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Present study was carried out on 32 pure Black Slavonian (BS) pigs and 32 crossbreds of Black Slavonian and Duroc (BSxDu); number of barrows and gilts was equal in both groups. Every three months, 4 barrows and 4 gilts from both groups were slaughtered for the analysis of tissue and primal parts development in the series of subsequent dissection trials covering a total fattening period of 12 months. The results showed that crossing the BS pigs with Duroc resulted in significant increase in the development of main tissues and primal parts. Significantly higher live weight, carcass weight and lean meat percentage was reported in BS pigs compared to BSxDu pigs (P<0.001). The exception was lean meat percentage determined at the age of 3 months (P>0.05). BSxDu pigs entered the experiment at significantly higher live weight (P<0.05) than BS pigs; this relationship continued during entire growth period. Muscle and fatty tissues followed the similar patterns of growth. Muscle tissue was produced in higher amounts than fat in case of BS pigs; in BSxDu pigs, fat overgrew muscle at the later stage of fattening. Although BS pigs exhibited lower formation of muscle tissue than BSxDu, their carcasses were significantly leaner. [ABSTRACT FROM AUTHOR]

Microsatellites (MS) have been, for the last two decades, widely used for parentage analysis in all types of livestock, including pigs. Conservation efforts on Banija spotted pigs included genetic characterization of the breed with MS markers. Since recent comparison of pedigree and MS data revealed some inconsistencies, the aim of this study was to develop a set of highly polymorphic and heterozygous MS markers, which could be used for parentage analysis and to prevent pedigree errors. 12 MS markers with the polymorphic information content (PIC) above 0.62 were chosen and combined into a single multiplex polymerase chain reaction (PCR). The combined non-exclusion probability for one candidate parent (NE-1P) was 0.00246149, the combined NE-1P given the genotype of a known parent of the opposite sex (NE-2P) was 0.00003739 and combined non-exclusion probability for a candidate parent pair (NE-PP) was 0.00000003. Due to a high information content of selected MS markers it was possible to obtain high accuracy in parentage assignment, which was confirmed by analyzing actual data with known genetic relationships. [ABSTRACT FROM AUTHOR]

The peculiarities of growth, development and fattening qualities of young pigs of different genotypes evaluated by the MC4R gene (marker of meat and fattening qualities, their association with productivity were determined). The true difference between animals of different genotypes (GG, AA and AG) is set at live weight at 3 months of age (4.9-5.2 kg), age of achievement live weight 100 kg (GG - Ag, 7.1 days), thickness of the sphinc at 6-7 thoracic vertebrae (GG - AA - 3.7 mm, GG - AG - 2.1 mm), body length and the chest circumference of the shoulder blades at the age of 6 months (AG - GG, 1.3-1.8 cm). According to O. Wangen's index, the GG genotype is an essential advantage in animals. Compared to the peers of the genotype AA and AG, the difference was 44.86-37.73%. [ABSTRACT FROM AUTHOR]

Abstract The Bama mini-pig (BM pig) is an inbred strain of the Bama Xiang pig (BX pig) and an important animal model used for studying human diseases. The extremely long inbreeding period renders a clear distinction between the features of the BM and BX strains, such as in their metabolism and olfactory system. However, there is limited information about differences between BM and BX animals at the genomic level. In this study, we generated genome sequencing data and used the assembly- vs -assembly approach to evaluate the phenotypic variations caused by inbreeding in these strains. Moreover, we detected differential expression of mutant genes related to the phenotypes in BX and BM pigs. We sequenced the genome of the BX pig strain and performed a series of analyses to reveal the comprehensive inbred genetic variants between BX and BM pigs. Here, the 2.56-Gb draft genome assembly for the BX pig and an N50 contig length of approximately 11.87 kb is described, and an N50 scaffold length of approximately 99 kb and the variations in the BX pig genome were identified by comparison with the BM pig reference genome. There were 1,424,354 single nucleotide polymorphisms (SNPs), 2,961,891 insertions and deletions (indels), 13,772 structural variants (SVs), and 20,606 copy number variants (CNVs) identified in the BX genome. Functional annotation of SVs and CNVs showed that the genes (ADGRE2 , GPR143 , olfactory receptor 52B4-like , olfactory receptor 10H1-like and SHROOM2) with both SVs and CNVs were enriched in the most of all KEGG pathways and gene ontology (GO) terms of mutant genes. ADGRE2, GPR143 and SHROOM2 were both found to have significant higher expression levels in BX pigs than in BM pigs. In the contrary, the expressions of olfactory receptor 52B4-like and olfactory receptor 10H1-like were significant lower in BX pigs than in BM pigs. In conclusion, sequence analysis of the BX pig genome revealed that the genome structure of the two pig strains has considerable genomic variation that was caused by the long inbreeding period. Moreover, qRT-PCR analysis of the mutant genes displayed a significant distinction that may be associated with phenotypic differences between these pig strains. Highlights • Genome of BM pig provides a unique opportunity to detect inbred variants in Bama pigs. • The genome of BX pig has been yielded. • Comprehensive inbred variation discovery in Bama pigs by the two genomes • Genetic mutant and different expression of several genes link to distinction of features between Bama pigs. [ABSTRACT FROM AUTHOR]

Changes in husbandry systems as well as consumers’ increasing demands for animal welfare lead to increasing importance of traits such as handleability and aggressiveness in pigs. However, before using such novel traits for selection decisions, information on genetic parameters for these traits for the specific population is required. Therefore, weight gain and behaviour-related traits were recorded in 1004 pigs (814 Pietrain x German Landrace crossbred, 190 German Landrace purebred) at different ages. Behaviour indicators and tests were assessed and conducted, respectively under commercial farm conditions and included scoring of skin lesions (twice) and behaviour during backtests (twice), injections (once), handling (twice) and weighing (three times). Since behaviour scores often exhibit suboptimal statistical properties for parametric analyses, variance components were estimated using an animal model assuming a normal (Gaussian, GA; all traits) and additionally a binary distribution of variables (BI; using a logit-link function for all behaviour traits). Heritabilities for behavioural traits ranged from 0.02 ± 0.04 (finishing pig handling test; BI) to 0.36 ± 0.08 (backtest 2; GA) suggesting that some of the traits are potentially useful for genetic selection (e.g. finishing pig weighing test: h2 (GA) = 0.20 ± 0.07). Only minor differences were observed for results from binary and Gaussian analyses of the same traits suggesting that either approach might yield valid results. However, four-fold cross-validation using correlations between breeding values of a sub-set of animals for the sample trait finishing pig weighing score indicated slight superiority of the logit model (r = 0.85 ± 0.04 vs. r = 0.77 ± 0.03). Generally, only weak to moderate associations were found between behavioural reactions to the same test at different ages (rp ≤ 0.11 for weighing at different ages; rp = 0.30 but rg (GA) = 0.84 ± 0.11 for the backtests) as well as between reactions to different tests. Therefore, for inclusion of behaviour traits into breeding programmes, and considering high labour input required for some tests such as the backtest, it is recommended to assess behaviour during situations that are relevant and identical to practical conditions, while the use of indicator traits generally does not appear to be a very promising alternative. [ABSTRACT FROM AUTHOR]

Insulin-like growth factor 2 (IGF2) is an important growth factor, which promotes growth and development in mammals during fetal and postnatal stages. Using CRISPR-Cas9 system, we generated multiple founder pigs containing 12 different mutant alleles around a regulatory element within the intron 3 of IGF2 gene. Crossing two male founders passed four mutant alleles onto F1 generation, and these mutations abolished repressor ZBED6 binding and rendered this regulatory element nonfunctional. Both founders and F1 animals showed significantly faster growth, without affecting meat quality. These results indicated that editing IGF2 intron 3-3072 site using CRISPR-Cas9 technology improved meat production in Bama pigs. This is the first demonstration that editing non-coding region can improve economic traits in livestock. [ABSTRACT FROM AUTHOR]

