Local Pig Research Articles

Construction of a gE-Deleted Pseudorabies Virus and Its Efficacy to the New-Emerging Variant PRV Challenge in the Form of Killed Vaccine.

The new-emerging PRV variants plague the vaccinated pigs and caused huge economic loss to local pig industry in China since 2011. The current commercial PRV vaccines cannot provide complete protection as the new-emerging PRV variants are antigenically different from the classical viruses. It is urgent to develop more safe and effective PRV vaccines based on the current circulating field isolates. In this study, a gE gene-deleted PRV based on the PRV HN1201, a representative PRV variant, was generated and the efficacy was tested on 3-week-old pigs in the form of killed vaccine. After fatal PRV HN1201 challenge, all vaccinated pigs survived without showing any clinical symptoms, but all unvaccinated pigs exhibited pseudorabies-specific respiratory and neurological signs with 100% mortality rate within 6 days after infection. The vaccinated pigs developed high level of gB and neutralizing antibodies after vaccination which may correlate to the protection provided by vaccine. Therefore, this gE gene-deleted PRV could be a promising vaccine candidate for the control of currently epidemic pseudorabies in China.

Differential expression of porcine TAP1 gene in the populations of pigs.

Transporter associated with antigen processing (TAP) transports peptides from the cytosol into the endoplasmic reticulum (ER) for subsequent loading onto the major histocompatibility complex (MHC) class I molecules. TAP is consisted of two subunits: TAP and TAP2. Using Real-time PCR technology, this study detected tissue expression profile and analyzed the differential expression of TAP1 gene in Sutai Escherichia coli-resistant group, Yorkshire and Meishan pigs. Tissue expression profile revealed that TAP1 gene expressed in all tissues we detected, and the expression levels were high in lung, immune tissues and intestines. Through the comparation of gene expression differention in different populations, TAP1 expression level of Sutai E. coli-resistant group was significantly higher than that of Yorkshire and Meishan populations in liver, spleen, lung, kidney, thymus, lymph, duodenum and jejunum (P<0.05). Meanwhile TAP1 gene was more highly expressed in Sutai E. coli-resistant group than that of Meishan population in stomach (P<0.05). In conclusion, the upregulation of TAP1 expression level in E. coli-resistant group could be related to E. coli F18 infection. In addition, Chinese local pigs may have special immune response and genetic mechanism in resisting E. coli F18 infection which is differing from MHC I moleculars.

From phenotyping towards breeding strategies: using in vivo indicator traits and genetic markers to improve meat quality in an endangered pig breed

In endangered and local pig breeds of small population sizes, production has to focus on alternative niche markets with an emphasis on specific product and meat quality traits to achieve economic competiveness. For designing breeding strategies on meat quality, an adequate performance testing scheme focussing on phenotyped selection candidates is required. For the endangered German pig breed ‘Bunte Bentheimer’ (BB), no breeding program has been designed until now, and no performance testing scheme has been implemented. For local breeds, mainly reared in small-scale production systems, a performance test based on in vivo indicator traits might be a promising alternative in order to increase genetic gain for meat quality traits. Hence, the main objective of this study was to design and evaluate breeding strategies for the improvement of meat quality within the BB breed using in vivo indicator traits and genetic markers. The in vivo indicator trait was backfat thickness measured by ultrasound (BFiv), and genetic markers were allele variants at the ryanodine receptor 1 (RYR1) locus. In total, 1116 records of production and meat quality traits were collected, including 613 in vivo ultrasound measurements and 713 carcass and meat quality records. Additionally, 700 pigs were genotyped at the RYR1 locus. Data were used (1) to estimate genetic (co)variance components for production and meat quality traits, (2) to estimate allele substitution effects at the RYR1 locus using a selective genotyping approach and (3) to evaluate breeding strategies on meat quality by combining results from quantitative-genetic and molecular-genetic approaches. Heritability for the production trait BFiv was 0.27, and 0.48 for backfat thickness measured on carcass. Estimated heritabilities for meat quality traits ranged from 0.14 for meat brightness to 0.78 for the intramuscular fat content (IMF). Genetic correlations between BFiv and IMF were higher than estimates based on carcass backfat measurements (0.39 v. 0.25). The presence of the unfavorable n allele was associated with increased electric conductivity, paler meat and higher drip loss. The allele substitution effect on IMF was unfavorable, indicating lower IMF when the n allele is present. A breeding strategy including the phenotype (BFiv) combined with genetic marker information at the RYR1 locus from the selection candidate, resulted in a 20% increase in accuracy and selection response when compared with a breeding strategy without genetic marker information.

