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Ubiquitin-like 5 (UBL5), which is supposed to be involved in regulation of feed intake, energy metabolism, obesity and type 2 diabetes, is located at position 62.1 cM on the pig chromosome 2 region harbouring quantitative trait loci for carcass and meat quality. The 4,354 bp genomic sequence (FR798948) of the porcine gene encompassing the promoter and entire gene was cloned by polymerase chain reaction. Comparative sequencing revealed 13 polymorphisms in noncoding regions. Synthesis of full-length cDNA sequences using rapid amplification of 5' and 3' ends showed three splice variants. Variants 1 and 2 differ in transcription length for the untranslated part of exon 1 with deduced protein of 73 amino acid (aa) residues and 100 % identities between human, mouse and other species. Variant 3, with 4 bp deletion at the 3' end of exon 2, encodes a truncated protein with 28 aa residues. In a Wild boar×Meishan F2 population (n = 334) with 47 recorded traits, loci FR798948:g.2788G>A and FR798948:g.2141T>C were associated at nominal P < 0.05 with fat deposition, growth and fattening and muscling but after adjustment for multiple testing (Benjamini and Hochberg, J R Stat Soc B 57:289-300, 1995) only eight fat deposition traits showed suggestive association with FR798948:g.2788G>A at adjusted P < 0.10. In a Meishan×Large White (MLW) cross (n = 562) with six trait records available, FR798948:g.2141T>C showed suggestive association with growth (adjusted P = 0.0690). As association mapping conducted in the outbred MLW population is more precise than in the three generation F2 population the UBL5 gene tends to be associated with growth rather than with fat accretion.

The serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 1 (SERPINE1) gene encodes plasminogen activator inhibitor type 1 (PAI), which is the major physiological inhibitor of tissue-type and urokinase-type plasminogen activators and plays a role in obesity and insulin resistance in women but not in men. We detected SNP FN396538:g.566G>A in intron 3 and a non-synonymous substitution NM&#95;213910:c.612A>G in exon 3 (p.Ile159Val) and mapped the gene to position 8.4 cM on the linkage map of chromosome 3. Association analyses were conducted on the 12th-15th generation of the Meishan × Large White (MLW) cross (n = 565), with records for weight at the end of test, lifetime daily gain, test time daily gain, loin depth and backfat depth, as well as on a European wild boar × Meishan (W × M) F(2) population (n = 333) with 47 traits recorded for carcass composition and meat quality. Analyses performed across the entire MLW population or in the male animals did not show any trait significantly associated with the loci studied. In female animals, both SNPs were associated with loin depth at nominal P < 0.05 with adjusted P values equal to 0.051 (g.566) and 0.057 (c.612). Differences between homozygotes were up to 0.65 SD. In the entire W × M population and female animals, SERPINE1 was significantly associated at adjusted P < 0.05 in descending order with muscling, growth and fat accretion and in male animals with meat quality (R-value). In the studied populations, allele effects were in opposite directions, which implies that the SNPs are markers that are in linkage disequilibrium with a causative mutation., (© 2011 The Authors, Animal Genetics © 2011 Stichting International Foundation for Animal Genetics.)

Quantitative trait loci (QTL) for fat deposition, growth and muscling traits have been previously mapped on the basis of low-density linkage maps in a wild boar x Meishan F2family to the chromosome X region flanked by SW2456 and SW1943. Improved QTL resolution was possible using data for F2 animals with a marker density of 2.7 cM distance in the SW2456 to SW1943 region, including AR, SERPINA7 and ACSL4 as candidate genes. The resolution of the QTL scan was increased substantially, as evidenced by the higher F-ratio values for all QTL. Maxima of F-ratio values for fat deposition, muscling and growth traits were 28.6, 18.2 and 16.5 respectively, and those QTL positions accounted for 7.9%, 5.0% and 4.5% of the F2 phenotypic variance (VF2) respectively. QTL for fatness and growth and for most muscling traits mapped near ACSL4, with the exception of the QTL for ham traits that mapped proximally, in the vicinity of AR. An analysis performed separately for F2 male animals showed the predominant QTL affecting fat deposition traits (up to 13.6% VF2) near AR and two QTL for muscling traits (up to 9.9% VF2) mapped close to ACSL4. In the F2 female animals, QTL affecting muscling (up to 12.1% VF2) mapped at ACSL4 and SW2456, and QTL for fat deposition (10% VF2) and growth (up to 10.5% VF2) mapped at ACSL4.

