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PubMed2004

Genetic complexity of an obesity QTL ( Fob3) revealed by detailed genetic mapping.

Obesity is proving to be a serious health concern in the developed world as well as an unwanted component of growth in livestock production. While recent advances in genetics have identified a number of monogenic causes of obesity, these are responsible for only a small proportion of human cases of obesity. By divergent selection for high and low fat content over 60 generations, we have created Fat (F) and Lean (L) lines of mice that represent a model of polygenic obesity similar to the situation in human populations. From previous crosses of these lines, four body fat quantitative trait loci (QTL) were identified. We have created congenic lines (F(chr15L)), by recurrent marker-assisted backcrossing, to introgress the QTL region with the highest LOD score, Fob3 on Chr 15, from the L-Iine into the F-line background. We have further mapped this QTL by progeny testing of recombinants, produced from crosses between the F-line and congenic F(chrl5L) mice, showing that the Fob3 QTL region is a composite of at least two smaller effect QTL-the proximal QTL Fob3a is a late-onset obesity QTL, whereas the distal Fob3b is an early-onset obesity QTL.

Analysis of Variance↗
PubMed1996

Positional cloning of the Chediak-Higashi syndrome gene: genetic mapping of the beige locus on mouse chromosome 13.

BACKGROUND: Chediak-Higashi syndrome (CHS) is a systemic disorder of human and mouse (beige, bg) that is characterized by aberrant intracellular protein kinesis and lysosomal trafficking. Affected individuals exhibit a severe primary immune deficiency that principally affects the function of granulocytes and cytolytic lymphocytes and partial oculocutaneous albinism, platelet dysfunction, and neurodegeneration. Chediak-Higashi syndrome is inherited as an autosomal recessive Mendelian trait in human and mouse and maps on proximal mouse Chromosome 13. METHODS: To clone positionally the defective gene in CHS, we have generated a large number of backcross mice who segregate for beige. Genomic DNA from these mice was genotyped for 26 genetic markers known to map on proximal mouse Chromosome 13. RESULTS: By segregation analysis, bg was localized to a 0.24 centiMorgan interval and was shown to cosegregate with 6 genetic markers (Nid, Estm9, D13Mit56, D13Mit162, D13Mit237, and D13Mit240). Two of these loci, Nid and Estm9, are genes and represent candidates for bg. Nidogen (Nid) encodes an extracellular matrix protein that is a component of basement membranes. Estm9 is a sequence that is transcribed ubiquitously in mouse embryos and encodes a protein of unknown function. Mutation analysis of Nid and Estm9 was undertaken in 6 bg alleles; no differences were observed between bg and coisogenic controls by analysis of Northern blots, Southern blots, or by quantitative reverse transcription and polymerase chain reaction. CONCLUSIONS: These studies indicate that a genomic rearrangement affecting Nid or Estm9 does not underlie bg. The bg locus has been localized on mouse Chromosome 13 with sufficient precision to enable rapid cloning of the bg non-recombinant interval and eventual identification of the gene for Chediak-Higashi syndrome among sequences within the interval.

Animals↗
PubMed1996

Centromere-linkage analysis and consolidation of the zebrafish genetic map.

The ease of isolating mutations in zebrafish will contribute to an understanding of a variety of processes common to all vertebrates. To facilitate genetic analysis of such mutations, we have identified DNA polymorphisms closely linked to each of the 25 centromeres of zebrafish, placed centromeres on the linkage map, increased the number of mapped PCR-based markers to 652, and consolidated the number of linkage groups to the number of chromosomes. This work makes possible centromere-linkage analysis, a novel, rapid method to assign mutations to a specific linkage group using half-tetrads.

Animals↗
PubMed1979

The genetic map of transfer RNA genes of yeast mitochondria: correction and extension.

Ninety five rho- mitochondrial DNA's of Saccharomyces cerevisiae were compared for their deletion structure by means of 15 genetic markers and 22 tRNA genes. The patterns of co-deletion and co-retention of different tRNA genes allowed us to determine their positions with respect to each other. The deduced order of tRNA genes was consistent with the order of the genetic markers established by independent genetic approaches. Our previously proposed mitochondrial tRNA gene map has been revised and extended. Transfer RNA genes, corresponding to all 20 aminoacids, and two isoacceptor tRNA genes were localized. The possible position of each tRNA gene has been indicated on the physical map of mitochondrial DNA. Seventeen tRNA genes are carried by a narrow region representing less than 20% of the wild type genome.

