be nar-rowed,when possible,to avoid negative effects of the AA on appetite in pigs.

Genome-wide association study identifies 12 new genetic loci associated with growth traits in pigs

Growth traits are among the most important economic traits in pigs and are regulated by polygenes with complex regulatory mechanisms.As the major indicators of growth performance,the backfat thickness(BFT),loin eye area(LEA),and days to 100 kg(D100)traits are commonly used to the genetics improvement in pigs.However,the available genetic markers for these traits are limited.To uncover novel loci and candidate genes associated with growth performance,we collected the phenotypic information of BFT,LEA,and D100 in 1,186 pigs and genotyped all these individuals using the Neogen GGP porcine 80K BeadChip.We performed a genome-wide association study(GWAS)using 4 statistical models,including mixed linear models(MLM),fixed and random model circulating probability unification(FarmCPU),settlement of MLM under progressively exclusive relationships(SUPER),Bayesian-information and linkage-disequilibrium Iteratively nested keyway(Blink),and identified 5,3,and 6 high-confidence single nucleotide polymorphisms(SNPs)associated with BFT,LEA,and D100,respectively.Variant annotation and quantitative trait locus(QTL)mapping analysis suggested that6 genes(SKAP2,SATB1,PDE7B,PPP1R16B,WNT3,and WNT9B)were potentially associated with growth performance in pigs.Transcriptome analysis suggested that the expression of Src Kinase Associated Phosphoprotein 2(SKAP2)was higher in prenatal muscles than in postnatal muscles,and the expression of Phosphodiesterase 7B(PDE7B)continuously increased during the prenatal stages and gradually decreased after birth,implying their potential roles in prenatal skeletal muscle development.Overall,this study provides new candidate loci and genes for the genetic improvement of pigs.

Amino acid and mineral digestibility,bone ash,and plasma inositol is increased by including microbial phytase in diets for growing pigs

Background The effect of microbial phytase on amino acid and energy digestibility is not consistent in pigs,which may be related to the phytase dosage or the adaptation length to the diet.Therefore,an experiment was conducted to test the hypotheses that increasing dietary phytase after an 18-day adaptation period:1)increases nutrient and energy digestibility;2)increases plasma P,plasma inositol,and bone ash of young pigs;and 3)demonstrates that maximum phytate degradation requires more phytase than maximum P digestibility.Results Data indicated that increasing inclusion of phytase[0,250,500,1,000,2,000,and 4,000 phytase units(FTU)/kg feed]in corn-soybean meal-based diets increased apparent ileal digestibility(AID)of Trp(quadratic;P<0.05),and of Lys and Thr(linear;P<0.05),and tended to increase AID of Met(linear;P<0.10).Increasing dietary phytase also increased AID and apparent total tract digestibility(ATTD)of Ca and P(quadratic;P<0.05)and increased ATTD of K and Na(linear;P<0.05),but phytase did not influence the ATTD of Mg or gross energy.Concentrations of plasma P and bone ash increased(quadratic;P<0.05),and plasma inositol also increased(linear;P<0.05)with increasing inclusion of phytase.Reduced concentrations of inositol phosphate(IP)6 and IP5(quadratic;P<0.05),reduced IP4 and IP3(linear;P<0.05),but increased inositol concentrations(linear;P<0.05)were observed in ileal digesta as dietary phytase increased.The ATTD of P was maximized if at least 1,200 FTU/kg were used,whereas more than 4,000 FTU/kg were needed to maximize inositol release.Conclusions Increasing dietary levels of phytase after an 18-day adaptation period increased phytate and IP ester degradation and inositol release in the small intestine.Consequently,increasing dietary phytase resulted in improved digestibility of Ca,P,K,Na,and the first 4 limiting amino acids,and in increased concentrations of bone ash and plasma P and inositol.In a corn-soybean meal diet,maximum inositol release requires approximately 3,200 FTU/kg more phytase than that required for maximum P digestibility.

