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ABSTRACT: Fatty acid (FA) composition is one of the most important parameters for the evaluation of meat quality. The stearoyl-CoA desaturase (SCD) gene is considered a positional candidate gene affecting FA composition in SSC14, based on previous quantitative trait loci studies. To evaluate the association of the SCD gene with FA composition in a Korean native pig × Landrace F(2) intercross population, we genotyped six single nucleotide polymorphisms (SNPs) of the SCD gene located in promoter region [2 SNPs (g.-353T>C, g.-233T>C)], exonic region [1 SNP (g.817C>T) in exon 2] and 3' UTR [3 SNPs (g.13311C>G, g.14384G>A, and g.14424C>T)] identified by massively parallel sequencing technology. Eighteen FA composition traits were measured in more than the 950 F(2) animals. A mixed-effect model was used to evaluate associations between these SNPs and FA composition traits in the F(2) intercross population. A detailed investigation detected that the five FA composition traits [palmitoleic acid (C16:1), stearic acid (C18:0), arachidic acid (C20:0), saturated FA, and unsaturated FA] were highly significant (P < 4.7 × 10(-5); C20:0) in association with the SNP g.-233T>C, SNP g.817C>T, SNP g.13311C>G and SNP g.14384G>A in the SCD gene, whereas SNP g.14424C>T was only significantly associated with palmitoleic acid (C16:1, P = 1.4 × 10(-3)). No significant association of FA composition traits with SNP g.-353T>C was detected. In particular, the SNP g.14384G>A accounted for 30.6 % of the additive genetic variance of palmitoleic acid (P = 1.9 × 10(-10)). These results suggest the SCD gene has a strong effect on FA composition in the crossbred pig population.
Molecular Biology Reports 11/2012; · 2.93 Impact Factor
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ABSTRACT: In this study, we conducted a genome-wide linkage analysis to identify the quantitative trait loci (QTL) that influence back fat thickness and carcass pH in an F(2) intercross between Landrace and Korean native pigs. Eight phenotypes related with back fat thickness and carcass pH were measured in more than 960 F(2) progeny. All experimental animals were subjected to genotypic analysis using 173 microsatellite markers located throughout the pig genome. The GridQTL program, based on the least squares regression model, was used to perform the QTL analysis. We identified 22 genome-wide significant QTL in 9 chromosomal regions (SSC1, 2, 5, 6, 7, 8, 12, 15, and 16) and 29 suggestive QTL in 16 chromosomal regions (SSC2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 14, 15, 16, 17, 18, and X). On SSC5, we detected a QTL affecting back fat thickness that accounted for 4.8 % of the phenotypic variance, which was the highest test statistic (F-ratio = 50.3 under the additive model, nominal P value = 2.5 × 10(-12)) observed in this study. Additionally, we showed that there were significant QTL on SSC16 affecting carcass pH traits. In conclusion, the QTL identified in this study together with associated positional candidate genes could play an important role in determining the genetic structure underlying the variation of back fat thickness and carcass pH in pigs.
Molecular Biology Reports 06/2012; 39(8):8327-33. · 2.93 Impact Factor
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ABSTRACT: Using a partial D-loop sequence of mtDNA, an intensive analysis was conducted of the maternal lineages of Jeju native pigs
(JNPs) from Korea. In total, 100 mtDNA sequences were obtained from Asian wild boars (AWBs), European wild boars (EWBs), Asian
domestic pigs (ADPs), European domestic pigs (EDPs), and JNPs and were used for phylogeny and network analyses. Two distinct
JNP groups — one (JNPA) in the Asian cluster and the other (JNPE) in the European cluster — were identified in the estimated
phylogenetic tree and network. The maternal lineage of JNPE was the closest to that of EWB and a clear haplogroup was identified
that shared an identical haplotype (hap04) among 15 individuals of JNPE and 2 individuals of EWB. A Landrace and an EWB shared
hap03 with a JNPE. EWB, Landrace, Large White, and Duroc formed two clear haplogroups with JNPE in a parsimonious median-joining
network analysis, suggesting that an obvious maternal contribution of EDP has occurred in JNPE in recent years. A pair-wise
mismatch analysis also indicated that JNPE may have experienced a sudden population expansion, suggesting a more recent establishment
compared with the gradual population expansion of JNPA. The JNPE group therefore should be further evaluated in order to decide
whether this group should be culled or accepted into further programs for maintenance of the JNP population as a pure breed.
