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Database : the Journal of Biological... May 2021Sus scrofa or pig was domesticated thousands of years ago. Through various indigenous breeds, different phenotypes were produced such as Chinese inbred miniature minipig...
Application of beta and gamma carbonic anhydrase sequences as tools for identification of bacterial contamination in the whole genome sequence of inbred Wuzhishan minipig (Sus scrofa) annotated in databases.
Sus scrofa or pig was domesticated thousands of years ago. Through various indigenous breeds, different phenotypes were produced such as Chinese inbred miniature minipig or Wuzhishan pig (WZSP), which is broadly used in the life and medical sciences. The whole genome of WZSP was sequenced in 2012. Through a bioinformatics study of pig carbonic anhydrase (CA) sequences, we detected some β- and γ-class CAs among the WZSP CAs annotated in databases, while β- or γ-CAs had not previously been described in vertebrates. This finding urged us to analyze the quality of whole genome sequence of WZSP for the possible bacterial contamination. In this study, we used bioinformatics methods and web tools such as UniProt, European Bioinformatics Institute, National Center for Biotechnology Information, Ensembl Genome Browser, Ensembl Bacteria, RSCB PDB and Pseudomonas Genome Database. Our analysis defined that pig has 12 classical α-CAs and 3 CA-related proteins. Meanwhile, it was approved that the detected CAs in WZSP are categorized in the β- and γ-CA families, which belong to Pseudomonas spp. and Acinetobacter spp. The protein structure study revealed that the identified β-CA sequence from WZSP belongs to Pseudomonas aeruginosa with PDB ID: 5JJ8, and the identified γ-CA sequence from WZSP belongs to P. aeruginosa with PDB ID: 3PMO. Bioinformatics and computational methods accompanied with bacterial-specific markers, such as 16S rRNA and β- and γ-class CA sequences, can be used to identify bacterial contamination in mammalian DNA samples.
Topics: Animals; Bacteria; Carbonic Anhydrases; DNA; RNA, Ribosomal, 16S; Sus scrofa; Swine; Swine, Miniature
PubMed: 34003248
DOI: 10.1093/database/baab029 -
Genes Oct 2020In the Carpathian Basin the wild boar () belongs among the most important game species both ecologically and economically, therefore knowing more about the basics of the...
In the Carpathian Basin the wild boar () belongs among the most important game species both ecologically and economically, therefore knowing more about the basics of the genetics of the species is a key factor for accurate and sustainable management of its population. The aim of this study was to estimate the genetic diversity and to elucidate the genetic structure and location of wild boar populations in the Carpathian Basin. A total of 486 samples were collected and genotyped using 13 STR markers. The number of alleles varied between 4 and 14, at 9 of the 13 loci the observed heterozygosity was significantly different ( < 0.05) from the expected value, showing remarkable introgression in the population. The population was separated into two groups, with an F value of 0.03, suggesting the presence of two subpopulations. The first group included 147 individuals from the north-eastern part of Hungary, whereas the second group included 339 samples collected west and south of the first group. The two subpopulations' genetic indices are roughly similar. The lack of physical barriers between the two groups indicates that the genetic difference is most likely caused by the high reproduction rate and large home range of the wild boars, or by some genetic traces' having been preserved from both the last ice age and the period before the Hungarian water regulation.
Topics: Animals; Female; Gene Flow; Genetic Variation; Genetics, Population; Genotype; Hungary; Male; Microsatellite Repeats; Sus scrofa
PubMed: 33066463
DOI: 10.3390/genes11101194 -
BMC Evolutionary Biology Feb 2015Identifying the phenotypic responses to domestication remains a long-standing and important question for researchers studying its early history. The great diversity in...
BACKGROUND
Identifying the phenotypic responses to domestication remains a long-standing and important question for researchers studying its early history. The great diversity in domestic animals and plants that exists today bears testament to the profound changes that domestication has induced in their ancestral wild forms over the last millennia. Domestication is a complex evolutionary process in which wild organisms are moved to new anthropogenic environments. Although modern genetics are significantly improving our understanding of domestication and breed formation, little is still known about the associated morphological changes linked to the process itself. In order to explore phenotypic variation induced by different levels of human control, we analysed the diversity of dental size, shape and allometry in modern free-living and captive wild, wild x domestic hybrid, domestic and insular Sus scrofa populations.