Chromosome Mapping↗
PubMed1995

Genetic mapping and non-Mendelian segregation of mating type loci in the oomycete, Phytophthora infestans.

DNA markers linked to the determinants of mating type in the oomycete, Phytophthora infestans, were identified and used to address the genetic basis of heterothallism in the normally diploid fungus. Thirteen loci linked to the A1 and A2 mating types were initially identified by bulked segregant analysis using random amplified polymorphic DNA markers (RAPDs) and subsequently scored in three crosses polymorphisms (SSCP), cleaved amplified polymorphisms (CAPS), or allele-specific polymerase chain reaction markers (AS-PCR). All DNA markers mapped to a single region, consistent with a single locus determining both mating types. Long-range restriction mapping also demonstrated the linkage of the markers to one region and delimited the mating type locus to a 100-kb region. The interval containing the mating type locus displayed non-Mendelian segregation as only two of the four expected genotypes were detected in progeny. This is consistent with a system of balance lethal loci near the mating type locus. A model for mating type determination is presented in which the balanced lethals exclude form progeny those with potentially conflicting combinations of mating type alleles, such as those simultaneously expressing A1 and A2 functions.

Base Sequence↗
PubMed1996

A physical and genetic map of Neisseria meningitidis B1940.

A physical map of the chromosome of Neisseria meningitidis B1940 has been constructed by one- and two-dimensional pulsed-field gel electrophoresis techniques. Complete macrorestriction maps for the enzymes Nhel (16 sites), Sgfl (13 sites), Sfil (11 sites) and l-Ceul (4 sites), as well as a partial restriction map for the restriction enzyme Spel (15 of c. 28 sites) could be established. Altogether, 59 restriction sites were mapped on a single circular chromosome of 2.3 Mbp. By restriction endonuclease digestion and Southern hybridization of cloned genetic markers, 39 genetic loci were assigned to this map. Comparison with the metabolic maps of Neisseria gonorrhoeae MS11-N198 and FA1090 revealed a high degree of conservation in the arrangement of gene loci among these two species, although four out of 24 genetic loci are located at different chromosomal positions, indicating several genomic rearrangements.

Chromosome Mapping↗
PubMed1997

Genetic mapping of susceptibility loci in the genes involved in rheumatoid arthritis.

Eighty-nine multicase rheumatoid arthritis families, each containing at least one affected sib pair, have been studied for evidence of genetic linkage to a panel of 315 microsatellite DNA markers. The families were located through the UK national data repository of the Arthritis and Rheumatism Council. Microsatellites were genotyped by semiautomated technology using Applied Biosystems sequencers (ABI 373). Using the SIBPAIR statistical package, linkage to HLA was confirmed (p < 0.0003). Several possible linkages outside HLA were noted, including at least one (p < 0.004) that merits further investigation.

Arthritis, Rheumatoid↗
PubMed2002

Identification of wheat-barley translocations by sequential GISH and two-colour FISH in combination with the use of genetically mapped barley SSR markers.

Five wheat-barley translocations in a wheat background were characterized through the combination of cytogenetic and molecular genetic approaches. The wheat chromosome segments involved in the translocations were identified using sequential GISH and two-colour FISH with the probes pSc119.2 and pAs1. The barley chromatin in these lines was identified using SSR markers. A total of 45 markers distributed over the total barley genome were selected from a recently published linkage map of barley and tested on the translocation lines. The following translocations were identified: 2DS.2DL-1HS, 3HS.3BL, 6BS.6BL-4HL, 4D-5HS, and 7DL.7DS-5HS. Wheat-barley disomic and ditelosomic addition lines for the chromosomes 3HS, 4H, 4HL, 5H, 5HL, and 6HS were used to determine the correct location of 21 markers and the position of the centromere. An intragenomic translocation breakpoint was detected on the short arm of the barley chromosome 5H with the help of SSR marker analysis. Physical mapping of the SSR markers on chromosomes 1H and 5H was carried out using the intragenomic and the interspecific translocation breakpoints, as well as the centromere, as physical landmarks.

Genetic Markers↗
PubMed2004

Variation in recombination rate may bias human genetic disease mapping studies.

