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PubMed1999

A radiation hybrid map of mouse chromosome 13.

A mouse radiation hybrid (RH) panel was used to make a framework map for the entire length of mouse chromosome (Chr) 13. Forty-one loci were typed, and while most used primers flanking simple sequence repeats, some genes were included. The most proximal and distal loci are D13Mit132 and D13Mit35. The estimate of map length for Chr 13 is 1328 cR. The map is compared with the same set of loci from the consensus map for Chr 13, which is 70 cM in length, and also with a recombinational map derived from an intraspecies cross typed for many of the same loci. The mouse RH panel gave good resolution for Chr 13 and at the distal end allowed separation of previously nonrecombinant markers that are present on a single 620-kb YAC clone. Data analysis was performed using the RH option for Map Manager QT. This framework RH map of Chr 13 is the second of a series of RH maps for mouse chromosomes.

Animals↗

PubMed1996

Analysis and comparison of the mouse and human immunoglobulin heavy chain JH-Cmu-Cdelta locus.

We report here 23,686 bases of contiguous DNA sequences from the mouse germline immunoglobulin heavy chain (H) constant (C) mu delta region. The sequence spans the joining (JH) regions, the mu constant region (C mu), the delta constant region (C delta) coding regions, a domain relic, the mu switch region (S mu), seven blocks of simple sequence repeats, a large unique sequence inverted repeat, a large unique sequence forward repeat, and all of the intervening material. A comparison of this 23.7-kb region with the corresponding human C mu/C delta region reveals clear homology in the coding and introns of C mu but not in the 5' flanking J gene segments nor in the intergenic and C delta regions. This mixed pattern of similarity between the human and the mouse sequences contrasts with high levels of similarity found in the T-cell receptor C alpha/C delta region and alpha and beta myosin genes and the very low levels found in the gamma-crystallin, XRCC1, and beta-globin gene clusters. The human and mouse comparison further suggests the incorporation of novel sequences into expressed genes of IgD.

Animals↗

PubMed1995

Barley microsatellites: allele variation and mapping.

Microsatellites have developed into a powerful tool for mapping mammalian genomes and first reports about their use in plants have been published. A database search of 228 barley sequences from GenBank and EMBL was made to determine which simple sequence repeat (SSR) motif prevails in barley. Nearly all types of SSRs were found. The (A)n and (T)n SSRs occurred more often than (C)n and (G)n for n > or = 10. Among the dinucleotide repeats, the (CG)n SSRs occurred least often. Trinucleotide repeats did not occur with n > 7 and there is no correlation between the GC content in the trinucleotide motifs and the number of observed SSRs. Analysing 15 different microsatellites with 11 barleys yielded 2.1 alleles per microsatellite. Sequencing 25 putative microsatellites showed that the resolution capacity of high-quality agarose gels was sufficient to determine differences of only three base pairs. Five microsatellites were mapped on three different chromosomes of a barley RFLP map.

Alleles↗

PubMed1994

Linkage analysis of the genetic determinants of high density lipoprotein concentrations and composition: evidence for involvement of the apolipoprotein A-II and cholesteryl ester transfer protein loci.

We have tested for evidence of linkage between the genetic loci determining concentrations and composition of plasma high density lipoproteins (HDL) with the genes for the major apolipoproteins and enzymes participating in lipoprotein metabolism. These genes include those encoding various apolipoproteins (apo), including apoA-I, apoA-II, apoA-IV, apoB, apoC-I, apoC-II, apoC-III, apoE, and apo(a), cholesteryl ester transfer protein (CETP), HDL-binding protein, lipoprotein lipase, and the low density lipoprotein (LDL) receptor. Polymorphisms of these genes, and nearby highly polymorphic simple sequence repeat markers, were examined by quantitative sib-pair linkage analysis in 30 coronary artery disease families consisting of a total of 366 individuals. Evidence for linkage was observed between a marker locus D16S313 linked to the CETP locus and a locus determining plasma HDL-cholesterol concentration (P = 0.002), and the genetic locus for apoA-II and a locus determining the levels of the major apolipoproteins of HDL, apoA-I and apoA-II (P = 0.009 and 0.02, respectively). HDL level was also influenced by the variation at the apo(a) locus on chromosome 6 (P = 0.02). Thus, these data indicate the simultaneous involvement of at least two different genetic loci in the determination of the levels of HDL and its associated lipoproteins.