KeywordsJeju native pig–Maternal lineage–Phylogeny–Network–Mismatch analysis
Genes & genomics 04/2012; 33(2):111-117. · 0.44 Impact Factor
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ABSTRACT: The KIT gene has been shown to have multiple functions in hematopoiesis, melanogenesis, and gametogenesis. In addition, mutations
of this gene cause pigmentation disorders in humans and mice and are responsible for coat color differences in pigs. While
characterizing polymorphisms in the porcine KIT gene, we detected alternative splicing (AS) of the NAGNAG splice acceptor site at the boundary of intron 4 and exon 5. This
AS event generated the E and I isoforms, characterized by insertion or deletion, respectively, of CAG at the borders of coding
sequence. AS patterns measured in tissue samples from two randomly selected animals did not identified any tissue-specific
outcomes. Analysis of AS patterns using three breeds demonstrated that Landrace and Large White pigs expressed both the E
and I isoforms. In contrast, a subset of specimens from Korean Native Pigs (KNP) yielded a single I isoform. Alignment of
the sequence from several species revealed that the region between the branch point sequence (BPS) and 3′ acceptor site is
conserved. However, it is appeared that the selection of either the proximal or distal splice site varied between species.
To test the breed specificity the NAGNAG splice acceptor site, we constructed two lineages of minigenes from KNP and Landrace
pigs harboring breed-specific mutations. The minigene splicing assay demonstrated that both types of minigenes expressed both
the E and I isoforms in two host cell lines, and no differences were detected in the AS pattern between the two breeds. We
conclude that the AS at the NAGNAG splice acceptor site on intron 4/exon 5 in the porcine KIT gene is the result of noise selection at the splice site by the splicing machinery. Therefore, this AS event in the porcine
KIT gene is unlikely to have any relationship with the coat color variations of Landrace and KNP breeds.
Keywords
KIT gene–Aalternative splicing–Pig–NAGNAG–Minigene
Genes & genomics 04/2012; 33(2):179-186. · 0.44 Impact Factor
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In-Cheol Cho,
Tao Zhong,
Bo-Young Seo,
Eun-Ji Jung,
Chae-Kyoung Yoo,
Jae-Hwan Kim,
Jae-Bong Lee,
Hyun-Tae Lim,
Byoung-Woo Kim, Jun-Heon Lee,
Moon-Suck Ko,
Jin-Tae Jeon
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ABSTRACT: The roan coat color is characterized by white hairs intermingled with colored hairs. Candidate genes based on comparative
phenotypes in horses and cattle involve the KIT and KIT ligand (MGF) genes. Here, we report the result of the whole genome scanning to detect genomic regions responsible for the roan coat color,
using a three-generation pedigree of 62 pigs in an intercross between Landrace and Korean native pig. These pigs were genotyped
using the PorcineSNP 60 BeadChip (Illumina, USA). The whole genome scan indicated that three genomic regions, 35∼36 Mb, 38∼39
Mb, and 58∼59 Mb on SSC8, were commonly and highly associated/linked with the roan phenotype in the case/control, sib-pair,
and linkage test, respectively. The porcine KIT was selected as a candidate gene, because it is located in one of the three significant regions and its function is related
to coat color formation. SNPs and Indels within coding sequence (CDS), promoter, and 3′-UTR of KIT were surveyed. Twenty-two SNPs in the CDS reported previously, as well as nine variations in promoter (2 SNPs) and 3′-UTR
(5 SNPs and 2 Indels) were detected. Although no causative mutations were identified, these results will help to elucidate
the genetic mechanisms involved in the expression of the roan phenotype and will aid in identifying key mutations responsible
for the roan phenotype in further studies.
