Genetic polymorphism of adenosine deaminase and mannose phosphate isomerase in blood of arctic foxes, Alopex lagopus

Blood samples of 70 foxes, including 10 families, have been investigated by horizontal starch gel electrophoresis for the enzymes adenosine deaminase (ADA) and mannose phosphate isomerase (MPI). The observed variation of the enzymes could be explained as a result of one locus with two codominant alleles and one with three respectively. The segregation in the families of the alleles assumed for the two loci is in accordance with this genetic model. The frequency of the two alleles at the Ada locus is about the same and the slowest anodic migrating allele at the Mpi locus is the most frequent.     

Allelic Variants at the Xanthine Dehydrogenase Locus Affecting Enzyme Activity in DROSOPHILA PSEUDOOBSCURA

Quantitative studies of enzyme activity on gels show about four-fold differences in enzyme activity of different xanthine dehydrogenase (XDH ) alleles. At least three different activity classes could be distinguished among the 23 strains isogenic for the XDH locus. No association of high activity with the high frequency electromorph was observed; instead, the low frequency electromorphs had 0.5 to 2 times the activity of the high frequency electromorph. The frequency of low activity, high activity and intermediate activity XDH alleles among these 23 lines is 0.13, 0.09, and 0.78, respectively.     

凡纳滨对虾微卫星位点在两个选育家系中遗传的初步研究

利用两个选育凡纳滨对虾全同胞家系研究了10个微卫星位点的遗传特征。通过ABI310或3100测序仪检测, 在所观察到的20个基因型比例（genotypic ratios）(10个微卫星位点 X 2个家系)中,有17个基因型比例符合孟德尔遗传。微卫星位点TUMXLv8.220在两个家系中均存在无效等位基因,从而3个不符合孟德尔遗传基因型中2个可由无效等位基因来解释。TUMXLv 3.1在06家系偏离了1：1：1：1的孟德尔预期比。3个微卫星位点（TUMXLv5.66,TUMXLv7.74,TUMXLv8.224）在两个家系中均表现单态。3个微卫星位点（TUMXLv5.45,TUMXLv7.56,TUMXLv8.256）在两个家系均既表现多态又遵循孟德尔共显性遗传, 是亲子鉴定和种群遗传分析的较好选择。结果显示在应用微卫星标记进行遗传分析之前利用全同胞家系进行遗传模式研究是非常必要的。     

An allelic series for the chalcone synthase locus in Arabidopsis

Five new alleles of the Arabidopsis chalcone synthase (CHS) locus, tt4, have been characterized at the gene, protein, and end product levels as a genetic approach to understanding structure-function relationships in a key enzyme of plant secondary metabolism. Together with two previously described mutants, these tt4 lines represent one of the first allelic series for a central enzyme of the flavonoid pathway and include both null alleles and alleles with leaky, apparently temperature-sensitive, phenotypes. A variety of effects on accumulation of CHS protein and flavonoid glycosides were observed among these lines, including alterations in the apparent stability and activity of the enzyme. Assembly of the CHS homodimer also appeared to be impacted in several cases. A three-dimensional model of the Arabidopsis CHS protein, based on the recently determined structure for alfalfa CHS, predicts significant effects on protein structure or folding for several of the mutations. This allelic series should provide a useful genetic resource for ongoing studies of flavonoid enzyme structure, function, and subcellular organization.     

Detecting linkage for genetically heterogeneous diseases and detecting heterogeneity with linkage data.

Interest in searching for genetic linkage between diseases and marker loci has been greatly increased by the recent introduction of DNA polymorphisms. However, even for the most well-behaved Mendelian disorders, those with clear-cut mode of inheritance, complete penetrance, and no phenocopies, genetic heterogeneity may exist; that is, in the population there may be more than one locus that can determine the disease, and these loci may not be linked. In such cases, two questions arise: (1) What sample size is necessary to detect linkage for a genetically heterogeneous disease? (2) What sample size is necessary to detect heterogeneity given linkage between a disease and a marker locus? We have answered these questions for the most important types of matings under specified conditions: linkage phase known or unknown, number of alleles involved in the cross at the marker locus, and different numbers of affected and unaffected children. In general, the presence of heterogeneity increases the recombination value at which lod scores peak, by an amount that increases with the degree of heterogeneity. There is a corresponding increase in the number of families necessary to establish linkage. For the specific case of backcrosses between disease and marker loci with two alleles, linkage can be detected at recombination fractions up to 20% with reasonable numbers of families, even if only half the families carry the disease locus linked to the marker. The task is easier if more than two informative children are available or if phase is known. For recessive diseases, highly polymorphic markers with four different alleles in the parents greatly reduce the number of families required.     

