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PubMed1985

Inheritance of allozyme variants in bishop pine (Pinus muricuta D. Don).

Isozyme phenotypes are described for 45 structural loci and 1 modifier locus in bishop pine (Pinus muricata D. Don,) and segregation data are presented for a subset of 31 polymorphic loci from 19 enzyme systems. All polymorphic loci had alleles that segregated within single-locus Mendelian expectations, although one pair of alleles at each of three loci showed significant segregation distortion. The consistency of resolution and segregation at many loci in bishop pine makes electrophoretic analyses feasible for many purposes in this species.

Electrophoresis, Polyacrylamide Gel↗

PubMed2004

Phytophthora sojae avirulence genes Avr4 and Avr6 are located in a 24kb, recombination-rich region of genomic DNA.

A cross between two different races (race 7xrace 25) of the soybean root and stem rot pathogen Phytophthora sojae was analyzed to characterize the genomic region flanking two cosegregating avirulence genes, Avr4 and Avr6. Both genes cosegregated in the ratio of 82:17 (avirulent:virulent) in an F(2) population, suggestive of a single locus controlling both phenotypes. A chromosome walk was commenced from RAPD marker OPE7.1C, 2.0cM distant from the Avr4/6 locus. Three overlapping cosmids were isolated which included genetic markers that flank the Avr4/6 locus. The chromosome walk spanned a physical distance of 67kb which represented a genetic map distance of 22.3cM, an average recombination frequency of 3.0kb/cM and 11.7-fold greater than the predicted average recombination frequency of 35.3kb/cM for the entire P. sojae genome. Six genes (cDNA clones) expressed from the Avr4/6 genomic region encompassed by the cosmid contig were identified. Single nucleotide polymorphisms and restriction fragment length polymorphisms showed these six genes were closely linked to the Avr4/6 locus. Physical mapping of the cDNA clones within the cosmid contig made it possible to deduce the precise linkage order of the cDNAs. None of the six cDNA clones appear to be candidates for Avr4/6. We conclude that two of these cDNA clones flank a physical region of approximately 24kb and 4.3cM that appears to include the Avr4/6 locus.

Algal Proteins↗

PubMed2003

A MAGE/NDN-like gene in zebrafish.

The human necdin/MAGE gene family has over 50 members, but most of the proteins encoded by these genes are of unknown function. We have now identified a single locus in Danio rerio that encodes a putative protein with significant coding sequence similarity to the mammalian NDN/MAGE genes. Analysis of the complete Fugu ribripes genome sequence also suggests that there is only a single MAGE-like gene in teleost fish. mage is expressed in the larval and adult brain, specifically the retina, the medial region of the telencephalon, periventricular gray zone of the optic tectum, and most highly in the cerebellar corpus. The discovery of a zebrafish NDN/MAGE gene expressed the developing brain facilitates studies of the MAGE homology domain in vertebrate development.

Amino Acid Sequence↗

PubMed2000

A likelihood-based extended admixture model of oligogenic inheritance in 'model-based' and 'model-free' analysis.

The admixture test of linkage heterogeneity is the most often and most successfully applied oligogenic-model linkage and/or LD analysis method. Full two-locus model linkage analysis is possible, but can be computationally intensive and difficult to interpret because of the need to specify so many indeterminate parameters. A novel, computationally efficient method is proposed for combining single locus lod scores which can allow for varying degrees of epistatic interaction. This method can be applied to two-point or multipoint (using complex-valued recombination fractions) linkage and/or linkage disequilibrium analysis to jointly test for multiple unlinked disease loci. Unlike the traditional admixture test, this algorithm permits joint analysis of multiple disease loci with different modes of inheritance for each, and can be applied to 'model-free' analysis as well through the use of 'pseudomarkers'. Software is available for computation of the various likelihood ratio tests described, for comparison of a variety of possible hypotheses regarding locus homogeneity, locus heterogeneity, and epistasis.

Algorithms↗

PubMed1998

Cloning of two loci for synapse protein Snap25 in zebrafish: comparison of paralogous linkage groups suggests loss of one locus in the mammalian lineage.

