Current Situation and Progress of Pig Model in Otology Research

Pig models are widely used in otological research. The establishment of common pig and miniature pig animal models has opened up new fields in otological research and is also an ideal large otological animal model. This article introduces the applications, current status, progress, advantages, and issues of using pigs as otologic animal models. It summarizes current research on pigs in the fields of hearing disorders, otitis, vertigo, cochlea, gene editing, and tissue engineering, among other otologic and audiological areas. These models are valuable for translating basic medical science into clinical applications. Based on this, platforms have been established for studying deafness and vertigo, cochlear implantation experiments, stem cell and gene therapy, and tissue engineering. These serve as ideal experimental models for the prevention and treatment of ear diseases, pointing toward new directions. This will bolster the promotion and application of pig models in the fields of tissue engineering and gene editing in the future.

Comparative analysis of primate and pig cells reveals primate-specific PINK1 expression and phosphorylation

PTEN-induced putative kinase 1(PINK1),a mitochondrial kinase that phosphorylates Parkin and other proteins,plays a crucial role in mitophagy and protection against neurodegeneration.Mutations in PINK1 and Parkin can lead to loss of function and early onset Parkinson's disease.However,there is a lack of strong in vivo evidence in rodent models to support the theory that loss of PINK1 affects mitophagy and induces neurodegeneration.Additionally,PINK1 knockout pigs(Sus scrofa)do not appear to exhibit neurodegeneration.In our recent work involving non-human primates,we found that PINK1 is selectively expressed in primate brains,while absent in rodent brains.To extend this to other species,we used multiple antibodies to examine the expression of PINK1 in pig tissues.In contrast to tissues from cynomolgus monkeys(Macaca fascicularis),our data did not convincingly demonstrate detectable PINK1expression in pig tissues.Knockdown of PINK1 in cultured pig cells did not result in altered Parkin and BAD phosphorylation,as observed in cultured monkey cells.A comparison of monkey and pig striatum revealed more PINK1-phosphorylated substrates in the monkey brain.Consistently,PINK1 knockout in pigs did not lead to obvious changes in the phosphorylation of Parkin and BAD.These findings provide new evidence that PINK1expression is specific to primates,underscoring the importance of non-human primates in investigating PINK1function and pathology related to PINK1 deficiency.

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.

Chromatin condensation but not DNA integrity of pig sperm is greater in the sperm-rich fraction

Background Protamination and condensation of sperm chromatin as well as DNA integrity play an essential role during fertilization and embryo development.In some mammals,like pigs,ejaculates are emitted in three separate fractions:pre-sperm,sperm-rich(SRF)and post sperm-rich(PSRF).These fractions are known to vary in volume,sperm concentration and quality,as well as in the origin and composition of seminal plasma(SP),with differences being also observed within the SRF one.Yet,whether disparities in the DNA integrity and chromatin condensation and pro-tamination of their sperm exist has not been interrogated.Results This study determined chromatin protamination(Chromomycin A3 test,CMA_(3)),condensation(Dibromobi-mane test,DBB),and DNA integrity(Comet assay)in the pig sperm contained in the first 10 m L of the SRF(SRF-P1),the remaining portion of the sperm-rich fraction(SRF-P2),and the post sperm-rich fraction(PSRF).While chromatin protamination was found to be similar between the different ejaculate fractions(P>0.05),chromatin condensation was seen to be greater in SRF-P1 and SRF-P2 than in the PSRF(P=0.018 and P=0.004,respectively).Regarding DNA integrity,no differences between fractions were observed(P>0.05).As the SRF-P1 has the highest sperm concentra-tion and ejaculate fractions are known to differ in antioxidant composition,the oxidative stress index(OSi)in SP,calcu-lated as total oxidant activity divided by total antioxidant capacity,was tested and confirmed to be higher in the SRF-P1 than in SRF-P2 and PSRF(0.42±0.06 vs.0.23±0.09 and 0.08±0.00,respectively;P<0.01);this index,in addition,was observed to be correlated to the sperm concentration of each fraction(Rs=0.973;P<0.001).Conclusion While sperm DNA integrity was not found to differ between ejaculate fractions,SRF-P1 and SRF-P2 were observed to exhibit greater chromatin condensation than the PSRF.This could be related to the OSi of each fraction.

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.

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.

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.

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.

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.