Polymorphism, genetic stability, and autosomal location of trimeric nucleoside phosphorylase in Peromyscus eremicus cell lines.

Nucleoside phosphorylase (NP: EC 2.4.2.1) has not been demonstrated to be an extensively polymorphic enzyme locus in mammals. We have studied NP electrophoretically in five independently derived cell lines established from Peromyscus eremicus as well as in various tissues of a sixth animal. Four different NP phenotypes involving three different alleles were resolved. The data suggest that (1) the enzyme is trimeric and its genetic locus is polymorphic in P. eremicus, (2) heterozygous enzyme phenotypes are stable during long-term culture, and (3) the enzyme locus is autosomal in Peromyscus.     

Origins of polymorphism at a polypurine hypervariable locus.

We present characterisation of a hypervariable locus, D8S210, mapped to the telomeric region of the short arm of chromosome 8. The locus is highly polymorphic with alleles varying in size from 1.8 kb to 24 kb. Sequence data from 7 alleles shows that the variable region is entirely polypurine on one strand with a tetranucleotide repeating unit GGAA at the margins and diverged versions of this motif internally. The margins are conserved between alleles; polymorphism occurring in the internal regions of the repeat. Alleles are inherited in a Mendelian manner and one new mutation has been observed in analysis of 51 meioses. Use of single copy flanking sequences to elaborate the polymorphism revealed loss of single copy DNA in 3 unrelated families and in 2 other unrelated individuals. Restriction mapping shows that this loss is similar for different sized alleles in all three families suggesting that it was an early event that may have involved a flanking Alu sequence. We present evidence that the polypurine region can adopt triplex conformations in vitro. Such structures may facilitate loss or gain of unique sequences in the genome, contribute to mutation at conformation transition points and drive the hypervariability (> 99% heterozygosity) of this locus.     

Linkage studies between the halothane (Hal), phosphohexose isomerase (Phi) and the S(A -O) and H red blood cell loci of Pietrain/ Hampshire and Landrace pigs

Frequency of blood group factors at the A-O and H loci were markedly altered within halothane positive (HP) and halothane negative (HN) composite synthetic Pietrain/Hampshire lines (PTH) over four generations of selection.
Linkage studies on the litters from 45 double backcross and 20 mixed and intercross matings, involving the S(A-O), H, Phi and Hal loci, were made in the PTH line and halothane positive and negative selected British Landrace lines. Crossing-over frequencies of 0.05 ± 0.04, 0.05 ± 0.03 and 0.1 ± 0.03 were established between Phi and Hal, H and Hal , and Phi and H respectively. An unequal crossing-over frequency between Phi and H was found when the alleles Ha and Hcd were compared. The difference in recombination frequency between the Ha and Hcd alleles amounted to 0.04 to 0.06.
No cross-overs were observed between the S(A -O ) and Phi, H or Hal loci in 15 families studied. The position of the S locus in relation to the other loci could not be established, but statistical evidence of association favours a haplotype sequence of Phi-Hal-S-H .     

Evolution of primate ABO blood group genes and their homologous genes

There are three common alleles (A, B, and O) at the human ABO blood group locus. We compared nucleotide sequences of these alleles, and relatively large numbers of nucleotide differences were found among them. These differences correspond to the divergence time of at least a few million years, which is unusually large for a human allelic divergence under neutral evolution. We constructed phylogenetic networks of human and nonhuman primate ABO alleles, and at least three independent appearances of B alleles from the ancestral A form were observed. These results suggest that some kind of balancing selection may have been operating at the ABO locus. We also constructed phylogenetic trees of ABO and their evolutionarily related alpha-1,3- galactosyltransferase genes, and the divergence time between these two families was estimated to be roughly 400 MYA.      

