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The number of vertebrae in pigs varies and is associated with meat productivity. Wild boars, which are ancestors of domestic pigs, have 19 vertebrae. In comparison, European commercial breeds have 21-23 vertebrae, probably owing to selective breeding for enlargement of body size. We previously identified two quantitative trait loci (QTL) for the number of vertebrae on Sus scrofa chromosomes (SSC) 1 and 7. These QTL explained an increase of more than two vertebrae. Here, we performed a map-based study to define the QTL region on SSC1. By using three F2 experimental families, we performed interval mapping and recombination analyses and defined the QTL within a 1.9-cM interval. Then we analyzed the linkage disequilibrium of microsatellite markers in this interval and found that 10 adjacent markers in a 300-kb region were almost fixed in European commercial breeds. Genetic variation of the markers was observed in Asian local breeds or wild boars. This region encoded an orphan nuclear receptor, germ cell nuclear factor (NR6A1, formerly known as GCNF), which contained an amino acid substitution (Pro192Leu) coincident with the QTL. This substitution altered the binding activity of NR6A1 to its corepressors, nuclear receptor-associated protein 80 (RAP80) and nuclear receptor corepressor 1 (NCOR1). In addition, somites of mouse embryos demonstrated expression of NR6A1 protein. Together, these results suggest that NR6A1 is a strong candidate for one of the QTL that influence number of vertebrae in pigs.

The objective of the research was to identify QTL affecting the number of vertebrae in swine, one of the major determining factors of growth and body composition. Previously, we reported a QTL for the number of vertebrae located on SSC1qter (terminal band of the q arm of SSC 1) in an F2 family produced by crossing a Göttingen miniature male with two Meishan females. Eight other swine families were subsequently produced by crosses between different breeds of European, Asian, and miniature pigs. In these families, the QTL on SSC1qter for the number of vertebrae was detected. Unlike the Asian alleles, all European alleles in this study had the effect of increasing the number of vertebrae by 0.44 to 0.69 and acted additively without dominance. The Göttingen miniature sire, for which we previously reported a smaller additive effect, seemed to be heterozygous at the QTL. In the present study, another QTL was found for the number of vertebrae on SSC7. This QTL was not fixed in the European pigs used as parents in our experimental families, and some of the European alleles increased the number of vertebrae. A half-sib analysis confirmed that this QTL was segregating in a commercial Large White population. Analysis in an F2 family in which the parental pigs were fixed for alternative alleles revealed that the effects of the QTL on SSC1 and on SSC7 were additive and similar in size. The two QTL acted independently without epistatic effects and explained an increase of more than two vertebrae.

Three generations of a swine family produced by crossing a Japanese wild boar and three Large White female pigs were used to map QTL for various production traits. Here we report the results of QTL analyses for skeletal muscle fiber composition and meat quality traits based on phenotypic data of 353 F(2) animals and genotypic data of 225 markers covering almost the entire pig genome for all of the F(2) animals as well as their F(1) parents and F(0) grandparents. The results of a genome scan using least squares regression interval mapping provided evidence that QTL (<1% genome-wise error rate) affected the proportion of the number of type IIA muscle fibers on SSC2, the number of type IIB on SSC14, the relative area (RA) of type I on SSCX, the RA of type IIA on SSC6, the RA of type IIB on SSC6 and SSC14, the Minolta a* values of loin on SSC4 and SSC6, the Minolta b* value of loin on SSC15, and the hematin content of the LM on SSC6. Quantitative trait loci (<5% genome-wise error rate) were found for the number of type I on SSC1, SSC14, and SSCX, for the number of type IIA on SSC14, for the number of type IIB on SSC2, for the RA of type IIA on SSC2, for the Minolta b* value of loin on SSC3, for the pH of loin on SSC15, and for the i.m. fat content on SSC15. Twenty-four QTL were detected for 11 traits at the 5% genome-wise level. Some traits were associated with each other, so the 24 QTL were located on 11 genomic regions. In five QTL located on SSC2, SSC6, and SSC14, each wild boar allele had the effect of increasing types I and IIA muscle fibers and decreasing type IIB muscle fibers. These effects are expected to improve meat quality.

