Assignment of 19 porcine type I loci by somatic cell hybrid analysis detects new regions of conserved synteny between human and pig

Association of adipocytokine IL-1A and IL-6 genes with intramuscular fat content and fatty acid composition in pigs

Several adipocytokines are involved in inflammatory and immune responses as well as regulated fat deposition and lipid metabolism in mammals. This study aimed to verify the polymorphisms of the porcine interleukin 1A (IL-1A) and interleukin 6 (IL-6) genes and to assess their association with intramuscular fat (IMF) content and fatty acid (FA) composition in commercial crossbred pigs. Two single nucleotide polymorphisms (SNPs) of the porcine IL-1A g.43722547A>G and IL-6 g.91508173C>T loci were found to be segregating in these crossbred pigs. Furthermore, the porcine IL-1A g.43722547A>G polymorphism was found to be significantly associated with myristic, palmitic, palmitoleic, and eicosadienoic acid levels. Moreover, the porcine IL-6 g.91508173C>T polymorphism was significantly associated with IMF content and homolinolenic acid levels. These results suggest that the polymorphisms of the porcine IL-1A and IL-6 genes correlated with lipid content and FA composition and confirmed the importance of the adipocytokine IL-1A and IL-6 genes as candidate genes for fatty acid composition in the muscles of pigs.

Expression of Mx Protein and Interferon-α in Pigs Experimentally Infected with Swine Influenza Virus

Expression of Mx protein and interferon-α (IFN-α) was examined by immunohistochemistry in pigs experimentally infected with swine influenza virus. In infected pigs euthanatized at 1 day postinoculation (dpi), the lumen of bronchioles were filled with large numbers of mononuclear cells, small numbers of neutrophils, sloughing epithelial cells, and proteinaceous fluid. Lesions at 3 and 5 dpi were similar but less severe. Alveolar spaces were filled with neutrophils. By 7 and 10 dpi, microscopic lesions were resolved. The immunohistochemical signals for Mx protein and IFN-α antigen were confined to cells in areas that had hybridization signal for swine influenza virus. In situ hybridization and immunohistochemistry of serial sections of lung indicated that areas containing numerous swine influenza virus RNA-positive cells also have numerous Mx and IFN-α antigen-positive cells. Mean immunohistochemical scores for Mx protein-positive cells were correlated with mean immunohistochemical scores for IFN-α antigen-positive cells ( rs = 0.8799, p < 0.05). These results indicated that Mx protein and IFN-α antigen were expressed in the lung from pigs experimentally infected with swine influenza virus, but their biological functions remain to be examined.

Porcine Mx1 fused to HIV Tat protein transduction domain (PTD) inhibits classical swine fever virus infection in vitro and in vivo

Background

Classical swine fever (CSF) caused by CSF virus (CSFV) is highly contagious andcauses significant economic losses in the pig industry throughout the world. Previously we demonstrated that porcine Mx1 (poMx1), when fused to HIV Tat protein transduction domain (PTD), inhibits CSFV propagation in PK-15 cells, but it is unknown whether PTD-poMx1 exhibits antiviral activity in other porcine lines and it is efficacious for controlling CSFV infection in pigs in China.

Methods

Two porcine cell lines, ST and 3D4/21, were used to investigate in vitro antiviral activity of PTD-poMx1 against CSFV using confocal microscopy, western blot, flow cytometry, and real-time RT-PCR. Furthermore, in vivo antiviral activity of PTD-poMx1 was assessed by means of rectal temperature, clinical score, pathological lesion, white blood cell count, viral load, etc.

Results

PTD-poMx1 entered both cell lines within 3 h and maintained for 16 h, but did not affect CSFV binding and uptake. Viral titers and qRT-PCR data showed that PTD-poMx1 inhibited CSFV replication in both cell lines, showing significant antiviral activity after infection. Injection of PTD-poMx1 into CSFV-challenged pigs attenuated CSFV symptoms and viremia in dose-dependent manner but did not completely block virus replication within 14 days post challenge, suggesting that PTD-poMx1 confers partial protection against a lethal challenge.

Conclusion

We demonstrated the anti-CSFV activity of PTD-poMx1 in vitro and in vivo. The results have shown that treatment with PTD-poMx1 alleviated symptoms and viral load in infected pigs. The results support our previous in vitro studies and suggest that PTD-poMx1 could be promising in reducing the clinical signs caused by CSFV.