The tyrosinase-positive oculocutaneous albinism gene shows locus homogeneity on chromosome 15q11-q13 and evidence of multiple mutations in southern African negroids.

Tyrosinase-positive oculocutaneous albinism (ty-pos OCA) is an autosomal recessive disorder of the melanin pigmentary system. South African ty-pos OCA individuals occur with two distinct phenotypes, with or without darkly pigmented patches (ephelides, or dendritic freckles) on exposed areas of the skin. These phenotypes are concordant within families, suggesting that there may be more than one mutation at the ty-pos OCA locus. Linkage studies carried out in 41 families have shown linkage between markers in the Prader-Willi/Angelman syndrome (PWS/AS) region on chromosome 15q11-q13 and ty-pos OCA. Analysis showed no obligatory crossovers between the alleles at the D15S12 locus and ty-pos OCA, suggesting that the D15S12 locus is very close to or part of the disease locus, which is postulated to be the human homologue, P, of the mouse pink-eyed dilution gene, p. Unlike caucasoid "ty-pos OCA" individuals, negroid ty-pos OCA individuals do not show any evidence of locus heterogeneity. Studies of allelic association between the polymorphic alleles detected at the D15S12 locus and ephelus status suggest that there was a single major mutation giving rise to ty-pos OCA without ephelides. There may, however, be two major mutations causing ty-pos OCA with ephelides, one associated with D15S12 allele 1 and the other associated with D15S12 allele 2. The two loci, GABRA5 and D15S24, flanking D15S12, are both hypervariable, and many different haplotypes were observed with the alleles at the three loci on both ty-pos OCA-associated chromosomes and "normal" chromosomes.(ABSTRACT TRUNCATED AT 250 WORDS)     

Length and sequence variation in the apolipoprotein B intron 20 Alu repeat.

We have developed a single-stranded conformation polymorphism (SSCP) protocol for typing both sequence and length variations in an Alu element located in intron 20 of the human apolipoprotein B (apo B) gene. Using the polymerase chain reaction (PCR), we simultaneously amplified and isotopically labeled the apo B intron 20 Alu. The Alu tail, which is composed of two arrays of variable numbers of tandem repeats, (TTTX)y (X = A or G) and (T)z, was separated from the rest of the PCR product by restriction enzyme digestion with PstI. Length variation in the Alu tail (IN20-REP) was thus separated from sequence variation in the Alu body (IN20-SEQ), rendering the SSCP patterns both eaiser to interpret and more informative. In a sample of 242 unrelated individuals from Nancy, France, we observed 11 SSCP alleles at the IN20-SEQ locus that differed only in sequence. At the IN20-REP locus, we observed 7 alleles that differed in both sequence and length. All alleles at both loci were subcloned and sequenced. One additional allele that did not undergo a detectable mobility shift in SSCP gels was uncovered at each locus during sequencing of the SSCP alleles. The additional IN20-SEQ allele was typed by restriction enzyme digestion. Although the number of IN20-SEQ and IN20-REP alleles was large, most were uncommon; the three most common alleles at each locus represented more than 94% of those sampled. We also typed the children of the 242 unrelated French individuals, enabling verification of the Mendelian segregation of the two loci and construction of haplotypes.(ABSTRACT TRUNCATED AT 250 WORDS)     

Phenotypes of Phosphoglucose isomerase,phosphoglucose mutase and general protein in some freshwater molluscs from Basrah,Iraq

Electrophoretic variants of phosphoglucose isomerase (EC.5.3.1.9) and phosphoglucose mutase (EC.2.7.5.1) have been studied in eight species of freshwater molluscs. Two phenotypes of phosphoglucose isomerase were observed in Melanopsis nodosa and one phenotype was observed in the rest of the species. One phenotype of phosphoglucose mutase was observed in all the species of molluscs studied. Phosphoglucose isomerase is inferred to be a dimer encoded at a single polymorphic locus in Melanoides nodosa. There are two alleles at this locus. Phosphoglucose mutase is inferred to be a monomer encoded at a single monomorphic locus in all species. The electrophoretic analysis revealed that phosphoglucose isomerase enzyme cannot be considered a good taxonomic criterion to differentiate the different members of the six families studied but, on the other hand, it is considered a good taxonomic criterion to differentiate Melanopsis nodosa and Theodoxus jordani. Phosphoglucose mutase is considered a good taxonomic criterion to differentiate the family Melanidae from the remaining five families studied. General protein can be considered a good taxonomic criterion to differentiate the family Corbicullidae from Melanidae, Viviparidae and Neritidae but, on the other hand, it seems to be a less useful taxonomic criterion to differentiate between the Viviparidae and Neritidae.     