Synaptosome-associated protein of 25 kDa (Snap25) is an intracellular protein that is defined as a target receptor for synapse vesicles prior to neurotransmitter release. Snap25 is highly conserved, with 61% identity between human and Drosophila melanogaster. Whereas mammals and chicken have a single locus for Snap25, the tetraploid goldfish has at least three loci. We report that the zebrafish has two loci with 91% amino acid identity to each other. The alternative splicing of exon 5 arose before the gene duplication. The expression patterns of the two loci are virtually identical in adult zebrafish. The two zebrafish snap25 loci are located in paralogous linkage groups that seem to correspond to human chromosome 20, which harbors the SNAP locus, and human chromosome 14. Because no additional Snap25 homologue has been reported for any mammal or chicken, snap25.2 may have been lost in the amniote or even tetrapod lineage.

Amino Acid Sequence↗

PubMed1985

Interaction of selection and biased gene conversion in a multigene family.

A model of the evolutionary dynamics of a multigene family in a finite population under the joint effects of selection and (possibly biased) gene conversion is analyzed. It is assumed that the loss or fixation of a polymorphism at any particular locus in the gene family occurs on a much faster time scale than the introduction of new alleles to a monomorphic locus by gene conversion. A general formula for the fixation of a new allele throughout a multigene family for a wide class of selection functions with biased gene conversion is given for this assumption. Analysis for the case of additive selection shows that (i) unless selection is extremely weak or bias is exceptionally strong, selection usually dominates the fixation dynamics, (ii) if selection is very weak, then even a slight conversion bias can greatly alter the fixation probabilities, and (iii) if both selection and conversion bias are sufficiently small, the substitution rate of new alleles throughout a multigene family is approximately the single locus mutation rate, the same result as for neutral alleles at a single-copy gene. Finally, I analyze a fairly general class of underdominant speciation models involving multigene families, concluding for these models under weak conversion that although the probability of fixation may be relatively high, the expected time to fixation is extremely long, so that speciation by "molecular drive" is unlikely. Furthermore, speciation occurs faster by fixing underdominant alleles of the same effect at single-copy genes than by fixing the same number of loci in a single multigene family under the joint effects of selection, conversion, and drift.

Alleles↗

PubMed1981

The polymorphism and structural homology of storage polypeptides (hordein) coded by the Hor-2 locus in barley (Hordeum vulgare L).

Two-dimensional mapping (isoelectric focusing followed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis) of the polypeptide components of "B" hordein fractions from eight barley varieties of widely different ancestry has been carried out. The relative positions of 47 different polypeptides were mapped, there being between 8 and 16 present in any one variety. The individual polypeptides differed in their distribution patterns; some were present in a number of varieties, while others were restricted to one or two. They also differed in their relative contributions to the total hordein fraction, both within and between varieties. The structural homology of the major polypeptides was compared by cleavage at methionine residues with cyanogen bromide and separation of the peptides on gradient gels. The polypeptides were classified into three groups which gave cleavage patterns with either two (class I), four (class II), or five (class III) low molecular weight bands. Class III polypeptides were found in all eight varieties, but in seven of the varieties class I or class II polypeptides were also present. With one exception, polypeptides migrating in the same position in different varieties gave identical or almost identical patterns. The three classes of polypeptides showed different distributions on the two-dimensional gels. Classes II and III polypeptides had a similar range of isoelectric points (pH 6.5-8.0), but all of the class II polypeptides were of slightly lower molecular weight. Class I polypeptides had a wider range of pI and molecular weight; the most alkaline and the lowest molecular weight polypeptides were in this group. The hordein fractions from a number of other barley varieties were compared with that of Julia. All had major polypeptides which migrated with ones present in Julia, but they differed in the relative amounts of these and in the absence of some polypeptides and the presence of others. B hordein is coded for by a single locus which has been suggested to be a complex multigenic family derived by duplication and divergence of a single gene. The data reported here provide support for this hypothesis and suggest that both mutations in the duplicated genes and recombination within the locus may have contributed to the polymorphism of the polypeptides.

Chromosome Mapping↗

PubMed2005

Analysis of genes for alcoholism using two-disease-locus models.

Using model-based two-locus methods for mapping genes, we analyzed the family data from the Collaborative Study on the Genetics of Alcoholism. Microsatellite data from 143 families ascertained through having three or more individuals affected with alcohol dependence were used for this investigation. Four regions showing evidence for linkage were identified using single-locus models from previous investigations. We investigated the genetic linkage, pattern of disease inheritance, and pair-wise genetic epistasis of these loci using the TLINKAGE program for two-disease-locus analysis.

Alcoholism↗

PubMed1986

Steroid 21-hydroxylase deficiency and the major histocompatibility complex.