This study characterized autochthonous pig breeds of Vietnam and compared them with breeds from other regions. A total of 343 animals were considered from 5 indigenous pig breeds of Vietnam (Muong Khuong, Co, Meo, Tap Na, and Mong Cai), 2 exotic breeds kept in Vietnam (Landrace and Yorkshire), 3 European commercial breeds (German Land-race, Piétrain, and Large White), the Chinese breed Meishan, and the European Wild Boar. Each individual was genotyped for 20 selected polymorphic microsatellite loci. The Vietnamese autochthonous breeds showed higher degrees of polymorphism, allelic diversity, and heterozygosity than the other pig breeds. Also, large genetic diversity was observed across the area of distribution, with village-specific subpopulations, which led to significant inbreeding coefficients. As expected, genetic distances showed large differences among European-based, Chinese, and Vietnamese indigenous breeds and reflected the geographical distribution of breeds. In comparison with the European breeds, the Vietnamese indigenous pig breeds harbored a considerable amount of genetic diversity and, therefore, will be of significance for livestock bioconservation.

The porcine orthologues of human chromosome HSA9q22.31 genes osteoglycin (OGN) and asporin (ASPN) were mapped to porcine chromosome SSC3 using linkage analysis and a somatic cell hybrid panel. This mapping was refined to SSC3q11 using fluorescence in situ hybridization. These results confirm the existence of a small conserved synteny group between SSC3 and HSA9. Polymorphisms were revealed in both genes, including a pentanucleotide microsatellite (SCZ003) in OGN and two single nucleotide polymorphisms (AM181682.1:g.780G>T and AM181682.1:g.825T>C) in ASPN. The two genes were included in a set of markers for quantitative trait loci (QTL) mapping on SSC3 in the Hohenheim Meishan x Piétrain F2 family. Major QTL for growth and carcass traits were centred in the ASPN-SW902 region.

The lamins are components of nuclear lamina and they have a profound influence on nuclear structure and functions. They are encoded by three genes, LMNA, LMNB1 and LMNB2. A genomic fragment of the porcine LMNA gene (822 bp; from exons 7 to 9) was amplified by polymerase chain reaction and comparatively sequenced. Four single nucleotide polymorphisms (SNPs) were identified in intronic sequences: G162A, G208A, T367G and C618T. The SNPs are within the restriction sites for enzymes Bsh1236I, HpaII, AluI and Bsh1236I respectively. Allele frequencies at SNPs G208A, T367G and C618T were determined by using eight pig breeds. Linkage analysis in the Hohenheim Meishan x Piétrain family placed the LMNA gene in the chromosome 4q linkage group, between MEF2D and GBA (MEF2D - 3.0 cM - LMNA - 0.2 cM - GBA). In radiation hybrid mapping LMNA was most significantly linked to SW270 on chromosome 4 (39 cR; LOD = 7.86). The LMNA gene is located in the quantitative trait loci region for some carcass traits on chromosome 4q.

A QTL analysis of multibreed experiments (i.e., crossed populations involving more than two founder breeds) offers clear advantages over classical two-breed crosses, among them increased power and a more comprehensive coverage of the total genetic variability in the species. An alternative to designed multibreed crosses is to reanalyze jointly several experiments involving different breeds. We report a multibreed, multitrait QTL analysis of SSCX that involves five different crosses, six breeds, and almost 3,000 genotyped individuals using a truly multibreed strategy to allow for any number of founder breed origins. Traits analyzed were growth, fat thickness, carcass length, and shoulder and ham weights. Generally, the joint analysis resulted in more significant QTL than the single-experiment analyses. We show that the QTL for fatness, which is highly significant (nominal P < 10(-43)), is of Asiatic origin (Meishan). The next most significant QTL (nominal P < 10(-15)) affected ham weight and seems to be segregating only between Large White and the rest of the breeds. A multitrait, multi-QTL analysis suggests that these are two distinct loci. Additionally, a locus segregating only between Iberian and Landrace affects live weight. The advantages of joint, multibreed analyses clearly outweigh their potential risks.