Objective: To aid in the development of a comprehensive list of functional variants in the swine genome, single nucleotide polymorphisms (SNP) were identified from whole genome sequence of 240 pigs. Interim data from 72 animals in this study was published in 2017. This communication extends our previous work not only by utilizing genomic sequence from additional animals, but also by the use of the newly released Sscrofa 11.1 reference genome. Results: A total of 26,850,263 high confidence SNP were identified, including 19,015,267 reported in our previously published results. Variation was detected in the coding sequence or untranslated regions (UTR) of 78% of the genes in the porcine genome: 1729 loss-of-function variants were predicted in 1162 genes, 12,686 genes contained 64,232 nonsynonymous variants, 250,403 variants were present in UTR of 15,739 genes, and 15,284 genes contained 90,939 synonymous variants. In total, approximately 316,000 SNP were classified as being of high to moderate impact (i.e. loss-of-function, nonsynonymous, or regulatory). These high to moderate impact SNP will be the focus of future genome-wide association studies. [ABSTRACT FROM AUTHOR]

Genetic reassortment between influenza A viruses (IAVs) facilitate emergence of pandemic strains, and swine are proposed as a “mixing vessel” for generating reassortants of avian and mammalian IAVs that could be of risk to mammals, including humans. However, how a transmissible reassortant emerges in swine are not well understood. Genomic analyses of 571 isolates recovered from nasal wash samples and respiratory tract tissues of a group of co-housed pigs (influenza-seronegative, avian H1N1 IAV–infected, and swine H3N2 IAV–infected pigs) identified 30 distinct genotypes of reassortants. Viruses recovered from lower respiratory tract tissues had the largest genomic diversity, and those recovered from turbinates and nasal wash fluids had the least. Reassortants from lower respiratory tracts had the largest variations in growth kinetics in respiratory tract epithelial cells, and the cold temperature in swine nasal cells seemed to select the type of reassortant viruses shed by the pigs. One reassortant in nasal wash samples was consistently identified in upper, middle, and lower respiratory tract tissues, and it was confirmed to be transmitted efficiently between pigs. Study findings suggest that, during mixed infections of avian and swine IAVs, genetic reassortments are likely to occur in the lower respiratory track, and tissue tropism is an important factor selecting for a transmissible reassortant. [ABSTRACT FROM AUTHOR]

Abstract To determine the genetic basis of pork eating quality traits and cooking loss, we herein performed a genome-wide association study (GWAS) for tenderness, juiciness, oiliness, umami, overall liking and cooking loss by using whole genome sequences of heterogeneous stock F6 pigs which were generated by crossing 4 typical western pig breeds (Duroc, Landrace, Large White and Pietrain) and 4 typical Asian pig breeds (Erhualian, Laiwu, Bamaxiang and Tibetan). We identified 50 associated loci (QTLs) and most of them are novel. Seven loci also showed pleiotropic associations with different traits. In addition, we identified multiple promising candidate genes for these traits, including PAK1 and AQP11 for cooking loss, EP300 for tenderness, SDK1 for juiciness, FITM2 and 5-linked MYH genes for oiliness, and TNNI2 and TNNT3 for overall liking. Our results provide not only a better understanding of the genetic basis for meat quality, but also a potential application in future breeding for these complex traits. [ABSTRACT FROM AUTHOR]

Summary: Inbreeding, which has several causes including genetic drift, population bottlenecks, mating of close relatives and selection, can leave tracts of runs of homozygosity (ROH) along genomes. Recently, decreasing performance on reproductive traits, which might have resulted from inbreeding, has been observed in Chinese pigs. In this study, 830 individuals from Western and Chinese pig breeds were genotyped using the reduced‐representation sequencing method. After imputation and quality control, 60 850 high‐confidence SNPs were retained for ROH detection. A simulation was performed to explore the reliability of ROH detection with imputed data. Different ROH‐related variables were compared between imputed and non‐missing genotypes used in ROH detection. Furthermore, ROH islands were evaluated and annotated to find genes influenced by inbreeding in these pigs. The simulation results showed that imputed data with 0.7 as the average missing genotype rate and three heterozygotes allowed in a sliding window have comparable ROH detected compared with data with no missing genotypes. Compared with Western pig breeds, Chinese pigs had more autosomes covered by ROH longer than 5 Mb, indicating higher inbreeding in Chinese pigs in recent times. Genes related to reproduction, immunity, meat quality and adaptability in Chinese pigs and several genes related to growth speed and immunity in Western pigs were observed in short ROH islands. The reproduction‐related gene PRM1 was found to be located in the most frequent long ROH island in Chinese pigs, which might explain the decreasing fertility in Chinese pig breeds. [ABSTRACT FROM AUTHOR]

Summary: Long noncoding RNAs (lncRNAs) constitute a large class of functional non‐coding RNAs that play important roles in many biological processes. Thousands of lncRNAs have been identified in mammals. Pig is an important farm animal and biomedical model. It is essential to create a Sus scrofa lncRNA database to enable further study of the function and evolution of lncRNAs. In this study, we built a systematic S. scrofa lncRNA database named lncRNAnet that contains 53 468 S. scrofa lncRNAs with their sequence characteristics, genomic locations, conservation, overlapping SNPs and QTLs, and transcript abundance across nine tissues in pigs. We also integrated 212 922 human and mouse lncRNAs sequences into lncRNAnet. This database will provide for a systematic S. scrofa lncRNA classification and help investigators browse, search for and analyze lncRNAs as well as do blast searches among human, mouse and pig lncRNAs. Thus, lncRNAnet should improve the understanding of the biological functions of lncRNA. The database is freely accessible at http://lnc.rnanet.org/. [ABSTRACT FROM AUTHOR]

Summary: Aggression in group‐housed pigs is a welfare concern and can negatively affect production. Skin lesions are reliable indicators of aggression and are moderately heritable, suggesting that selective breeding may reduce aggression. To further understand the genetic control of behavioral traits, such as the aggressive response to regrouping, associated single nucleotide polymorphisms (SNPs) can be identified within the genome, and the region in which these SNPs are located can be related to known genes. To investigate SNPs associated with aggression, 1093 purebred Yorkshire pigs were strategically remixed into new groups of familiar and unfamiliar animals at three life stages and lesion counts were recorded. Genomic best linear unbiased prediction (GBLUP) models were fitted for each trait. The genetic additive effect was obtained from a genetic relationship matrix constructed from the 50 924 SNPs. SNP effects and their variances were estimated from the GBLUP objects. SNPs that were associated with a significant portion of the trait variance were identified for lesions to the anterior (three SNPs, FDR <5%) and central (one SNP, FDR <5%) portions of the body in grow‐finish pigs. These SNPs were located on chromosome 11, suggesting that chromosome 11 contains a region explaining variation in lesion counts that should be further explored to identify genes underlying biological control of aggression. [ABSTRACT FROM AUTHOR]

The aim of this study was to evaluate MYH7 single nucleotide polymorphism (SNP) (NC_010449.4: g.7:75667956G>A) in relation to growth and carcass traits in pigs reared in Poland. Previous study has shown that g.7:75667956G>A substitution in pigs influences miR-208b and MYH7 expression, and is associated with proportion of muscle fibre types. The presented study was conducted on 582 pigs belonging to six breeds: Polish Landrace, Polish Large White, Puławska, Pietrain, Duroc and Hampshire. Statistical analysis (GLM procedure) was performed for first three breeds separately and for whole group together. Our study showed that investigated SNP was associated with test daily gain, average daily gain, age at slaughter and number of days in experiment (P ≤ 0.05 or P ≤ 0.01) in Polish Large White, Puławska and whole group. Among carcass traits MYH7 variants influenced mean backfat thickness from 5 measurements (P ≤ 0.05) in the same groups. We also noticed some associations for slaughter efficiency, weight of loin without backfat and skin, loin eye area and meat percentage (P ≤ 0.05 or P ≤ 0.01) but results were not consistent among breeds and whole group. Obtained results indicate that MYH7 SNP could be used as a genetic marker for improvement of some growth traits and backfat thickness in pigs. [ABSTRACT FROM AUTHOR]