In vitro inhibition of the replication of classical swine fever virus by porcine Mx1 protein

Classical swine fever virus (CSFV) is the causative pathogen of classical swine fever (CSF), a highly contagious disease of swine. Mx proteins are interferon-induced dynamin-like GTPases present in all vertebrates with a wide range of antiviral activities. Although Zhao et al. (2011) have reported that human MxA can inhibit CSFV replication, whether porcine Mx1 (poMx1) has anti-CSFV activity remains unknown. In this study, we generated a cell line designated PK-15/EGFP-poMx1 which expressed porcine Mx1 protein constitutively, and we observed that the proliferation of progeny virus in this cell line was significantly inhibited as measured by virus titration, indirect immune fluorescence assay, Q-PCR and Western blot. Furthermore, when PTD-poMx1 fusion protein expressed in Escherichia coli (Zhang et al., 2013) was used to treat CSFV-infected PK-15 cells, the results showed that PTD-poMx1 inhibited CSFV replication in a dose-dependent manner. Additionally, the proliferation of progeny virus was inhibited as measured by virus titration and Q-PCR. Overall, the results demonstrated that poMx1 effectively inhibited CSFV replication, suggesting that poMx1 may be a valuable therapeutic agent against CSFV infection.

Restriction of porcine endogenous retrovirus by porcine APOBEC3 cytidine deaminases

Xenotransplantation of porcine cells, tissues, and organs shows promise to surmount the shortage of human donor materials. Among the barriers to pig-to-human xenotransplantation are porcine endogenous retroviruses (PERV) since functional representatives of the two polytropic classes, PERV-A and PERV-B, are able to infect human embryonic kidney cells in vitro, suggesting that a xenozoonosis in vivo could occur. To assess the capacity of human and porcine cells to counteract PERV infections, we analyzed human and porcine APOBEC3 (A3) proteins. This multigene family of cytidine deaminases contributes to the cellular intrinsic immunity and act as potent inhibitors of retroviruses and retrotransposons. Our data show that the porcine A3 gene locus on chromosome 5 consists of the two single-domain genes A3Z2 and A3Z3. The evolutionary relationships of the A3Z3 genes reflect the evolutionary history of mammals. The two A3 genes encode at least four different mRNAs: A3Z2, A3Z3, A3Z2-Z3, and A3Z2-Z3 splice variant A (SVA). Porcine and human A3s have been tested toward their antiretroviral activity against PERV and murine leukemia virus (MuLV) using novel single-round reporter viruses. The porcine A3Z2, A3Z3 and A3Z2-Z3 were packaged into PERV particles and inhibited PERV replication in a dose-dependent manner. The antiretroviral effect correlated with editing by the porcine A3s with a trinucleotide preference for 5' TGC for A3Z2 and A3Z2-Z3 and 5' CAC for A3Z3. These results strongly imply that human and porcine A3s could inhibit PERV replication in vivo, thereby reducing the risk of infection of human cells by PERV in the context of pig-to-human xenotransplantation.

Molecular characterization and chromosomal mapping of porcine brain and muscle Arnt-like protein-1 gene

As a transcription factor regulating circadian rhythm, brain and muscle Arnt-like protein-1 (BMAL1) plays an important role in lipid homeostasis. The Chinese indigenous and western pig breeds show marked difference in fat deposition, the structure and function of porcine BMAL1 (pBMAL1) between them might be different. In present study, the molecular characteristics and chromosomal location of pBMAL1 were analyzed. The results indicated that pBMAL1 cDNA had a coding region of 1,878 bp and shared 94.36, 89.85 and 89.79% identity with human, mouse and rat BMAL1, respectively, and the pBMAL1 protein had 99.20, 98.24 and 97.92% identity to those of human BMAL1b, mouse BMAL1b and rat BMAL1b, respectively. Compared with other mammals, pBMAL1 was more closely related to human BMAL1. The expression of pBMAL1 was detected in kidney, stomach, spleen, bladder, gallbladder, lumbar spinal cord, medulla oblongata, heart, longissimus dorsi muscle, liver, small intestine, large intestine, lung and backfat tissues. In adipose tissues, it was detected in mesentery fat, leaf fat, caul fat, backfat and cardiac fat, however, the expression level was not significantly different. Alternative usage of exon 2 was revealed to result in two pBMAL1 transcripts. Finally, by using a whole genome porcine radiation hybrid (RH) panel (IMpRH), the pBMAL1 gene was mapped to SSC 2p11-q21.

Polymorphisms in the promoter region of the porcine antiviral MX1 and MX2 genes

The porcine MX1 and MX2 promoters were characterized in this study. Sequencing of the 332-bp MX1 promoter region identified 15 substitutions and insertions at three positions in 21 pigs from 15 breeds, in which nine genotypes were classified. Among the nine genotypes, no statistically significant differences in the promoter activities were observed after interferon (IFN-alpha 2b) treatment of transiently transfected cells containing constructs with luciferase reporter plasmids. The 341-bp MX2 promoter region contained regulatory sequences for ISRE, GC box, Sp1 and AP-1, as well as a TATA box. Nucleotide sequences of the MX2 promoter region revealed four substitutions and one deletion, in which six genotypes were classified. Among the six genotypes, a statistically significant difference (P < 0.05) in MX2 promoter activities after IFN-alpha 2b treatment was detected in transiently transfected cells.