KeywordsKIT–Korean native pig–Roam–CDS
Genes & genomics 04/2012; 33(1):17-23. · 0.44 Impact Factor
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ABSTRACT: Pigs have been considered as donors for xenotransplantation in the replacement of human organs and tissues. However, porcine endogenous retroviruses (PERVs) might transmit new infectious disease to humans during xenotransplantation. To investigate PERV integration sites, 45 PERV-positive BAC clones, including 12 PERV-A, 16 PERV-B, and 17 PERV-C clones, were identified from the NIH miniature pig BAC library. The analysis of 12 selected full-length sequences of PERVs, including the long terminal repeat (LTR) region, identified the expected of open reading frame length, an indicative of active PERV, in all five PERV-C clones and one of the four PERV-B clones. Premature stop codons were observed in only three PERV-A clones. Also, eleven PERV integration sites were mapped using a 5000-rad IMpRH panel. The map locations of PERV-C clones have not been reported before, thus they are novel PERV clones identified in this study. The results could provide basic information for the elimination of site-specific PERVs in selection of pigs for xenotransplantation.
Journal of Biomedicine and Biotechnology 01/2012; 2012:482568. · 2.44 Impact Factor
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ABSTRACT: An apparatus for generating atmospheric pressure plasma (APP) jet was used to investigate the inactivation of Listeria monocytogenes on the surface of agar plates and slices of cooked chicken breast and ham. He, N₂ (both 7 L/min), and mixtures of each with O₂ (0.07 L/min) were used to produce the plasma jets. After treatment for 2 min with APP jets of He, He + O₂, N₂, or N₂ + O₂, the numbers of L. monocytogenes on agar plates were reduced by 0.87, 4.19, 4.26, and 7.59 log units, respectively. Similar treatments reduced the L. monocytogenes inoculated onto sliced chicken breast and ham by 1.37 to 4.73 and 1.94 to 6.52 log units, respectively, according to the input gas used with the N₂ + O₂ mixture being the most effective. Most APP jets reduced the numbers of aerobic bacteria on the meat surfaces to <10² CFU/g, and the numbers remained below that level of detection after storage at 10 °C for 7 days. The results indicate that APP jets are effective for the inactivation of L. monocytogenes on sliced meats and for prolonging the shelf-life of such foods.
Food Microbiology 12/2011; 28(8):1468-71. · 3.28 Impact Factor
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ABSTRACT: The highly polymorphic porcine major histocompatibility complex (MHC), or the swine leukocyte antigens (SLA), has been repeatedly associated with variations in swine immune response to pathogens and vaccines as well as with production traits. The SLA antigens are also important targets for immunological recognition of foreign tissue grafts. We recently established a resource population of Korean native pigs as models for human transplantation and xenotransplantation research. In this study, 115 animals derived from three generations of the Korean native pigs were genotyped for three SLA class I (SLA-2, SLA-3 and SLA-1) and three SLA class II loci (DRB1, DQB1, DQA) using PCR with sequence-specific primers (PCR-SSP) at the allele group resolution. A total of seven SLA haplotypes (Lr-5.34, Lr-7.23, Lr-31.13, Lr-56.23, Lr-56.30, Lr-59.1, Lr-65.34), comprising six unique class I and five unique class II haplotypes, were characterized in the founding animals. Class I haplotype Lr-65.0 and class II haplotype Lr-0.34 were novel; and together with Lr-56.0 these haplotypes appeared to be breed-specific. In the progeny population, Lr-7.23 and Lr-56.30 appeared to be the most prevalent haplotypes with frequencies of 34.7% and 31.6%, respectively; the overall homozygosity was 27.4%. This resource population of SLA-defined Korean native pigs will be useful as large animal models for various transplantation and xenotransplantation experiments, as well as for dissecting the roles of SLA proteins in swine disease resistance and production traits.