RESULTS
We show that domestication has created completely new dental phenotypes not found in wild boar (although the amount of variation amongst domestic pigs does not exceed that found in the wild). Wild boar tooth shape also appears to be biogeographically structured, likely the result of post-glacial recolonisation history. Furthermore, distinct dental phenotypes were also observed among domestic breeds, probably the result of differing types and intensity of past and present husbandry practices. Captivity also appears to impact tooth shape. Wild x domestic hybrids possess second molars that are strictly intermediate in shape between wild boar and domestic pigs (third molars, however, showing greater shape similarity with wild boar) while their size is more similar to domestic pigs. The dental phenotypes of insular Sus scrofa populations found on Corsica and Sardinia today (originally introduced by Neolithic settlers to the islands) can be explained either by feralization of the original introduced domestic swine or that the founding population maintained a wild boar phenotype through time.
CONCLUSIONS
Domestication has driven significant phenotypic diversification in Sus scrofa. Captivity (environmental control), hybridization (genome admixture), and introduction to islands all correspond to differing levels of human control and may be considered different stages of the domestication process. The relatively well-known genetic evolutionary history of pigs shows a similar complexity at the phenotypic level.
Topics: Animals; Animals, Domestic; Evolution, Molecular; Genetic Variation; Humans; Hybridization, Genetic; Phenotype; Sus scrofa; Tooth
PubMed: 25648385
DOI: 10.1186/s12862-014-0269-x -
Gut Microbes May 2020It is well established that pig gut microbiota plays a critical role in maintaining metabolic homeostasis as well as in a myriad of physiological, neurological and... (Review)
Review
It is well established that pig gut microbiota plays a critical role in maintaining metabolic homeostasis as well as in a myriad of physiological, neurological and immunological functions; including protection from pathogens and digestion of food materials - some of which would be otherwise indigestible by the pig. A rich and diverse gut microbial ecosystem (balanced microbiota) is the hallmark of good health; while qualitative and quantitative perturbations in the microbial composition can lead to development of various diseases. Alternatively, diseases caused by stressors or other factors have been shown to negatively impact the microbiota. This review focuses primarily on how commensal microorganisms in the gastrointestinal tract of pigs influence biochemical, physiological, immunological, and metabolic processes within the host animal.
Topics: Animals; Brain; Breeding; Diet; Environmental Exposure; Gastrointestinal Microbiome; Gastrointestinal Tract; Host Microbial Interactions; Immunity; Sus scrofa
PubMed: 31760878
DOI: 10.1080/19490976.2019.1690363 -
Journal of Experimental Zoology. Part... Dec 2022Domestication has led to many changes in domestic animal biology, including their anatomy. The shape of the inner ear, part of the mammalian ear, has been found...
Domestication has led to many changes in domestic animal biology, including their anatomy. The shape of the inner ear, part of the mammalian ear, has been found particularly relevant for discriminating domesticated species, their hybrids or differentiating the wild and domestic populations of a single species. Here we assessed the use of the size and shape of the semicircular canals (SCC) of the inner ear as a marker of pig domestication. We studied a total of 63 petrosal bones belonging to wild boar (Sus scrofa, two populations) and domestic pigs (extensively and intensively reared specimens) that were µCT-scanned and from which the size and the shape of the inner ear were quantified through geometric morphometrics, analyzing the 3D coordinates of 6 landmarks and 60 sliding semilandmarks localized on the SCC and the common crus. The domestic pigs have larger SCC than the wild boar from which they also strongly differ in shape (correct cross validation of 95.5%, confidence interval: 92.3%-98.1%). Strong shape differences were detected between the two populations of wild boar, as well as a sexual size dimorphism. All together the results highlight the taxonomic discriminant power of the SCC of the inner ear shape, and its relevance for domestication studies.
Topics: Animals; Swine; Domestication; Semicircular Canals; Sus scrofa
PubMed: 35226406
DOI: 10.1002/jez.b.23127 -
BMC Genomics Oct 2021In recent years, animal welfare and health has become more and more important in pig breeding. So far, numerous parameters have been considered as important biomarkers,...
BACKGROUND
In recent years, animal welfare and health has become more and more important in pig breeding. So far, numerous parameters have been considered as important biomarkers, especially in the immune reaction and inflammation. Previous studies have shown moderate to high heritabilities in most of these traits. However, the genetic background of health and robustness of pigs needs to be extensively clarified. The objective of this study was to identify genomic regions with a biological relevance for the immunocompetence of piglets. Genome-wide Association Studies (GWAS) in 535 Landrace (LR) and 461 Large White (LW) piglets were performed, investigating 20 immune relevant traits. Besides the health indicators of the complete and differential blood count, eight different cytokines and haptoglobin were recorded in all piglets and their biological dams to capture mediating processes and acute phase reactions. Additionally, all animals were genotyped using the Illumina PorcineSNP60v2 BeadChip.