Single-cell profiling of the pig cecum at various developmental stages

The gastrointestinal tract is essential for food digestion,nutrient absorption,waste elimination,and microbial defense.Single-cell transcriptome profiling of the intestinal tract has greatly enriched our understanding of cellular diversity,functional heterogeneity,and their importance in intestinal tract development and disease.Although such profiling has been extensively conducted in humans and mice,the single-cell gene expression landscape of the pig cecum remains unexplored.Here,single-cell RNA sequencing was performed on 45572 cells obtained from seven cecal samples in pigs at four different developmental stages(days(D)30,42,150,and 730).Analysis revealed 12 major cell types and 38 subtypes,as well as their distinctive genes,transcription factors,and regulons,many of which were conserved in humans.An increase in the relative proportions of CD8^(+)T and Granzyme A(low expression)natural killer T cells(GZMA^(low)NKT)cells and a decrease in the relative proportions of epithelial stem cells,Tregs,RHEX^(+)T cells,and plasmacytoid dendritic cells(pDCs)were noted across the developmental stages.Moreover,the post-weaning period exhibited an up-regulation in mitochondrial genes,COX2 and ND2,as well as genes involved in immune activation in multiple cell types.Cell-cell crosstalk analysis indicated that IBP6^(+)fibroblasts were the main signal senders at D30,whereas IBP6^(−)fibroblasts assumed this role at the other stages.NKT cells established interactions with epithelial cells and IBP6^(+)fibroblasts in the D730 cecum through mediation of GZMA-F2RL1/F2RL2 pairs.This study provides valuable insights into cellular heterogeneity and function in the pig cecum at different development stages.

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.

Digital measuring the ocular morphological parameters of guinea pig eye in vivo with Python

AIM:To quantitatively measure ocular morphological parameters of guinea pig with Python technology.METHODS:Thirty-six eyeballs of eighteen 3-weekold guinea pigs were measured with keratometer and photographed to obtain the horizontal,coronal,and sagittal planes respectively.The corresponding photo pixels-actual length ratio was acquired by a proportional scale.The edge coordinates were identified artificially by ginput function.Circle and conic curve fitting were applied to fit the contour of the eyeball in the sagittal,coronal and horizontal view.The curvature,curvature radius,eccentricity,tilt angle,corneal diameter,and binocular separation angle were calculated according to the geometric principles.Next,the eyeballs were removed,canny edge detection was applied to identify the contour of eyeball in vitro.The results were compared between in vivo and in vitro.RESULTS:Regarding the corneal curvature and curvature radius on the horizontal and sagittal planes,no significant differences were observed among results in vivo,in vitro,and the keratometer.The horizontal and vertical binocular separation angles were 130.6°±6.39°and 129.8°±9.58°respectively.For the corneal curvature radius and eccentricity in vivo,significant differences were observed between horizontal and vertical planes.CONCLUSION:The Graphical interface window of Python makes up the deficiency of edge detection,which requires too much definition in Matlab.There are significant differences between guinea pig and human beings,such as exotropic eye position,oblique oval eyeball,and obvious discrepancy of binoculus.This study helps evaluate objectively the ocular morphological parameters of small experimental animals in emmetropization research.

Feeding Practices and Use of Lysine and Methionine in Pigrationing on Intensified Pig Breeding in the West Center and Hauts Bassins Regions of Burkina Faso

The aim of the study was to assess feeding practices and the use of lysine and methionine in pig rationing on intensified and semi-intensive pig breeding in the Koudougou and Bobo-Dioulasso areas. To this end, a cross-sectional survey was carried out on 87 breeding in these towns. A Discriminant Factorial Analysis (DFA) confirming a k-means classification of the data collected was used to retain 71 breeding divided into three breeding classes: Class A (32.4% of breeding), Class B (14.08%) and Class C (53.52%). The results show that the majority of pig breeders were men between the ages of 36 and 59. Average herd sizes were 35 ± 28;79 ± 42 and 89 ± 21 pigs for Classes A, B and C respectively. The main breeds of pig found on the breeding were crossbred, Large white, local, Landrace and Duroc. Class A (26.1%), B (30%) and C (15.8%) breeders were familiar with both lysine and methionine. Class A breeders distributed feed staggered (65.2%) and in rations (34.8%). Lysine (13%) and methionine (8.7%) were purchased at 5250 FCFA/kg. Those in class B distributed feed staggered (50%) and in the form of rations (50%), in which they incorporated lysine (30%) and methionine (30%) purchased at a cost of 2500 FCFA/kg and 3000 FCFA/kg respectively. Rationing and staggered feeding were practiced by 23.7% and 76.3% of Class C breeders respectively. Only lysine purchased at 3400 FCFA/kg was incorporated into rations by 10.5% of breeders. The high cost of lysine and methionine was incriminated by Class A (100%), B (33.3%) and C (50%) breeders. In conclusion, intensive pig breeding, the practice of rationing and the incorporation of the amino acids lysine and methionine are of ascending importance from classes C, A to B. The high cost of feedstuffs, particularly lysine and methionine, compromises their use in rations, which could have a negative impact on expected breeding performance. The screening and use of feeds rich in and/or enriched with these amino acids, through the development or adaptation of technologies, could improve the efficiency of rations and the productivity of intensive pig breeding in Burkina Faso.