Core and variable antimicrobial resistance genes in the gut microbiomes of Chinese and European pigs

Monitoring the prevalence of antimicrobial resistance genes(ARGs)is vital for addressing the global crisis of antibiotic-resistant bacterial infections.Despite its importance,the characterization of ARGs and microbiome structures,as well as the identification of indicators for routine ARG monitoring in pig farms,are still lacking,particularly concerning variations in antimicrobial exposure in different countries or regions.Here,metagenomics and random forest machine learning were used to elucidate the ARG profiles,microbiome structures,and ARG contamination indicators in pig manure under different antimicrobial pressures between China and Europe.Results showed that Chinese pigs exposed to high-level antimicrobials exhibited higher total and plasmid-mediated ARG abundances compared to those in European pigs(P<0.05).ANT(6)-Ib,APH(3')-IIIa,and tet(40)were identified as shared core ARGs between the two pig populations.Furthermore,the core ARGs identified in pig populations were correlated with those found in human populations within the same geographical regions.Lactobacillus and Prevotella were identified as the dominant genera in the core microbiomes of Chinese and European pigs,respectively.Forty ARG markers and 43 biomarkers were able to differentiate between the Chinese and European pig manure samples with accuracies of 100%and 98.7%,respectively.Indicators for assessing ARG contamination in Chinese and European pigs also achieved high accuracy(r=0.72-0.88).Escherichia flexneri in both Chinese and European pig populations carried between 21 and 37 ARGs.The results of this study emphasize the importance of global collaboration in reducing antimicrobial resistance risk and provide validated indicators for evaluating the risk of ARG contamination in pig farms.

Genetically modified pigs with CD163 point mutation are resistant to HP-PRRSV infection

Porcine reproductive and respiratory syndrome(PRRS)is a globally prevalent contagious disease caused by the positive-strand RNA PRRS virus(PRRSV),resulting in substantial economic losses in the swine industry.Modifying the CD163 SRCR5 domain,either through deletion or substitution,can eff1ectively confer resistance to PRRSV infection in pigs.However,large fragment modifications in pigs inevitably raise concerns about potential adverse effects on growth performance.Reducing the impact of genetic modifications on normal physiological functions is a promising direction for developing PRRSV-resistant pigs.In the current study,we identified a specific functional amino acid in CD163 that influences PRRSV proliferation.Viral infection experiments conducted on Marc145 and PK-15CD163 cells illustrated that the mE535G or corresponding pE529G mutations markedly inhibited highly pathogenic PRRSV(HP-PRRSV)proliferation by preventing viral binding and entry.Furthermore,individual viral challenge tests revealed that pigs with the E529G mutation had viral loads two orders of magnitude lower than wild-type(WT)pigs,confirming effective resistance to HP-PRRSV.Examination of the physiological indicators and scavenger function of CD163 verified no significant differences between the WT and E529G pigs.These findings suggest that E529G pigs can be used for breeding PRRSV-resistant pigs,providing novel insights into controlling future PRRSV outbreaks.

Evaluating the performance of genomic selection on purebred population by incorporating crossbred data in pigs

Genomic selection(GS)has been widely used in livestock,which greatly accelerated the genetic progress of complex traits.The population size was one of the significant factors affecting the prediction accuracy,while it was limited by the purebred population.Compared to directly combining two uncorrelated purebred populations to extend the reference population size,it might be more meaningful to incorporate the correlated crossbreds into reference population for genomic prediction.In this study,we simulated purebred offspring(PAS and PBS)and crossbred offspring(CAB)base on real genotype data of two base purebred populations(PA and PB),to evaluate the performance of genomic selection on purebred while incorporating crossbred information.The results showed that selecting key crossbred individuals via maximizing the expected genetic relationship(REL)was better than the other methods(individuals closet or farthest to the purebred population,CP/FP)in term of the prediction accuracy.Furthermore,the prediction accuracy of reference populations combining PA and CAB was significantly better only based on PA,which was similar to combine PA and PAS.Moreover,the rank correlation between the multiple of the increased relationship(MIR)and reliability improvement was 0.60-0.70.But for individuals with low correlation(Cor(Pi,PA or B),the reliability improvement was significantly lower than other individuals.Our findings suggested that incorporating crossbred into purebred population could improve the performance of genetic prediction compared with using the purebred population only.The genetic relationship between purebred and crossbred population is a key factor determining the increased reliability while incorporating crossbred population in the genomic prediction on pure bred individuals.