Molecular cloning, mapping, and tissue expression of the porcine cluster of differentiation 14 (CD14) gene

CD14 plays an important role in initiating the innate response to lipopolysaccharide from Gram-negative bacteria. The gene and corresponding cDNA of porcine CD14 were sequenced and characterized. The porcine CD14 gene consists of two exons and a short intron (80 bp) located immediately after the ATG translation start codon. This structure is very similar to the CD14 gene of human, rat, mouse, rabbit, horse, and cow. The sequence of the porcine CD14 protein is 59-76% identical to that of rat, mouse, rabbit, human, horse, and cow CD14 protein. A highly conserved structure of the CD14 protein with respect to the leucine-rich repeats domain and the N-glycosylation sites was observed between species. Porcine CD14 was assigned to porcine chromosome 2q21 by a radiation hybrid panel. Using RT-PCR analysis, porcine CD14 transcripts were detected in liver, spleen, thymus, white matter, and skeletal muscle.

Differential Anti-Influenza Activity among Allelic Variants at TheSus Scrofa Mx1Locus

A promising way to oppose infectious challenges would be to improve the resistance of the target species through genetic selection. Theoretically, a candidate gene is available against influenza viruses since a resistance trait was fortuitously discovered in the A2G mouse strain. This trait was demonstrated to be correlated with the expression of a specific isoform of the type I interferon (IFN)-dependent protein MX, an isoform coded by a specific allele at the mouse Mx1 locus. Two allelic polymorphisms were described recently in the Sus scrofa homologous gene. In this study, the frequencies and distribution of both alleles were evaluated among European domestic pig and wild boar populations by PCR-RFLP, and the anti-influenza activity conferred by both MX1 isoforms was evaluated in vitro using transfection of Vero cells followed by flow cytometric determination of the fraction of influenza virus-infected cells among MX-producing and MX-nonproducing cell populations. A significant difference in the anti-influenza activity brought by the two MX1 isoforms was demonstrated, which suggests that a significant improvement of innate resistance of pigs by genetic selection might be feasible provided the differences found here in vitro are epidemiologically relevant in vivo.

Sequence identification, tissue distribution, mapping and polymorphism of the porcine sar1b gene

The predicted full-length cDNA sequence of the porcine Sar1b gene was characterized by assembling pig ESTs from GenBank. The coding sequence (CDS) shares high sequence identity with the corresponding sequences of human (93%) and mouse (91%). The reverse transcription-polymerase chain reaction (RT-PCR) displayed that porcine Sar1b gene is expressed in all eight tissues (liver, small intestine, stomach, heart, lung, spleen, muscle and fat). Analysis of the somatic cell hybrid panel (SCHP) and the INRA-University of Minnesota porcine radiation hybrid (IMpRH) panel indicated the gene maps to SSC2 (1/2 q24)-q29 and most closely links to the interleukin-4 (IL4) gene. One base-pair deletion polymorphism in the 3' untranslated region (UTR) detected by PCR-single strand conformational polymorphism (PCR-SSCP) analysis shows allele frequency differences between Meishan, Yushan Black, Dahuabai, Qingping, Tibetan, Landrace, Large White and Duroc. The association analysis using pigs of Tongcheng, Landrace x (Large White x Tongcheng) and Large White x (Landrace x Tongcheng) suggested that the deletion polymorphism was associated with the porcine muscle pH value.

Genetic approaches to the improvement of fertility traits in the pig

One of the major determinants for litter size in pigs is prenatal mortality. It occurs most frequently during the first few weeks of gestation and can be attributed to abnormalities in developmental processes during embryogenesis including trophoblastic elongation and blastocyst implantation. Improvement of litter size has been attempted by means of phenotypic selection. However, another promising approach in pursuit of this aim has been the use of genotypic information. Reproductive traits in general are well-suited for application of marker-assisted selection (MAS). The possibility of exerting selection criteria at the molecular level shortens the generation interval as the selection decision can take place early in the life of an animal. Moreover, in consideration of the sex-limited nature of reproductive traits, genotypic information allows for selection in the gender in which the trait cannot be directly observed. Accordingly, there has been considerable interest in mapping and identifying genes involved in the regulation of reproductive traits and in elucidating their expression patterns. This review offers a comprehensive, if not exhaustive, account of the efforts being made and the approaches currently used in this field. One approach has been to choose candidate genes a priori because of the physiological importance of the proteins they encode and their role in the reproduction of other mammals. The usefulness of candidate genes is then examined by association studies between genetic polymorphisms identified in the respective candidate genes and the phenotypic reproductive traits. The other approach discussed uses pre-existing or designed families for linkage analyses in order to map the location of quantitative trait loci (QTL) for the reproductive trait of interest. The results reported were not consistent among different studies but the QTL regions detected may be useful for identification of positional candidate genes in further molecular genetic studies. However, a better understanding of porcine reproduction requires that these functional genomic approaches are merged and integrated with detailed analyses of the proteome to establish linkages between predisposition and physiology.