Histological and immunohistochemical changes of the thyroid gland during the foetal and postnatal period of development in indigenous Large White crossbred pigs

The present study was carried out to ascertain the morphometric, histological and immunohistochemical changes (expression of calcitonin and somatostatin) in the thyroid gland of indigenous local pig crosses during the foetal and postnatal period of development. A total of thirty foetal thyroids (40) grouped into early and late foetal period, fifteeen (15) prepubertal and ten (10) pubertal thyroids obtained from slaughtered pigs in the local abattoir were used. Histomorphometrically, all the measured parameters increased with development in all thyroid age group. The mean values were significantly different at P˂0.05 among ages. Histologically, significant age-related variations in the structure of the foetal and postnatal thyroids were observed in the follicles, colloid, colloid vacuoles, follicular cells and interfollicular connective tissue. Calcitonin was demonstrated in the foetal and postnatal parafollicular cells, while somatostatin was only localised in the pubertal parafollicular cells. The study provides strong evidence of thyroid functionality during the late foetal period that changes with age during the development.

Histomorphological Study of the Respiratory System of Mizo Local Pig (zo vawk)

The present study provides a baseline data on histology of respiratory system of Mizo local pig (Zo Vawk). The Occurrence of nasal glands was high in the respiratory region of nasal cavity which might enhance the efficiency of humidifying the inhaled air. The visceral pleura and interlobar and interlobular septa were thick containing elastic fibres which might increase the elasticity of the lung. The respiratory bronchioles were well developed in Mizo local pig which might enhance their respiratory efficiency in higher altitude and lesser atmospheric oxygen tension in Mizoram. Frequent occurrence of alveolar macrophages might be attributed to the better resistance to respiratory diseases of the indigenous pigs of Mizoram (Zo Vawk).

Genetic characterization of local Criollo pig breeds from the Americas using microsatellite markers.

Little is known about local Criollo pig genetic resources and relationships among the various populations. In this paper, genetic diversity and relationships among 17 Criollo pig populations from 11 American countries were assessed with 24 microsatellite markers. Heterozygosities, F-statistics, and genetic distances were estimated, and multivariate, genetic structure and admixture analyses were performed. The overall means for genetic variability parameters based on the 24 microsatellite markers were the following: mean number of alleles per locus of 6.25 ± 2.3; effective number of alleles per locus of 3.33 ± 1.56; allelic richness per locus of 4.61 ± 1.37; expected and observed heterozygosity of 0.62 ± 0.04 and 0.57 ± 0.02, respectively; within-population inbreeding coefficient of 0.089; and proportion of genetic variability accounted for by differences among breeds of 0.11 ± 0.01. Genetic differences were not significantly associated with the geographical location to which breeds were assigned or their country of origin. Still, the NeighborNet dendrogram depicted the clustering by geographic origin of several South American breeds (Criollo Boliviano, Criollo of northeastern Argentina wet, and Criollo of northeastern Argentina dry), but some unexpected results were also observed, such as the grouping of breeds from countries as distant as El Salvador, Mexico, Ecuador, and Cuba. The results of genetic structure and admixture analyses indicated that the most likely number of ancestral populations was 11, and most breeds clustered separately when this was the number of predefined populations, with the exception of some closely related breeds that shared the same cluster and others that were admixed. These results indicate that Criollo pigs represent important reservoirs of pig genetic diversity useful for local development as well as for the pig industry.

Development of a modified QUick, Easy, CHeap, Effective, Rugged and Safe method for the determination of multi-class antimicrobials in vegetables by liquid chromatography tandem mass spectrometry