Apolipoprotein A-II↗

PubMed1993

Inter-ethnic polymorphism of the beta-globin gene locus control region (LCR) in sickle-cell anemia patients.

Sequence polymorphisms within the 5'HS2 segment of human locus control region is described among sickle cell anemia patients. Distinct polymorphic patterns of a simple sequence repeat are observed in strong linkage disequilibrium with each of the five major beta s haplotypes. Potential functional relevance of this polymorphic region in globin gene expression is discussed.

Algeria↗

PubMed1993

Genetic mapping of the erythropoietin receptor gene.

We describe a novel, highly informative (polymorphism information content, PIC, = 0.86) simple sequence repeat polymorphism at the 5' end of the gene encoding the human erythropoietin receptor (EPOR) previously assigned to 19p13.2 by in situ hybridization. Fourteen different allelic size variants were identified in 12 families of the CEPH (Centre d'Etude du Polymorphisme Humain) family panel of 40 families. In pairwise linkage 16 of the 65 chromosome 19 markers reported to the CEPH database gave a lod score exceeding 3.0 when tested against EPOR. The most likely location of EPOR within a framework of 10 markers including orientation and information on reported physical assignments was pter-[INSR-D19S177-D19S176]-D19S24-LDLR-++ +EPOR-cen-D19S7-D19S49-D19S75-D19S47-AP OC2-qter, placing EPOR as the most proximal of the tested loci on the short arm. On an 11-point map the position and order for all other loci except INSR were supported by the data with odds exceeding 1,000:1. The polymorphism at the 5' end of EPOR should provide a useful landmark marker for future mapping studies of this region.

Base Sequence↗

PubMed1994

Characterization of 65 bovine microsatellites.

Microsatellites or simple sequence repeat (SSR) polymorphisms are used widely in the construction of linkage maps in many species. High levels of polymorphism coupled with the ease of analysis of the polymerase chain reaction (PCR) have resulted in this type of maker being one of the most widely used for genetic analysis. In this paper we describe 58 polymorphic bovine microsatellites that were isolated from insert size selected bovine genomic libraries. Primer sequences, number of alleles, and heterozygosity levels in cattle reference families are reported. Chromosomal locations for 47 of these microsatellites as well as for 7 previously described systems derived from entries in the Genbank or EMBL databases have been determined. The markers map to 24 syntenic or chromosomal locations. Polymorphic bovine microsatellites were estimated to occur, on average, every 320 kb, and there is no evidence of clustering in the genome. Thirty of the bovine-derived microsatellite systems gave specific and polymorphic products in sheep, adding to the number of useful markers in that species.

Animals↗

PubMed1995

Genetic map of 16 polymorphic markers forming three linkage groups assigned to rat chromosome 4.

Sixteen polymorphic markers, including markers for eight new loci, forming three linkage groups, were assigned to rat Chromosome (Chr) 4 by linkage analysis of the progeny of an F2 intercross of Fischer (F344/N) and Lewis (LEW/N) inbred rats. One gene, Igk, was mapped by restriction fragment length polymorphism (RFLP) analysis. One marker for Tcrb was identified by the polymorphic insertion of a repetitive LINE element. The remaining 14 markers contained polymorphic simple sequence repeats (SSRs). Ten were identified in genes (Tgfa, Npy, Prss1, Prss2, Aldr1, Iapp, Prp, Eno2, Cacnl1a1, and Il6), one was identified in a sequence related to a gene (Egr4l1), and three were identified in anonymous DNA segments. The SSR markers were highly polymorphic in 16 inbred rat strains. These markers expand the genetic map of the rat and should be useful in future genetic studies of inbred rats.

