Genomic Diversity in Pig (Sus scrofa) and its Comparison with Human and other Livestock

We have reviewed the current pig (Sus scrofa) genomic diversity within and between sites and compared them with human and other livestock. The current Porcine 60K single nucleotide polymorphism (SNP) panel has an average SNP distance in a range of 30 - 40 kb. Most of genetic variation was distributed within populations, and only a small proportion of them existed between populations. The average heterozygosity was lower in pig than in human and other livestock. Genetic inbreeding coefficient (F(IS)), population differentiation (F(ST)), and Nei's genetic distance between populations were much larger in pig than in human and other livestock. Higher average genetic distance existed between European and Asian populations than between European or between Asian populations. Asian breeds harboured much larger variability and higher average heterozygosity than European breeds. The samples of wild boar that have been analyzed displayed more extensive genetic variation than domestic breeds. The average linkage disequilibrium (LD) in improved pig breeds extended to 1 - 3 cM, much larger than that in human (~ 30 kb) and cattle (~ 100 kb), but smaller than that in sheep (~ 10 cM). European breeds showed greater LD that decayed more slowly than Asian breeds. We briefly discuss some processes for maintaining genomic diversity in pig, including migration, introgression, selection, and drift. We conclude that, due to the long time of domestication, the pig possesses lower heterozygosity, higher F(IS), and larger LD compared with human and cattle. This implies that a smaller effective population size and less informative markers are needed in pig for genome wide association studies.     

Rhodanese distribution in porcine (Sus scrofa) tissues

The enzyme rhodanese (thiosulfate/cyanide sulfurtransferase) is an ubiquitous enzyme and its activity is present in all living organisms from bacteria to man. Evidence has been accumulated to indicate that this enzyme plays a central role in cyanide detoxification. A comparison was made of rhodanese activity in different tissues of young male and adult male and female pig (Sus scrofa). The highest activity of rhodanese was in liver and kidney cortex of all animals. Among the remaining tissues examined, the kidney medulla and the stomach epithelium tended to have higher levels than other tissues, although this was not significant (P>0.05). The rhodanese activity of heart ventricle tissue of 6-month-old male animals was higher than 7-week-old male animals (P<0.05), and 6-month-old male animals had higher rhodanese activity in lung tissue, compared to 6-month-old female pigs (P<0.05). Medulla and spleen of younger male animals exhibited higher levels of activity (P<0.10) compared to older male pigs. The results of this study may indicate the involvement of rhodanese in cyanide detoxification in pig tissues, which have greater potential to be exposed to higher levels of cyanide.     

Vascular-associated lymphoid tissue in swine (Sus scrofa)

Focal accumulations of mononuclear cells in the arterial wall of healthy humans at predilection sites for atherosclerotic lesions have been described as 'vascular-associated lymphoid tissue' (VALT). Here we investigated whether pigs (Sus scrofa), a commonly used animal model for studying cardiovascular disease, have VALT. Samples of major arteries were collected from 10 conventional crossbred pigs (age, 2 to 24 mo) and processed for routine light microscopy, immunohistochemistry, and immunofluorescence. Single or small aggregates of mononuclear cells were noted in the intima and occasionally the inner portion of the tunica media and adventitia at branching sites. The infiltrating cells were primarily CD3+CD4+ T cells, with some macrophages. No CD8+ T cells were present. Infiltrating leukocytes and overlying endothelial cells frequently expressed major histocompatibility class II molecules. Two Ossabaw pigs on low-fat diet had similar leukocytic aggregates at locations where animals of the same breed but fed a high-fat and high-cholesterol diet developed atherosclerotic lesions. Further, the densities of CD3+ T lymphocytes and in these areas were decreased in 2 sedentary and 2 exercised Ossabaw pigs on an atherogenic diet compared with conventional crossbred and Ossabaw pigs on a normal diet. This study shows that focal aggregates of lymphocytes occur in the vasculature of pigs at locations predisposed to development of atherosclerotic lesions. These cellular aggregates are similar to the structures described as VALT in human arteries and reinforce the value of the pig as a model for the study of human cardiovascular disease.     

Genomic structure, promoter analysis, and expression of the porcine (Sus scrofa) Mx1 gene

Allelic polymorphisms at the mouse Mx1 locus affect the probability of survival after experimental influenzal disease, raising the possibility that marker-assisted selection using the homologous locus could improve the innate resistance of pigs to natural influenza infections. Several issues need to be resolved before efficient large scale screening of the allelic polymorphism at the porcine (Sus scrofa) Mx1 locus can be implemented. First, the Mx1 genomic structure has to be established and sufficient flanking intronic sequences have to be gathered to enable simple PCR amplification of the coding portions of the gene. Then, a basic knowledge of the promoter region needs to be obtained as an allelic variation there can significantly alter absolute levels and/or tissue-specificity of MX protein expression. The results gathered here show that the porcine Mx1 gene and promoter share the major structural and functional characteristics displayed by their homologs described in cattle, mouse, chicken, and man. The crucial function of the proximal interferon-sensitive response elements motif for gene expression is also demonstrated. The sequence data compiled here will allow an extensive analysis of the polymorphisms present among the widest spectrum possible of porcine breeds with the aim to identify an Mx1 allele providing antiviral resistance.     