The availability of the human genome sequence and variability information (as from the International HapMap project) will enhance our ability to map genetic disorders and choose targets for therapeutic intervention. However, several factors, such as regional variation in recombination rate, can bias conclusions from genetic mapping studies. Here, we examine the impact of regional variation in recombination rate across the human genome. Through computer simulations and literature surveys, we conclude that genetic disorders have been mapped to regions of low recombination more often than expected if such diseases were randomly distributed across the genome. This concentration in low recombination regions may be an artifact, and disorders appearing to be caused by a few genes of large effect may be polygenic. Future genetic mapping studies should be conscious of this potential complication by noting the regional recombination rate of regions implicated in diseases.

Bias↗
PubMed2005

Genetic mapping of the distribution of minima on the potential energy surface of disordered systems.

We show that genetic algorithms and energy minimizations in combination provide a highly efficient tool for mapping low-energy minima on the erratic and complex potential-energy surfaces of grossly disordered materials. The distribution of energy minima mimics with sufficient accuracy the low-energy portion of the parent distribution of minima and allows accurate calculation of configurational Boltzmann averaged structural and thermodynamic properties in cases where a small fraction of the minima is thermally accessible. The distribution of energy minima obtained using genetic algorithms is biased, and consequently the properties converge slowly at high temperatures. In contrast, an optimized set of a few randomly chosen configurations provides a statistical representable selection for the accurate calculation of configurational-averaged properties at high temperatures, but gives a poor description of the low-energy portion of minima. Thus the properties calculated using the random algorithm are hampered by the presence of systematic errors in cases where a small fraction of the minima is thermally accessible. The inherently slow convergence of both the genetic algorithm and the random selection at intermediate temperatures is tackled by combining the lower fraction of the distribution of minima obtained using genetic algorithms with the intermediate and upper fraction from the random (nonbiased) selection of configurations. For this purpose we introduce a cut-and-scale-type scheme. The resulting combined distribution allows accurate calculation of properties at all temperatures.

Journal Article↗
PubMed1995

Relative positions of two clusters of human alpha-L-fucosyltransferases in 19q (FUT1-FUT2) and 19p (FUT6-FUT3-FUT5) within the microsatellite genetic map of chromosome 19.

Five on the seven cloned human fucosyltransferase genes have been mapped to two clusters, one on 19q and the other on 19p. Comparative DNA sequence analysis showed the Généthon microsatellite D19S596 lies 2.2 kb downstream of the coding region of FUT1, indicating that the cluster comprising the closely linked FUT1 and FUT2 genes is located 4 cM distal to D19S412 (lod score 13.7) and 9 cM proximal to D19S571 (lod score 11.7). Polymorphic markers of FUT3, FUT5, and FUT6 were used for linkage analysis with 14 Généthon microsatellites in Indonesian families. These three loci constitute a cluster on 19p, located between the Généthon microsatellites D19S216 and D19S567, which are known to be only 1 cM distant from each other. Two cross-overs, one between FUT6 and FUT3 and the other between FUT3 and FUT5, suggest the gene order 19pter-D19S216-FUT6-FUT3-FUT5-D19S567++ +-cen. Comparison of genetic and physical maps suggests that the FUT6-FUT3-FUT5 cluster is located on 19p13.3 and the FUT1-FUT2 cluster on 19q13.3. FUT6, FUT3 and FUT5 genes share more than 85% homology and encode three similar, but distinct alpha(1,3) fucosyltransferases. FUT1 and FUT2 share about 70% homology and encode two distinct alpha(1,2)fucosyltransferases. No sequence homology was found between the genes of the two clusters. The members of each of these two clusters have probably emerged by duplication and divergent evolution of two unrelated ancestor genes.

Base Sequence↗
PubMed1979

Genetic mapping of the ecotropic murine leukemia virus-inducing locus of BALB/c mouse to chromosome 5.

By means of an approach that combined the techniques of somatic cell genetics and Mendelian breeding studies, the inducibility locus, designated Cv, for ecotropic murine leukemia virus in BALB/c mice, was mapped to chromosome 5, 23 units from the locus for phosphoglucomutase-1, with gene order Cv-Pgm-1-Gus. This low-efficiency inducibility locus is therefore not allelic with the chromosome 7 loci previously described for two other mouse strains with high virus inducibility. These studies provide further evidence that endogenous ecotropic viruses represent viral genomes inserted at different chromosomal sites in the various mouse strains.

Animals↗
PubMed1995

Multiple trait analysis of genetic mapping for quantitative trait loci.