A novel porcine gene, alpha-1-antichymotrypsin 2 (SERPINA3-2), a member of the serpin superfamily, was isolated from a porcine genomic library and sequenced. The genomic organization of the approximately 9.0 kb gene was determined on the basis of the porcine liver cDNA of SERPINA3-1 and SERPINA3-2, and comprises five exons and four introns. The coding sequence of SERPINA3-2 shares 86% identity with the paralogue, SERPINA3-1. Porcine SERPINA3-2 was found to be an orthologue of human SERPINA3 (71% identity of the coding sequences) and both genes have a similar genomic organization. Polymorphisms were found in intron 4 of the porcine gene using polymerase chain reaction-restriction fragment length polymorphism. The gene was mapped by linkage analysis and radiation hybrid mapping to the distal end of chromosome 7q, to the gene cluster of the protease inhibitors including PI1 (SERPINA1), PI2, PI3, PI4 (apparently paralogues of SERPINA3), and PO1A and PO1B. SERPINA3-2 is the first porcine serpin gene whose genomic organization has been determined.

During genotyping of 38 microsatellites for QTL (quantitative trait loci) mapping in three F2 swine populations, five mutant alleles were detected in a total of 66,436 parent-offspring transfers of microsatellite alleles, which gives an overall mutation rate of 7.52 x 10(-5) per locus per generation. No significant (P > 0.05) association between mutation rates and other factors (i.e., GC contents in the flanking regions, heterozygosity, and repeat number) was revealed. Detailed sequencing showed that four out of five mutant alleles were caused by insertions of one to five repeats, respectively. The other mutant allele was produced by either an insertion of three repeats or a change of 30 base pairs (a deletion of 16 CT repeats and an insertion of one CA repeat). An insertion of one base pair in the flanking region of a microsatellite was also detected. Together, these data indicate that expansions are more common than contractions among microsatellites and that the mutation processes are very complicated, do not fit with the strict stepwise mutation model and may vary from locus to locus.

Skeletal muscle fibre characteristics are key determinants of meat quality. High fibre diameters and shifting towards higher white fibre proportions lead to increasing R-values (degree of desamination of adenosine) and lactate-production, resulting in high incidences of pale, soft, exudative (PSE) meat and stress susceptibility in European and American pig breeds. Development of muscle fibres including their enzymes, is regulated by the MyoD-gene family together with transcription factors like FOS. We report on the associations between the chromosomal region of FOS with skeletal muscle fibre and metabolism traits. The BB genotype representing the European Pietrain breed had 10.9% more white fibres with fibre diameters decreased by 6.1%, with 3.9% higher R-values and 8.5% higher lactate levels than the AA genotype of the Chinese Meishan. Lactate levels and R-values per microm of fibre diameter were increased to 18.4 and 11.6% in the BB genotype. The contrast between the two quantitative trait loci (QTL) alleles associated with a polymorphism in the FOS gene explained up to 5.13% of the total variance. A new TaiI-restriction fragment length polymorphism (RFLP) connected to a Asn258/Ser mutation, located in a transcription activator region, was used to map FOS between markers S0115 and Sw581 on SSC7. The QTLs for skeletal muscle fibre and metabolism traits have been mapped to the marker interval around FOS. The present data suggest that variability in FOS gene may underlie phenotypic variation in skeletal muscle fibre and metabolism traits in the pig.