Genetic susceptibility to keloid disease: mutation screening of the TGFβ3 gene

Keloid disease (KD) is a fibroproliferative dermal tumour of unknown aetiology. The increased familial clustering in KD, its increased prevalence in certain races and its presence in identical twins suggest a strong genetic predisposition to keloid formation. Transforming growth factor beta isoforms (TGFbeta) play a central role in wound healing and fibrosis and have been implicated in KD pathogenesis. Recent data has suggested that TGFbeta(3) has an important role in scar formation. There is little known about the genetic variation present within the TGFbeta(3) gene, which contains seven exons and six introns spanning 43,000 base pairs of the human genome. Exons one to seven and the promoter region (1000 bp upstream from exon 1 in the 5'-flanking regions) were screened in 95 Caucasian KD cases and 95 Caucasian controls for the presence of novel mutations using a high throughput DHPLC mutation detection technology. There were no mutations identified in any of the exonic regions, however, multiple nondisease associated mutations were found in the promoter region of the TGFbeta(3) gene. These data demonstrate that there is no association between the exonic and promoter regions of TGFbeta(3) gene and keloid scarring in our cohort of Caucasian patients.

Development of a single nucleotide polymorphism map of porcine chromosome 2

Single nucleotide polymorphism markers are developed on SSC2, predominantly on the p-arm. Several studies reported a quantitative trait loci (QTL) for backfat thickness in this region. Single nucleotide polymorphisms were identified by comparative re-sequencing of polymerase chain reaction (PCR) products from a panel of eight individuals. The panel consisted of five Large Whites (each from a different Dutch breeding company), a Meishan, a Pietrain and a Wild Boar. In total, 67 different PCR products were sequenced and 301 SNPs were identified in 32,429 bp of consensus sequence, an average of one SNP in every 108 bp. After correction for sample size, this polymorphism rate corresponds to a heterozygosity value of one SNP in every 357 bp. For 63% of the SNPs, there was variation among the five Large Whites, and these SNPs are relevant for linkage and association studies in commercial populations. Comparing the Whites with other breeds revealed higher variation rates with: (i) Meishan, 89%; (ii) Pietrain, 69%; (iii) Wild Boar, 70%. Because many of the experimental populations to identify QTL are based on crosses between these breeds, these SNPs are relevant for the fine mapping of the QTL identified within these crosses.

Molecular cloning of the porcine inhibin-betaB gene and reassignment to chromosome 15

Inhibins are gonadal glycoproteins belonging to the transforming growth factor-beta superfamily that act to suppress pituitary follicle stimulating hormone and are composed of a common alpha-subunit linked by disulphide bonds to either a betaA- or betaB-subunit. The porcine inhibin-alpha, -betaA (INHBA) and -betaB (INHBB) subunit genes have previously been mapped to chromosomes 15, 18 and 12, respectively. Over 6.7 kb of the INHBB gene was sequenced from a porcine genomic cosmid clone and found to contain two microsatellites, one in intron 1 and the other in the 3'-untranslated region. Both microsatellites mapped to pig chromosome 15 at relative position 48 cm. This sequence was greater than 99% identical to two previously reported partial non-contiguous cDNAs for porcine INHBB. Non-coding regions also had a high degree (79-88%) of identity with the corresponding regions of the human gene. Based on sequence information and mapping of two novel microsatellite markers, we reassigned porcine INHBB to chromosome 15, which is consistent with comparative physical and linkage maps of this chromosome and human chromosome 2.

Chromosomal assignments for porcine genes encoding enzymes in hepatic metabolic pathways

Increasing the number of mapped genes will facilitate (1) the identification of potential candidate genes for a trait of interest within quantitative trait loci regions and (2) comparative mapping. The metabolic activities of the liver are essential for providing fuel to peripheral organs, for regulation of amino acid, carbohydrate and lipid metabolism and for homoeostasis of vitamins, minerals and electrolytes. We aimed to identify and map genes coding for enzymes active in the liver by somatic cell genetics in order to contribute to the improvement of the porcine gene map. We mapped 28 genes of hepatic metabolic pathways including six genes whose locations could be confirmed and 22 new assignments. Localization information in human was available for all but one gene. In total 24 genes were assigned to in the expected chromosomal regions on the basis of the currently available information on the comparative human and pig map while for four genes our results suggest a new correspondence or extended regions of conservation between porcine and human chromosomes.