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Highlights • Processing fluids (PF) constitute a useful sample to detect PRRSV infections at processing. • PRRSV can circulate in the farm at a low prevalence, increasing the chances of a re-break. • Young parity female litters should be targeted for PRRSV detection. • Current practice to bleed 30 pigs could be underestimating PRRSV prevalence in the herd. • The decrease in sensitivity at the litter level can be compensated by sampling more litters to detect PRRSV at the herd level. Abstract Collection of serum samples of pigs at weaning to monitor for porcine reproductive and respiratory syndrome virus (PRRSV) has become a common practice to determine PRRSV herd infection status. Diagnostic sensitivity of this practice is low in herds undergoing PRRSV elimination once prevalence of infection is near zero. Thus, the goal of this study was to characterize the dynamics of PRRSV infection in 3 day-old pigs overtime using serum and serosanguineous fluids obtained as part of castration and tail docking practices (processing fluids (PF)). Secondary goal was to estimate sensitivity and specificity of PF in the 3 day old population. A 6000 breed-to-wean sow herd was monitored every three weeks for 23 weeks after a PRRSV outbreak by collecting both PF and individual serum samples from all pigs in the selected litters. Out of the 77 litters tested, 23 (29.8%) were identified as positive using the PF and the serum samples, with a Cohen's kappa statistic of 0.81 (95% CI: 0.59–1) between the results obtained in each sample type. The sensitivity and specificity of the PF relative to the results in serum was 87% (95% CI: 66%–97%) and 94% (95% CI: 85%–99%) respectively. The percentage of PRRSV positive litters decreased over time and litters from gilts were more likely to test positive than those from older sows. Overall, the study demonstrates that PF can be a convenient and reliable specimen to monitor PRRSV infection in breeding herds. [ABSTRACT FROM AUTHOR]

Highlights • Extremely high faecal carriage rate of mcr-1 in Chinese pig production. • E. coli is the dominant host bacteria of mcr-1. • Mcr-1 -positive E. coli isolates are not resistant to carbapenems and tigecycline. • The representative mcr-1 -positive E. coli isolates showed diverse PFGE patterns. Abstract The mcr-1 gene is a plasmid-borne and globally distributed colistin-resistance gene, which threatens the last-line role of colistin in treatment of infections caused by multi-drug resistant(MDR) Gram-negative bacteria in humans. The aim of this study was to obtain a comprehensive understanding of mcr-1 prevalence in the pig industry in China. A total of 600 faecal samples were collected from 60 swine farms in 18 provinces of China. Faecal DNA was extracted and subjected to PCR screening to detect the presence of mcr-1. Positive samples were randomly selected for isolation of colistin-resistant bacteria. A total of 152 mcr-1 -positive isolates collected from different provinces were characterized by antimicrobial susceptibility testing and pulsed-field gel electrophoresis (PFGE) typing. Extremely high rate of faecal carriage of mcr-1 (457/600, 76.2%) was observed, with positive rates ranging from 45.0%–100% among the provinces. All colistin-resistant colonies were identified as Escherichia coli and mcr-1 -positive. The 152 representative mcr-1 -positive E. coli isolates showed high level resistance to ampicillin (79.60%), tetracycline(94.74%), doxycycline(93.42%), florfenicol(78.29%), enrofloxacin(44.08%), and ciprofloxacin(38.82%) and low level resistance to ceftiofur(26.32%), cefoxitin(0.66%), and amikacin(0.66%). No resistant isolates were detected for gentamicin, meropenem, and tigecycline. The mcr-1 -positive E. coli strains exhibited highly diverse PFGE patterns, which suggested that horizontal transfer through plasmids or other mobile elements was the main mechanism for the wide dissemination of mcr-1 in pig farms. Similar studies are warranted to continuously monitor colistin resistance and mcr-1 prevalence in food-animal production. [ABSTRACT FROM AUTHOR]

Highlights • From 2000, Korean CSFV changed from genotype 3 to 2 (subgenotypes 2.1b and 2.1d). • Subgenotype 2.1d(prevalent in Korea) was detected in wild boar and breeding pigs. • The mean substitution rate for circulating Korean CSFVs is 2.2114(×10−3 s/s/y). Abstract The 5′ UTR (n=102) and full-length E2 (n=37) genes of classical swine fever viruses (CSFVs) circulating in South Korea over the past 30 years (1987–2017) were examined to determine the evolutionary rate and estimated time of the most recent common ancestor (tMRCA). From 2000, the Korean classical swine fever (CSF) antigen changed from genotype 3 to 2, which comprises subgenotypes 2.1b (2002–2013) and 2.1d (2011–2017). There are genotypic variations in the full-length E2 gene of Korean CSFV genotypes 2.1b and 2.1d (seven separate amino acid substitutions); these are useful distinguishing markers. The mean substitution rate (×103 substitutions/site/year) for Korean CSFV was estimated to be 2.2088 (95% highest posterior density (HPD): lower, 1.7045; upper, 2.7574) and the mean tMRCA was estimated to be 1901 (95% HPD: lower, 1865; upper, 1933). The effective population size of Korean CSFV genotype 2 increased rapidly from 2002 to 2003, after which it remained constant. The occurrence of CSF in Korea is expected to decline in the future; however, it will likely be more prevalent in wild boar than in domestic pigs. Thus, there is a risk of transmission from wild boar to breeding pigs. [ABSTRACT FROM AUTHOR]

This study was conducted to detect the presence of porcine DNA in meatballs using polymerase chain (PCR) reaction assay targeted mitochondrial DNA (mtDNA) species-specific gene. Meatballs spiked with 1.0% (w/w) and 5.0% (w/w) porcine meat and gelatin, respectively, were prepared and heat-treated using five (n=5) cooking methods: boiling, pan-frying, roasting, microwaving and autoclaving. Two pairs of mtDNA primers were targeted in short sequences using polymerase chain reaction (PCR) analysis, producing 212- and 83-bp amplicons. Electrophoresis analysis showed positive results for porcine DNA at 1.0% and 5.0% for both porcine meat and gelatin for all of the different cooking techniques. Thus, PCR analysis using species-specific primers was demonstrated to be very useful for the detection of porcine DNA in cooked meatballs. [ABSTRACT FROM AUTHOR]

Understanding the influence of genetic variations in olfactory receptor (OR) genes on the olfaction-influenced phenotypes such as behaviors, reproduction, and feeding is important in animal biology. However, our understanding of the complexity of the OR subgenome is limited. In this study, we analyzed 1120 typing results of 20 representative OR genes belonging to 13 OR families on 14 pig chromosomes from 56 individuals belonging to seven different breeds using a sequence-based OR typing method. We showed that the presence of copy number variations, conservation of locus-specific diversity, abundance of breed-specific alleles, presence of a loss-of-function allele, and low-level purifying selection in pig OR genes could be common characteristics of OR genes in mammals. The observed nucleotide sequence diversity of pig ORs was higher than that of dogs. To the best of our knowledge, this is the first report on the individual- or population-level characterization of a large number of OR family genes in livestock species., (© 2023. The Author(s).)