Steroid 21-hydroxylase (21-OHase) deficiency is an HLA-linked recessive disorder of cortisol biosynthesis that can occur in several forms which differ in severity. Because they are in genetic linkage disequilibrium with different HLA antigens, the inheritance of these forms is consistent with the existence of several alleles at a single locus. When severe 21-OHase deficiency occurs in association with the HLA haplotype A3;Bw47;DR7, there is a simultaneous null allele at one of the C4 loci. This was hypothesized to result from a single deletion or rearrangement affecting the 21-OHase and C4 loci and perhaps the HLA-B gene as well. To test this hypothesis and identify the 21-OHase gene, a cDNA clone was isolated that encoded the cytochrome P450 specific for steroid 21-hydroxylation in the bovine adrenal gland. This clone hybridized to two genes in normal human DNA, but to only one gene in DNA from an individual homozygous for A3;Bw47;DR7. All individuals heterozygous for A3;Bw47;DR7 carry a heterozygous deletion of a cytochrome P450 gene. Cosmid clones have been used to locate the 21-OHase genes both in man and mouse. In both species, there are two 21-OHase genes each located immediately 3' of one of the two C4 genes, and oriented in the same direction as the C4 genes. In man, the gene located 3' of the C4B gene is deleted in 21-OHase deficiency on the Bw47 haplotype, but the gene 3' of the C4A gene is deleted in hormonally normal individuals on the A1;B8;C4AQ0, C4B1;DR3 haplotype. Thus the 21-OHase B gene is normally active in man, but the 21-OHase A gene is not.

Adrenal Hyperplasia, Congenital↗

PubMed1997

Host specificity, evolutionary relationships and macrogeographic differentiation among Ascaris populations from humans and pigs.

We describe a variety of restriction site polymorphisms in the introns of Ascaris nuclear genes and in the ribosomal DNA spacers. We use these markers, in addition to previously described mitochondrial variation, to clarify our understanding of the epidemiology of Ascaris in Guatemalan villages where humans and pigs occur in sympatry and to describe the genetic structure of host-associated Ascaris populations from world-wide locations. Intron sequences were amplified from individual worms and alleles defined by endonuclease digestion. Two loci were monomorphic, while 4 length variants and 22 point mutations were detected in the other 7 loci. Within sympatric Guatemalan populations no single locus from either the nuclear or mitochondrial genome was fixed for alternative alleles, although allele frequencies were significantly different at many loci. Phenograms constructed from multilocus nuclear genotypes of individual worms failed to reveal a single case of cross-infection, and demonstrate that divergent mtDNA genotypes are segregating within host-associated populations. On a world-wide scale, the data suggest that extant worm populations result from a single host shift, although characterization of genetic variation in additional loci will be necessary to confirm this. The direction and the geographical origin of the host shift were unresolved. Overall 65% of nuclear genetic variation was found within populations, host (human or pig) explained 18%, while geographical variation within host-associated populations explained 17%. The results (a) demonstrate the utility of introns for studying the epidemiology of parasites showing limited allozyme variation (b) suggest that programmes aiming to control Ascaris infection in the human population can safely ignore zoonotic infection from pigs and (c) illustrate the problems inherent in using single genetic markers to make inferences about the epidemiology of closely related parasite taxa.

Animals↗

PubMed1985

Adrenal 21-hydroxylase cytochrome P-450 genes within the MHC class III region.

Genes encoding several serum complement components and the gene(s) for steroid 21-hydroxylase (21-OH) have been located in the class III region of the major histocompatibility complex (MHC). All these genes are highly polymorphic in man, and these polymorphisms have been used to draw conclusions about the structure and function of these genes. For example, electrophoretic polymorphisms of the fourth component of complement (C4) have been shown to be controlled by two closely linked genes, which also control expression of the red cell antigens Rodgers and Chido. Steroid 21-OH deficiency (D) can occur in several forms which differ in severity, and because of genetic linkage disequilibrium with different HLA antigens the inheritance of these forms is consistent with the existence of several alleles at a single locus. When severe 21-OH D occurs in association with the HLA haplotype A3;Bw47;DR7, there is a simultaneous null allele at one of the C4 loci. This was hypothesized to result from a single deletion or rearrangement affecting the 21-OH and C4 loci and perhaps the HLA-B gene as well. To test this hypothesis and identify the 21-OH gene, a cDNA clone was isolated which encoded the cytochrome P450 specific for steroid 21-hydroxylation in the bovine adrenal gland. This clone hybridized to two genes in normal human DNA, but to only one gene in DNA from an individual homozygous for A3;Bw47;DR7. All individuals heterozygous for A3;Bw47;DR7 carry a heterozygous deletion of a gene. These experiments showed that at least one structural gene for the cytochrome P450 specific for 21-hydroxylation is located in the MHC, probably very near the C4 genes, and a mutation in this gene results in 21-OH D. Cosmid clones have been used to locate the 21-OH genes both in man and mouse. In both species, there are two 21-OH genes, each located immediately 3' of one of the two C4 genes, and oriented in the same direction as the C4 genes. In man, the gene located 3' of the C4B gene is deleted in 21-OH D on the Bw47 haplotype, but the gene 3' of the C4A gene is deleted in hormonally normal individuals on the A1;B8;C4AQO;C4B1;DR3 haplotype. Thus the 21-OH B gene is normally active in man, but the 21-OH A gene is not.