Supplementation of vitamin E or a botanical extract as antioxidants to improve growth performance and health of growing pigs housed under thermoneutral or heat-stressed conditions

Background Heat stress has severe negative consequences on performance and health of pigs,leading to significant economic losses.The objective of this study was to investigate the effects of supplemental vitamin E and a botanical extract in feed or drinking water on growth performance,intestinal health,and oxidative and immune status in grow-ing pigs housed under heat stress conditions.Methods Duplicate experiments were conducted,each using 64 crossbred pigs with an initial body weight of 50.7±3.8 and 43.9±3.6 kg and age of 13-week and 12-week,respectively.Pigs(n=128)were housed individually and assigned within weight blocks and sex to a 2×4 factorial arrangement consisting of 2 environments(thermo-neutral(21.2℃)or heat-stressed(30.9℃))and 4 supplementation treatments(control diet;control+100 IU/L of D-α-tocopherol in water;control+200 IU/kg of DL-α-tocopheryl-acetate in feed;or control+400 mg/kg of a botanical extract in feed).Results Heat stress for 28 d reduced(P≤0.001)final body weight,average daily gain,and average daily feed intake(-7.4 kg,-26.7%,and-25.4%,respectively)but no effects of supplementation were detected(P>0.05).Serum vitamin E increased(P<0.001)with vitamin E supplementation in water and in feed(1.64 vs.3.59 and 1.64 vs.3.24),but not for the botanical extract(1.64 vs.1.67 mg/kg)and was greater when supplemented in water vs.feed(P=0.002).Liver vitamin E increased(P<0.001)with vitamin E supplementations in water(3.9 vs.31.8)and feed(3.9 vs.18.0),but not with the botanical extract(3.9 vs.4.9 mg/kg).Serum malondialdehyde was reduced with heat stress on d 2,but increased on d 28(interaction,P<0.001),and was greater(P<0.05)for antioxidant supplementation compared to control.Cellular proliferation was reduced(P=0.037)in the jejunum under heat stress,but increased in the ileum when vitamin E was supplemented in feed and water under heat stress(interaction,P=0.04).Tumor necrosis factor-αin jejunum and ileum mucosa decreased by heat stress(P<0.05)and was reduced by vitamin E sup-plementations under heat stress(interaction,P<0.001).Conclusions The addition of the antioxidants in feed or in drinking water did not alleviate the negative impact of heat stress on feed intake and growth rate of growing pigs.

Impact of an oligosaccharide-based polymer on the metabolic profiles and microbial ecology of weanling pigs experimentally infected with a pathogenic E.coli

Background Our previous study has reported that supplementation of oligosaccharide-based polymer enhances gut health and disease resistance of pigs infected with enterotoxigenic E.coli(ETEC)F18 in a manner similar to carbadox.The objective of this study was to investigate the impacts of oligosaccharide-based polymer or antibiotic on the host metabolic profiles and colon microbiota of weaned pigs experimentally infected with ETEC F18.Results Multivariate analysis highlighted the differences in the metabolic profiles of serum and colon digesta which were predominantly found between pigs supplemented with oligosaccharide-based polymer and antibiotic.The relative abundance of metabolic markers of immune responses and nutrient metabolisms,such as amino acids and carbohydrates,were significantly differentiated between the oligosaccharide-based polymer and antibiotic groups(q<0.2 and fold change>2.0).In addition,pigs in antibiotic had a reduced(P<0.05)relative abundance of Lachnospiraceae and Lactobacillaceae,whereas had greater(P<0.05)Clostridiaceae and Streptococcaceae in the colon digesta on d 11 post-inoculation(PI)compared with d 5 PI.Conclusions The impact of oligosaccharide-based polymer on the metabolic and microbial profiles of pigs is not fully understood,and further exploration is needed.However,current research suggest that various mechanisms are involved in the enhanced disease resistance and performance in ETEC-challenged pigs by supplementing this polymer.