For many species several similar QTL mapping populations have been produced and analyzed independently. Joint analysis of such data could be used to increase power to detect QTL and evaluate population differences. In this study, data were collated on almost 3000 pigs from seven different F(2) crosses between Western commercial breeds and either the European wild boar or the Chinese Meishan breed. Genotypes were available for 31 markers on chromosome 4 (on average 8.3 markers per population). Data from three traits common to all populations (birth weight, mean backfat depth at slaughter or end of test, and growth rate from birth to slaughter or end of test) were analyzed for individual populations and jointly. A QTL influencing birth weight was detected in one individual population and in the combined data, with no significant interaction of the QTL effect with population. A QTL affecting backfat that had a significantly greater effect in wild boar than in Meishan crosses was detected. Some evidence for a QTL affecting growth rate was detected in all populations, with no significant differences between populations. This study is the largest F(2) QTL analysis achieved in a livestock species and demonstrates the potential of joint analysis.

To screen the whole porcine chromosome 12 for QTL affecting economically important traits, ten genetic markers were genotyped in two F2 populations generated from the cross of genetically diverse breeds: European Wild pig and commercial pig breed Pietrain (W x P), and Chinese Meishan and Pietrain (M x P). Fifty-one traits were recorded. A least squares method was used for chromosome-wide screening for QTL. An association analysis between genotypes at the GH locus and traits was also carried out. The least squares analysis did not reveal the presence of genome-wide significant QTL affecting the traits, while the association study showed significant (P < 0.01) associations between GH genotypes and fatness traits in M x P, but not in W x P. F2 pigs carrying the genotype C1A2/C4A2 at the GH locus displayed the thinnest backfat (21.76 mm), while the ones carrying the genotype C2A2/C2A2 had the thickest (31.41 mm).

The complete porcine c-fos proto-oncogene (FOS) with flanking regions was cloned and sequenced. FOS consists of four exons at amino acids 1-47, 48-131, 132-167, and 168-380 and includes all the typical motifs of the fos proto-oncogene. The promoter contains consensus sequences for CRE, SRE, CaRE, and the E-Box, as well as an AP-1 site. Homologies between human and swine were between 89.7% and 96.3% in the exons. Based on somatic cell hybrid panel screening and known homologies between swine chromosome 7 and human chromosome 14, the porcine c-fos gene was assigned to chromosome 7q23., (Copyright 2000 S. Karger AG, Basel.)

Serum samples of Meishan (13 animals) and Meishan x Wild Boar crosses (361 animals) were analysed by means of two-dimensional electrophoresis. Some new variants in protease inhibitor systems PO1A, PO1B and PI2 are reported.

The role of the porcine GH gene was investigated in 292 F2 animals of mating Wild Boar x Piétrain and in 310 F2 animals of mating Meishan x Piétrain. Forty-three traits of fattening, carcass composition, meat quality and stress resistance were recorded. For the analysis of associations between GH gene variants and quantitative traits, two restriction fragment length polymorphisms were examined. In the Meishan x Piétrain family eight traits related to fatness were significantly associated with GH genotypes, while in the Wild Boar x Piétrain family no significant associations were found. In the Meishan x Piétrain cross, the GH locus explained 11.7% to 17.7% of the total phenotypic variance in the F2 population. The possibility of multiple alleles at the GH locus is discussed. Based on these results, we conclude that the GH locus should be further investigated in commercial breeds to determine its suitability for use in marker-assisted selection programmes.

A two-point linkage analysis was performed between blood group (14), allotype (8), polymorphic protein (11), DNA type I (2), and microsatellite (2) loci in Wild Boar x Pietrain and Meishan x Pietrain three-generation families. The following new pairwise linkages were detected: LPR-EAN (Zmax = 60.68, theta = 0.055), EAD-GH1 (Zmax = 17.43, theta = 0.246), EAO-P3 (Zmax = 15.81, theta = 0.239), and P3-S0003 (Zmax = 5.43, theta = 0.312). This study and published mapping data enabled the localization of LPR (LPR allotype) to chromosome 9, EAD (erythrocyte antigen D) to chromosome 12, and EAO (erythrocyte antigen O) and P3 (P3 allotype) to the q arm of chromosome 6 with gene order S0003-P3-EAO, EAO being the most distal.