Animals↗

PubMed1993

Genes encoding the H,K-ATPase alpha and Na,K-ATPase alpha 3 subunits are linked on mouse chromosome 7 and human chromosome 19.

We have used linkage analysis and fluorescence in situ hybridization to determine the chromosomal organization and location of the mouse (Atp4a) and human (ATP4A) genes encoding the H,K-ATPase alpha subunit. Linkage analysis in recombinant inbred (BXD) strains of mice localized Atp4a to mouse Chromosome (Chr) 7. Segregation of restriction fragment length polymorphisms in backcross progeny of Mus musculus x Mus spretus mating confirmed this assignment and indicates that Atp4a and Atp1a3 (gene encoding the murine Na,K-ATPase alpha 3 subunit) are linked and separated by a distance of approximately 2 cM. Analysis of the segregation of simple sequence repeats suggested the gene order centromere-D7Mit21-D7Mit57/Atp1a3-D7Mit72/Atp 4a. A human Chr 19-enriched cosmid library was screened with both H,K-ATPase alpha and Na,K-ATPase alpha 3 subunit cDNA probes to isolate the corresponding human genes (ATP4A and ATP1A3, respectively). Fluorescence in situ hybridization with gene-specific cosmid clones localized ATP4A to the q13.1 region, and proximal to ATP1A3, which maps to the q13.2 region, of Chr 19. These results indicate that ATP4A and ATP1A3 are linked in both the mouse and human genomes.

Animals↗

PubMed1993

Genetic map of seven polymorphic markers comprising a single linkage group on rat chromosome 5.

Seven polymorphic markers comprising a single linkage group were assigned to rat Chromosome (Chr) 5 by linkage analysis of the progeny of an F2 intercross of Fischer (F344/N) and Lewis (LEW/N) inbred rats. Three genes, alpha-L-fucosidase 1 (FUCA1), mitochondrial superoxide dismutase (SOD2), and glucose transporter (GLUT1), were mapped by restriction fragment length polymorphism (RFLP) analysis. Two genes, glucose transporter (GTG3) and elastase II (ELAII), one pseudogene for alpha tubulin (TUBAPS), and one sequence related to the 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase gene (PFKFBP1-related sequence) were mapped by simple sequence repeat (SSR) polymorphism analysis. The loci are in the following order: SOD2, GTG3/GLUT1, FUCA1, ELAII/PFKFBP1-related sequence, and TUBAPS. This linkage group covered 68.3 cM of rat Chr 5. The SSR markers were highly polymorphic in 13 inbred rat strains (SHR/N, WKY/N, MNR/N, MR/N, LOU/MN, BN/SsN, BUF/N, WBB1/N, WBB2/N, ACI/N, LER/N, F344/N, and LEW/N). These markers, located on rat Chr 5, will be useful in genetic studies of inbred rats.

Animals↗

PubMed1993

Characterizations of candidate genes for IDD susceptibility from the diabetes-prone NOD mouse strain.

The nucleotide sequences of the NOD and C57BL/6J alleles of Glut-2, Sod-2, and Il-2 were determined by RT-PCR sequencing. Each of these loci is located in intervals that strongly correlated with susceptibility to diabetes in an (NOD/Uf x C57BL/6J)F1 x NOD/Uf backcross. No significant variations in the alleles of Glut-2 at 16 cM on Chromosome (Chr) 3 or Sod-2 at 8 cM on Chr 17 were detected. However, the Il-2 allele in NOD at 20 cM on Chr 3 was found to differ from that in C57BL/6J by a complex mutation involving the contraction of a simple sequence repeat (SSR). Il-2 in NOD differs from the allele in C57BL/6J via a complex mutation involving a deletion of four CAG codons from the SSR together with a length-compensatory four-codon duplication of a segment 5' from the SSR. Two nonsynonymous mutations in the coding region 5' to the SSR were also detected. Only these two allelic forms of Il-2 were detected in a survey of 13 standard inbred lines and 4 wild mouse strains. We propose to designate these alleles as Il-2a (for alleles such as C57BL/6J that contain 12 CAG repeats) and Il-2b (for alleles such as NOD), which occurred in a variety of standard inbred strains and in all four wild Mus musculus domesticus tested. The distribution of these Il-2 alleles among inbred strains correlated with the detection of Chr 3 as an interval effecting diabetes susceptibility in three separate genetic crosses.(ABSTRACT TRUNCATED AT 250 WORDS)

Alleles↗

PubMed1994

Glucokinase gene in gestational diabetes mellitus: population association study and molecular scanning.