Characteristics of sodium transport in pig (Sus scrofa) erythrocytes

Sodium content, sodium transport (ouabain-sensitive efflux rate of sodium, oMosNa; and ouabain-sensitive efflux rate constant of sodium, oKosNa), [3H]ouabain binding capacity, and Na+, K+-ATPase activity were measured in erythrocytes from young pigs (Sus scrofa). The sodium content, sodium transport, and the number of sodium pumps (assessed by ouabain binding capacity) were lower in the pig compared to the human erythrocytes. The efflux rate constant of sodium, oKosNa was 36% and the ouabain binding capacity was 60% of those in human, suggesting the degree of activation of sodium pump units is much lower.     

Comparative cytogenetic studies in Sus verrucosus,Sus celebensis and Sus scrofa vittatus (Suidae,Mammalia)

Chromosome studies on the Javan warty pig (Sus verrucosus), the Sulawesi warty pig (S. celebensis) and a subspecies of the wild boar, S. scrofa vittatus, have revealed diploid chromosome numbers of 38. The morphology and C-band size of chromosome 10 are different in S. verrucosus and the two other species. Both S. verrucosus and S. celebensis have a Y chromosome that is larger than the Y chromosome of domestic and wild S. scrofa, and is submetacentric rather than metacentric. There are differences between all three species in the G-banding pattern of the long arm of the Y chromosome. The presence of 2n=38 chromosomes in the Javan warty pig and the Sulawesi warty pig provides new strong evidence that the basic chromosome number in the genus Sus is 38. The differences in karyotype between these pigs (chromosome 10 and the Y chromosome) confirm that they are separate species.     

Craniometrical analysis of Bulgarian wild boar (Sus scrofa) populations

Skull characters of wild boars ( Sus scrofa L.) from four regions of Bulgaria were compared using stepwise discriminant, cluster of cases and principal component analyses (PCA). Classification functions were derived for discriminating individuals from different areas. Specimens from the north-eastern part of the country (Dobrudja and the Balkan Range) were found well separated from those from the south (Rila-Rhodopes & Strandja Mountains). PCA showed the differences being mostly related to the size rather than to the shape of both the cranium and the mandible. Natural migrations, intergradation areas between different subspecies, as well as restocking and hybridization with semi-domestic pigs are discussed as possible factors influencing the solution of the problem of the intraspecific systematics of the wild boar in Bulgaria.     

Daily selection of habitat in wild boar (Sus scrofa)

Spatial segregation of the sexes is observed in numerous species of ungulates, but are there other forms of segregation in species where spatial segregation is not present, such as in the wild boar? This study investigates the differences in habitat selection between two categories of individuals whose ecological requirements are supposedly divergent: subadult males, and females with dependent piglets. The proportion of the day spent in each category of habitat was used as a parameter representative of daily decisions. The overall results fit with the hypothesis that females with piglets avoid insecure habitats, and that both categories select habitats on the basis of food richness. In addition, it was found that the pattern of habitat selection depends on the total time spent moving slowly. A short duration of slow movement was observed only in males, but the time dedicated to efficient foraging (in rich habitats) was sufficient in all observations of all animals. Subadult males, therefore, do not differ from each other in foraging efficiency, but in the time spent on slow movement in secure habitats. Those spending more time active in secure habitats have the opportunity of performing more potentially beneficial activities such as social interactions and sexual contacts.     

The contribution of social effects to heritable variation in finishing traits of domestic pigs (Sus scrofa)

Social interactions among individuals are ubiquitous both in animals and in plants, and in natural as well as domestic populations. These interactions affect both the direction and the magnitude of responses to selection and are a key factor in evolutionary success of species and in the design of breeding schemes in agriculture. At present, however, very little is known of the contribution of social effects to heritable variance in trait values. Here we present estimates of the direct and social genetic variance in growth rate, feed intake, back fat thickness, and muscle depth in a population of 14,032 domestic pigs with known pedigree. Results show that social effects contribute the vast majority of heritable variance in growth rate and feed intake in this population. Total heritable variance expressed relative to phenotypic variance was 71% for growth rate and 70% for feed intake. These values clearly exceed the usual range of heritability for those traits. Back fat thickness and muscle depth showed no heritable variance due to social effects. Our results suggest that genetic improvement in agriculture can be substantially advanced by redirecting breeding schemes, so as to capture heritable variance due to social effects.     