Low crude protein formulation with supplemental amino acids for its impacts on intestinal health and growth performance of growing-finishing pigs

Background Low crude protein(CP)formulations with supplemental amino acids(AA)are used to enhance intestinal health,reduce costs,minimize environmental impact,and maintain growth performance of pigs.However,extensive reduction of dietary CP can compromise growth performance due to limited synthesis of non-essential AA and limited availability of bioactive compounds from protein supplements even when AA requirements are met.Moreover,implementing a low CP formulation can increase the net energy(NE)content in feeds causing excessive fat deposition.Additional supplementation of functional AA,coupled with low CP formulation could further enhance intestinal health and glucose metabolism,improving nitrogen utilization,and growth performance.Three experiments were conducted to evaluate the effects of low CP formulations with supplemental AA on the intestinal health and growth performance of growing-finishing pigs.Methods In Exp.1,90 pigs(19.7±1.1 kg,45 barrows and 45 gilts)were assigned to 3 treatments:CON(18.0%CP,supplementing Lys,Met,and Thr),LCP(16.0%CP,supplementing Lys,Met,Thr,Trp,and Val),and LCPT(16.1%CP,LCP+0.05%SID Trp).In Exp.2,72 pigs(34.2±4.2 kg BW)were assigned to 3 treatments:CON(17.7%CP,meeting the requirements of Lys,Met,Thr,and Trp);LCP(15.0%CP,meeting Lys,Thr,Trp,Met,Val,Ile,and Phe);and VLCP(12.8%CP,meeting Lys,Thr,Trp,Met,Val,Ile,Phe,His,and Leu).In Exp.3,72 pigs(54.1±5.9 kg BW)were assigned to 3 treatments and fed experimental diets for 3 phases(grower 2,finishing 1,and finishing 2).Treatments were CON(18.0%,13.8%,12.7%CP for 3 phases;meeting Lys,Met,Thr,and Trp);LCP(13.5%,11.4%,10.4%CP for 3 phases;meeting Lys,Thr,Trp,Met,Val,Ile,and Phe);and LCPG(14.1%,12.8%,11.1%CP for 3 phases;LCP+Glu to match SID Glu with CON).All diets had 2.6 Mcal/kg NE.Results In Exp.1,overall,the growth performance did not differ among treatments.The LCPT increased(P<0.05)Claudin-1 expression in the duodenum and jejunum.The LCP and LCPT increased(P<0.05)CAT-1,4F2hc,and B0AT expressions in the jejunum.In Exp.2,overall,the VLCP reduced(P<0.05)G:F and BUN.The LCP and VLCP increased(P<0.05)the backfat thickness(BFT).In Exp.3,overall,growth performance and BFT did not differ among treatments.The LCPG reduced(P<0.05)BUN,whereas increased the insulin in plasma.The LCP and LCPG reduced(P<0.05)the abundance of Streptococcaceae,whereas the LCP reduced(P<0.05)Erysipelotrichaceae,and the alpha diversity.Conclusions When implementing low CP formulation,CP can be reduced by supplementation of Lys,Thr,Met,Trp,Val,and Ile without affecting the growth performance of growing-finishing pigs when NE is adjusted to avoid increased fat deposition.Supplementation of Trp above the requirement or supplementation of Glu in low CP formulation seems to benefit intestinal health as well as improved nitrogen utilization and glucose metabolism.

Oils with different degree of saturation:effects on ileal digestibility of fat and corresponding additivity and bacterial community in growing pigs

Background Oils are important sources of energy in pig diets.The combination of oils with different degree of saturation contributes to improve the utilization efficiency of the mixed oils and may reduce the cost of oil supplemented.An experiment was conducted to evaluate the effects of oils with different degree of saturation on the fat digestibility and corresponding additivity and bacterial community in growing pigs.Methods Eighteen crossbred(Duroc×Landrace×Yorkshire)barrows(initial body weight:29.3±2.8 kg)were surgically fitted with a T-cannula in the distal ileum.The experimental diets included a fat-free basal diet and 5 oil-added diets.The 5 oil-added diets were formulated by adding 6%oil with different ratio of unsaturated to saturated fatty acids(U:S)to the basal diet.The 5 oils were palm oil(U:S=1.2),canola oil(U:S=12.0),and palm oil and canola oil were mixed in different proportions to prepare a combination of U:S of 2.5,3.5 and 4.5,respectively.Results The apparent and standardized ileal digestibility(AID and SID)of fat and fatty acids increased linearly(P<0.05)as the U:S of dietary oils increased except for SID of fat and C18:2.The AID and SID of fat and fatty acids differed among the dietary treatments(P<0.05)except for SID of unsaturated fatty acids(UFA)and C18:2.Fitted one-slope broken-line analyses for the SID of fat,saturated fatty acids(SFA)and UFA indicated that the breakpoint for U:S of oil was 4.14(R^(2)=0.89,P<0.01),2.91(R^(2)=0.98,P<0.01)and 3.84(R^(2)=0.85,P<0.01),respectively.The determined SID of fat,C18:1,C18:2 and UFA in the mixtures was not different from the calculated SID of fat,C18:1,C18:2 and UFA.However,the determined SID of C16:0,C18:0 and SFA in the mixtures were greater than the calculated SID values(P<0.05).The abundance of Romboutsia and Turicibacter in pigs fed diet containing palm oil was greater than that in rapeseed oil treatment group,and the two bacteria were negatively correlated with SID of C16:0,C18:0 and SFA(P<0.05).Conclusions The optimal U:S for improving the utilization efficiency of mixed oil was 4.14.The SID of fat and UFA for palm oil and canola oil were additive in growing pigs,whereas the SID of SFA in the mixture of two oils was greater than the sum of the values of pure oils.Differences in fat digestibility caused by oils differing in degree of saturation has a significant impact on bacterial community in the foregut.