Precise mapping of breakpoints in conserved synteny between human chromosome 1 and pig chromosomes 4, 6 and 9

Previous comparative mapping suggested that at least five pig chromosomes (Sscr4, 6, 9, 10 and 14) share homology with human chromosome 1 (Hsap1). A significant quantitative trait loci (QTL) for fat deposition has been identified on Sscr4 that appears to be near the junction region between Sscr4 and Sscr9 relative to Hsap1. It is of interest to define the boundaries of conserved synteny between pig chromosomes and Hsap1 to use human map information to identify putative comparative positional candidates for this QTL. Eleven genes, including Janus kinase 1 (JAK1), Prostaglandin E receptor3 (PTGER3), urate oxidase (UOX), coagulation factor 3 (F3), vascular cell adhesion molecule 1 (VCAM1), ribosomal protein L5 (RPL5), POU domain, class 2, transcription factor 1 (POU2F1), coagulation factor 5 (F5), Prostaglandin endoperoxide synthase-2 (PTGS2), myosin binding protein H (MYBPH) and Antithrombin III (SERPINC1), were selected to refine the boundaries of the blocks of conserved synteny between Hsap1 and pig chromosomes. Pig sequence tagged sites (STSs) were developed and used to physically map these 11 genes using a somatic cell hybrid panel. Eight loci have been mapped by using fluorescent in situ hybridization (FISH) to improve map resolution. Heterologous FISH was used to refine the location of VCAM1 on human chromosomes. In addition, human yeast artificial chromosomes (YACs) were mapped by heterologous FISH on pig metaphases to refine the boundaries of the regions of homology between Sscr4 and Sscr9 on Hsap1. Results from this study suggest the precise break in conserved synteny on Hsap1 corresponding to the Sscr4/6 and Sscr4/9 transitions are most likely on the Hsap1p22 and Hsap1q24-25 regions, respectively. Further, our data predict that Hsap1q21-24 is a candidate region for the backfat QTL localized to Sscr4.

An updated linkage and comparative map of porcine chromosome 18

Swine chromosome 18 (SSC18) has the poorest marker density in the USDA-MARC porcine linkage map. In order to increase the marker density, seven genes from human chromosome 7 (HSA7) expected to map to SSC18 were selected for marker development. The genes selected were: growth hormone releasing hormone receptor (GHRHR), GLI-Kruppel family member (GLI3), leptin (LEP), capping protein muscle Z-line alpha 2 subunit (CAPZA2), beta A inhibin (INHBA), T-cell receptor beta (TCRB) and T-cell receptor gamma (TCRG). Large-insert clones (YACs, BACs and cosmids) that contained these genes, as well as two previously mapped microsatellite markers (SW1808 and SW1984), were identified and screened for microsatellites. New microsatellite markers were developed from these clones and mapped. Selected clones were also physically assigned by fluorescence in situ hybridization (FISH). Fifteen new microsatellite markers were added to the SSC18 linkage map resulting in a map of 28 markers. Six genes have been included into the genetic map improving the resolution of the SSC18 and HSA7 comparative map. Assignment of TCRG to SSC9 has identified a break in conserved synteny between SSC18 and HSA7.

Comparative porcine gene mapping relative to human chromosomes 9, 10, 20 and 22

Comparative anchor tagged sequence (CATS) consensus primers from loci mapped to human chromosomes 9, 10, 20, and 22 have been used to amplify homologous loci in pigs. Of 53, CATS primers tested in pigs, only 23 yielded products homologous to the human locus (42% success). Ten loci were physically mapped (43% success rate for verified products, but only 19% for primers tested). Due to lack of polymorphism, linkage mapping was possible only for AMBP. Map locations were consistent with human/pig ZOO-FISH, except for ADRA1A, whose position is still equivocal in humans. These CATS primers have made very limited contributions to pig/human comparative gene mapping because of low efficiency of amplification of orthologous porcine product, frequent amplification from rodent template in a somatic hybrid panel and low level of polymorphism.

Molecular characterization and chromosome assignment of the porcine gene for leukemia inhibitory factor LIF

Leukemia inhibitory factor (LIF) is a pleiotropic cytokine involved in early conceptus development in pig. We isolated a PAC clone containing the porcine LIF gene and determined the complete DNA sequence of the gene, which spans about 6.3 kb and consists of five exons including three alternative first exons (1D, 1M, 1T) spliced onto common second and third exons. The LIF-D transcript encodes a protein of 202 amino acids sharing 87, 84, and 78% identity with respectively human, ovine, and murine leukemia inhibitory factors. The LIF-M and LIF-T transcripts both encode a truncated protein of 158 amino acids. Two SNP markers within untranslated regions of the LIF cDNA were identified. One SNP is located in the 5'-UTR of the alternative exon 1T while the other SNP is located in the 3'-UTR of exon 3. Based on fluorescence in situ hybridization and radiation hybrid mapping, the porcine LIF gene was assigned to chromosome 14q2.1-->q2.2.