Molecules and Cells 05/2010; 29(5):493-9. · 2.18 Impact Factor
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ABSTRACT: In order to elucidate the precise phylogenetic relationships of Korean wild boar (Sus scrofa coreanus), a partial mtDNA D-loop region (1,274 bp, NC_000845 nucleotide positions 16576-1236) was sequenced among 56 Korean wild boars. In total, 25 haplotypes were identified and classified into four distinct subgroups (K1 to K4) based on Bayesian phylogenetic analysis using Markov chain Monte Carlo methods. An extended analysis, adding 139 wild boars sampled worldwide, confirmed that Korean wild boars clearly belong to the Asian wild boar cluster. Unexpectedly, the Myanmarese/Thai wild boar population was detected on the same branch as Korean wild boar subgroups K3 and K4. A parsimonious median-joining network analysis including all Asian wild boar haplotypes again revealed four maternal lineages of Korean wild boars, which corresponded to the four Korean wild boar subgroups identified previously. In an additional analysis, we supplemented the Asian wild boar network with 34 Korean and Chinese domestic pig haplotypes. We found only one haplotype, C31, that was shared by Chinese wild, Chinese domestic and Korean domestic pigs. In contrast to our expectation that Korean wild boars contributed to the gene pool of Korean native pigs, these data clearly suggest that Korean native pigs would be introduced from China after domestication from Chinese wild boars.
Molecules and Cells 10/2009; 28(5):423-30. · 2.18 Impact Factor
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ABSTRACT: Three isoforms of pig PDE4B were cloned and classified as two forms: PDE4B1 and PDE4B3, which contain UCR1 and UCR2; and PDE4B2, which contains only UCR2. The amino acid sequences of each isoform showed good conservation in human and rat. PDE4B2 is expressed in a wide range of tissues, but PDE4B1 and PDE4B3 are not. Using an informative SNP for the Iberian x Landrace intercross detected from intron 12, a linkage map was constructed. The location of PDE4B was estimated at 123.6 cM outside of the QTL-CI (124-128 cM) for IMF. However, the QTL-CI for IMF was reconfirmed with high significance, and its position was narrowed down to an interval of 4 cM (the region defined by markers PDE4B and SW1881). Using radiation hybrid mapping, LEPR, LEPROT, DNAJC6, AK3L1 and AK3L2 were selected as positional and/or functional candidates related to the QTL.
BMB reports 07/2008; 41(6):466-71. · 1.72 Impact Factor
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Seung-Hwan Lee,
Eung-Woo Park,
Yong-Min Cho,
Sung-Kon Kim, Jun-Heon Lee,
Jin-Tae Jeon,
Chang-Soo Lee,
Seok-Ki Im,
Sung-Jong Oh,
J M Thompson,
Duhak Yoon
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ABSTRACT: Marbling of cattle meat is dependent on the coordinated expression of multiple genes. Cattle dramatically increase their intramuscular fat content in the longissimus dorsi muscle between 12 and 27 months of age. We used the annealing control primer (ACP)-differential display RT-PCR method to identify differentially expressed genes (DEGs) that may participate in the development of intramuscular fat between early (12 months old) and late fattening stages (27 months old). Using 20 arbitrary ACP primers, we identified and sequenced 14 DEGs. BLAST searches revealed that expression of the MDH, PI4-K, ferritin, ICER, NID-2, WDNMI, telethonin, filamin, and desmin (DES) genes increased while that of GAPD, COP VII, ACTA1, CamK II, and nebulin decreased during the late fattening stage. The results of functional categorization using the Gene Ontology database for 14 known genes indicated that MDH, GAPD, and COP VII are involved in metabolic pathways such as glycolysis and the TCA cycle, whereas telethonin, filamin, nebulin, desmin, and ACTA1 contribute to the muscle contractile apparatus, and PI4-K, CamK II, and ICER have roles in signal transduction pathways regulated by growth factor or hormones. The final three genes, NID-2, WDNMI, and ferritin, are involved in iron transport and extracellular protein inhibition. The expression patterns were confirmed for seven genes (MDH, PI4-K, ferritin, ICER, nebulin, WDNMI, and telethonin) using real-time PCR. We found that the novel transcription repressor ICER gene was highly expressed in the late fattening stage and during bovine preadipocyte differentiation. This information may be helpful in selecting candidate genes that participate in intramuscular fat development in cattle.