A new allele Maejm and a more precise genetic analysis of the Ml factor previously assigned to the M system are described after screening three generation families (Wild Boar x Pietrain, Meishan x Pietrain) for the M blood group system using a complete set of 13 M reagents. From informative families with proven parental M genotypes it was shown that the Ml antigen is controlled by an allele from another system. We propose to designate this new system P and to change the factor designation from Ml to Pa.

Loci containing (GT)n repeats were isolated from three different plasmid libraries with inserts of porcine genomic DNA between 140 and 200, 200 and 300, and 350 and 400 bp. Sequencing showed that the average repeat length and the fraction of perfect repeats were increased in the libraries containing longer inserts (> or = 200 bp). The polymorphism of (GT)n loci containing at least 10 repeat units was analyzed using the polymerase chain reaction and an automated DNA sequencer. Nearly all tested loci are polymorphic and can therefore be used as marker loci for gene mapping and for other applications. The (GT)n loci were categorized into three classes: (1) loci containing the (GT)n repeats associated with a SINE element, (2) loci containing the (GT)n repeats associated with one or more other simple repeats, and (3) loci containing (GT)n as the only detected repetitive element. At most loci of the first class, the (GT)n repeat was in a fixed configuration adjacent to the 3' end of the SINE. The findings support the notion of clustering of different repeat types in the mammalian genome.

The alkaline phosphatases from serum, liver, bone and intestine of pigs were separated by starch and polyacrylamide gel electrophoresis. Treatments with neuraminidase, urea, heat, L-homoarginine and L-phenylalanine were performed. Variants of serum alkaline phosphatases were derived from different tissues and hence must be under the control of at least two different loci. Within the intestinal phosphatases, polymorphic electrophoretic patterns were observed among 195 animals.

Kind and probability of homoplasy across allelic microsatellite fragments can be investigated using DNA of genetically diverse pig breeds. In this study, nine microsatellite loci (SW1897,SW2427,SW489,SW957,TNFB,IFNG,SW2410,SW2019andS0215) were analysed using DNA samples of pigs from Vietnam (Indigenous breeds Co, Meo, Muong Khuong, Tap Na) and Germany (European Wild Boar, Piétrain). In a total of 39 sequences, 20 differences within isomorphic alleles were observed in comparison with the respective reference sequences. They affected five of the nine tested microsatellite loci. The majority (18) of SNPs occurred in the 5′-flanking regions of the microsatellite repeats, 10 were found in the 3′-flanking regions and only one SNP occurred within the repeat of the Wild Boar sequence ofSW2427. The compound microsatellitesIFNGandS0215were unaffected by size homoplasy (SH) within our material. We conclude that the fragment length analysis of microsatellites is a reliable tool for intraspecific phylogenetic studies because SH rates within a species were low. [ABSTRACT FROM AUTHOR]

Three informative pig F2 families based on European Wild Boar (W), Meishan (M) and Pietrain (P) crosses have been used for genome-wide linkage and quantitative trait loci (QTL) analysis. Altogether 129 microsatellites, 56 type I loci and 46 trait definitions (specific to growth, fattening, fat deposition, muscling, meat quality, stress resistance and body conformation) were included in the study. In the linkage maps of M × P, W × P and W × M families, average spacing of markers were 18.4, 19.7 and 18.8 cM, the numbers of informative meioses were 582, 534 and 625, and the total lengths of autosomes measured were 27.3, 26.0 and 26.2 Morgan units, respectively. Maternal maps were on average 1.3 times longer than paternal maps. QTLs contributing more than 3% of F2 phenotypic variance could be identified at p < 0.05 chromosome-wide level. Differences in the numbers and positions of QTLs were observed between families. Genome-wide significant QTL effects were mapped for growth and fattening traits on eight chromosomes (1, 2, 4, 13, 14, 17, 18 and X), for fat deposition traits on seven chromosomes (1, 2, 3, 4, 6, 7 and X), for muscling traits on 11 chromosomes (1, 2, 3, 4, 6, 7, 8, 12, 14, 15 and X), for meat quality and stress resistance traits on seven chromosomes (2, 3, 6, 13, 16, 18 and X), and QTLs for body-conformation traits were detected on 14 chromosomes. Closely correlated traits showed similar QTL profiles within families. Major QTL effects for meat quality and stress resistance traits were found on SSC6 in the interval RYR1-A1BG in the W × P and M × P families, and could be attributed to segregation of the RYR1 allele T derived from Pietrain, whereas no effect in the corresponding SSC6 interval was found in family W × M, where Wild Boar and Meishan both contributed the RYR1 allele C. QTL positions were mostly similar in two of the three families for body conformation traits and for growth, fattening, fat deposition and muscling traits, especially on SSC4 (interval SW1073-NGFB). QTLs with large effects were also mapped on SSC7 in the major histocompatibility complex (MHC) (interval CYP21A2-S0102) and affected body length, weight of head and many other traits. The identification of DNA variants in genes causative for the QTLs requires further fine mapping of QTL intervals and a positional cloning. However, for these subsequent steps, the genome-wide QTL mapping in F2 families represents an essential starting point and is therefore significant for animal breeding. [ABSTRACT FROM AUTHOR]