The main mechanism of innate immunity is the complement system. Its components include the protein products of the C1R and C5 genes, which are involved in the classical activation pathway as well as the inflammatory and cytolytic immune responses, respectively. The aim of this study was to determine the relationship between PCR-restriction fragment length polymorphism in C1R (726T > C) and C5 (1044A > C) genes, and the values of hematological and biochemical blood indices in suckling crossbred (Polish Large White × Polish Landrace × Duroc × Pietrain) piglets (n = 473), considering their age (younger, 21 ± 3 days, n = 274; older, 35 ± 3 days, n = 199) and health status. The frequencies of the C5 genotypes deviated from the Hardy-Weinberg expectations. Younger piglets, healthy piglets, piglets that deviated from physiological norms and older piglets with the C1R TT genotype all had lower white and red blood cell indices. In piglets with the C5 CC genotype, younger piglets, piglets that deviated from physiological norms and older piglets, a greater number and/or percentage of monocytes were recorded in the blood. Older piglets also showed an increase in the number of leukocytes and granulocytes, along with a tendency for a decrease in the percentage of lymphocytes in their blood. We concluded that a polymorphism in the C1R gene may exhibit a functional association or genetic linkage with other genes involved in the process of erythropoiesis. Furthermore the relationship between the C5 gene polymorphism and the number and/or percentage of monocytes in the blood may modify the body's defense abilities. Piglets with the CC genotype, having an increased number/proportion of these cells in their blood, probably display a weakened immune response to pathogens or a chronic stimulation of the immune system.

Background: Feed efficiency is a research priority to support a sustainable meat production. It is recognized as a complex trait that integrates multiple biological pathways orchestrated in and by various tissues. This study aims to determine networks between biological entities to explain inter-individual variation of feed efficiency in growing pigs., Results: The feed conversion ratio (FCR), a measure of feed efficiency, and its two component traits, average daily gain and average daily feed intake, were obtained from 47 growing pigs from a divergent selection for residual feed intake and fed high-starch or high-fat high-fiber diets during 58 days. Datasets of transcriptomics (60 k porcine microarray) in the whole blood and metabolomics (1H-NMR analysis and target gas chromatography) in plasma were available for all pigs at the end of the trial. A weighted gene co-expression network was built from the transcriptomics dataset, resulting in 33 modules of co-expressed molecular probes. The eigengenes of eight of these modules were significantly ([Formula: see text]) or tended to be ([Formula: see text]) correlated to FCR. Great homogeneity in the enriched biological pathways was observed in these modules, suggesting co-expressed and co-regulated constitutive genes. They were mainly enriched in genes participating to immune and defense-related processes, and to a lesser extent, to translation, cell development or learning. They were also generally associated with growth rate and percentage of lean mass. In the whole network, only one module composed of genes participating to the response to substances, was significantly associated with daily feed intake and body adiposity. The plasma profiles in circulating metabolites and in fatty acids were summarized by weighted linear combinations using a dimensionality reduction method. Close association was thus found between a module composed of co-expressed genes participating to T cell receptor signaling and cell development process in the whole blood and related to FCR, and the circulating concentrations of polyunsaturated fatty acids in plasma., Conclusion: These systemic approaches have highlighted networks of entities driving key biological processes involved in the phenotypic difference in feed efficiency between animals. Connecting transcriptomics and metabolic levels together had some additional benefits., (© 2023. The Author(s).)

The aim of this study was to estimate genetic parameters for the reproductive traits of boars based on single-nucleotide polymorphism data. A total of 109,836 semen samples from 2249 boars were collected between 2010 and 2022. Five basic traits were assessed: sperm volume, sperm concentration, motility, number of abnormal sperm, and, for the first time for the local population, libido. In addition, two derived traits were assessed: total sperm count and number of functional sperm. Genetic parameters were estimated using the single-step genomic best linear unbiased prediction method (ssGBLUP). Dam and sire breeds were evaluated separately. The five basic traits were evaluated using five-trait models, while the two derived traits were evaluated using single-trait models. The heritability coefficients had lower values for all sperm quality traits with both methods. For the basic traits, the heritability ranged from 0.099 to 0.342. The greatest difference between dam and sire breeds was observed for the heritability of the sperm concentration trait (0.099 and 0.271, respectively). The heritability of the libido trait was twice as high for boars of sire breeds as it was for boars of dam breeds. The genetic parameters estimated with ssGBLUP can be used in routine genetic evaluations to improve the pig breeding process.

Mitochondrial DNA (mtDNA) variations and associated effects on economic traits have been widely reported in farm animals, as these genetic polymorphisms can affect the efficiency of energy production and cell metabolism. In studies related to metabolism, the deposition of fat was highly correlated with mitochondria. However, the effect of mtDNA polymorphisms on porcine backfat thickness (BFT) remained unclear. In this study, 243 pigs were collected to analyse the relationship between BFT and mtDNA polymorphisms. There were considerable differences in BFT, ranging from 5 mm to 18 mm. MtDNA D-loop sequencing discovered 48 polymorphic sites. Association analysis revealed that 30 variations were associated with BFT ( P  < 0.05). The polymorphism m.794A > G showed the maximum difference in BFT between A and G carriers, which differed at ∼2.5 mm ( P  < 0.001). The 48 polymorphic sites generated 22 haplotypes (H1-H22), which clustered into 4 haplogroups (HG1-HG4). HG1 had a lower BFT value than other three haplogroups ( P  < 0.01), whereas H4 in HG1 exhibited the lowest BFT of all haplotypes analyzed ( P  < 0.01). The results of this study highlight an association between mtDNA polymorphisms and BFT, and suggest the potential application of mtDNA in pig molecular breeding practices.

Traditional pig breeding has a long cycle and high cost, and there is an urgent need to use new technologies to revitalize the pig breeding industry. The recently emerged CRISPR/Cas9 genome editing technique shows great potential in pig genetic improvement, and has since become a research hotspot. Base editor is a new base editing technology developed based on the CRISPR/Cas9 system, which can achieve targeted mutation of a single base. CRISPR/Cas9 technology is easy to operate and simple to design, but it can lead to DNA double strand breaks, unstable gene structures, and random insertion and deletion of genes, which greatly restricts the application of this technique. Different from CRISPR/Cas9 technique, the single base editing technique does not produce double strand breaks. Therefore, it has higher accuracy and safety for genome editing, and is expected to advance the pig genetic breeding applications. This review summarized the working principle and shortcomings of CRISPR/Cas9 technique, the development and advantages of single base editing, the principles and application characteristics of different base editors and their applications in pig genetic improvement, with the aim to facilitate genome editing-assisted genetic breeding of pig.

To study the characteristics of genes and metabolites related to intramuscular fat (IMF) content with less influence by breed background and individual differences, the skeletal muscle samples from 40 Beijing black pigs with either high or low IMF content were used to perform transcriptome and metabolome analyses. About 99 genes (twofold-change) were differentially expressed. Up-regulated genes in the high IMF pigs were mainly related to fat metabolism. The key genes in charge of IMF deposition are ADIPOQ , CIDEC , CYP4B1 , DGAT2 , LEP , OPRL1 , PLIN1 , SCD , and THRSP . KLHL40 , TRAFD1 , and HSPA6 were novel candidate genes for the IMF trait due to their high abundances. In the low IMF pigs, the differentially expressed genes involved in virus resistance were up-regulated. About 16 and 18 differential metabolites (1.5 fold-change) were obtained in the positive and negative modes, respectively. Pigs with low IMF had weaker fatty acid oxidation due to the down-regulation of various carnitines. Differentially expressed genes were more important in determining IMF deposition than differential metabolites because relatively few differential metabolites were obtained, and they were merely the products under the physiological status of diverged IMF content. This study provided valuable information for further studies on IMF deposition.

