Mapping four genes from human chromosome 4 to porcine chromosome 8 further develops the comparative map for an economically important chromosome of the swine genome

Because porcine chromosome (SSC) 8 has become the focal point of many efforts aimed at identifying quantitative trait loci affecting ovulation rate, genes distributed across human chromosome (HSA) 4 were physically mapped in the pig. A more refined comparative map of this region for these two species was produced. In this study, four genes were selected based on their location in the human genome, the availability of nucleotide sequence and their genomic organization. The genes selected were fibroblast growth factor basic (FGF2; HSA 4q25-27), gonadotropin releasing hormone receptor (GNRHR; HSA 4q13), phosphodiesterase 6 B (PDE6B; HSA 4p16.3) and aminopeptidase S (PEPS; HSA 4p11-q12). Genomic libraries were screened via PCR and clones were physically assigned using fluorescence in situ hybridization (FISH). These four genes from HSA 4 were physically mapped to SSC 8p2.3 (PDE6B), 8p1.1 (PEPS), 8q1.1-1.2 (GNRHR) and 8q2.2-2.4 (FGF2). These assignments provide additional benchmarks for the comparative map and help define the level of gene order conserved between HSA 4 and SSC 8.     

Genetic mapping: X chromosome

Starting with the male chiasma distribution for chromosome 2, a significantly better fit is obtained to lod scores for the X chromosome if terminalization of distal chiasmata is assumed. The linkage data are not consistent with a uniform distribution of chiasmata, absence of terminalization, or restriction of terminalization to the distal band. As information about the genetic map of the X chromosome increases, the map will be freed from assumptions about chiasma distribution. At present, however, even fragmentary data on the male are useful to construct a genetic map that, by converting physical assignments to equivalent genetic recombinations, has no inconsistencies between genetic and physical map orders.     

Use of PCR markers for mapping swine chromosome 12

Using PCR analysis of pig-mink and pig-Chinese hamster hybrid cell lines and heterologous and homologous primers of various types, chromosomal and subchromosomal mapping of genes TOP2A, THRA, BRCA1, GAS, HLR1, MYL4, LIS1, MCP1, ENO3, CRYB1, P4HB, STAT5B, and H3F3B to pig chromosome 12 was carried out. The efficiency of using different types of heterologous primers for pig chromosome mapping was compared.     

Mapping of growth hormone releasing hormone receptor to swine chromosome 18

The growth hormone releasing hormone receptor (GHRHR) was mapped in the pig for study as a potential candidate gene in controlling pig quantitative growth and carcass characteristics. Primers were designed from the pig GHRHR sequence to amplify a 1·65-kb intronic fragment between exons 6 and 7. By using a pig–rodent somatic cell hybrid panel, GHRHR was mapped to pig chromosome 18 (SSC18) with 100% concordance, and the regional assignment was SSC18q24 with 89% concordance. The polymerase chain reaction–restriction fragment length polymorphisms (PCR–RFLPs) with Mse I and Taq I were developed to confirm this assignment with linkage analysis by using the European Pig Gene Mapping Project (PiGMaP) reference families. Pig GHRHR was mapped with strong linkage to SSC18 markers S0062 and S0120 (lod > 8). The GHRHR and IGFBP3 were found to map near to each other on human chromosome 7 (HSA7), and the pig IGFBP3 gene has been mapped to SSC18 by others. Our mapping of pig GHRHR increases the comparative information available on the SSC18 maps and further confirms the synteny conservation between HSA7 and SSC18.     

High-resolution comparative mapping between human chromosomes 4 and 8 and bovine chromosome 27 provides genes and segments serving as positional candidates for udder health in cattle

To get more information about the order of genes located in Bos taurus (BTA) chromosome 27 segments, supposed to harbor loci influencing clinical mastitis and somatic cell count, and to identify genes that serve as positional candidates for the mentioned traits, we constructed a high-resolution, comparative, and comprehensive gene map for BTA27. The map includes 57 loci in a 5000-rad cattle-hamster whole genome radiation hybrid panel supported by 50 syntenic assignments in a cattle-murine somatic hybrid cell panel. Thirty-eight new loci (36 genes, 2 microsatellites) together with repeated mappings of 5 genes and 7 microsatellites and integration of existing data from 7 microsatellites were used to generate a comprehensive RH5000 map. The RH map, constructed at lod score criterion 8 using the software RHMAP v.3.0, consisted of three linkage groups 23, 22, and 590 cR5000 in length. Gene assignments on BTA27 and the localization of 8 more genes on BTA8 and BTA14 previously predicted on BTA8/BTA27 and BTA14/BTA27 narrowed down significantly the chromosome break points between the three cattle chromosomes and segments on Homo sapiens chromosomes HSA4 and HSA8. Defined evolutionary break points increase the accuracy of comparative in silico mapping of further human genes in conserved chromosome segments of BTA27.     