A modified quick, easy, cheap, efficient, rugged and safe (QuEChERS) method coupled with liquid chromatography tandem mass spectrometry (LC-MS/MS) was developed for rapid determination of 26 veterinary antimicrobials in vegetables. Samples were extracted by single-phase extraction with acetonitrile-methanol (85:15, v/v) and citric buffer solution, followed by liquid–liquid partitioning with the addition of anhydrous magnesium sulfate and sodium chloride. A dispersive solid-phase extraction with primary secondary amine was applied for cleanup. Concentration and solvent exchange was performed prior to LC-MS/MS analysis. All matrix-matched calibration curves were linear with correlation coefficients (r) over 0.99. Recoveries for all the analytes spiked at 0.5 (1 or 1.5), 5 and 50ng/mL were in the range of 60.0–98.0%, except for sulfaquinoxaline, sulfaclozine and doxycycline, with relative standard deviations below 25% for the low concentration level, 20% for the medium and 15% for the high. The decision limits and the detection capabilities of the analytes ranged from 0.005 to 0.5μg/kg and from 0.02 to 1.5μg/kg, respectively. The method was developed and validated in accordance with romaine lettuce matrix, and higher recovery rates were obtained from the other five kinds of vegetables including white radish, Chinese cabbage, cucumber, string bean and green pepper. Matrix effects of different vegetables were evaluated and signal suppression effect was observed for the majority of 26 analytes. Finally, the method was applied to the analysis of real samples collected from the agricultural areas in the vicinity of local pig farms, and the phenomenon of vegetables contaminated by antimicrobials residues is provoking.

The complete mitochondrial genome of Congjiang miniature pig (Sus scrofa)

Congjiang miniature pig is one of the most important local pig breeds in China. It is the first time that the complete mitochondrial genome sequence of Lantang pig is reported in this work, which is determined through the PCR-based method. The total length of the mitogenome is 16,772 bp, which contains 1 control region (D-loop region), 2 ribosomal RNA genes, 13 PCGs and 22 tRNA genes. The total base composition of Congjiang miniature pig mitochondrial genome is 34.78% for A, 26.21% for C, 25.78% for T and 13.22% for G and in the order A>C>T>G. The complete mitochondrial genome of Congjiang miniature pig provides an important data in genetic mechanism and the evolution genomes.

Genome sequencing and analysis of Mangalica, a fatty local pig of Hungary.

BackgroundMangalicas are fatty type local/rare pig breeds with an increasing presence in the niche pork market in Hungary and in other countries. To explore their genetic resources, we have analysed data from next-generation sequencing of an individual male from each of three Mangalica breeds along with a local male Duroc pig. Structural variations, such as SNPs, INDELs and CNVs, were identified and particular genes with SNP variations were analysed with special emphasis on functions related to fat metabolism in pigs.ResultsMore than 60 Gb of sequence data were generated for each of the sequenced individuals, resulting in 11× to 19× autosomal median coverage. After stringent filtering, around six million SNPs, of which approximately 10% are novel compared to the dbSNP138 database, were identified in each animal. Several hundred thousands of INDELs and about 1,000 CNV gains were also identified. The functional annotation of genes with exonic, non-synonymous SNPs, which are common in all three Mangalicas but are absent in either the reference genome or the sequenced Duroc of this study, highlighted 52 genes in lipid metabolism processes. Further analysis revealed that 41 of these genes are associated with lipid metabolic or regulatory pathways, 49 are in fat-metabolism and fatness-phenotype QTLs and, with the exception of ACACA, ANKRD23, GM2A, KIT, MOGAT2, MTTP, FASN, SGMS1, SLC27A6 and RETSAT, have not previously been associated with fat-related phenotypes.ConclusionsGenome analysis of Mangalica breeds revealed that local/rare breeds could be a rich source of sequence variations not present in cosmopolitan/industrial breeds. The identified Mangalica variations may, therefore, be a very useful resource for future studies of agronomically important traits in pigs.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-761) contains supplementary material, which is available to authorized users.

Genetic structure of wild boar (Sus scrofa) populations from East Asia based on microsatellite loci analyses.

BackgroundWild boar, Sus scrofa, is an extant wild ancestor of the domestic pig as an agro-economically important mammal. Wild boar has a worldwide distribution with its geographic origin in Southeast Asia, but genetic diversity and genetic structure of wild boar in East Asia are poorly understood. To characterize the pattern and amount of genetic variation and population structure of wild boar in East Asia, we genotyped and analyzed microsatellite loci for a total of 238 wild boar specimens from ten locations across six countries in East and Southeast Asia.ResultsOur data indicated that wild boar populations in East Asia are genetically diverse and structured, showing a significant correlation of genetic distance with geographic distance and implying a low level of gene flow at a regional scale. Bayesian-based clustering analysis was indicative of seven inferred genetic clusters in which wild boars in East Asia are geographically structured. The level of genetic diversity was relatively high in wild boars from Southeast Asia, compared with those from Northeast Asia. This gradient pattern of genetic diversity is consistent with an assumed ancestral population of wild boar in Southeast Asia. Genetic evidences from a relationship tree and structure analysis suggest that wild boar in Jeju Island, South Korea have a distinct genetic background from those in mainland Korea.ConclusionsOur results reveal a diverse pattern of genetic diversity and the existence of genetic differentiation among wild boar populations inhabiting East Asia. This study highlights the potential contribution of genetic variation of wild boar to the high genetic diversity of local domestic pigs during domestication in East Asia.