基于PigsTrack跟踪器的群养生猪多目标跟踪

基于视频的生猪行为跟踪和识别对于实现精细化养殖具有重要价值。为了应对群养生猪多目标跟踪任务中由猪只外观相似、遮挡交互等因素带来的挑战,研究提出了基于PigsTrack跟踪器的群养生猪多目标跟踪方法。PigsTrack跟踪器利用高性能YOLOX网络降低目标误检与漏检率,采用Transformer模型获取具有良好区分特性的目标外观特征;基于OC-SORT(observation-centric sort)的思想,通过集成特征匹配、IoU匹配和遮挡恢复匹配策略实现群养生猪的准确跟踪。基于PBVD(pigs behaviours video dataset)数据集的试验结果表明,PigsTrack跟踪器的HOTA(higher order tracking accuracy),MOTA(multiple object tracking accuracy)和IDF1得分(identification F1 score)分别为85.66%、98.59%和99.57%,相较于现有算法的最高精度,分别提高了3.71、0.03和2.05个百分点,证明了PigsTrack跟踪器在解决外观相似和遮挡交互引起的跟踪过程中身份跳变问题方面的有效性。随后,利用Slowfast网络对PigsTrack跟踪器的跟踪结果进行了典型行为统计,结果显示PigsTrack在群养生猪个体行为统计方面更准确。此外,通过在ABVD(aggressive-behavior video)数据集上的试验,PigsTrack跟踪器的HOTA、MOTA和IDF1得分分别为69.14%、94.82%和90.11%,相对于现有算法的最高精度,提高了5.33、0.57和8.60个百分点,验证了PigsTrack跟踪器在群养生猪跟踪任务中的有效性。总而言之,PigsTrack跟踪器能够有效应对外观相似和遮挡交互等挑战,实现了准确的生猪多目标跟踪,并在行为统计方面展现出更高的准确性,为生猪养殖领域的研究和实际应用提供了有价值的指导。

Effects of different starch structures on energy metabolism in pigs

Background Starch is a major component of carbohydrates and a major energy source for monogastric animals.Starch is composed of amylose and amylopectin and has different physiological functions due to its different structure.It has been shown that the energy supply efficiency of amylose is lower than that of amylopectin.However,there are few studies on the effect of starch structure on the available energy of pigs.The purpose of this study was to measure the effect of different structures of starch in the diet on the net energy(NE)of pigs using a comparative slaughter method and to establish a prediction equation to estimate the NE of starch with different structures.Fifty-six barrows(initial BW 10.18±0.11 kg)were used,and they were housed and fed individually.Pigs were divided into 7 treatments,with 8 replicates for each treatment and 1 pig for each replicate.One of the treatments was randomly selected as the initial slaughter group(ISG).Pigs in the remaining treatments were assigned to 6 diets,fed with basic diet and semi-pure diets with amylose/amylopectin ratio(AR)of 3.09,1.47,0.25,0.15 and 0.12,respectively.The experiment lasted for 28 d.Results Results showed that compared with the high amylose(AM)groups(AR 3.09 and 1.47),the high amylopectin(AP)group(AR 0.15)significantly increased the final BW,average daily weight gain and average daily feed intake of pigs(P<0.05),but the F:G of the AM group was lower(P<0.01).In addition,AR 0.15 and 0.12 groups have higher(P<0.01)nutrient digestibility of dry matter,crude protein,gross energy and crude ash.Meanwhile,compared with other groups,AR 0.15 group has a higher(P<0.05)NE intake and energy retention(RE).The regressive equation for predicting with starch structures was established as RE=1,235.243-48.298AM/AP(R^(2)=0.657,P=0.05).Conclusions In conclusion,NE intake and RE of pigs augmented with the increase of dietary amylopectin content,indicating that diets high in amylopectin were more conducive to promoting the growth of pigs in the late conserva-tion period.