Background: Breast carcinoma amplified sequence 2 ( BCAS2 ) participates in pre-mRNA splicing and DNA damage response, which is implicated in spermatogenesis and meiosis initiation in mouse. Nevertheless, the physiological roles of BCAS2 in the testes of large mammals especially boars remain largely unknown., Methods: In this study, testes were collected from Hezuo pig at three development stages including 30 days old (30 d), 120 days old (120 d), and 240 days old (240 d). BCAS2 CDS region was firstly cloned using RT-PCR method, and its molecular characteristics were identified using relevant bioinformatics software. Additionally, the expression patterns and cellular localization of BCAS2 were analyzed by quantitative real-time PCR (qRT-PCR), Western blot, immunohistochemistry and immunofluorescence., Results: The cloning and sequence analysis indicated that the Hezuo pig BCAS2 CDS fragment encompassed 678 bp open reading frame (ORF) capable of encoding 225 amino acid residues, and possessed high identities with some other mammals. The results of qRT-PCR and Western blot displayed that BCAS2 levels both mRNA and protein were age-dependent increased ( p < 0.01). Additionally, immunohistochemistry and immunofluorescence results revealed that BCAS2 protein was mainly observed in nucleus of gonocytes at 30 d testes as well as nucleus of spermatogonia and Sertoli cells at 120 and 240 d testes. Accordingly, we conclude that BCAS2 is critical for testicular development and spermatogenesis of Hezuo pig, perhaps by regulating proliferation or differentiation of gonocytes, pre-mRNA splicing of spermatogonia and functional maintenance of Sertoli cells, but specific mechanism still requires be further investigated., Competing Interests: The authors declare that they have no competing interests., (© 2023 Tang et al.)

This study aimed to assess and compare the performance of different machine learning models in predicting selected pig growth traits and genomic estimated breeding values (GEBV) using automated machine learning, with the goal of optimizing whole-genome evaluation methods in pig breeding. The research employed genomic information, pedigree matrices, fixed effects, and phenotype data from 9968 pigs across multiple companies to derive four optimal machine learning models: deep learning (DL), random forest (RF), gradient boosting machine (GBM), and extreme gradient boosting (XGB). Through 10-fold cross-validation, predictions were made for GEBV and phenotypes of pigs reaching weight milestones (100 kg and 115 kg) with adjustments for backfat and days to weight. The findings indicated that machine learning models exhibited higher accuracy in predicting GEBV compared to phenotypic traits. Notably, GBM demonstrated superior GEBV prediction accuracy, with values of 0.683, 0.710, 0.866, and 0.871 for B100, B115, D100, and D115, respectively, slightly outperforming other methods. In phenotype prediction, GBM emerged as the best-performing model for pigs with B100, B115, D100, and D115 traits, achieving prediction accuracies of 0.547, followed by DL at 0.547, and then XGB with accuracies of 0.672 and 0.670. In terms of model training time, RF required the most time, while GBM and DL fell in between, and XGB demonstrated the shortest training time. In summary, machine learning models obtained through automated techniques exhibited higher GEBV prediction accuracy compared to phenotypic traits. GBM emerged as the overall top performer in terms of prediction accuracy and training time efficiency, while XGB demonstrated the ability to train accurate prediction models within a short timeframe. RF, on the other hand, had longer training times and insufficient accuracy, rendering it unsuitable for predicting pig growth traits and GEBV.

Background: Toxoplasmosis is a zoonosis with a worldwide presence that is caused by the intracellular parasite Toxoplasma gondii. Active regulation of apoptosis is an important immune mechanism by which host cells resist the growth of T. gondii or avoid excessive pathological damage induced by this parasite. Previous studies found that upregulated expression of microRNA-185 (miR-185) during T. gondii infection has a potential role in regulating the expression of the ARAF gene, which is reported to be associated with cell proliferation and apoptosis., Methods: The expression levels of miR-185 and the ARAF gene were evaluated by qPCR and Western blot, respectively, in mice tissues, porcine kidney epithelial cells (PK-15) and porcine alveolar macrophages (3D4/21) following infection with the T. gondii ToxoDB#9 and RH strains. The dual luciferase reporter assay was then used to verify the relationship between miR-185 and ARAF targets in PK-15 cells. PK-15 and 3D4/21 cell lines with stable knockout of the ARAF gene were established by CRISPR, and then the apoptosis rates of the cells following T. gondii infection were detected using cell flow cytometry assays. Simultaneously, the activities of cleaved caspase-3, as a key apoptosis executive protein, were detected by Western blot to evaluate the apoptosis levels of cells., Results: Infection with both the T. gondii ToxoDB#9 and RH strains induced an increased expression of miR-185 and a decreased expression of ARAF in mice tissues, PK-15 and 3D4/21 cells. MiR-185 mimic transfections showed a significantly negative correlation in expression levels between miR-185 and the ARAF gene. The dual luciferase reporter assay confirmed that ARAF was a target of miR-185. Functional investigation revealed that T. gondii infection induced the apoptosis of PK-15 and 3D4/21 cells, which could be inhibited by ARAF knockout or overexpression of miR-185. The expression levels of cleaved caspase-3 protein were significantly lower in cells with ARAF knockout than in normal cells, which were consistent with the results of the cell flow cytometry assays., Conclusions: Toxoplasma gondii infection could lead to the upregulation of miR-185 and the downregulation of ARAF, which was not related to the strain of T. gondii and the host cells. Toxoplasma gondii infection could regulate the apoptosis of host cells via the miR-185/ARAF axis, which represents an additional strategy used by T. gondii to counteract host-cell apoptosis in order to maintain survival and reproduce in the host cells., (© 2023. BioMed Central Ltd., part of Springer Nature.)

Background: Although the accumulation of whole-genome sequencing (WGS) data has accelerated the identification of mutations underlying complex traits, its impact on the accuracy of genomic predictions is limited. Reliable genotyping data and pre-selected beneficial loci can be used to improve prediction accuracy. Previously, we reported a low-coverage sequencing genotyping method that yielded 11.3 million highly accurate single-nucleotide polymorphisms (SNPs) in pigs. Here, we introduce a method termed selective linkage disequilibrium pruning (SLDP), which refines the set of SNPs that show a large gain during prediction of complex traits using whole-genome SNP data., Results: We used the SLDP method to identify and select markers among millions of SNPs based on genome-wide association study (GWAS) prior information. We evaluated the performance of SLDP with respect to three real traits and six simulated traits with varying genetic architectures using two representative models (genomic best linear unbiased prediction and BayesR) on samples from 3579 Duroc boars. SLDP was determined by testing 180 combinations of two core parameters (GWAS P-value thresholds and linkage disequilibrium r 2 ). The parameters for each trait were optimized in the training population by five fold cross-validation and then tested in the validation population. Similar to previous GWAS prior-based methods, the performance of SLDP was mainly affected by the genetic architecture of the traits analyzed. Specifically, SLDP performed better for traits controlled by major quantitative trait loci (QTL) or a small number of quantitative trait nucleotides (QTN). Compared with two commercial SNP chips, genotyping-by-sequencing data, and an unselected whole-genome SNP panel, the SLDP strategy led to significant improvements in prediction accuracy, which ranged from 0.84 to 3.22% for real traits controlled by major or moderate QTL and from 1.23 to 11.47% for simulated traits controlled by a small number of QTN., Conclusions: The SLDP marker selection method can be incorporated into mainstream prediction models to yield accuracy improvements for traits with a relatively simple genetic architecture, however, it has no significant advantage for traits not controlled by major QTL. The main factors that affect its performance are the genetic architecture of traits and the reliability of GWAS prior information. Our findings can facilitate the application of WGS-based genomic selection., (© 2023. ’Institut National de Recherche en Agriculture, Alimentation et Environnement (INRAE).)

This study investigated the effects of dietary supplementation with taurine (TAU) on the meat quality, muscle fiber type, and mitochondrial function of finishing pigs. The results demonstrated that TAU significantly increased the a * value while decreasing b * 45 min , L * 24 h , and drip loss 24 h and drip loss 48 h in the longissimus dorsi (LD) muscle. Dietary supplemented with TAU reduced the content of lactate and the glycolytic potential (GP) in the LD muscle. Dietary supplemented with TAU enhanced the oxidative fiber-related gene expression as well as increased succinic dehydrogenase and malate dehydrogenase activities while reducing lactate dehydrogenase activity. Furthermore, dietary supplementation with TAU increased the contents of mtDNA and ATP and mitochondrial function-related gene expression. Moreover, TAU enhanced the mRNA expressions of calcineurin ( CaN ) and nuclear factor of activated T cells c1 ( NFATc1 ) and protein expressions of CNA and NFATc1. The results indicate that dietary TAU supplementation improves meat quality and mitochondrial biogenesis and function and promotes muscle fiber-type conversion from the glycolytic fiber to the oxidative fiber via the CaN/NFATc1 pathway.