Assignment of T cell receptor (TCR) alpha-chain gene (A), beta-chain gene (B), gamma-chain gene (G), and delta-chain gene (D) loci on swine chromosomes by in situ hybridization and radiation hybrid mapping

Using the cDNA sequence of porcine T-cell receptor (TCR) alpha-, beta-, gamma-, and delta-chain genes, we screened a porcine BAC library to isolate clones containing these genes. The isolated BAC clones were confirmed to carry these TCR genes by partial nucleotide sequencing. Among the clones obtained in the present screening, two clones carried both the TCR alpha-chain gene (TRA) and the TCR delta-chain gene (TRD) while one clone each carried only the sequence of either TRA or TRD. This observation demonstrated that TRA and TRD are localized in close proximity on a swine chromosome. Also two clones contained the sequence of the TCR beta-chain gene (TRB), and two clones contained the sequence of TCR gamma-chain gene (TRG). Fluorescence in situ hybridization using the above BAC clones as probes revealed that TRA and TRD, TRB, and TRG loci reside on swine chromosomes 7q15.3-->q21, 18q11.3-->q12, and 9q21-->q22, respectively. The chromosome positions of TRA and TRB are consistent with those determined by somatic cell hybrid analysis (Rettenberger et al., 1996). In addition, RH mapping of these genes was performed using the INRA-University of Minnesota RH panel DNA. The result confirmed the position of TRA and TRB reported earlier (http://imprh.toulouse.inra.fr/), and further demonstrated that TRG was located 11 cR away from genetic marker SW989 toward the marker S0019.

Homologies between human and dolphin chromosomes detected by heterologous chromosome painting

Human chromosome-specific probes for the entire karyotype were hybridized to metaphase spreads of the Atlantic bottlenose dolphin, Tursiops truncatus, to directly compare the evolutionary conservation of chromosomal segments between these two distantly related species. All human chromosomal paints, except the Y probe, hybridized to Tursiops counterparts, and every dolphin chromosome was painted except for the smallest submetacentric pair. In our analysis, 36 segments of conserved synteny common to the human and dolphin genomes were identified. The distribution of conserved chromosomal segments and the specific rearrangement patterns found between the two genomes are presented and discussed.

Construction of a whole-genome radiation hybrid panel for high-resolution gene mapping in pigs

We have developed a panel of 152 whole-genome radiation hybrids by fusing irradiated diploid pig lymphocytes or fibroblasts with recipient hamster permanent cells. The number and size of the porcine chromosome fragments retained in each hybrid clone were checked by fluorescence in situ hybridization with a SINE probe or by primed in situ labeling (PRINS) with SINE-specific primers. A strategy based on the interspersed repetitive sequence polymerase chain reaction (IRS-PCR) was developed for selected clones to determine if the large fragments painted by the SINE probe corresponded to one pig chromosome or to different fragments of several chromosomes. This strategy was buttressed by a double PRINS approach using primers specific for alpha-satellite sequences of two different groups of swine chromosomes. Genome retention frequency was estimated for each clone by PCR with 32 markers localized on different porcine chromosomes. Of the 152 hybrids produced, 126 were selected on the basis of cytogenetic content and chromosome retention frequency to construct a radiation hybrid map of swine chromosome 8. Our initial results for this chromosome indicate that the resolution of the radiation hybrid map is 18 times higher than that obtained by linkage analysis.

Comparative mapping between human chromosome 3 and porcine chromosome 13

Zoo-FISH and somatic cell hybrid panels have earlier demonstrated extended synteny conservation between human chromosome 3 (HSA3) and pig chromosome 13 (SSC13). In the present study, eight human genes viz., ADCY5, CASR, COL7A1, COL8A1, ITIH1, RHO, SIAT1 and XPC, spread along the length of HSA3, were chosen for expanding the comparative map between the two chromosomes. Using human and rat cDNAs, or human- and porcine-specific PCR products as probes, 8 porcine lambda clones were isolated. After subcloning and partial sequence determination, identity of the clones with regards to the specific genes was established. The eight type 1 markers thus obtained were biotin labeled and FISH mapped to pig metaphase spreads. All lambda clones localized to SSC13. In combination with the hitherto published mapping data of coding sequences on SSC13, a preliminary comparative status depicting the relative organization of this chromosome with respect to HSA3 was developed. The comparative map thus obtained bears significance in searching for candidate genes of economically important traits mapped to SSC13.