Untangling the hybrid nature of modern pig genomes: a mosaic derived from biogeographically distinct and highly divergent Sus scrofa populations.

The merging of populations after an extended period of isolation and divergence is a common phenomenon, in natural settings as well as due to human interference. Individuals with such hybrid origins contain genomes that essentially form a mosaic of different histories and demographies. Pigs are an excellent model species to study hybridization because European and Asian wild boars diverged ~1.2 Mya, and pigs were domesticated independently in Europe and Asia. During the Industrial Revolution in England, pigs were imported from China to improve the local pigs. This study utilizes the latest genomics tools to identify the origin of haplotypes in European domesticated pigs that are descendant from Asian and European populations. Our results reveal fine-scale haplotype structure representing different ancient demographic events, as well as a mosaic composition of those distinct histories due to recently introgressed haplotypes in the pig genome. As a consequence, nucleotide diversity in the genome of European domesticated pigs is higher when at least one haplotype of Asian origin is present, and haplotype length correlates negatively with recombination frequency and nucleotide diversity. Another consequence is that the inference of past effective population size is influenced by the background of the haplotypes in an individual, but we demonstrate that by careful sorting based on the origin of haplotypes, both distinct demographic histories can be reconstructed. Future detailed mapping of the genomic distribution of variation will enable a targeted approach to increase genetic diversity of captive and wild populations, thus facilitating conservation efforts in the near future.

GROSS ANATOMY OF THE RESPIRATORY SYSTEM OF MIZO LOCAL PIG (ZO VAWK)

The present investigation provides a baseline data on gross anatomy of respiratory system of Mizo local pig (Zo vawk). The values of the biometrical measurements were less corresponding to the smaller shape, size and lesser body weight of Mizo local pigs. They have relatively longer nasal cavities corresponding to the long facial part of the head. The laryngeal prominence is found absent on the ventral surface of thyroid cartilage. The first tracheal ring is slightly wider and larger and no fusion between tracheal rings. The right extra pulmonary bronchus is shorter and wider than left extra pulmonary bronchus. The surface lobulations are clearly visible on the lung corresponding to the thick interlobar and interlobular connective tissue.

Canis lupus familiaris involved in the transmission of pathogenic Yersinia spp. in China

To investigate canines carrying pathogens associated with human illness, we studied their roles in transmitting and maintaining pathogenic Yersinia spp. We examined different ecological landscapes in China for the distribution of pathogenic Yersinia spp. in Canis lupus familiaris, the domestic dog. The highest number of pathogenic Yersinia enterocolitica was shown from the tonsils (6.30%), followed by rectal swabs (3.63%) and feces (1.23%). Strains isolated from plague free areas for C. lupus familiaris, local pig and diarrhea patients shared the same pulsed-field gel electrophoresis (PFGE) pattern, indicating they may be from the same clone and the close transmission source of pathogenic Y. enterocolitica infections in these areas. Among 226 dogs serum samples collected from natural plague areas of Yersinia pestis in Gansu and Qinghai Provinces, 49 were positive for F1 antibody, while the serum samples collected from plague free areas were all negative, suggested a potential public health risk following exposure to dogs. No Y. enterocolitica or Yersinia pseudotuberculosis was isolated from canine rectal swabs in natural plague areas. Therefore, pathogenic Yersinia spp. may be regionally distributed in China.

Seroprevalence of Lawsonia intracellularis antibodies in intensive pig farms in China.