Exome Capture with Heterologous Enrichment in Pig (Sus scrofa)

The discovery of new protein-coding DNA variants related to carcass traits is very important for the Italian pig industry, which requires heavy pigs with higher thickness of subcutaneous fat for Protected Designation of Origin (PDO) productions. Exome capture techniques offer the opportunity to focus on the regions of DNA potentially related to the gene and protein expression. In this research a human commercial target enrichment kit was used to evaluate its performances for pig exome capture and for the identification of DNA variants suitable for comparative analysis. Two pools of 30 pigs each, crosses of Italian Duroc X Large White (DU) and Commercial hybrid X Large White (HY), were used and NGS libraries were prepared with the SureSelectXT Target Enrichment System for Illumina Paired-End Sequencing Library (Agilent). A total of 140.2 M and 162.5 M of raw reads were generated for DU and HY, respectively. Average coverage of all the exonic regions for Sus scrofa (ENSEMBL Sus_scrofa.Sscrofa10.2.73.gtf) was 89.33X for DU and 97.56X for HY; and 35% of aligned bases uniquely mapped to off-target regions. Comparison of sequencing data with the Sscrofa10.2 reference genome, after applying hard filtering criteria, revealed a total of 232,530 single nucleotide variants (SNVs) of which 20.6% mapped in exonic regions and 49.5% within intronic regions. The comparison of allele frequencies of 213 randomly selected SNVs from exome sequencing and the same SNVs analyzed with a Sequenom MassARRAY® system confirms that this “human-on-pig” approach offers new potentiality for the identification of DNA variants in protein-coding genes.     

Genetic diversity in wild (Sus scrofa scrofa) and domestic (Sus scrofa domestica) pigs and their hybrids based on polymorphism of a fragment of the D-loop region in the mitochondrial DNA

We examined the variation in mitochondrial DNA by sequencing the D-loop region in wild and domestic (large-white breed) pigs, in hybrids between domestic and wild pigs, and in Monteiro pigs. A D-loop fragment of approximately 330 bp was amplified by PCR. Sequencing of DNA amplicons identified haplotypes previously described as European and Asian types. Monteiro pigs and wild pigs had European haplotypes and domestic pigs had both European and Asian haplotypes.     

The Complete Mitochondrial DNA Sequence of the Pig (Sus scrofa)

The complete mitochondrial genome sequence of the pig, Sus scrofa, was determined. The length of the sequence presented is 16,679 nucleotides. This figure is not absolute, however, due to pronounced heteroplasmy caused by variable numbers of the motif GTACACGTGC in the control region of different molecules. A phylogenetic study was performed on the concatenated amino acid and nucleotide sequences of 12 protein-coding genes of the mitochondrial genome. The analysis identified the pig (Suiformes) as a sister group of a cow/whale clade, making Artiodactyla paraphyletic. The split between pig and cow/whale was molecularly dated at 65 million years before present. Received: 2 December 1997 / Accepted: 20 February 1998     

Characterization of a polymorphic IGLV gene in pigs (Sus scrofa)

Swine, unlike other artiodactyls, but similar to humans, utilize both lambda and kappa light chain isotypes almost equally in the generation of their antibody repertoire. The porcine antibody light chain loci have previously been characterized in a single Duroc sow in which was seen extensive allelic variation between light chain genes on homologous chromosomes. However, the extent of variation between individuals is completely unknown. Using deep sequencing of cDNA-derived amplicons from five pigs, we report the identification and characterization of an IGLV gene that is functional and highly expressed in some animals, yet completely absent in others. Our findings provide a possible rationale for the known individual-to-individual variation in antibody responses to vaccination, infectious challenge, and subsequent disease outcome.     

Intrinsic rate of spermatogenesis in free-ranging feral pigs (Sus scrofa sp)

The aim of this research was to evaluate the intrinsic rate of spermatogenesis in adult free-ranging feral pigs. Twelve adult male free-ranging feral pigs were captured, sedated, and orchidectomized, and then were released and observed to complete recovery and return to their natural environment. Fragments of the testes were embedded in plastic resin and used to prepare slides for histometric analysis. Characteristics investigated included cell populations in the seminiferous epithelium in stage 1 of the cycle of the seminiferous epithelium, intrinsic rate of spermatogenesis and Sertoli cell index. The efficiency coefficient of spermatogonial mitosis was 7.59, the meiotic index was 3.03, the overall yield of spermatogenesis was 23.97 and the cell loss ratio during the meiotic prophase was 1.04. Each Sertoli cell supported an average of 0.92 type A spermatogonia, 7.01 primary spermatocytes in preleptotene/leptotene, 7.30 primary spermatocytes in pachytene and 22.16 round spermatids. In conclusion, the results of the present study indicate that the supporting capacity of Sertoli cells in free-ranging feral pigs is among the greatest values reported for most domestic animals, and the overall yield of spermatogenesis is comparable to that reported in wild boars.