PIG3启动子结合元件(TGYCC)n与肿瘤易感性的研究进展

PIG3是受p53调控的下游靶基因,通过参与合成活性氧及对氧化应激的调控参与细胞凋亡过程。PIG3的启动子区有一段串联重复序列(TGYCC)n(Y=C或T),其转录调控与这段五核苷酸重复序列密切相关。本文对(TGYCC)n这段串联重复序列在PIG3转录调控中的作用进行综述,探讨其多态性与肿瘤易感性的关系。

Impact of Sharp Fluctuations of Live Pig Prices on Financial Capacity of Pig Breeding Enterprises : An Analysis Based on the Data of Listed Enterprises from 2018 to 2021

Based on the general equilibrium theory of microeconomics,this study first analyzed the causes of sharp fluctuations in live pig prices,and then explored the financial capabilities of enterprises during the sharp fluctuations of live pig prices by using the financial data of 4 typical top listed enterprises from 2018 to 2021.By comparing the changes in the capabilities of enterprises,the impact of price on the financial capability of enterprises and differences were identified.The research results showed that the price of live pigs played a decisive role in enterprise profits,and there were huge differences in the fluctuation period.In the sharp increase period of price,price temptation is easy to cause enterprises to over-invest,resulting in excessive growth of enterprise assets,and increasing the business risk of enterprises.Based on the above conclusions,some policy suggestions were put forward to promote the stable development of industry from the three levels of enterprises,industries and government departments.

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.

Genetic gain and inbreeding from simulation of different genomic mating schemes for pig improvement

Background Genomic selection involves choosing as parents those elite individuals with the higher genomic estimated breeding values(GEBV)to accelerate the speed of genetic improvement in domestic animals.But after multi-generation selection,the rate of inbreeding and the occurrence of homozygous harmful alleles might increase,which would reduce performance and genetic diversity.To mitigate the above problems,we can utilize genomic mating(GM)based upon optimal mate allocation to construct the best genotypic combinations in the next generation.In this study,we used stochastic simulation to investigate the impact of various factors on the efficiencies of GM to optimize pairing combinations after genomic selection of candidates in a pig population.These factors included:the algorithm used to derive inbreeding coefficients;the trait heritability(0.1,0.3 or 0.5);the kind of GM scheme(focused average GEBV or inbreeding);the approach for computing the genomic relationship matrix(by SNP or runs of homozygosity(ROH)).The outcomes were compared to three traditional mating schemes(random,positive assortative or negative assortative matings).In addition,the performance of the GM approach was tested on real datasets obtained from a Large White pig breeding population.Results Genomic mating outperforms other approaches in limiting the inbreeding accumulation for the same expected genetic gain.The use of ROH-based genealogical relatedness in GM achieved faster genetic gains than using relatedness based on individual SNPs.The GROH-based GM schemes with the maximum genetic gain resulted in 0.9%-2.6%higher rates of genetic gainΔG,and 13%-83.3%lowerΔF than positive assortative mating regardless of heritability.The rates of inbreeding were always the fastest with positive assortative mating.Results from a purebred Large White pig population,confirmed that GM with ROH-based GRM was more efficient than traditional mating schemes.Conclusion Compared with traditional mating schemes,genomic mating can not only achieve sustainable genetic progress but also effectively control the rates of inbreeding accumulation in the population.Our findings demonstrated that breeders should consider using genomic mating for genetic improvement of pigs.

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.

Pig macrophages with site-specific edited CD163 decrease the susceptibility to infection with porcine reproductive and respiratory syndrome virus

Porcine reproductive and respiratory syndrome(PRRS)is recognized as one of the most infectious viral diseases of swine.Although Cluster of differentiation 163(CD163)is identified as an essential receptor for mediating PRRS virus(PRRSV)infection,the important residues involved in infection on CD163 are still unclear.Therefore,it is very important to identify these key residues to study the mechanism of PRRSV infection and to generate anti-PRRSV pigs.In this study,we first generated immortalized porcine alveolar macrophage(IPAM)cell lines harboring 40-residues(residues 523-562,including R561(arginine(R)at position 561))deletion of CD163.PRRSV infection experiments showed that these IPAM cell lines were completely resistant to PRRSV infection.We then generated cloned pigs carrying CD163-R561A(an arginine(R)to alanine(A)substitution at position 561 of CD163).PRRSV challenge experiments in porcine alveolar macrophages(PAMs)isolated from the CD163-R561A pigs showed significantly lower susceptibility to PRRSV than that of CD163-R561 PAMs.Through this study,we show that CD163523-562 contains essential residues for mediating PRRSV infection,and that CD163 R561 significantly contributes to PRRSV infection but is not essential for infection.These functional sites can therefore serve as new targets for understanding the mechanism of PRRSV infection.Furthermore,CD163-R561A pigs can be used as an important model for improving pig germplasm with resistance against PRRSV.