Adrenal Glands↗

PubMed1985

Cystic fibrosis locus defined by a genetically linked polymorphic DNA marker.

A polymorphic DNA marker has been found genetically linked, in a set of 39 human families, to an autosomal recessive gene that causes cystic fibrosis (CF), a disease affecting one in 2000 Caucasian children. The DNA marker (called D0CRI-917) is also linked to the PON locus, which by independent evidence is linked to the CF locus. The best estimates of the genetic distances are 5 centimorgans between the DNA marker and PON and 15 centimorgans between the DNA marker and the CF locus, meaning that the location of the disease gene has been narrowed to about 1 percent of the human genome (about 30 million base pairs). Although the data are consistent with the interpretation that a single locus causes cystic fibrosis, the possibility of genetic heterogeneity remains. The discovery of a linked DNA polymorphism is the first step in molecular analysis of the CF gene and its causative role in the disease.

Aryldialkylphosphatase↗

PubMed1990

Genetic relationships among strains of avian Escherichia coli associated with swollen-head syndrome.

Genetic diversity among 22 Escherichia coli strains isolated from chickens with swollen-head syndrome (SHS), an acute respiratory disease of domestic poultry, and 93 strains isolated from birds with colibacillosis was assessed on the basis of allelic variation at 20 enzyme-encoding loci detected by multilocus enzyme electrophoresis. SHS isolates from Spain and Canada were polymorphic at 14 loci and were classified into 19 multilocus genotypes, defining clones that differed on average at 34% of the loci. In most cases, SHS isolates of different clonal genotypes were distinct in O:H serotype and expressed different fimbrial antigens. Comparisons with 93 isolates obtained from birds with colibacillosis revealed enzyme polymorphisms at 17 of 20 loci, with an average of 3.5 alleles per locus. In the total sample, 56 clonal genotypes were distinguished, with 27 (23%) of the isolates belonging to one of three common clones. Both SHS and colibacillosis isolates were genetically diverse, with an average single-locus diversity of 0.36, indicating that a wide variety of naturally occurring bacterial clones is associated with these acute avian infections. Six previously defined groups of clones identified in diseased birds from the United States were represented in isolates from Spain, indicating that similar clones occur in widely separated geographic areas. In addition, one group of SHS isolates was closely related to a recognized widespread clone complex incriminated in human septicemia and meningitis. The results suggest that certain strains implicated in SHS infections belong to a clone complex whose members have special attributes that promote involvement in invasive diseases in humans and animals.

Alleles↗

PubMed1984

The occurrence of the alpha G-Philadelphia-globin allele on a double-locus chromosome.

Hb G-Philadelphia, an alpha-globin allele, is expressed as either 20%, 30%, or 40% of the total hemoglobin. Restriction analyses published thus far have shown that among persons with 30% and 40% hemoglobin (Hb) G the alpha G allele is seen only in a single-locus haplotype. We now report the identification of a second haplotype in which the alpha G allele is found in tandem with an alpha A allele. This haplotype has been found present in DNA from the members of one family in which Hb G is expressed as 20% of the total hemoglobin, determined by both cellulose acetate electrophoresis and high-performance liquid chromatography (HPLC). Synthesis was balanced in all individuals. The identification of a variant alpha-globin allele in two distinct haplotypes presents the possibility of independent mutation. However, an alternative explanation cannot be ruled out; namely, that the original allele may have become distributed among the two haplotypes by unequal crossing-over.

Alleles↗

PubMed1987

The use of measured genotype information in the analysis of quantitative phenotypes in man. II. The role of the apolipoprotein E polymorphism in determining levels, variability, and covariability of cholesterol, betalipoprotein, and triglycerides in a sample of unrelated individuals.