Identification, Inheritance, and Variation of Microsatellite Markers in the Black Scallop Mimachlamys varia

Five polymorphic microsatellite loci were identified in the black scallop Mimachlamys varia after construction of a genomic library enriched for (GT)n. To examine the transmission pattern of microsatellite alleles, several families were created and genotypes scored for three loci. The expected Mendelian ratios were found in 12 of 14 segregations examined. Unexpected segregations may be explained by a genotyping error (allelic dropout), given that when a specific allele was treated as dominant, the phenotypic ratios conformed to Mendelian expectations. The five loci were also examined in two samples from the Spanish coast. The two localities displayed similar mean values for the number of alleles per locus (7.2-8.4), allelic richness (7.2-7.9), and observed (0.389-0.484) and expected heterozygosity (0.545-0.618). Significant Hardy-Weinberg deviations were observed at three loci, with heterozygote deficiency occurring in all cases. Global multilocus θ value and allele frequencies at one locus revealed significant differentiation between the two localities.     

Genetics of alcohol dehydrogenase and aldehyde dehydrogenase from Monodelphis domestica cornea: further evidence for identity of corneal aldehyde dehydrogenase with a major soluble protein

A didelphid marsupial, the gray short-tailed opossum (Monodelphis domestica), was used as a model species to study the biochemical genetics of alcohol dehydrogenases (ADHs) and aldehyde dehydrogenase (ALDH) in corneal tissue. Isoelectric point variants of corneal ALDH (designated ALDH3) and a major soluble protein in corneal extracts were observed among eight families of animals used in studying the genetics of these proteins. Both phenotypes exhibited identical patterns following PAGE-IEF and were inherited in a normal Mendelian fashion, with two alleles at a single locus (ALDH3) showing codominant expression. The data provided evidence for genetic identity of corneal ALDH with this major soluble protein, and supported biochemical evidence, recently reported for purified bovine corneal ALDH, that this enzyme constitutes a major portion of soluble corneal protein (Abedinia et al. 1990). Isoelectric point variants for corneal ADH were also observed, with patterns for the two major forms (ADH3 and ADH4) and one minor form (ADH5) being consistent with the presence of two ADH subunits (designated gamma and delta), and variant phenotypes existing for the gamma subunit. The genetics of this enzyme was studied in the eight families, and the results were consistent with codominant expression of two alleles at a single locus (designated ADH3). It is relevant that a major detoxification function has been proposed for corneal ADH and ALDH, in the oxidoreduction of peroxidic aldehydes induced by available oxygen and UV-B light (Holmes & VandeBerg, 1986a). In addition, a direct role for corneal ALDH as a UV-B photoreceptor in this anterior eye tissue has also been proposed (Abedinia et al. 1990).     

The anonymous PAS45 probe detects RFLPs in 13q31

An anonymous DNA probe PAS45 was isolated. This probe detects an RFLP with two alleles 1 and 2 at the same locus, with the different restriction enzymes (Bg1II, EcoRI, HindIII, PstI, MspI, XbaI). The observed polymorphism is explained by a chromosome rearrangement involving these enzyme cleavage sites. The frequency of alleles 1 and 2 was 0.875 and 0.125, respectively, in a sample of 48 unrelated individuals in France. Codominant inheritance of alleles 1 and 2 was demonstrated in 13 families with 30 offspring. The PAS45 probe was localized on chromosome 13 by somatic cell hybrid analysis and on 13q31 by in situ hybridization. The rearrangement on 13q31 is present in one out of four healthy individuals in France.     