Insights into the architecture of human-induced polygenic selection in Duroc pigs

Background:As one of the most utilized commercial composite boar lines,Duroc pigs have been introduced to China and undergone strongly human-induced selection over the past decades.However,the efficiencies and limitations of previous breeding of Chinese Duroc pigs are largely understudied.The objective of this study was to uncover directional polygenic selection in the Duroc pig genome,and investigate points overlooked in the past breeding process.Results:Here,we utilized the Generation Proxy Selection Mapping(GPSM)on a dataset of 1067 Duroc pigs with 8,766,074 imputed SNPs.GPSM detected a total of 5649 putative SNPs actively under selection in the Chinese Duroc pig population,and the potential functions of the selection regions were mainly related to production,meat and carcass traits.Meanwhile,we observed that the allele frequency of variants related to teat number(NT)relevant traits was also changed,which might be influenced by genes that had pleiotropic effects.First,we identified the direction of selection on NT traits by G,and further pinpointed large-effect genomic regions associated with NT relevant traits by selection signature and GWAS.Combining results of NT relevant traits-specific selection signatures and GWAS,we found three common genome regions,which were overlapped with QTLs related to production,meat and carcass traits besides“teat number”QTLs.This implied that there were some pleiotropic variants underlying NT and economic traits.We further found that rs346331089 has pleiotropic effects on NT and economic traits,e.g.,litter size at weaning(LSW),litter weight at weaning(LWW),days to 100 kg(D100),backfat thickness at 100 kg(B100),and loin muscle area at 100 kg(L100)traits.Conclusions:The selected loci that we identified across methods displayed the past breeding process of Chinese Duroc pigs,and our findings could be used to inform future breeding decision.

Characteristics of glucose and lipid metabolism and the interaction between gut microbiota and colonic mucosal immunity in pigs during cold exposure

Background Cold regions have long autumn and winter seasons and low ambient temperatures.When pigs are unable to adjust to the cold,oxidative damage and inflammation may develop.However,the differences between cold and non-cold adaptation regarding glucose and lipid metabolism,gut microbiota and colonic mucosal immunological features in pigs are unknown.This study revealed the glucose and lipid metabolic responses and the dual role of gut microbiota in pigs during cold and non-cold adaptation.Moreover,the regulatory effects of dietary glucose supplements on glucose and lipid metabolism and the colonic mucosal barrier were evaluated in cold-exposed pigs.Results Cold and non-cold-adapted models were established by Min and Yorkshire pigs.Our results exhibited that cold exposure induced glucose overconsumption in non-cold-adapted pig models(Yorkshire pigs),decreasing plasma glucose concentrations.In this case,cold exposure enhanced the ATGL and CPT-1αexpression to promote liver lipolysis and fatty acid oxidation.Meanwhile,the two probiotics(Collinsella and Bifidobacterium)depletion and the enrichment of two pathogens(Sutterella and Escherichia-Shigella)in colonic microbiota are not conducive to colonic mucosal immunity.However,glucagon-mediated hepatic glycogenolysis in cold-adapted pig models(Min pigs)maintained the stability of glucose homeostasis during cold exposure.It contributed to the gut microbiota(including the enrichment of the Rikenellaceae RC9 gut group,[Eubacterium]coprostanoligenes group and WCHB1-41)that favored cold-adapted metabolism.Conclusions The results of both models indicate that the gut microbiota during cold adaptation contributes to the protection of the colonic mucosa.During non-cold adaptation,cold-induced glucose overconsumption promotes thermogenesis through lipolysis,but interferes with the gut microbiome and colonic mucosal immunity.Furthermore,glucagon-mediated hepatic glycogenolysis contributes to glucose homeostasis during cold exposure.