Recent advances in molecular biology provide measures of genotypes at loci involved in lipid metabolism. Genotypes for apolipoprotein E (apo E) and quantitative levels of total plasma cholesterol, betalipoprotein, and triglycerides were measured in a sample of 223 unrelated individuals from Nancy, France. The frequencies of the epsilon 2, epsilon 3, and epsilon 4 alleles are 0.13, 0.74, and 0.13, respectively, in this sample. Significant differences among apo E genotypes were detected for these lipoprotein phenotypes. The average effect of the epsilon 2 allele was to reduce total plasma cholesterol and betalipoprotein levels by 0.52 mmol/L and 0.98, respectively, while the epsilon 4 allele raised these levels by 0.26 mmol/L and 0.61, respectively. Apo E genotype specific correlations suggest that this locus also has an effect on the coordinated metabolism between cholesterol and triglycerides. We infer that approximately 17% of the genetic variability in total plasma cholesterol may be attributable to this apo E polymorphism. No other single locus has been identified with such a large contribution to cardiovascular disease risk factors in the general population.

Alleles↗

PubMed1994

Genetic markers for the Booroola fecundity (Fec) gene in sheep.

Animals from the Booroola line of Australian Merino sheep are characterized by a high ovulation rate that can be attributed to the presence of a codominant allele (FecB). The specific function of the gene has not been identified. Effective use of the trait within the sheep breeding industry requires one or more genetic markers that can distinguish between alternative alleles at the locus Fec. With a combination of DNA minisatellite markers and polymorphic protein markers, a cluster of seven minisatellite fragments has been identified as being linked to the Fec gene and to the ovine A blood group locus. The minisatellite fragments have been derived from multilocus probes and hence cannot be used to define the chromosomal location of the Fec gene or to serve as diagnostic markers for Fec. The derivation of cloned single locus markers from the minisatellite fragments will enable finer scale mapping of the Fec and the A blood group locus in sheep.

Animals↗

PubMed2003

Frequent microsatellite alterations in a predominantly younger age of onset breast cancer population.

Microsatellite instability (MSI) and loss of heterozygosity (LOH) was investigated in paired tumour and normal tissue DNA from 108 predominantly premenopausal breast cancer patients (under age 45 years at presentation) for 25 simple repeat loci interspersed across 11 chromosomes. MSI was observed at a single locus in 69 (64%) patients; 41 of these had instability at more than one site. Greatest frequency of MSI was at loci D2S1356 (33%), D2S2739 (22%), D3S1766 (21%) and D13S796 (20%). LOH was seen at a single site in 55% of patients and at two or more sites in 27 patients with greatest frequency at D2S1356 (33%), D2S443 (19%) and D17S1299 (18%). Both mutations were found in the same patient but at different loci. Clearly, choice of loci is a determining factor in assessing genomic instability. The relatively high frequency of MSI may also reflect peculiarities of this younger patient population. Occurrence of MSI or LOH was unrelated to clinical stage, nodal status, tumour size or grade or steroid receptor status. It was independent of mutations detected in exons 5-9 of the p53 gene. There was no significant association with survival. The lack of such correlations reflects a random disabling mechanism that may equally affect genes promoting cell death as well as growth.

Adult↗

PubMed2000

[Genetic structure of geographically different populations of candida albicans].

Codominant single-locus markers were developed by amplifying genomic DNA of C. albicans with pairs of random primers. Monomorphic PCR products were screened for polymorphisms by the SSCP technique. Sequencing confirmed that SSCP's were mostly due to single nucleotide substitutions in the polymorphic fragments. A total of 85 polymorphic loci were observed within 13 PCR fragments. Populations from Africa displayed less genotype variation than the populations from Europe and USA. Two genetically similar African C. albicans populations exhibiting an atypical biotype were strictly clonal and perhaps represent a geographically distributed clone. Analyses of "typical" C. albicans populations of different geographical origin provided however evidence for both clonality and recombination. Evidence for clonality was supported by the absence of segregation genotypes, and by deviation of genotypic frequencies from Hardy-Weinberg expectations. Tests for nonrandom association of alleles across loci revealed less evidence for linkage disequilibrium than expected for strictly clonal populations. Although all C. albicans populations tested were primarily clonal, evidence for recombination suggests that sexual reproduction or some other form of genetic exchange occurs in this species.

Africa↗