Several quantitative trait loci (QTL) have been detected on SSC1qter (Sus scrofa chromosome 1qter), including QTL for the number of vertebrae, as reported in our previous study. To provide the tools for analysis of QTLs on SSC1qter, we constructed a comparative map of swine and human. In addition, we identified 26 swine STSs and mapped 16 of them on SSC1qter using the INRA - University of Minnesota porcine radiation hybrid (IMpRH) panel. We screened a BAC library using these swine STSs and developed 35 new polymorphic microsatellite markers from the BAC clones, of which 26 were informative in our reference family. We also mapped nine microsatellite markers we had isolated previously. Consequently a total of 44 new polymorphic microsatellite markers were located within a 60-cM region of SSC1qter, spanning from SW1092 to the telomere.

In the present paper, we proposed a statistical procedure based on composite interval mapping for accurate analysis of quantitative trait loci (QTL) for individuals sampled from an outcrossing population with two-generation families consisting of the sampled individuals and F1 progenies obtained by crossing them as parental individuals. In the proposed procedure, haplotypes of markers of parental individuals were reconstructed based on the genotypes of F1 progenies and QTL analyses with composite interval mapping were conducted separately for each of parents as well as jointly for both parents. A least squares method was applied to the composite interval mapping, where some of markers were selected as cofactors to absorb the variation induced by QTL located elsewhere in the genome. The procedure was evaluated for the efficiency in detecting QTL and the precision of estimates of locations and effects of QTL using simulations. It was shown that QTL with interaction between paternal and maternal alleles was effectively detected by joint analysis of both parents, while a QTL segregating only in one parent, closely linked to a QTL segregating only in the other parent, was successfully detected by analyzing separately each of the parents with inclusion of markers of both parents. The proposed procedure can provide detailed genetic information useful for marker assisted breeding in an outcrossing species such as forest trees.

Comparative mapping studies facilitate the identification of genes located in quantitative trait locus (QTL) regions in domestic animals by utilizing information from the human genome. Radiation hybrid (RH) mapping is effective for this purpose because of its high resolution in ordered gene mapping on chromosomes. We constructed an RH map of pig chromosome 7, by adding 23 markers associated with genes. This RH map clearly demonstrated the mosaic of homology between pig chromosome 7 (SSC7) and human chromosomes 6, 14 and 15 at a 'gene' level, and was confirmed by linkage analysis. Clarification of the homology of SSC7 to human chromosomes will contribute to the elucidation of the gene(s) responsible for QTL detected on this chromosome.

The development of informative polymorphic markers is essential for QTL mapping. We developed 50 microsatellite markers from BAC clones containing genes that were predicted to map swine chromosome 4 (SSC4) according to comparative analysis between human and swine chromosomes, and constructed a linkage map that consisted of 37 markers including 24 markers closely linked to genes in BAC clones. Microsatellite markers were developed by direct-sequencing of BAC clones and our results demonstrated that this method was effective for developing microsatellite markers in specific regions on chromosomes. Effective development of microsatellite markers closely linked to genes can further accelerate the comparative studies of chromosomes between different species.