Improving the accuracy of genomic prediction for meat quality traits using whole genome sequence data in pigs

Background Pork quality can directly affect customer purchase tendency and meat quality traits have become valu-able in modern pork production.However,genetic improvement has been slow due to high phenotyping costs.In this study,whole genome sequence(WGS)data was used to evaluate the prediction accuracy of genomic best linear unbiased prediction(GBLUP)for meat quality in large-scale crossbred commercial pigs.Results We produced WGS data(18,695,907 SNPs and 2,106,902 INDELs exceed quality control)from 1,469 sequenced Duroc×(Landrace×Yorkshire)pigs and developed a reference panel for meat quality including meat color score,marbling score,L*(lightness),a*(redness),and b*(yellowness)of genomic prediction.The prediction accuracy was defined as the Pearson correlation coefficient between adjusted phenotypes and genomic estimated breeding values in the validation population.Using different marker density panels derived from WGS data,accuracy differed substantially among meat quality traits,varied from 0.08 to 0.47.Results showed that MultiBLUP outperform GBLUP and yielded accuracy increases ranging from 17.39%to 75%.We optimized the marker density and found medium-and high-density marker panels are beneficial for the estimation of heritability for meat quality.Moreover,we conducted genotype imputation from 50K chip to WGS level in the same population and found average concord-ance rate to exceed 95%and r^(2)=0.81.Conclusions Overall,estimation of heritability for meat quality traits can benefit from the use of WGS data.This study showed the superiority of using WGS data to genetically improve pork quality in genomic prediction.

A promising resilience parameter for breeding:the use of weight and feed trajectories in growing pigs

Background Increasing resilience is a priority in modern pig breeding.Recent research shows that general resilience can be quantified via variability in longitudinal data.The collection of such longitudinal data on weight,feed intake and feeding behaviour in pigs has been facilitated by the development of technologies such as automated feeding stations.The goal of this study was to investigate resilience traits,which were estimated as deviations from longitudinal weight,feed intake and feeding behaviour data during the finishing phase.A dataset with 324,207 records between the age of 95 and 155 days on 5,939 Pietrain pigs with known pedigree and genomic information was used.We provided guidelines for a rigid quality control of longitudinal body weight data,as we found that outliers can significantly affect results.Gompertz growth curve analysis,linear modelling and trajectory analyses were used for quantifying resilience traits.Results To our knowledge,this is the first study comparing resilience traits from longitudinal body weight,feed intake and feeding behaviour data in pigs.We demonstrated that the resilience traits are lowly to moderately heritable for deviations in body weight(h2=2.9%–20.2%),in feed intake(9.4%–23.3%)and in feeding behaviour(16.2%–28.3%).Additionally,these traits have good predictive abilities in cross-validation analyses.Deviations in individual body weight and feed intake trajectories are highly correlated(rg=0.78)with low to moderate favourable genetic correlations with feed conversion ratio(rg=0.39–0.49).Lastly,we showed that some resilience traits,such as the natural logarithm of variances of observed versus predicted body weights(lnvarweight),are more robust to lower observation frequencies and are repeatable over three different time periods of the finishing phase.Conclusions Our results will help future studies investigating resilience traits and resilience-related traits.Moreover,our study provides first results on standardization of quality control and efficient data sampling from automated feeding station data.Our findings will be valuable for breeding organizations as they offer evidence that pigs’general resilience can be selected on with good accuracy.Moreover,this methodology might be extended to other species to quantify resilience based on longitudinal data.