RESULTS
In summary, GWAS detected 25 genome-wide and 452 chromosome-wide significant SNPs associated with 17 immune relevant traits in the two maternal pig lines LR and LW. Only small differences were observed considering the maternal immune records as covariate within the statistical model. Furthermore, the study identified across- and within-breed differences as well as relevant candidate genes. In LR more significant associations and related candidate genes were detected, compared with LW. The results detected in LR and LW are partly in accordance with previously identified quantitative trait loci (QTL) regions. In addition, promising novel genomic regions were identified which might be of interest for further detailed analysis. Especially putative pleiotropic regions on SSC5, SSC12, SSC15, SSC16 and SSC17 are of major interest with regard to the interacting structure of the immune system. The comparison with already identified QTL gives indications on interactions with traits affecting piglet survival and also production traits.
CONCLUSION
In conclusion, results suggest a polygenic and breed-specific background of immune relevant traits. The current study provides knowledge about regions with biological relevance for health and immune traits. Identified markers and putative pleiotropic regions provide first indications in the context of balancing a breeding-based modification of the porcine immune system.
Topics: Animals; Genetic Association Studies; Genotype; Immune System; Phenotype; Quantitative Trait Loci; Sus scrofa; Swine
PubMed: 34610786
DOI: 10.1186/s12864-021-07997-1 -
Animal Genetics Aug 2021In Europe, swine represent economically important farm animals and furthermore have become a preferred preclinical large animal model for biomedical studies,...
In Europe, swine represent economically important farm animals and furthermore have become a preferred preclinical large animal model for biomedical studies, transplantation and regenerative medicine research. The need for typing of the swine leukocyte antigen (SLA) is increasing with the expanded use of pigs as models for human diseases and organ-transplantation experiments and their use in infection studies and for design of veterinary vaccines. In this study, we characterised the SLA class I (SLA-1, SLA-2, SLA-3) and class II (DRB1, DQB1, DQA) genes of 549 farmed pigs representing nine commercial pig lines by low-resolution (Lr) SLA haplotyping. In total, 50 class I and 37 class II haplotypes were identified in the studied cohort. The most common SLA class I haplotypes Lr-04.0 (SLA-1*04XX-SLA-3*04XX(04:04)-SLA-2*04XX) and Lr-32.0 (SLA-1*07XX-SLA-3*04XX(04:04)-SLA-2*02XX) occurred at frequencies of 11.02 and 8.20% respectively. For SLA class II, the most prevalent haplotypes Lr-0.15b (DRB1*04XX(04:05/04:06)-DQB1*02XX(02:02)-DQA*02XX) and Lr-0.12 (DRB1*06XX-DQB1*07XX-DQA*01XX) occurred at frequencies of 14.37 and 12.46% respectively. Meanwhile, our laboratory has contributed to several vaccine correlation studies (e.g. Porcine Reproductive and Respiratory Syndrome Virus, Classical Swine Fever Virus, Foot-and-Mouth Disease Virus and Swine Influenza A Virus) elucidating the immunodominance in the T-cell response with antigen specificity dependent on certain SLA-I and SLA-II haplotypes. Moreover, these SLA-immune response correlations could facilitate tailored vaccine development, as SLA-I Lr-04.0 and Lr-32.0 as well as SLA-II Lr-0.15b and Lr-0.12 are highly abundant haplotypes in European farmed pigs.
Topics: Animals; Breeding; Europe; Genetic Variation; Histocompatibility Antigens Class I; Sus scrofa
PubMed: 34028065
DOI: 10.1111/age.13090 -
International Journal of Molecular... Mar 2019This study aimed to characterize the full-length cDNA of MARK4 in , and evaluated its potential role in the regulation of lipid accumulation in pig placental...