Loci affecting swine intramuscular fat content, backfat thickness, carcass weight, and daily weight gain were assigned to regions of swine chromosome (SSC) 4, which were shown to correspond to human chromosome (HSA) 1p22--> q25 by ZOO-FISH, bidirectional chromosome painting, as well as by the linkage map of genes. In order to select candidate genes responsible for the above traits from the human genome database, precise correspondence between SSC4 and HSA1 is a prerequisite. In the present study, 27 genes, PTGFR, GBP1, GBP2, GFI1, GCLM, ABCD3, EXTL2, KCNA3, ADORA3, KCND3, WNT2B, NRAS, SYCP1, PTGFRN, IGSF2, NOTCH2, S100A10, SHC1, SSR2, LMNA, CCT3, CD5L, PEA15, FCER1G, EAT2, DDR2, and LAMB3, located in the HSA1 region corresponding to SSC4 or possibly SSC4, were assigned to the IMpRH map. The alignment of genes from centromere to telomere in the SSC4 q arm is basically conserved in HSA1p22-->q25 with the direction from the q arm to the p arm, which is in good agreement with results from linkage mapping. In addition, the present study first demonstrated that WNT2B residing in the middle of the HSA1 region was assigned to SSC18 with a high lod score (> 5), and that at least three intrachromosomal rearrangements occurred in the region in the process of swine and human evolution. PTGFR, and LAMB3 localized at both ends of the HSA1 region were assigned to SSC6 and SSC9, respectively, which is consistent with regional correspondence reported earlier. In the course of the above analysis, microsatellite markers were developed in the proximity of eleven genes localized on SSC4, and three genes on other swine chromosomes., (Copyright 2003 S. Karger AG, Basel)

We cloned and sequenced a cDNA that contains the coding sequence of the porcine interleukin-18 receptor alpha chain (PoIL-18Ralpha). Based on the conserved nucleotide sequences between human (HuIL-18Ralpha) and murine IL-18Ralpha (MuIL-18Ralpha), we performed reverse transcription-polymerase chain reaction (RT-PCR) with total RNA prepared from porcine peripheral blood lymphocytes (PBLs) stimulated with PoIL-12 to clone the cDNA of PoIL-18Ralpha. The open reading frame (ORF) of the PoIL-18Ralpha cDNA is 1620 base pairs (bp) in length and encodes 539 amino acids. The predicted amino acid sequence showed 68.2% and 50.2% identity to the human and murine amino acid sequences, respectively. Stimulation with concanavalin A (ConA) and IL-12, but not with IL-4, was shown to upregulate the expression of IL-18Ralpha mRNA in pig PBLs by RT-PCR analysis. Flow cytometric analysis also demonstrated that IL-18Ralpha was constitutively expressed on PoPBLs, and this expression was augmented by ConA stimulation. Furthermore, the PoIL-18Ralpha gene was mapped by fluorescence in situ hybridization (FISH) to porcine chromosome 3 (3q13-q14), near the location at which the IL-1beta gene had already been mapped. The present results will be helpful for understanding PoIL-18 and interferon gamma (IFN-gamma)-mediated T helper 1 (Th1) cell development.

Composite interval mapping (CIM) has been successfully applied to the detection of QTL in experimental animals and plants. However, practical analyses based on CIM have been reported mainly for populations derived from cross between inbred lines. There are few studies on QTL analyses with CIM in outbred populations. To evaluate the applicability of CIM to outbred populations is prerequisite for the fine mapping of QTL in industrial animals such as pig and chicken. Some markers are usually not fully informative in outbred populations. In application of CIM to outbred populations, the influence of inclusion of such uninformative markers used as covariates on the efficiency of CIM should be investigated. In this paper a least-squares method for CIM was formalized in an F(2) population derived by crossing two outbred lines. The efficiencies of CIM were evaluated for outbred populations in comparison with simple interval mapping (SIM) for several cases of marker informativeness using simulations. By incorporating markers linked to a tested position as well as those unlinked, CIM showed a higher efficiency to separate two linked QTL over SIM. The efficiency of dissection was enhanced as the marker informativeness was increased. The power of CIM to detect an isolated QTL was improved by excluding markers linked to a tested position from covariates and higher than SIM regardless of marker informativeness. In conclusion, CIM is a useful procedure for the analysis of QTL in outbred populations even under low marker informativeness.