Inbreeding depression is expected to be more pronounced in fitness-related traits, such as pig litter size. Recent studies have suggested that the genetic determinism of inbreeding depression may be heterogeneous across the genome. Therefore, the objective of this study was to conduct a genomic scan of the whole pig autosomal genome to detect the genomic regions that control inbreeding depression for litter size in two varieties of Iberian pigs (Entrepelado and Retinto). The datasets consisted of 2069 (338 sows) and 2028 (327 sows) records of litter size (Total Number Born and Number Born Alive) for the Entrepelado and Retinto varieties. All sows were genotyped using the Geneseek GGP PorcineHD 70 K chip. We employed the Unfavorable Haplotype Finder software to extract runs of homozygosity (ROHs) and conducted a mixed-model analysis to identify highly significant differences between homozygous and heterozygous sows for each specific ROH. A total of eight genomic regions located on SSC2, SSC5, SSC7, SSC8, and SSC13 were significantly associated with inbreeding depression, housing some relevant genes such as FSHR, LHCGR, CORIN, AQP6, and CEP120.

Meat adulteration is a major global concern that poses a threat to public health and consumer rights. However, current detection techniques, such as quantitative polymerase chain reaction (qPCR) and gas chromatography-mass spectrometry, are time-consuming and require sophisticated equipment. In this study, we developed a rapid onsite identification method for animal-derived ingredients by utilizing a fast nucleic acid lysis buffer to expedite the release of sample nucleic acids and combined it with dual-recombinase-aided amplification (dual-RAA) technology and visual multiplex lateral flow strips (MLFSs). Our method successfully detected duck- and bovine-derived, porcine- and bovine-derived, duck- and ovine-derived, and porcine- and ovine-derived meat in a rapid 20 min onsite detection assay, with a detection limit of 10 1 copies/50 μL reaction system for target genes. Moreover, our method accurately detected adulterated meat with proportions as low as 1:999. These findings have significant implications for food safety and the protection of consumer rights.

The vascular endothelium of xenografted pig organs represents the initial site of rejection after exposure to recipient immune cells. In this study, we aimed to develop a promoter specific to porcine vascular endothelial cells as a step toward overcoming xenograft rejection. Transcriptome analysis was performed on porcine aortic endothelial cells (PAECs), ear skin fibroblasts isolated from GGTA knockout (GTKO) pigs, and the porcine renal epithelial cell line pk-15. RNA sequencing confirmed 243 differentially expressed genes with expression changes of more than 10-fold among the three cell types. Employing the Human Protein Atlas database as a reference, we identified 34 genes exclusive to GTKO PAECs. The endothelial cell-specific adhesion molecule ( ESAM ) was selected via qPCR validation and showed high endothelial cell specificity and stable expression across tissues. We selected 1.0 kb upstream sequences of the translation start site of the gene as the promoter ESAM1.0. A luciferase assay revealed that ESAM1.0 promoter transcriptional activity was significant in PAECs, leading to a 2.8-fold higher level of expression than that of the porcine intercellular adhesion molecule 2 ( ICAM2 ) promoter, which is frequently used to target endothelial cells in transgenic pigs. Consequently, ESAM1.0 will enable the generation of genetically modified pigs with endothelium-specific target genes to reduce xenograft rejection.

The production of semen in boars involves multiple reproductive glands, including the testis (Tes), epididymis (Epi), vesicular gland (VG), prostate gland (PG), and bulbourethral gland (BG). However, previous studies on boar reproduction primarily focused on the testis, with little attention paid to the other glands. Here, we integrated single-molecule long-read sequencing with short-read sequencing to characterize the RNA landscape from five glands of Banna mini-pig inbred line (BMI) and Diannan small-ear pigs (DSE). We identified 110,996 full-length isoforms from 22,298 genes, and classified the alternative splicing (AS) events in these five glands. Transcriptome-wide variation analysis indicated that the number of single nucleotide polymorphisms (SNPs) in five tissues of BMI was significantly lower than that in the non-inbred pig, DSE, revealing the effect of inbreeding on BMI. Additionally, we performed small-RNA sequencing and identified 299 novel miRNAs across all glands. Overall, our findings provide a comprehensive overview of the RNA landscape within these five glands, paving the path for future investigations on reproductive biology and the impact of inbreeding on pig transcriptome., (© 2023. Springer Nature Limited.)

Genomic prediction (GP) has greatly advanced animal and plant breeding over the past two decades. GP in joint populations is a feasible method to improve the accuracy of genomic estimated breeding values in small populations. However, there is still a need to understand the factors that influence GP in joint populations. This study used simulated data and real data from Duroc pig populations to examine the impact of linkage disequilibrium (LD), causal variants effect sizes (CVESs), and minor allele frequencies (MAF) of SNPs on the accuracy of genomic prediction in joint populations. Three prediction methods were used: genomic best linear unbiased prediction (GBLUP), single-step GBLUP and multi-trait GBLUP. Results from the simulated datasets showed that the accuracies of GP in joint populations were always higher than those in a single population when only LD inconsistencies existed. However, single-step GBLUP accuracy in joint populations decreased as the correlation of MAF between populations decreased, while the accuracy of GBLUP is consistently higher in joint populations than in a single population. As the correlation of CVES between populations decreased, the accuracy of both GBLUP and single-step GBLUP in joint populations declined. Analysis of real Duroc populations showed low genetic correlation, similar to the simulated relationship between the most distant populations. In most cases in Duroc populations, GP have higher accuracies in joint populations than in individual population. In conclusion, the consistency of CVES plays a more important role in multi-population GP. The genetic relatedness of the Duroc populations is so weak that the prediction accuracy of GP in joint populations is reduced in some traits. Multi-trait GBLUP is a competitive method for the joint breeding evaluation., (Copyright © 2023 The Author(s). Published by Elsevier B.V. All rights reserved.)

Umbilical hernia (UH) and inguinal hernia (IH) are among the most common defects in pigs, affecting their welfare and resulting in economic losses. In this study, we aimed to verify the association of previously reported differences in transcript levels of the ACAN , COL6A5 , MMP13 , and VIT genes with the occurrence of UH and IH. We examined mRNA levels in muscle and connective tissue from 68 animals-34 affected by UH and 34 controls. In a second cohort, we examined inguinal channel samples from 46 pigs (in four groups). We determined DNA methylation levels in muscle tissue for the UH and control animals. The transcript level of MMP13 changed in the UH cases, being upregulated and downregulated in muscle and connective tissue, respectively, and the VIT gene also showed an increased muscular mRNA level. The transcript of the ACAN gene significantly decreased in old pigs with IH. We further observed an increased DNA methylation level for one CpG site within the MMP13 gene in UH individuals. We conclude that these alterations in gene mRNA levels in the UH animals depend on the tissue and can sometimes be a consequence of, not a cause of, the affected phenotype.