The effects of dietary supplementation with mushroom or selenium enriched mushroom powders on the growth performance and intestinal health of post-weaned pigs

Background There is an urgent need to identify natural bioactive compounds that can enhance gastrointestinal health and promote pig growth performance in the absence of pharmacological levels of zinc oxide(ZnO).The objectives of this study were to:1)compare the effects of mushroom powder supplemented with inorganic selenium(inSeMP)to mushroom powder enriched with organic selenium(orgSeMP)to pharmacological levels of ZnO on growth performance and faecal scores(FS)for the first 21 d post-weaning(Period 1);and 2)compare the molecular and microbial effects of inSeMP and orgSeMP in these pigs on d 39 post-weaning(Period 2).Methods In Period 1,pigs(3 pigs/pen;8 pens/treatment)were assigned to:(1)basal diet(control);(2)basal diet+zinc oxide(ZnO)(3100 mg/kg d 1–14,1550 mg/kg d 15–21);(3)basal diet+mushroom powder supplemented with inorganic selenium(inSeMP)containing selenium(selenite)content of 0.3 mg/kg feed;(4)basal diet+mushroom powder enriched with organic selenium(orgSeMP)containing selenium(selenocysteine)content of 0.3 mg/kg feed.Mushroom powders were included at 6.5 g/kg of feed.Results In Period 1,there was no effect of diets on average daily gain(ADG)and gain:feed(G:F)ratio(P>0.05).The orgSeMP supplemented pigs had a lower average daily feed intake(ADFI)compared to all other groups(P<0.05).The ZnO supplemented pigs had reduced FS compared to the basal and mushroom group,while the orgSeMP supplemented pigs had lower FS compared to the basal group during the 21 d experimental period(P<0.05).In Period 2,there was no effect of diets on ADFI,ADG and G:F ratio(P>0.05).The orgSeMP supplementation increased the caecal abundance of bacterial members of the Firmicutes and Bacteroidetes phylum,including Lactobacillus,Agathobacter,Roseburia,and Prevotella and decreased the abundance of Sporobacter compared to the basal group,while inSeMP increased the caecal abundance of Prevotella and decreased the caecal abundance of Sporobacter compared to the basal group(P<0.05).Dietary supplementation with inSeMP increased expression of TLR4 and anti-inflammatory cytokine gene IL10 and decreased nutrient transporter gene FABP2 compared to the orgSeMP group(P<0.05).Conclusion OrgSeMP is a novel and sustainable way to incorporate selenium andβ-glucans into the diet of weaned pigs whilst improving FS and modulating the caecal microbiota.

Phytogenic feed additives alleviate pathogenic Escherichia coli-induced intestinal damage through improving barrier integrity and inhibiting inflammation in weaned pigs

Background:This study was conducted to investigate the effects of each phytogenic feed additive(PFA;PFA1,bitter citrus extract;PFA2,a microencapsulated blend of thymol and carvacrol;PFA3,a mixture of bitter citrus extract,thymol,and carvacrol;PFA4,a premixture of grape seed,grape marc extract,green tea,and hops;PFA5,fenugreek seed powder)on the growth performance,nutrient digestibility,intestinal morphology,and immune response in weaned pigs infected with Escherichia coli(E.coli).Results:A total of 634-week-old weaned pigs were placed in individual metabolic cages and assigned to seven treatment groups.The seven treatments were as follows:1)NC;basal diet without E.coli challenge,2)PC;basal diet with E.coli challenge,3)T1;PC+0.04%PFA1,4)T2;PC+0.01%PFA2,5)T3;PC+0.10%PFA3,6)T4;PC+0.04%PFA4,7)T5;PC+0.10%PFA5.The experiments lasted in 21 d,including 7 d before and 14 d after the first E.coli challenge.In the E.coli challenge treatments,all pigs were orally inoculated by dividing a total of 10 mL of E.coli F18 for 3 consecutive days.The PFA-added groups significantly increased(P<0.05)average daily gain and feed efficiency and decreased(P<0.05)the fecal score at d 0 to 14 post-inoculation(PI).Tumor necrosis factorαwas significantly lower(P<0.05)in the PFA-added groups except for T1 in d 14 PI compared to the PC treatment.The T3 had a higher(P<0.05)immunoglobulin G and immunoglobulin A concentration compared to the PC treatment at d 7 PI.Also,T3 showed significantly higher(P<0.05)villus height:crypt depth and claudin 1 expression in ileal mucosa,and significantly downregulated(P<0.05)the expression of calprotectin compared to the PC treatment.Conclusions:Supplementation of PFA in weaned pigs challenged with E.coli alleviated the negative effects of E.coli and improved growth performance.Among them,the mixed additive of bitter citrus extract,thymol,and carvacrol showed the most effective results,improving immune response,intestinal morphology,and expression of tight junctions.