This study aimed to characterize the full-length cDNA of MARK4 in , and evaluated its potential role in the regulation of lipid accumulation in pig placental trophoblasts and analyzed signaling pathways involved, thereby providing insights into mechanisms for placental lipotoxicity induced by excessive back-fat during pregnancy of sows. The cDNA obtained with 5' and 3' RACE amplification covered 3216 bp with an open reading frame of 2259 bp encoding 752 amino acids. Multiple alignments and phylogenetic analysis revealed MARK4 protein of had a high homology (95%⁻99%) to that of other higher vertebrates. After transfection, enhanced MARK4 significantly promoted lipogenesis in pig trophoblasts, as evidenced by accelerated lipid accumulation and consistently increased mRNA expressions of lipogenic genes DGAT1, LPIN1, LPIN3, LPL, PPARδ and SREBP-1c. Meanwhile, PPARγ remarkably inhibited the stimulating effect of MARK4 on non-receptor-mediated lipid accumulation in trophoblasts. Further analyses revealed WNT signaling enhanced lipid accumulation and activation of MARK4 in pig trophoblast cells. Finally, we demonstrated that WNT/β-catenin signal pathway is involved in MARK4 activated lipogenesis. These results suggest that MARK4 promotes lipid accumulation in porcine placental trophoblasts and can be considered as a potential regulator of lipotoxicity associated with maternal obesity in the pig placenta.
Topics: Animals; Cells, Cultured; Enzyme Activation; Female; Lipogenesis; Models, Molecular; Phylogeny; Placenta; Pregnancy; Protein Conformation; Protein Serine-Threonine Kinases; Sus scrofa; Trophoblasts; Wnt Signaling Pathway
PubMed: 30857324
DOI: 10.3390/ijms20051206 -
Laboratory Animals Apr 2021Pigs are used to model humans in gastrointestinal (GI) studies because of their comparable size, physiology and behaviour: both are monogastric omnivores. A porcine...
Pigs are used to model humans in gastrointestinal (GI) studies because of their comparable size, physiology and behaviour: both are monogastric omnivores. A porcine surgical model for testing novel, tethered ultrasound capsule endoscopes (USCE) requires a clean, motile small intestine. Recommendations for human GI tract preparation before the mechanically similar process of video capsule endoscopy describe using oral purgatives, while high-carbohydrate drinks are recommended before colorectal surgery. Reports of the GI preparation of pigs exist but lack technical details, that is, administration, efficacy and side effects. This report details feeding a high-energy liquid diet to 11 female pigs undergoing surgery and USCE which was readily accepted and easily administered, and which produced a clean, motile small intestine and caused no detectable physiological/behavioural abnormalities.
Topics: Animal Husbandry; Animals; Capsule Endoscopes; Capsule Endoscopy; Diet; Female; Intestine, Small; Models, Animal; Sus scrofa
PubMed: 33045909
DOI: 10.1177/0023677220960509 -
BMC Genetics Nov 2014Genomic selection and genomic wide association studies are widely used methods that aim to exploit the linkage disequilibrium (LD) between markers and quantitative trait...
BACKGROUND
Genomic selection and genomic wide association studies are widely used methods that aim to exploit the linkage disequilibrium (LD) between markers and quantitative trait loci (QTL). Securing a sufficiently large set of genotypes and phenotypes can be a limiting factor that may be overcome by combining data from multiple breeds or using crossbred information. However, the estimated effect of a marker in one breed or a crossbred can only be useful for the selection of animals in another breed if there is a correspondence of the phase between the marker and the QTL across breeds. Using data of five pure pig (Sus scrofa) lines (SL1, SL2, SL3, DL1, DL2), one F1 cross (DLF1) and two commercial finishing crosses (TER1 and TER2), the objectives of this study were: (i) to compare the equality of LD decay curves of different pig populations; and (ii) to evaluate the persistence of the LD phase across lines or final crosses.
RESULTS
Almost all of the lines presented different extents of LD, except for the SL2 and DL3, both of which exhibited the same extent of LD. Similar levels of LD over large distances were found in crossbred and pure lines. The crossbred animals (DLF1, TER1 and TER2) presented a high persistence of phase with their parental lines, suggesting that the available porcine single nucleotide polymorphism (SNP) chip should be dense enough to include markers that have the same LD phase with QTL across crossbred and parental pure lines. The persistence of phase across pure lines varied considerably between the different line comparisons; however, correlations were above 0.8 for all line comparisons when marker distances were smaller than 50 kb.
CONCLUSIONS
This study showed that crossbred populations could be very useful as a reference for the selection of pure lines by means of the available SNP chip panel. Here, we also pinpoint pure lines that could be combined in a multiline training population. However, if multiline reference populations are used for genomic selection, the required density of SNP panels should be higher compared with a single breed reference population.
Topics: Alleles; Animals; Gene Frequency; Genetic Markers; Hybridization, Genetic; Linkage Disequilibrium; Sus scrofa
PubMed: 25421851
DOI: 10.1186/s12863-014-0126-3