Recent human decedent model studies 1,2 and compassionate xenograft use 3 have explored the promise of porcine organs for human transplantation. To proceed to human studies, a clinically ready porcine donor must be engineered and its xenograft successfully tested in nonhuman primates. Here we describe the design, creation and long-term life-supporting function of kidney grafts from a genetically engineered porcine donor transplanted into a cynomolgus monkey model. The porcine donor was engineered to carry 69 genomic edits, eliminating glycan antigens, overexpressing human transgenes and inactivating porcine endogenous retroviruses. In vitro functional analyses showed that the edited kidney endothelial cells modulated inflammation to an extent that was indistinguishable from that of human endothelial cells, suggesting that these edited cells acquired a high level of human immune compatibility. When transplanted into cynomolgus monkeys, the kidneys with three glycan antigen knockouts alone experienced poor graft survival, whereas those with glycan antigen knockouts and human transgene expression demonstrated significantly longer survival time, suggesting the benefit of human transgene expression in vivo. These results show that preclinical studies of renal xenotransplantation could be successfully conducted in nonhuman primates and bring us closer to clinical trials of genetically engineered porcine renal grafts., (© 2023. The Author(s).)

Cold exposure is an essential factor affecting breeding efforts in cold regions. Muscle, as an important tissue for homeothermic animals, can produce heat through shivering thermogenesis (ST) and non-shivering thermogenesis (NST) under cold exposure. Long non-coding RNAs (lncRNAs) play important roles in regulating gene expression. However, the regulatory mechanisms of lncRNAs and their role in the thermogenesis of pigs are unclear. We examined lncRNAs in the skeletal muscle of an indigenous pig breed, the Enshi black pig, when the pigs were exposed to acute or chronic cold. Three pigs were maintained inside a pig house (control group), three pigs were maintained outside the pig house for 55 d (chronic cold group), and three pigs were suddenly exposed to the conditions outside the pig house for 3 days (acute cold group). After the experiment, the longissimus dorsi of each pig were collected, and their lncRNA profiles were sequenced and analyzed. Each sample obtained nearly 12.56 Gb of clean data. A total of 11,605 non-coding RNAs were obtained, including 10,802 novel lncRNAs. The number of differentially expressed lncRNAs (DElncRNAs) was identified under acute cold (427) and cold acclimation (376), with 215 and 192 upregulated lncRNAs, respectively. However, only 113 lncRNAs were commonly upregulated by acute cold and cold acclimation. In addition, 65% of the target genes were trans-regulated by DElncRNAs. The target genes were enriched in signal transduction, immune system, cell growth and death pathways, and amino acid and carbohydrate metabolism. Compared to cold acclimation, acute cold stress-induced more DElncRNAs and response pathways. In conclusion, low temperatures altered the expression levels of lncRNAs and their target genes in muscle tissue. Some potential mechanisms were revealed, including ion migration and the metabolism of amino acids and carbohydrates.

Ningxiang pigs are a renowned indigenous pig breed in China, known for their meat quality, disease resistance, and environmental adaptability. In recent decades, consumer demand for meats from indigenous breeds has grown significantly, fueling the selection and crossbreeding of Ningxiang pigs (NXP). The latter has raised concerns about the conservation and sustainable use of Ningxiang pigs as an important genetic resource. To address these concerns, we conducted a comprehensive genomic study using 2242 geographically identified Ningxiang pigs. The estimated genomic breed composition (GBC) suggested 2077 pigs as purebred Ningxiang pigs based on a ≥94% NXP-GBC cut-off. The remaining 165 pigs were claimed to be crosses, including those between Duroc and Ningxiang pigs and between Ningxiang and Shaziling pigs, and non-Ningxiang pigs. Runs of homozygosity (ROH) were identified in the 2077 purebred Ningxiang pigs. The number and length of ROH varied between individuals, with an average of 32.14 ROH per animal and an average total length of 202.4 Mb per animal. Short ROH (1-5 Mb) was the most abundant, representing 66.5% of all ROH and 32.6% of total ROH coverage. The genomic inbreeding estimate was low (0.089) in purebred Ningxiang pigs compared to imported western pig breeds. Nine ROH islands were identified, pinpointing candidate genes and QTLs associated with economic traits of interest, such as reproduction, carcass and growth traits, lipid metabolism, and fat deposition. Further investigation of these ROH islands and candidate genes is anticipated to better understand the genomics of Ningxiang pigs.

Corpus luteum cysts are a serious reproductive disorder that affects the reproductive performance of sows. In this study, transcriptome and metabolome datasets of porcine normal and cyst luteal granulosa cells were generated to explore the molecular mechanism of luteal cyst formation. We obtained 28.9 Gb of high-quality transcriptome data from luteum tissue samples and identified 1048 significantly differentially expressed genes between the cyst and normal corpus luteum samples. Most of the differentially expressed genes were involved in cancer and immune signaling pathways. Furthermore, 22,622 information-containing positive and negative ions were obtained through gas chromatography-mass spectrometry, and 1106 metabolites were successfully annotated. Important differentially abundant metabolites and pathways were identified, among which abnormal lipid and choline metabolism were involved in the formation of luteal cysts. The relationships between granulosa cells of luteal cysts and cancer, immune-related signaling pathways, and abnormalities of lipid and choline metabolism were elaborated, providing new entry points for studying the pathogenesis of porcine luteal cysts.

Background: China has one third of the worldwide indigenous pig breeds. The Henan province is one of the earliest pig domestication centers of China (about 8000 years ago). However, the precise genetic characteristics of the Henan local pig breeds are still obscure. To understand the origin and the effects of selection on these breeds, we performed various analyses on lineage composition, genetic structure, and detection of selection sweeps and introgression in three of these breeds (Queshan, Nanyang and Huainan) using genotyping data on 125 Queshan, 75 Nanyang, 16 Huainan pigs and 878 individuals from 43 Eurasian pig breeds., Results: We found no clear evidence of ancestral domestic pig DNA lineage in the Henan local breeds, which have an extremely complicated genetic background. Not only do they share genes with some northern Chinese pig breeds, such as Erhualian, Hetaodaer, and Laiwu, but they also have a high admixture of genes from foreign pig breeds (33-40%). Two striking selection sweeps in small regions of chromosomes 2 and 14 common to the Queshan and Nanyang breeds were identified. The most significant enrichment was for lipid kinase activity (GO:0043550) with the genes FII, AMBRA1, and PIK3IP1. Another interesting 636.35-kb region on chromosome 14 contained a cluster of spermatogenesis genes (OSBP2, GAL3ST1, PLA2G3, LIMK2, and PATZ1), a bisexual sterility gene MORC2, and a fat deposition gene SELENOM. Reproduction and growth genes LRP4, FII, and ARHGAP1 were present in a 238.05-kb region on SSC2 under selection. We also identified five loci associated with body length (P = 0.004) on chromosomes 1 and 12 that were introgressed from foreign pig breeds into the Henan breeds. In addition, the Chinese indigenous pig breeds fell into four main types instead of the previously reported six, among which the Eastern type could be divided into two subgroups., Conclusions: Admixture of North China, East China and foreign pigs contributed to high genetic diversity of Henan local pigs. Ontology terms associated with lipid kinase activity and spermatogenesis and growth shaping by introgression of European genes in Henan pigs were identified through selective sweep analyses., (© 2023. ’Institut National de Recherche en Agriculture, Alimentation et Environnement (INRAE).)

Background: Artificial selection on quantitative traits using breeding values and selection indices in commercial livestock breeding populations causes changes in allele frequency over time at hundreds or thousands of causal loci and the surrounding genomic regions. In population genetics, this type of selection is called polygenic selection. Researchers and managers of pig breeding programs are motivated to understand the genetic basis of phenotypic diversity across genetic lines, breeds, and populations using selection mapping analyses. Here, we applied generation proxy selection mapping (GPSM), a genome-wide association analysis of single nucleotide polymorphism (SNP) genotypes (38,294-46,458 markers) of birth date, in four pig populations (15,457, 15,772, 16,595 and 8447 pigs per population) to identify loci responding to artificial selection over a period of five to ten years. Gene-drop simulation analyses were conducted to provide context for the GPSM results. Selected loci within and across each population of pigs were compared in the context of swine breeding objectives., Results: The GPSM identified 49 to 854 loci as under selection (Q-values less than 0.10) across 15 subsets of pigs based on combinations of populations. The number of significant associations increased when data were pooled across populations. In addition, several significant associations were identified in more than one population. These results indicate concurrent selection objectives, similar genetic architectures, and shared causal variants responding to selection across these pig populations. Negligible error rates (less than or equal to 0.02%) of false-positive associations were found when testing GPSM on gene-drop simulated genotypes, suggesting that GPSM distinguishes selection from random genetic drift in actual pig populations., Conclusions: This work confirms the efficacy and the negligible error rates of the GPSM method in detecting selected loci in commercial pig populations. Our results suggest shared selection objectives and genetic architectures across swine populations. The identified polygenic selection highlights loci that are important to swine production., (© 2023. ’Institut National de Recherche en Agriculture, Alimentation et Environnement (INRAE).)