Human chromosome 3 and pig chromosome 13 show complete synteny conservation but extensive gene-order differences

A comparative map of human chromosome 3 (HSA 3) and pig chromosome 13 (SSC 13) was constructed using physically assigned pig sequence-tagged sites (STSs). Pig STSs representing 11 HSA 3 genes, including v-Raf-1 murine leukemia viral oncogene homolog 1 (RAF1), retinoic acid beta receptor (RARB), cholecystokinin (CCK), pituitary transcription factor 1 (POU1F1), ceruloplasmin (CP), guanine nucleotide binding protein, alpha-inhibiting polypeptide 2 (GNAI2), sucrase-isomaltase (SI), rhodopsin (RHO), dopamine receptor D3 (DRD3), growth-associated protein 43 (GAP43), and somatostatin (SST), were developed. Ten pig STSs were regionally mapped using a somatic cell hybrid panel (SCHP) to SSC 13 with 80-100% concordance. Large-insert probes were obtained by screening a pig yeast artificial chromosome (YAC) library with primers for each STS. Several YACs were identified for DRD3, GAP43, POU1F1, RHO, SI, and SST for fluorescence in situ hybridization (FISH) mapping. Single gene and bi-color FISH with each pairwise combination were used to further define the gene order on SSC 13. While these data confirm chromosome painting results showing that HSA 3 probes hybridize to a major portion of SSC 13, they also demonstrate extensive gene-order differences between man and pig within this large conserved synteny group. Interestingly, several conserved chromosomal regions have been detected between pig and mouse that are not conserved between man and mouse, suggesting that the SSC 13 gene arrangement may be the closest to that of the ancestral eutherian chromosome.

Comparative karyotype of pig and cattle using whole chromosome painting probes

The extent and distribution of conserved chromosomal segments between pig and cattle chromosomes were established using hybridization of porcine chromosome painting probes on bovine metaphases. A total of 44 segments of conserved synteny were identified, resulting in a nearly complete coverage of the bovine karyotype. This study provides new data on chromosome evolution of mammals.

FISH mapping of seven cDNA sequences in the pig

Fluorescence in situ hybridization (FISH) technique was applied to localize seven clones derived from a porcine (SSC) intestinal directionally cloned cDNA library. The size of the clones ranged from 1.1 to 1.3 kb. Three of the clones corresponded to histidyl-tRNA synthetase (HARS), immunoglobulin alpha (IGA) and lysozyme (LYZ) and mapped to SSC2q28-q29, 7q2.6 and 5p11 respectively. The available human-pig comparative painting data and sequence homology comparisons assisted in a tentative identification of the other three clones as glutathione-S-transferase (GST), glutathione-S-transferase mu (GSTM1) and immunoglobulin lambda gene cluster (IGL@). These clones mapped to SSC14q21, 5q2.4 and 14q22-q23 respectively. The remaining clone representing an EST mapped to 1p24-p25. These localizations contribute to the transcript map in pig and are significant as comparative markers. Difficulties associated with the mapping of small sequences using FISH are discussed.

Linkage assignment of eleven genes to the porcine genome

We report comparative linkage mapping of eleven genes in the swine genome by RFLP analysis. These genes include: Acid phosphatase type 5 (ACP5), Cholecystokinin Type B Receptor (CCKBR), Antibiotic Peptide (FALL39), Insulin-like Growth Factor 1 Receptor (IGF1R), Integrin Alpha M (ITGAM), Integrin Beta 2 (ITGbeta2), Opioid Receptor Mu-1 (OPRM1), Pro-hormone Converter (PC1/3), Retinol Binding Protein 3 (RBP3), Ribosomal DNA (RNR1), and Zona Pellucida Glycoprotein 1 (ZP1). The CCKBR and ITGbeta2 loci define the ends of the linkage groups on Chromosomes (Chro) (SSC) 9p and 13qter, respectively.

Mapping of 22 expressed sequence tags isolated from a porcine small intestine cDNA library

Complementary DNA sequences were selected from a resource of tentatively identified clones from a porcine small intestine cDNA library. Forty PCR primer pairs were designed to amplify 101-309 base pairs of the 3' untranslated region of the genes. The PCR conditions were optimized by altering both formamide and magnesium concentrations on samples of pig, mouse, and hamster DNA. Twenty primer pairs that, under stringent conditions, were pig-specific and amplified the expected fragments were chosen for regional assignment in a pig/rodent hybrid cell panel. Furthermore, 22 primer pairs were chosen to amplify DNA from the parental animals of the PiGMaP shared reference families in order to detect possible polymorphisms. Primer pairs that generated polymorphisms were used for genetic mapping. A total of 22 porcine expressed sequence tags (ESTs) were cytogenetically or genetically mapped by this approach. Twelve of the mapped ESTs could be added to the human-porcine comparative map.