Mutations of the glucokinase gene result in early-onset familial Type 2 (non-insulin-dependent) diabetes mellitus, and several members of the mutant glucokinase kindreds were originally diagnosed as having gestational diabetes. This study examined the glucokinase gene in 270 American Black women, including 94 with gestational diabetes whose diabetes resolved after pregnancy (gestational diabetes only), 77 with gestational diabetes who developed Type 2 diabetes after pregnancy (overt diabetes), and 99 normal control subjects who were recruited during the peripartum period. Two simple sequence repeat polymorphisms flanking either end of the glucokinase gene were evaluated. No association was found between glucokinase alleles and gestational diabetes only or overt diabetes, after adjustment for multiple comparisons. To detect single base changes, all 11 exons and proximal islet and liver promoter regions were examined by polymerase chain reaction plus single-stranded conformational polymorphism analysis in 45 gestational diabetes only patients who had not yet developed Type 2 diabetes. Nine coding region variants were identified: Ala11 (GCC) to Thr11 (ACC) in islet exon 1, and 8 variants either in untranslated regions or in the third base of a codon. Four variant sites were found in introns, but none in splicing consensus sequences. Analysis of the promoter regions revealed two common variants, G-->A at islet -30 (24%), and G-->A at liver -258 (42%). The frequencies of the promoter variants, determined by allele specific polymerase chain reaction analysis, but did not differ among the three groups. Thus, no significant coding sequence glucokinase mutations were found in 90 alleles from 45 patients with gestational diabetes.(ABSTRACT TRUNCATED AT 250 WORDS)

Adult↗

PubMed1995

Genetic mapping of the polycystic kidney gene, pcy, on mouse chromosome 9.

The murine polycystic kidney disease gene, pcy, is an autosomal recessive trait located on chromosome 9. To determine the genetic locus of pcy, 222 intraspecific backcross mice were obtained by mating C57BL/6FG-pcy and Mus molossinus. Restriction fragment length polymorphism analysis of 70 of the 222 backcross progeny showed that pcy, dilute coat color (d), and cholecystokinin (Cck) were located in the order d--pcy--Cck from the centromere. Simple sequence repeat length polymorphism analysis of DNA of all 222 backcross mice was carried out using four markers which were located near the central regions of d and Cck. One and eight recombinations were detected between D9Mit24 and pcy and between D9Mit16 and pcy, respectively. However, no recombinant was observed among pcy, D9Mit14, and D9Mit148. These findings strongly suggest that D9Mit14 and D9Mit148 are located near the pcy gene and are good markers for chromosomal walking to this gene.

Animals↗

PubMed1995

Differentiation of Fusarium sambucinum Fuckel sensu lato and related species by RAPD PCR.

DNA polymorphisms generated by the random amplified polymorphic DNA polymerase chain reaction (RAPD PCR) were used to analyse 41 isolates investigated in the European Fusarium sambucinum Project (EFSP). Employing ten arbitrary (10-mer) oigonucleotides and simple repeat sequences (M13, (GACA)4) as single primers, informative banding patterns typical for identifying European populations of Fusarium sambucinum Fuckel s. str., F. torulosum (Berk. & Curt.) Nirenberg and F. venenatum Nirenberg were obtained.

Base Sequence↗

PubMed1992

Generation and characterization of a human chromosome 9 cosmid library.