Copy number variation (CNV) represents a significant reservoir of genetic diversity within the genome and exhibits a strong association with economically valuable traits in livestock. The manifestation of aggressive behavior in pigs has detrimental effects on production efficiency, immune competency, and meat quality. Nevertheless, the impact of CNV on the aggressive behavior of pigs remains elusive. In this investigation, we employed an integrated analysis of genome and transcriptome data to investigate the interplay between CNV, gene expression changes, and indicators of aggressive behavior in weaned pigs. Specifically, a subset of pigs comprising the most aggressive pigs (MAP, n = 12) and the least aggressive pigs (LAP, n = 11) was purposefully selected from a herd of 500 weaned pigs following a mixing procedure based on their composite aggressive score (CAS). Subsequently, we thoroughly analyzed copy number variation regions (CNVRs) across the entire genome using next-generation sequencing techniques, ultimately revealing the presence of 6869 CNVRs. Using genome-wide association study (GWAS) analysis and evaluating variance-stabilizing transformation (V ST ) values, we successfully identified distinct CNVRs that distinguished the MAP and LAP counterparts. Among the prioritized CNVRs, CNVR-4962 (designated as the top-ranked p -value and V ST value, No. 1) was located within the Solute Carrier Organic Anion Transporter Family Member 3A1 (SLCO3A1) gene. The results of our analyses indicated a significantly higher ( p < 0.05) copy number of SLCO3A1 in the MAP compared to the LAP. Furthermore, this increased copy number exhibited a positive correlation with the CAS of the pigs ( p < 0.05). Furthermore, we integrated genomic data with transcriptomic data from the temporal lobe to facilitate the examination of expression quantitative trait loci (eQTL). Importantly, these observations were consistent with the mRNA expression pattern of SLCO3A1 in the temporal lobe of both MAP and LAP ( p < 0.05). Consequently, our findings strongly suggest that CNVs affecting SLCO3A1 may influence gene expression through a dosage effect. These results highlight the potential of SLCO3A1 as a candidate gene associated with aggressive traits in pig breeding programs.

Enhancing meat production and quality is the eternal theme for pig breeding industries. Fat deposition has always been the focus of research in practical production because it is closely linked to pig production efficiency and pork quality. In the current study, multi-omics techniques were performed to explore the modulatory mechanisms of backfat (BF) accumulation at three core developmental stages for Ningxiang pigs. Our results identified that 15 differentially expressed genes (DEGs) and 9 significantly changed metabolites (SCMs) contributed to the BF development via the cAMP signaling pathway, regulation of lipolysis in adipocytes, and biosynthesis of unsaturated fatty acids. Herein, we found a series of candidate genes such as adrenoceptor beta 1 (ADRB1), adenylate cyclase 5 (ADCY5), ATPase Na+/K+ transporting subunit beta 1 (ATP1B1), ATPase plasma membrane Ca 2+ transporting 3 (ATP2B3), ATPase Na+/K+ transporting subunit alpha 2 (ATP1A2), perilipin 1 (PLIN1), patatin like phospholipase domain containing 3 (PNPLA3), ELOVL fatty acid elongase 5 (ELOVL5) and metabolites like epinephrine, cAMP, arachidonic acid, oleic acid, linoleic acid, and docosahexaenoic acid existed age-specificeffects and played important roles in lipolysis, fat accumulation, and fatty acid composition. Our findings provide a reference for molecular mechanisms in BF tissue development and the optimization of carcass quality., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier B.V. All rights reserved.)

Background: Heat stress (HS) is known to exert negative effects on the poultry and breeding industry, resulting in severe economic losses. Bile acids (BAs), an important component of bile, play a crucial role in improving the production performance of livestock and poultry, alleviating stress injury, and ensuring the health of livestock and poultry. At present, porcine BAs are widely used because of their therapeutic effects on HS; however, it remains unclear whether the same effects are exerted by sheep BAs, which are different from porcine BAs and have different compositions. In this study, we compared the anti-HS effects of porcine BAs and sheep BAs in the diet by establishing an HS model of chicks and investigating the chicken performance, HS-related genes' expression, oxidative stress markers, jejunal histoarchitecture, inflammatory cytokines' expression, jejunal secreted immunoglobulin A concentration, and cecal bacterial flora., Results: The results showed that the addition of sheep BAs to the diet increased the average daily weight gain and the feed conversion ratio of chicks. Under HS, sheep BAs were more effective than porcine BAs in improving the activities of lactate dehydrogenase and glutamic pyruvic transaminase in serum and the content/activity of malondialdehyde, superoxide dismutase, and reduced glutathione in serum and tissue, in reducing the messenger RNA (mRNA) expression of heat shock proteins (HSP60, HSP70, and HSP90) in the liver and jejunum, and in improving the histological structure and the expression of tight junction proteins (occludin and zonula occludens-1) and enriching intestinal bacterial flora. However, porcine BAs were significantly inferior to sheep BAs in reducing the mRNA expression of inflammatory factors (interleukin-6, interleukin-1β, and tumor necrosis factor-α)., Conclusion: The effect of sheep BAs was more significant than porcine BAs was in alleviating HS injury in chicks, suggesting that sheep BAs have great potential as new feed nutrition and health additive to improve poultry production performance and prevent HS. © 2023 Society of Chemical Industry., (© 2023 Society of Chemical Industry.)

Improved feed efficiency is an essential goal for the sustainability of pig production in economic and environmental terms. Traits such as feed conversion rate (FCR), residual feed intake (RFI), residual body weight gain (RG) and feeding behaviour, such as duration (TPV) and feeding rate per visit (FR) can now be measured by automatic feeding systems. The aim of this study was to evaluate the benefits of incorporating feeding behaviour traits into a selection index to improve feed efficiency in a nucleus of purebred Pietrain pigs. Data on body weight, feed intake and duration were recorded at each visit in 1608 animals. The information contained in 843,605 visits was grouped by animal ID to obtain a set of feed efficiency and feeding behaviour traits. These traits were obtained in three periods (first, second and total period). Bayesian models were built to estimate the posterior marginal distribution of the variance components. The heritabilities were between 0.44 and 0.59 for feeding behaviour traits and between 0.31 and 0.49 for feed efficiency traits. The FCR and RFI showed a considerable genetic correlation with daily feed intake (~0.65). FCR showed a genetic correlation with feeding behaviour traits, such as feed intake per visit (FPV) (0.44) and FR (0.33). Furthermore, the fast-eating pigs were less efficient. This was due to the positive genetic correlation found between the FR and the FCR (0.33) and the RFI (0.23), and the negative correlation found with the RG (-0.28). On the other hand, the inclusion of the feeding behaviour traits into a selection index slightly increased the selection response for FCR (4%) and RFI (1.8%). However, there was an increase of up to 19% in the selection response for RG and an improvement in accuracy from 0.59 to 0.70. Therefore, we concluded that it would be interesting to include feeding behaviour traits in a selection index to improve the selection response and accuracy of feed efficiency traits., (© 2023 The Authors. Journal of Animal Breeding and Genetics published by John Wiley & Sons Ltd.)