Discusses the linkage assignments of the porcine ATP1A1 and IVL genes, and the RH mapping of the ATP1A1, ATP1B1, V-ATPase (CGI-11) and IVL genes. Chromosomal localization; Primer sequences; Mendelian inheritance; Allele frequency.

Focuses on the linkage and QTL mapping of the Hohenheim F[sub 2] pig families. Identification of genes contributing to quantitative phenotypic variation; Genome-wide scans of marker loci to map gene effects on numerous traits; Names of the people acknowledged for their contributions to this research.

The nucleotide sequence data referred to in this paper have been submitted to GenBank and have been assigned the accession number X97040.c-myc is an ubiquitous nuclear phosphoprotein involved in the regulation of cell-growth, differentiation and apoptosis. Higher nuclear levels of c-myc block adipogenesis and trigger the onset of myogenesis and folliculogenesis. The c-myc proto-oncogene has the potential of a mediator between second messengers such as calcium and cAMP and gene expression. As both are involved in stress-susceptibility and carcass quality in the pig, this study investigates associations between c-myc genotypes and carcass quality traits as well as interactions with the Ryr1 genotype in this species. An association between c-myc and carcass fat traits was evident, but did not reach genome-wide significance levels. Significance niveaus, explained variance and mean differences between the homozygotes of the Ryr1-gene which clearly decreased from the AA-genotype to the BB-genotype of c-myc are indicating a gene interaction between both genes. Mean differences in lean percentage (expressed in SD) decreased by 89.2% in ME × PI and by 86.3% in WS × PI. The existing but weakly developed significances of the association between c-myc and carcass fat traits are discussed under the aspect of epistatic nullification. [ABSTRACT FROM AUTHOR]

Future prophylaxis needs new concepts, including natural disease resistance of hosts against infectious agents. Genomic approaches to detect and improve disease resistance in farm animals and the molecular mechanisms involved in host–parasite interactions depend to a high degree on the trait differences between founder breeds, i.e. on the animal model. The present study evaluates differences in susceptibility/resistance against Sarcocystis miescheriana in the European Pietrain (PI) and the Chinese Meishan (ME) pig breeds, based on 25 individuals, infected orally with 5×104 sporocysts of S. miescheriana. Significant differences appeared in clinical, serological, haematological and parasitological findings. The major discriminating period post infection (p.i.) was between days 42 and 45. Severity of signs was negatively correlated with specific immunoglobulin titres during the first 3 weeks p.i. and positively with the load of bradyzoites in muscle tissues of the pigs. Loads of bradyzoites in muscle tissues were 20 times higher in PI than in ME. Sarcocystis-specific differences between the two breeds were in the range of 1–2 standard deviations. The study lays the foundation for further experiments to analyse chromosomal regions, candidate genes, and thus the molecular basis of Sarcocystis susceptibility/resistance as a model for host–parasite interaction in protozoan infectious disease. [Copyright &y& Elsevier]