Journal of biochemistry and molecular biology 10/2007; 40(5):757-64. · 2.02 Impact Factor
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ABSTRACT: Aside from single nucleotide polymorphisms, copy number variations (CNVs) are the most important factors in susceptibility to genetic disorders because they affect expression levels of genes. In previous studies, pyrosequencing, mini-sequencing, real-time PCR, invader assays and other techniques have been used to detect CNVs. However, the higher the copy number in a genome, the more difficult it is to resolve the copies, so a more accurate method for measuring CNVs and assigning genotype is needed.
PCR followed by a quantitative oligonucleotide ligation assay (qOLA) was developed for quantifying CNVs. The accuracy and precision of the assay were evaluated for porcine KIT, which was selected as a model locus. Overall, the root mean squares of bias and standard deviation of qOLA were 2.09 and 0.45, respectively. These values are less than half of those in the published pyrosequencing assay for analyzing CNV in porcine KIT. Using a combined method of qOLA and another pyrosequencing for quantitative analysis of KIT copies with spliced forms, we confirmed the segregation of KIT alleles in 145 F1 animals with pedigree information and verified the correct assignment of genotypes. In a diagnostic test on 100 randomly sampled commercial pigs, there was perfect agreement between the genotypes obtained by grouping observations on a scatter plot and by clustering using the nearest centroid sorting method implemented in PROC FASTCLUS of the SAS package. In a test on 159 Large White pigs, there were only two discrepancies between genotypes assigned by the two clustering methods (98.7% agreement), confirming that the quantitative ligation assay established here makes genotyping possible through the accurate measurement of high KIT copy numbers (>4 per diploid genome). Moreover, the assay is sensitive enough for use on DNA from hair follicles, indicating that DNA from various sources could be used.
We have established a high resolution quantification method using an oligonucleotide ligation assay to measure CNVs, and verified the reliability of genotype assignment for random animal samples using the nearest centroid sorting method. This new method will make it more practical to determine KIT CNV and to genotype the complicated Dominant White/KIT locus in pigs. This procedure could have wide applications for studying gene or segment CNVs in other species.
BMC Genetics 01/2007; 8:81. · 2.47 Impact Factor
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ABSTRACT: Using the Phred/Phrap/Polyphred/Consed pipeline established in the National Livestock Research Institute of Korea, we predicted candidate coding single nucleotide polymorphisms (cSNPs) from 7,600 expressed sequence tags (ESTs) derived from three cDNA libraries (liver, M. longissimus dorsi, and intermuscular fat) of Hanwoo (Korean native cattle) steers. From the 7,600 ESTs, 829 contigs comprising more than two EST reads were assembled using the Phrap assembler. Based on the contig analysis, 201 candidate cSNPs were identified in 129 contigs, in which transitions (69%) outnumbered transversions (31%). To verify whether the predicted cSNPs are real, 17 SNPs involved in lipid and energy metabolism were selected from the ESTs. Twelve of these were confirmed to be real while five were identified as artifacts, possibly due to expressed sequence tag sequence error. Further analysis of the 12 verified cSNPs was performed using the program BLASTX. Five were identified as nonsynonymous cSNPs, five were synonymous cSNPs, and two SNPs were located in 3'-UTRs. Our data indicated that a relatively high SNP prediction rate (71%) from a large EST database could produce abundant cSNPs rapidly, which can be used as valuable genetic markers in cattle.
Journal of biochemistry and molecular biology 04/2006; 39(2):183-8. · 2.02 Impact Factor
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ABSTRACT: Pigs are an important large animal model for transplantation and a potential source of xenografts. Swine leukocyte antigen (SLA) molecules are strong mediators of alloreactive and xenoreactive immune responses. We have characterized the SLA alleles of a new pig line bred for transplantation research, the Westran (Westmead Hospital transplantation) pig, described in a companion paper.
Three sixth generation inbred Westran pigs and a Large White pig control were used to assess SLA alleles. We examined the SLA-1, SLA-3, SLA-6, SLA-2, DQA1, DQB1, DRA1 and DRB1 loci using reverse transcription-polymerase chain reaction and sequencing-based method.