Several quantitative trait loci (QTLs) (vertebrate number, birth weight, age at puberty, growth rate, gestation length, and backfat depth) have been independently mapped to the distal region of swine Chromosome (SSC) 1q in several resource populations. In order to improve the map resolution and refine these QTLs more precisely on SSC1q, we have isolated and mapped additional microsatellites (ms), using chromosome microdissection and radiation hybrid (RH) mapping. Five copies of the telomeric region of SSC1q were microdissected from metaphase spreads and pooled. The chromosomal fragment DNA was randomly amplified by using degenerate oligonucleotide primed polymerase chain reaction (DOP-PCR), enriched for ms, and subcloned into a PCR vector. Screening of subsequent clones with ms probes identified 23 unique ms sequences. Fifteen of these (65%) were subjected to radiation hybrid (RH) mapping by using the INRA-University of Minnesota porcine RH panel (IMpRH); and the remaining eight were not suited for the RH mapping. Twelve microsatellites were assigned to SSC1q telomeric region of IMpRH map (LOD >6), and three remain unlinked (LOD <6). Out of the 15 microsatellite markers, 9 were polymorphic in NIAI reference population based on the Meishan and Göttingen miniature pig. In summary, we have used microdissection and radiation hybrid mapping to clone and map 12 new microsatellites to the swine gene map to increase the resolution of SSC1q in the region of known QTLs.

Background and Purpose: Rat chromosome 20 is one of special interest because it contains some diabetogenic genes, such as a major histocompatibilitiy complex (MHC)-linked genetic components and quantitative trait loci. We studied rat chromosome 20, using the backcross progeny between BB/Wor and PVG.R23 rats, and confirmed the genetic linkage map by use of another backcross panel., Methods: Backcross panels were done between BB/Wor and PVG.R23 rats, and BN and KZC rats. Length variations of simple sequence length polymorphism markers were analyzed by use of polymerase chain reaction (PCR) analysis. Alleles of RT1-Bb and RT1-Db were analyzed by use of the PCR-restriction fragment length polymorphism method. Genetic maps of rat chromosome 20 were constructed, using the Map Manager computer program., Results: Fifty-two loci were mapped on rat chromosome 20. Genetic length was 57.9 cM, with average spanning of 1.11 cM between markers. The positions of RT1-N1, Tnf, and RT1-Bb into the MHC region were separated and confirmed by results of two backcross panels in our linkage studies., Conclusions: The genetic linkage map of rat chromosome 20 was improved, and was a useful tool for genetic analysis of a diabetogenic gene(s) and for producing MHC congenic strains.

The chromosomal location of the swine tenascin gene (HXB) was determined by fluorescence in situ hybridization and simultaneous R-banding. Swine tenascin cDNA was labeled with biotin, and used as a probe. Hybridization was detected by the FITC-labeled streptavidin/biotinylated antistreptavidin antibody system. The signals revealed that the tenascin gene is localized on swine chromosome 1q21.1-->q21.3.

We have molecularly cloned portions of equine satellite-type DNA and investigated the organization of the DNA sequence of the cloned segments. Sequence analysis and dot-blot analysis, using the cloned sequence (ES200) as a probe, indicate that the satellite-type DNA sequence consists mainly of 221-bp tandem repeats and represents 3.7-11% of the equine genome. Southern blot analysis further shows that (1) no sequences homologous to ES200 exist in the human, swine, and bovine genomes and that (2) the fragment pattern of the satellite-type DNA produced by ApaI cleavage shows a slight difference among equine DNA samples, indicating a slight sequence variation between individual horses. To localize the satellite-type DNA in the horse genome, chromosome spreads on glass slides were first subjected to G-banding to identify each chromosome and then hybridized in situ with biotin-labeled ES200. The chromosome banding, together with the hybridization, demonstrates that the satellite sequences are preferentially localized on the centromeric regions of all chromosomes except chromosomes 2, 9, and 11.

We investigated the distribution of PRE-1 sequences (a swine major SINE) on the swine chromosomes. The investigation demonstrated that PRE-1 sequences are unevenly distributed along the chromosomes as in the case of the human and mouse SINES. The distribution pattern, however, has no simple correlation with Q-band pattern as that of human and mouse SINES. The prominent difference is as follows; PRE-1 is localized on centromeric regions, but human and mouse SINES are not [KORENBERG and RYKOWSKI (1988). Cell, 53: 391-400; BOYLE, BALLARD, and WARD (1990). Proc. Natl. Acad. Sci. U.S.A. 87: 7751-7761].