Mapping of quantitative trait loci affecting behaviour in swine

Behavioural indices in vertebrates are under genetic control at least to some extent. In spite of significant behavioural problems in farm animals, information on the genetic background of behaviour is sparse. The aim of this study was to map QTL for behavioural indices in swine under healthy conditions and after infection with Sarcocystis miescheriana , as behaviour can be significantly influenced by disease . This well-described parasite model subsequently leads to acute (day 14 p.i.), subclinical (day 28 p.i.) and chronic disease (day 42 p.i.), allowing the study and comparison of the behaviour of pigs under four different states of health or disease. The study was based on a well-described Pietrain/Meishan F₂ family that has recently allowed the detection of QTL for disease resistance. We have mapped six genome-wide significant and 24 chromosome-wide significant QTL for six behavioural indices in swine. Six of these QTL (i.e. 20% of total QTL) showed effects on behavioural traits of the healthy pigs (day 0). Some of them (QTL on SSC11 and 18) lost influence on behavioural activities during disease, while the effects of others (QTL on SSC5, SSC8) partly remained during the whole experiment, although with different effects on the distinct behavioural indices. The disease model has been of high relevance to detect effects of gene loci on behavioural indices. Considering the importance of segregating alleles and environmental conditions that allow the identification of the phenotype, we conclude that there are indeed QTL with interesting effects on behavioural indices in swine.     

Continued mapping of chromosome 2 genes

This report describes our continued efforts to elucidate the genetic fine structure of the central portion of the mouse chromosome (Chr) 2. Mice from our panel of 28 Chr 2 congenic strains were tested: (1) for the presence of the antigens which stimulate Chr 2-reactive lymphocyte clones in mixed lymphocyte reactive lymphocyte clones in mixed lymphocyte reaction (MLR); (2) for the antigens of histocompatibility (H) genes H-42 ^a and H-45 ^a as determined by allograft rejection; and (3) for their ability to respond to the H-Y antigen in a cell-mediated lysis assay. The results obtained in this study have allowed additional mapping of immunoogically involved Chr 2 genes. The gene encoding the antigen which stimulates lymphocyte clone 1C11 can be considered wholly different from other Chr 2 H genes on the basis of chromosomal recombination. We have assigned the symbol H-48 to this gene. The following gene order has been established: [H-3, B2m, pa], we, [H-42, H-48], H-45, IR-H-Y, Hd-1, un, H-13, A ^w. The order of the bracketed genes is not known. H-44 maps centromeric to IR-H-Y. The genes encoding the antigens that stimulate lymphocyte clones 2G7, 2C10, 1F6, 1B10, and 1H10 map centromeric to H-45.     

Mapping of quantitative trait loci for clinical–chemical traits in swine

Clinical–chemical traits are diagnostic parameters essential for characterization of health and disease in veterinary practice. The traits show significant variability and are under genetic control, but little is known about the fundamental genetic architecture of this variability, especially in swine. We have identified QTL for alkaline phosphatase (ALP), lactate (LAC), bilirubin (BIL), creatinine (CRE) and ionized sodium (Na⁺), potassium (K⁺) and calcium (Ca⁺⁺) from the serum of 139 F₂ pigs from a Meishan/Pietrain family before and after challenge with Sarcocystis miescheriana , a protozoan parasite of muscle. After infection, the pigs passed through three stages representing acute disease, subclinical disease and chronic disease. Forty-two QTL influencing clinical–chemical traits during these different stages were identified on 15 chromosomes. Eleven of the QTL were significant on a genome-wide level; 31 QTL were chromosome-wide significant. QTL showed specific health/disease patterns with respect to the baseline values of the traits as well as the values obtained through the different stages of disease. QTL influencing different traits at different times were found primarily on chromosomes 1, 3, 7 and 14. The most prominent QTL for the investigated clinical–chemical traits mapped to SSC3 and 7. Baseline traits of ALP, LAC, BIL, Ca⁺⁺ and K⁺ were influenced by QTL regions on SSC3, 6, 7, 8 and 13. Single QTL explained up to 21.7% of F₂ phenotypic variance. Our analysis confirms that variation of clinical–chemical traits is associated with multiple chromosomal regions.     

Mapping of quantitative trait loci on porcine chromosome 4

A F₂ population derived from a cross between European Large White and Chinese Meishan pigs was established in order to study the genetic basis of breed differences for growth and fat traits. Chromosome 4 was chosen for initial study as previous work had revealed quantitative trait loci (QTLs) on this chromosome affected growth and fat traits in a Wild Boar × Large White cross. Individuals in the F₂ population were typed for nine markers spanning a region of approximately 124 c m . We found evidence for QTLs affecting growth between weaning and the end of test (additive effect: 43·4 g/day) and fat depth measured in the mid-back position (additive effect: 1·82 mm). There was no evidence of interactions between the QTLs and sex, grandparents or F₁ sires, suggesting that the detected QTLs were fixed for alternative alleles in the Meishan and Large White breeds. Comparison of locations suggests that these QTLs could be the same as those found in the Wild Boar × Large White cross.     