We present in this paper models and statistical methods for performing multiple trait analysis on mapping quantitative trait loci (QTL) based on the composite interval mapping method. By taking into account the correlated structure of multiple traits, this joint analysis has several advantages, compared with separate analyses, for mapping QTL, including the expected improvement on the statistical power of the test for QTL and on the precision of parameter estimation. Also this joint analysis provides formal procedures to test a number of biologically interesting hypotheses concerning the nature of genetic correlations between different traits. Among the testing procedures considered are those for joint mapping, pleiotropy, QTL by environment interaction, and pleiotropy vs. close linkage. The test of pleiotropy (one pleiotropic QTL at a genome position) vs. close linkage (multiple nearby nonpleiotropic QTL) can have important implications for our understanding of the nature of genetic correlations between different traits in certain regions of a genome and also for practical applications in animal and plant breeding because one of the major goals in breeding is to break unfavorable linkage. Results of extensive simulation studies are presented to illustrate various properties of the analyses.

Algorithms↗
PubMed2003

Genetic mapping of allelic loss on chromosome 6q within heterogeneous prostate carcinoma.

A number of genetic events have been reported in prostate carcinogenesis, including frequent loss of heterozygosity (LOH) on chromosomes 8q, 10q, 16q and 18q. In samples of heterogeneous, multifocal prostate carcinomas, we focused on chromosome 6q using PCR-based techniques with 15 microsatellite markers to identify the specific 6q deletion within tumors. LOH of one or more polymorphic markers was detected in 10 of 21 tumors (48%). Two of these 10 tumors demonstrated LOH in all cancerous foci at specific loci and 4 tumors showed deletion in one focus. Different deletion patterns were found in 3 tumors when different polymorphic markers were used. In 90% of tumors showing LOH in one or more foci, however, two common regions of LOH were identified; one at 1.81 cM on 6q15-16.3 between markers D6S1631 and D6S1056, and the other at 5.11 cM on 6q16-21 between markers D6S424 and D6S283. By RT-PCR analysis, the TAK1 gene located at these loci did not correlate with LOH status, indicating that TAK1 is not a target gene in prostate carcinoma. The 6q deletion occurs heterogeneously and LOH was more frequent in tumors of higher pathological stages, implying that this alteration is a late event in prostate carcinogenesis. Because prostate carcinomas are genetically multicentric and of multifocal origin, it remains unclear whether the foci containing 6q deletions specifically expand within tumors or to what extent they contribute to the histological heterogeneity characteristic of the disease.

Aged↗
PubMed1992

A directional, high-frequency chromosomal mobilization system for genetic mapping of Rhizobium meliloti.

A system for mapping of the Rhizobium meliloti chromosome that utilizes transposon Tn5-Mob, which carries the mobilization site of IncP plasmid RP4 (R. Simon, Mol. Gen. Genet. 196:413-420, 1984), was developed. Insertions of Tn5-Mob that were located at particular sites on the R. meliloti chromosome were isolated and served as origins of high-frequency chromosomal transfer when IncP tra functions were provided in trans. This approach is, in principle, applicable to any gram-negative bacterium in which Tn5 can transpose and into which IncP plasmids can conjugate.

Chromosome Mapping↗
PubMed2006

Genetic mapping of a major gene affecting onion bulb fructan content.

The non-structural dry matter content of onion bulbs consists principally of fructose, glucose, sucrose and fructans. The objective of this study was to understand the genetic basis for the wide variation observed in the relative amounts of these carbohydrates. Bulb carbohydrate composition was evaluated in progeny from crosses between high dry matter storage onion varieties and sweet, low dry matter varieties. When samples were analysed on a dry weight basis, reducing sugar and fructan content exhibited high negative correlations and bimodal segregation suggestive of the action of a major gene. A polymorphic SSR marker, ACM235, was identified which exhibited strong disequilibrium with bulb fructan content in F(2:3) families from the 'W202A' x 'Texas Grano 438' mapping population evaluated in two environments. This marker was mapped to chromosome 8 in the interspecific population 'Allium cepa x A. roylei'. Mapping in the 'Colossal Grano PVP' x 'Early Longkeeper P12' F2 population showed that a dominant major gene conditioning high-fructan content lay in the same genomic region. QTL analysis of total bulb fructan content in the intraspecific mapping population 'BYG15-23' x 'AC43' using a complete molecular marker map revealed only one significant QTL in the same chromosomal region. This locus, provisionally named Frc, may account for the major phenotypic differences in bulb carbohydrate content between storage and sweet onion varieties.

Breeding↗