Characterization, chromosomal localization, and genetic variation of the porcine heart fatty acid-binding protein gene

The purpose of this study was to detect genetic variation in the porcine H-FABP gene, a candidate gene for meat quality traits in pigs. Lambda phages containing the porcine H-FABP gene were isolated by plaque hybridization with human H-FABP cDNA. The coding and flanking intronic sequences of the porcine H-FABP gene were determined as well as 1.6 kb of the 5' upstream region. The various potential regulatory sequences in this region are in accordance with the function and expression of the protein in muscle and mammary tissue. Furthermore, comparison with the homolog region of the mouse identified a highly conserved 13-bp element (CTTCCT [A/C] TTTCGG) that may be involved in regulation of expression. The porcine H-FABP gene was localized on Chromosome (Chr) 6 by porcine sequence-specific PCR on DNA from a pig/rodent cell hybrid panel. In addition, part of the H-FABP gene was screened for genetic variation by PCR-RFLP analysis. Three PCR-RFLPs were detected, one in the upstream region (HinfI) and two in the second intron (HaeIII and MspI). In most pig breeds the corresponding alleles have a variable distribution, possibly a consequence of selective breeding. This genetic variation will enable us to investigate the role of the H-FABP locus in porcine production and meat quality traits.

Genomic mapping of chemokine and transforming growth factor genes in swine

Five chemokine genes, transforming growth factors alpha, beta 2 and 3 (TGFBA, TGFB-2, and TGFB-3), interleukin 8 (IL-8), and monocyte chemoattractant protein 2 (MCP-2), were mapped to porcine linkage groups on Chromosomes 3q, 10p, 7q, 8, and 12q, respectively. Restriction fragment length polymorphisms (RFLPs) for these genes were developed by Southern blot hybridization after digestion of porcine genomic DNA with BamHI and MspI (TGFBA), BamHI and PvuII (TGFB-2), HindIII (TGFB-3), BglII (IL-8), and PstI (MCP-2) and used to genotype the USDA-MARC Swine Reference Population pigs. Sufficient informative meioses, 61 (TGFBA), 58 (TGFB-2), 28 (TGFB-3), 38 (IL-8), and 156 (MCP-2), were available to pursue two-point pairwise linkage analysis with over 1,000 existing loci in the USDA-MARC genome database to establish initial linkage (LOD > 3). Multi-point analysis with CRIMAP determined the most likely order for each new marker. The assignment of the five chemokine genes in swine concurs with previous porcine/human chromosomal homologies based on results from ZOO-FISH and chromosomal painting experiments. These findings add five new informative Type I markers within a single gene family to the swine genome and may help us understand the genetic basis for disease resistance in livestock.

Polymerase chain reaction-based polymorphisms in the porcine cholecystokinin (CCK) gene and assignment to chromosome 13

Polymorphisms were identified in the porcine cholecystokinin (CCK) gene by digestion of products from polymerase chain reaction (PCR) with the restriction enzyme DpnII. Individuals from the European pig gene mapping project (PiGMaP) consortium reference families (eight full-sib families, 91 total progeny) were genotype to determine linkage relationships between the CCK gene and previously mapped loci. Linkage analysis revealed that the CCK gene is located on porcine chromosome 13.

Partial characterization of porcine obesity gene (OBS) and its localization to chromosome 18 by somatic cell hybrids

Degenerate primers based on human and mouse obesity gene (OBS) sequencing data were used in the reverse transcriptase-polymerase chain reaction (RT-PCR) of total RNA from pig white adipose tissue. Both strands of the resultant pig- specific 325 bp DNA fragment were sequenced. Comparison of the obtained sequence with known sequences revealed an 86% identity with the human and 84% identity with the mouse OBS cDNA. The OBS gene was physically mapped to pig chromosome 18 by PCR analysis of somatic cell hybrids, using pig-specific primers. This result is consistent with the recent assignment of the human OBS gene to chromosome 7 and the observation made by comparative mapping that by using a human chromosome 7 specific library two segments of conserved synteny were detected on porcine chromosomes 9 and 18. We conclude the border of conserved synteny to be in the 7q31-7q32 region of the human chromosome.

Mapping of the porcine urate oxidase and transforming growth factor beta 2 genes by fluorescence in situ hybridization

We have mapped two genes from human chromosome 1, urate oxidase (UOX) and transforming growth factor beta 2 (TGFB2), by fluorescence in situ hybridization (FISH) in the pig genome. Porcine-specific polymerase chain reaction (PCR) primers for both genes were designed from the porcine cDNA sequence. With the help of these primers yeast artificial chromosome (YAC) clones for UOX and TGFB2 were isolated from a pig YAC library. These DNA probes were used for FISH analysis. TGFB2 was localized to SSC 10p16. With the YAC probe for UOX two porcine chromosome regions 6q26 and 6q32, revealed specific signals. These results, help to refine the comparative mapping data between human and pig.