Development of a deer mouse whole-genome radiation hybrid panel and comparative mapping of Mus chromosome 11 loci

A 5000-rad whole-genome radiation hybrid cell panel (BW5000) was developed for mapping the deer mouse (Peromyscus maniculatus bairdii) genome. The panel consists of 103 cell lines and has an estimated marker retention frequency of 63.9% (range, 28%–88%) based on PCR typing of 30 Type I (coding gene) and 25 Type II (microsatellite) markers. Using the composite Mus map, Type I markers were selected from six Mus chromosomes, 22 of which are on Mus Chr 11. Fifteen of the Mus Chr 11 markers were simultaneously mapped on an interspecific (P. maniculatus × P. polionotus) backcross panel to test the utility of the radiation hybrid panel, create a framework map, and help establish gene order. The radiation hybrids have effectively detected linkage in the deer mouse genome between markers as far apart as 6.7 cM and resolved markers that are, in the Mus genome, as close as 0.2 Mb. Combined results from both panels have indicated a high degree of gene order conservation of the telomeric 64 cM of Mus Chr 11 in the deer mouse genome. The remaining centromeric portion also shows gene order conservation with the deer mouse but as a separate linkage group. This indicates a translocation of that portion of Mus Chr 11 in P. maniculatus and is consistent with rearrangement breakpoints observed between Mus and other mammalian genomes, including rat and human. Furthermore, this separate linkage group is likely to reside in a chromosomal region of inversion polymorphism between P. maniculatus and P. polionotus.     

Mapping of body weight loci on mouse Chromosome X

Inheritance of overweight in humans appears to be under polygenic control. Study on the mouse model may help to determine candidate regions in human genome for the search of overweight genes. Inbred mouse strains showed wide variation in body weight and can provide an experimental model for the study of inheritance of overweight. By genetic linkage analysis, we report the mapping of two loci, named Bw1 and Bw2 (body weight 1 and 2), on Chromosome (Chr) X that strongly affect adult body weight in two interspecific testcross male populations (HSB and ASB) of mice. In addition, another locus, named Bw3, is also mapped on Chr X in ASB populations. These loci account for up to 24% of the phenotypic variation in both populations. Considering the conserved synteny between mouse and human Chr X, these results provide candidate regions on Chr X that can be tested for linkage with overweight in humans.     

Synteny mapping of human chromosome 8 loci in cattle

Four genes having homologous loci on the short arm of human chromosome 8 have been mapped to two different bovine syntenic groups. The gene coding for the tissue-type plasminogen activator mapped with GSR, a human chromosome 8 marker, of syntenic group U14 while lipoprotein lipase and the medium and light neurofilament polypeptide genes were shown to be syntenic with the human chromosome 9 marker GGTB2 of syntenic group U18.     

Multipoint mapping studies of six loci on chromosome 11

The six loci, beta-globin (HBBC), parathyroid hormone (PTH), oncogene c-Ha-ras-1 (HRAS1), insulin (INS), calcitonin (CAL) and catalase (CAT) loci, have been mapped to 11p in the order: CAT-CAL-PTH-HBBC-(HRAS1-INS). The purpose of the current study was to examine the linkage relationships, especially the multipoint relationships of these loci in detail. In the 18 families studied, a significant sex difference in recombination was found for the HBBC: HRAS1 linkage with more recombination in the male parent than the female parent (22 vs. 2%). The results of the multipoint analyses provided further evidence for the order CAT-CAL-PTH-HBBC-(HRAS1-INS); however, the order of the last two tightly linked loci is still not clear.     

Intervening sequences in paralogous genes: a comparative genomic approach to study the evolution of X chromosome introns

The enlargement of the genome size and the decrease in genome compactness with increase in the number and size of introns is a general pattern during the evolution of eukaryotes. Among the possible mechanisms for modifying intron size, it has been suggested that the insertion of transposable elements might have an important role in driving intron evolution. The analysis of large portions of the human genome demonstrated that a relatively recent (50 to 100 MYA) accumulation of transposable elements appears to be biased, favoring a preferential insertion of LINE1 transposons into sex chromosomes rather than into autosomes. In the present work, the effect of chromosomal location on the increase in size of introns was evaluated with a comparative analysis performed on pairs of human paralogous genes, one located on the X chromosome and the second on an autosome. A phylogenetic analysis was also performed on the X-encoded proteins and their paralogs to confirm orthology-paralogy and to approximately estimate the time of gene duplication. Statistical analysis of total intron length for each pair of paralogous genes provided no evidence for a larger size of introns in the gene copies located on the X chromosome. On the opposite, introns of autosomal genes were found to be significantly longer than introns of their X-linked paralogs. Likewise, LINE1 elements were not significantly more frequent in X-chromosome introns, whereas the frequency of SINE elements showed a marginally significant bias toward autosomal introns.