BackgroundPorcine proliferative enteropathy caused by Lawsonia intracellularis (L. intracellularis) is a major concern to the pig industry worldwide. Although 8.3 billion pigs are produced each year in China, few reports on the prevalence of L.intracellularis infection are available. The aim of the current study was to estimate the seroprevalence of L. intracellularis antibodies in intensive pig farms in China.ResultsA total of 1060 serum samples were collected from 14 commercial pig farms located throughout China. Animals from all age groups were sampled including pre-weaning piglets, weaners, fattening pigs, adult sows and boars. Antibodies against L. intracellularis were detected using a specific blocking ELISA. Of the 1060 serum samples, 602 were identified as positive using the ELISA test. The apparent seroprevalence of L. intracellularis seropositivity was 57% (95% CI 50 to 64%). The true prevalence (that is, prevalence corrected for the imperfect sensitivity and specificity of the testing method) was 77% (95% CI 70 to 83%).ConclusionsThe highest true prevalence was observed in sows and boars, suggesting that within a herd these stock classes are a reservoir for infection. The prevalence of L. intracellularis seropositivity in local breed pigs was significantly less than that in imported breeds. A higher seroprevalence was found in pigs in herds in Central and Northern China, which may correspond to the greater use of the intensive production systems in these areas. We conclude that L. intracellularis is widely prevalent in commercial pigs in China.

Positive Correlation Between the Efficiency of Induced Pluripotent Stem Cells and the Development Rate of Nuclear Transfer Embryos When the Same Porcine Embryonic Fibroblast Lines Are Used As Donor Cells

Induced pluripotent stem cells (iPSCs) and nuclear transfer (NT) are two of the primary routes to reprogram differentiated cells back to the pluripotent state. However, it is still unknown whether there is any correlation between the reprogramming efficiency of iPSCs and NT if the same donor cells are employed. In this study, six porcine embryonic fibroblast (PEF) lines from Landrace (L1, L6, L9) or Congjiang local pigs (C4, C5, C6) were used for iPSC induction and NT. Furthermore, the resultant iPSCs from four PEF lines (L1, L6, C4, and C5) were used for NT (iPSC-NT), and the expression of exogenous genes was detected in iPSC-NT embryos by real-time PCR. The results showed that the efficiency of iPSC lines established from different PEF lines were significantly different. When the same PEF lines were used as donor cells for NT, the blastocysts rates were also different among different PEF lines and positively related with iPSCs induction efficiency. When the iPSCs were used as donor cells for NT, compared with the source PEFs, the blastocysts rates were significantly decreased. Real-time PCR results indicated that exogenous genes (Oct4, c-Myc) continued to be expressed in iPSC-NT embryos. In summary, our results demonstrate that there was a positive correlation between iPSCs and NT reprogramming efficiency, although the mechanism of these two routes is different. This may provide a new method to select the appropriate donor cells for inducing iPSCs.

Oxfendazole flukicidal activity in pigs

Although oxfendazole (OFZ) is a well know broad-spectrum benzimidazole anthelmintic, the assessment of its potential trematodicidal activity remains unexplored. OFZ administration at single high doses has been recommended to control Taenia solium cysticercus in pigs. The current study investigated the flukicidal activity obtained after a single high (30mg/kg) oral dose of OFZ in pigs harbouring a natural Fasciola hepatica infection. Sixteen (16) local ecotype pigs were randomly allocated into two (2) experimental groups of 8 animals each named as follow: Untreated control and OFZ treated, in which animals received OFZ (Synanthic®, Merial Ltd., 9.06% suspension) orally at 30mg/kg. At seven (7) days post-treatment, all the animals were sacrificed and direct adult liver fluke counts were performed following the WAAVP guidelines. None of the animals involved in this experiment showed any adverse event during the study. OFZ treatment as a single 30mg/kg oral dose showed a 100% efficacy against F. hepatica. In conclusion, the trial described here demonstrated an excellent OFZ activity against F. hepatica in naturally infected pigs, after its administration at a single oral dose of 30mg/kg.

Light Microscopic Study on the Peripheral Lymphnodes of Mizo Local Pig (Zo Vawk)

The present study provides a baseline data on histology of peripheral lymph nodes of Mizo local pig (Zo Vawk). The mean adult body weight was recorded 34.48±2.18 Kg in male and 21.17±2.29 Kg in female. The parenchyma of the peripheral lymph nodes revealed cortex like tissue, medulla like tissue and reticulum. Several lymphoid segments of various sizes in the cortex like tissues, referred to as “nodules”, were confirmed. Two types of hiluses were recorded viz. afferent type (A-type) and efferent type (E-type). The cortex like tissue contained primary and secondary types of nodules; however, most of the nodules were secondary. The cell population of the nodule was mainly lymphoblast cells, some with mitotic figures, lymphocytes, few macrophages along with reticular cells and plasma cells and occasional neutrophils. More concentration of immunogenic cells like macrophages was observed in the nodule which might be attributed to the better resistance to disease in Mizo local pig (Zo Vawk).