All of the Westran pigs had a single allele at each locus, except for the SLA-1 locus. Typing of the SLA-1 locus in additional animals indicated that this is most likely the result of a duplication of the SLA-1 locus rather than heterozygosity. The lack of SLA heterozygosity is consistent with the previous finding of low microsatellite marker heterozygosity and is the result of both the recent deliberate inbreeding of these pigs and their derivation from a feral stock from Kangaroo Island, South Australia, established by the release of a single pair in 1803.
After comparing DNA and protein sequences of the Westran SLA alleles with published GenBank SLA sequences, the SLA class I alleles found in the Westran pigs were all novel, while the SLA-DR and DQB1 alleles have been previously described in other pig breeds. Characterization of the SLA alleles in the Westran pigs has identified novel alleles and will be useful for designing protocols for modulation of immune responses to allografts and xenografts.
Xenotransplantation 08/2005; 12(4):303-7. · 2.33 Impact Factor
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ABSTRACT: Pigs were introduced into Australia and New Zealand in the 18th and 19th centuries, with some establishing feral populations. With few records of pig introductions into these two countries, molecular phylogenetic analysis was used to assess their origins. Mitochondrial (mt) control region sequence and nuclear glucosephosphate isomerase pseudogene (GPIP) restriction fragments were used, as distinct European and Asian domestic pig and Wild Boar control region clades and GPIP genotypes can be recognised. Feral pig control region sequences clustered with either European or Asian domestic pig sequences and both Asian and European GPIP alleles were segregating. It was not possible to distinguish direct importation of Asian domestic animals into Australia and New Zealand from indirect introgression of Asian domestic sequences via Europe. However, the clustering of three feral control region sequences of pigs from northern Australia with Asian Wild Boar implies unrecorded introduction of Wild Boar or crossbred animals into Australia. However, two of these feral pigs had European GPIP alleles. In combination, analyses of control region and GPIP markers suggest that both European and Asian pigs have contributed in similar frequencies to the origins of Australian feral pigs.
Molecular Phylogenetics and Evolution 12/2004; 33(2):339-48. · 3.61 Impact Factor
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ABSTRACT: Phylogenetic relationships of Northeast Asian cattle to various other cattle breeds including Bos taurus, Bos indicus, and Bison bison were assessed using mtDNA D-loop sequences. A neighbor-joining tree was constructed using sequences determined for 4 Cheju Black, 4 Cheju Yellow, 4 Korean Yellow cattle (Bos taurus), and 2 American Brahman cattle (Bos indicus), and also published sequences for 31 Japanese Black cattle, 45 European breed cattle, 6 African zebus, 2 African taurines, and 6 Indian zebus. Five American bisons (Bison bison) were used as an outgroup. The neighbor-joining tree showed that American bisons and Indian zebus are clearly separate from other cattle breeds, respectively, and African cattle clustered together, although with a low bootstrap probability (< 50%). Results indicate that cattle in Northeast Asia, Europe, and Africa are closely related to each other-suggesting their recent divergence, but are separate from Indian zebus.
Biochemical Genetics 05/2003; 41(3-4):91-8. · 0.86 Impact Factor
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ABSTRACT: Since porcine endogenous retroviruses (PERVs) can infect cultured human cells, they are a potential hazard to xenotransplantation. For this reason, endogenous retroviruses from the Westran (Westmead Hospital transplantation) inbred line of pigs were analyzed by using consensus primers for the type A and type B viruses to amplify 1.8-kb envelope gene fragments. After preliminary analysis with restriction enzymes KpnI and MboI, 31 clones were sequenced. Between types A and B, five recombinant clones were identified. Fifty-five percent of clones (17 of 31) had premature stop codons within the envelope protein-encoding region. Endogenous retroviruses in Westran pigs were physically mapped by fluorescence in situ hybridization (FISH) using PERV-A and PERV-B envelope clones as probes to identify at least 32 integration sites (19 PERV-A sites and 13 PERV-B sites). The chromosomal sites of integration in the Westran strain are quite different from those in the European Large White pig. The recombinant clones suggest that defective PERVs could become infective through recombination and further that PERVs might recombine with human endogenous retroviruses in xenotransplants.
Journal of Virology 07/2002; 76(11):5548-56. · 5.40 Impact Factor