PCR-RFLP typing of the bovine myoglobin gene

We have identified substitutions in the 3₁ untranslated region of the bovine myoglobin gene, one of which affects an MboII restriction enzyme site resulting in a bi-allelic restriction fragment length polymorphism. Co-dominant inheritance of the alleles in three reference families was observed using a polymerase chain reaction—restriction fragment length polymorphism assay. The distribution of the alleles seems characteristic of cattle type—one of the alleles was not detected in purely taurine breeds. Furthermore, we mapped, using the polymerase chain reaction on a bovine–rodent somatic cell hybrid panel, the myoglobin gene to bovine chromosome five. It is therefore syntenic with γ-interferon and insulin-like growth factor in which we have not found polymorphism. The myoglobin locus therefore serves as a type one marker on bovine chromosome five.     

Haplotype analysis of phenylalanine hydroxylase alleles in polish families with phenylketonuria

Eight polymorphic restriction enzyme sites at phenylalanine hydroxylase locus from the parental chromosomes in Polish families with phenylketonuria were analyzed. Among 28 chromosomes studied, we identified haplotypes found within the Danish population. Haplotype 2 has been found in 25% of affected alleles. One of the patients studied is homozygous for this haplotype.     

Partial deletion of the beta-globin gene: a common beta-thalassaemia allele in Asian Indians

We have examined 11 families of Asian Indian origin, who are segregating beta-thalassaemia alleles, for coupled restriction enzyme site markers. A beta-thalassaemia deletion allele, which removes over 600 base pairs, is a common cause of thalassaemia in this population. This deletion can be conveniently detected in AvaII restriction enzyme digests. Consequently AvaII digests are particularly informative in this population because both the deletion and a coupled restriction site polymorphism may be simultaneously observed.     

Evidence that the penetrance of mutations at the RP11 locus causing dominant retinitis pigmentosa is influenced by a gene linked to the homologous RP11 allele.

A subset of families with autosomal dominant retinitis pigmentosa (RP) display reduced penetrance with some asymptomatic gene carriers showing no retinal abnormalities by ophthalmic examination or by electroretinography. Here we describe a study of three families with reduced-penetrance RP. In all three families the disease gene appears to be linked to chromosome 19q13.4, the region containing the RP11 locus, as defined by previously reported linkage studies based on five other reduced-penetrance families. Meiotic recombinants in one of the newly identified RP11 families and in two of the previously reported families serve to restrict the disease locus to a 6-cM region bounded by markers D19S572 and D19S926. We also compared the disease status of RP11 carriers with the segregation of microsatellite alleles within 19q13.4 from the noncarrier parents in the newly reported and the previously reported families. The results support the hypothesis that wild-type alleles at the RP11 locus or at a closely linked locus inherited from the noncarrier parents are a major factor influencing the penetrance of pathogenic alleles at this locus.     

Exploiting EST databases for the development and characterization of EST-SSRs in the Pacific oyster (Crassostrea gigas)

A total of 147 microsatellite-containing expressed sequence tags (ESTs) (3.63%) were detected from 4053 ESTs of the Pacific oyster (Crassostrea gigas) in GenBank. The average density of simple sequence repeats (SSRs) was 1 per 8.25 kb of EST after redundancy elimination. Dinucleotide repeat motifs appeared to be the most abundant type. Sixteen new polymorphic EST-SSRs were developed. The number of alleles per locus varied from 3 to 12, with an average of 5.9 alleles per locus. Marker transferability was tested on 2 other Crassostrea species, and 14 loci gave successful amplifications in both species. Twenty EST-SSRs were tested on 3 families of C. gigas for examination of inheritance mode of EST-SSRs. Thirty-five tests of segregation ratios revealed 5 significant departures from expected Mendelian ratios, 4 of which confirmed Mendelian expectations when accounting for the presence of null alleles. Null alleles were detected at 3 loci (15.0%) of the 20 loci, and the frequency of null alleles at EST-SSRs was lower than that in genomic SSRs in C. gigas. The results obtained in this study suggest that C. gigas EST-SSRs will complement the currently available genomic SSR markers and may be useful for comparative mapping, marker-assisted selection, and evolutionary studies.