Genome‐wide scans to detect positive selection in Large White and Tongcheng pigs

Due to the direction, intensity, duration and consistency of genetic selection, especially recent artificial selection, the production performance of domestic pigs has been greatly changed. Therefore, we reasoned that there must be footprints or selection signatures that had been left during domestication. In this study, with porcine 60K BeadChip genotyping data from both commercial Large White and local Chinese Tongcheng pigs, we calculated the extended haplotype homozygosity values of the two breeds using the long-range haplotype method to detect selection signatures. We found 34 candidate regions, including 61 known genes, from Large White pigs and 25 regions comprising 57 known genes from Tongcheng pigs. Many selection signatures were found on SSC1, SSC4, SSC7 and SSC14 regions in both populations. According to quantitative trait loci and network pathway analyses, most of the regions and genes were linked to growth, reproduction and immune responses. In addition, the average genetic differentiation coefficient FST was 0.254, which means that there had already been a significant differentiation between the breeds. The findings from this study can contribute to further research on molecular mechanisms of pig evolution and domestication and also provide valuable references for improvement of their breeding and cultivation.

Determination of 26 veterinary antibiotics residues in water matrices by lyophilization in combination with LC–MS/MS

A sensitive, simple and reliable multi-residue method was developed for the determination of 26 widely used veterinary antibiotics including 6 macrolides, 2 pleuromutilins, 4 tetracyclines, 2 lincosamides, 6 fluoroquinolones and 6 sulfonamides in different water matrices using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Water samples were lyophilized to dryness. Target compounds were separated on Zorbax SB-Aq column (150mm×2.1mm i.d., 3.5μm) and determined by LC-MS/MS operating in positive electrospray ionization mode. Spiked at concentration levels of 0.02, 0.4 and 4μgL(-1), recoveries of all target compounds were over 70% except sulfaquinoxaline (59.0% at 0.02μgL(-1)) with relative standard deviations below 20%. Limits of detection (LOD) and limits of quantification (LOQ) of 26 drugs ranged from 0.1 to 6.5ngL(-1) and from 0.3 to 19ngL(-1), respectively. The developed method was successfully applied to the analysis of 26 antibiotics residues in fish pond water, groundwater, biogas digester water, and lagoon wastewater samples collected from local pig farms.

Whole-genome sequence analysis reveals differences in population management and selection of European low-input pig breeds.

BackgroundA major concern in conservation genetics is to maintain the genetic diversity of populations. Genetic variation in livestock species is threatened by the progressive marginalisation of local breeds in benefit of high-output pigs worldwide. We used high-density SNP and re-sequencing data to assess genetic diversity of local pig breeds from Europe. In addition, we re-sequenced pigs from commercial breeds to identify potential candidate mutations responsible for phenotypic divergence among these groups of breeds.ResultsOur results point out some local breeds with low genetic diversity, whose genome shows a high proportion of regions of homozygosis (>50%) and that harbour a large number of potentially damaging mutations. We also observed a high correlation between genetic diversity estimates using high-density SNP data and Next Generation Sequencing data (r = 0.96 at individual level). The study of non-synonymous SNPs that were fixed in commercial breeds and also in any local breed, but with different allele, revealed 99 non-synonymous SNPs affecting 65 genes. Candidate mutations that may underlie differences in the adaptation to the environment were exemplified by the genes AZGP1 and TAS2R40. We also observed that highly productive breeds may have lost advantageous genotypes within genes involve in immune response – e.g. IL12RB2 and STAB1–, probably as a result of strong artificial in the intensive production systems in pig.ConclusionsThe high correlation between genetic diversity computed with the 60K SNP and whole genome re-sequence data indicates that the Porcine 60K SNP Beadchip provides reliable estimates of genomic diversity in European pig populations despite the expected bias. Moreover, this analysis gave insights for strategies to the genetic characterization of local breeds. The comparison between re-sequenced local pigs and re-sequenced commercial pigs made it possible to report candidate mutations to be responsible for phenotypic divergence among those groups of breeds. This study highlights the importance of low input breeds as a valuable genetic reservoir for the pig production industry. However, the high levels of ROHs, inbreeding and potentially damaging mutations emphasize the importance of the genetic characterization of local breeds to preserve their genomic variability.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-601) contains supplementary material, which is available to authorized users.