A cosmid library has been constructed from the hamster-human hybrid cell line PK-87-9, which contains chromosome 9 as its sole known human component. Ten thousand colonies were produced, of which approximately 200, or 2%, contain human material. Fifty of these 200 were regionally mapped by an Alu-primed PCR product hybridization procedure. These cosmids were localized to all regions of chromosome 9, but were especially concentrated in the distal portion of 9q. The map location derived by the Alu-primed PCR product hybridization procedure was compared to the map location derived by fluorescent in situ hybridization. Assignment of chromosomal location by the two methods was correspondent in all but a few cases. The presumptive presence of HTF islands was investigated for 130 cosmids by digestion with the restriction enzyme NotI. Twenty percent of cosmids contained at least one NotI site. A number of simple sequence repeat polymorphisms identified from the cosmid set were characterized and will provide a link between the genetic and physical maps for this chromosome.

Animals↗

PubMed1995

Analysis of aldehyde oxidase and xanthine dehydrogenase/oxidase as possible candidate genes for autosomal recessive familial amyotrophic lateral sclerosis.

Recently, point mutations in superoxide dismutase 1 (SOD1) have been shown to lead to a subset of autosomal dominantly inherited familial amyotrophic lateral sclerosis (ALS). These findings have led to the hypothesis that defects in oxygen radical metabolism may be involved in the pathogenesis of ALS. Therefore, we decided to analyze other enzymes involved in oxygen radical metabolism for possible involvement in other forms of ALS. We report here analysis of two genes encoding the molybdenum hydroxylases aldehyde oxidase (AO) and xanthine dehydrogenase/oxidase (XDH) for involvement in ALS. Of particular interest, one gene identified as encoding aldehyde oxidase is shown to map to 2q33, a region recently shown to contain a gene responsible for a familial form of ALS with autosomal recessive inheritance (FALS-AR). The AO gene appears to be located within 280,000 bp of simple sequence repeat marker D2S116, which shows no recombination with the FALS-AR locus. The AO gene is highly expressed in glial cells of human spinal cord. In addition, we mapped a gene for XDH to 2p22, a region previously shown to contain a highly homologous but different form of XDH. Neither of these XDH genes appears to be highly expressed in human spinal cord. This evidence suggests that AO may be a candidate gene for FALS-AR.

Aldehyde Oxidase↗

PubMed1996

Comparative diagnoses of twin zygosity by SSLP variant analysis, questionnaire, and dermatoglyphic analysis.

Zygosity diagnosis has been performed in 79 pairs of twins using three methods. Simple sequence repeat length polymorphism (SSLP) analysis allows an efficient classification (MZ or DZ) with only a few markers following a simplified technique of extraction and amplification. A method based on a full questionnaire completed by parents about twin similarity correctly classifies 97.46% of the pairs; 92.41% are correctly classified using only four questions as suggested by logistic regression analysis. The third method, using dermatoglyphic analyses, correctly classifies 86.76% of pairs. To lower the cost of DNA diagnosis we stress the possibility of limiting its use to pairs with scores in the overlap area between MZ and DZ twins with a validated questionnaire.

Child↗

PubMed1993

Four polymorphic markers on rat chromosome 12 form a single linkage group.

Four PCR-typable polymorphic markers were mapped to rat chromosome 12 by linkage analysis of F2 intercross progeny of Fischer (F344/N) and Lewis (LEW/N) rat strains. The markers formed a single linkage group, covering 27.7 cM, with the following order and distance between markers: plasminogen activator inhibitor (Planh)--0.0 cM--phosphoenolpyruvate carboxykinase-related sequence 2 (Pepckr2)--15.4 cM--anonymous marker (D12N155)--12.3 cM--serine dehydratase (Sdh). All markers were identified and genotyped by PCR analysis of simple sequence repeats. The gene encoding Planh was previously assigned to rat chromosome 12, which allowed us to assign the entire linkage group to this chromosome. These markers were highly polymorphic in 13 additional inbred rat strains (BUF/N, BN/SsN, WKY/N, MNR/N, LER/N, WBB1/N, WBB2/N, MR/N, LOU/MN, SHR/N, ACI/N, SR/Jr, and SS/Jr). These markers should be useful tools for further genetic studies in rats.

Animals↗