Molecular analysis of common aldolase B alleles for hereditary fructose intolerance in North Americans.

The diagnosis of hereditary fructose intolerance (HFI) presents a difficult challenge that often involves procedures of high risk to the patient. A relatively noninvasive method that involves molecular analysis of common alleles would offer a decided advantage. The molecular defects in the aldolase B gene were studied in 31 HFI subjects (23 pedigrees, 47 apparently independent alleles) from the United States and Canada. We screened for the three most common European alleles by direct hybridization of allele-specific oligodeoxyribonucleotides (ASOs) to portions of the aldolase B gene that were amplified by PCR. Fifty-five percent of mutant North American alleles were A149P (ala149----pro), the most common mutation in the European population. The other two alleles, A174D (ala174----asp) and N334K (asn334----lys), represent 11 and 2% of North American alleles, respectively. Nine patients, representing 32% of independent alleles studied, had an HFI allele that was not of this common missense class. This North American allele distribution is significantly different from that in Europe, where 13% of HFI alleles are not of this type. Preliminary screening of amplified DNA with this set of ASOs indicated that 80% of symptomatic HFI patients can be identified in the American population by this simple genetic test.     

A minisatellite and a microsatellite polymorphism within 1.5 kb at the human muscle glycogen phosphorylase (PYGM) locus can be amplified by PCR and have combined informativeness of PIC 0.95.

We sequenced a genomic clone (pMCMP1), previously reported to detect a VNTR polymorphism at the PYGM locus, and found a dinucleotide repeat segment (CA)14(GA)25 and a complex (AT)-repeat-rich segment containing 63 repeats spanning 160 bp. Resolution of PCR-amplified genomic DNA from the (CA)(GA) repeat region on DNA sequencing gels revealed a highly informative polymorphism with alleles differing by 2-bp intervals and ranging in size from 156 to 190 bp. Among three racial groups, a total of 18 alleles were observed. Fourteen alleles were observed in Caucasians (PIC 0.89), 12 alleles in American Blacks (PIC 0.89), and 9 alleles in Pima Indians (PIC 0.73). PCR amplification of the (AT) repeat region and resolution of the products on DNA sequencing gels revealed a complex variable length polymorphism with alleles distributed in size from 367 to 970 bp. Twenty-eight alleles were found in American Blacks (PIC 0.94), 6 alleles in Pima Indians (PIC 0.70), and 11 alleles in Caucasians (PIC 0.71). Comparison of the previously described VNTR RFLP alleles visualized by Southern hybridization to the PCR products described in this report demonstrated that the polymorphism described in both assays was identical. However, a larger number of alleles could be detected from the PCR-amplified products. Combined informativeness, PIC 0.95, for the two polymorphisms was determined from haplotype analysis of 100 Caucasian chromosomes. Therefore, for genotyping purposes, informativeness is maximized from using both polymorphisms.     

Population genetics of the highly polymorphic locus D16S7 and its use in paternity evaluation.

We have developed a DNA RFLP test to resolve paternity cases in which the accused man is included at a low probability of paternity by conventional testing. The DNA probe p79-2-23 was used to determine the allele frequency distribution for the locus D16S7 in the North American black, Caucasian, and Hispanic racial groups. Approximately 3,500 TaqI-digested DNAs were analyzed from the three populations studied. An apparent continuum of alleles was detected varying in size from 2.9 kb to 8.3 kb. Estimates of the average probability of exclusion were found to be .90 and .79 for the North American black and Caucasian populations, respectively. Gene frequency data for common and rare alleles indicated a potential paternity index ranging from 2 to 450.     

Genetic studies of human apolipoproteins. XVII: Population genetics of apolipoprotein polymorphisms in American Samoa

Variation in human apolipoprotein genes is a major source of phenotypic differences in human lipid metabolism. Data regarding genetic variation at apolipoprotein loci in various populations are only beginning to accumulate, and they suggest that different populations vary widely in distribution of apolipoprotein alleles. Using isoelectric focusing-immunoblotting techniques, we screened 67 serum samples from self-identified Samoan residents of American Samoa to investigate structural variation at six apolipoprotein loci: A-I, A-II, A-IV, C-II, E, and H. The APO A-I, A-II, and C-II loci were found to be monomorphic by isoelectrical focusing. In Samoans, the common three-allele polymorphism was observed for APO E, with no striking differences in frequencies from Caucasian populations. The three common alleles of the APO H locus also were identified; however, frequencies of the less common alleles (APO H*I and APO H*3) were different from those observed elsewhere for Caucasians.     

MICA polymorphism in South American Indians

We have studied the MICA alleles of 196 unrelated subjects from three South American Indian tribes (Toba, Wichi and Terena). They are members of isolated tribes located in the Gran Chaco area in northeastern Argentina and in Mato Grosso do Sul in South Central Brazil. Of 55 previously known alleles, nine were observed in South American Indians, compared with 16 that were found in North American Caucasians, suggesting a more restricted allelic distribution of MICA in these tribes. In South American Indians, MICA*00201 was the most frequent allele, with a gene frequency of 33% in Toba, 47% in Wichi and 44% in Terena. MICA*00201, MICA*027 (external domain sequence like MICA*008/TM allele A5) and MICA*010 accounted for more than 90% of all the MICA genes in South American Indians. In North American Caucasians, MICA*00801 (*008/A5.1) accounted for 42% of the genes and was the most common allele. We observed a high degree of linkage disequilibrium between certain alleles of MICA and of HLA-B in the South American Indian populations. Phylogenetic trees constructed using gene frequencies of the transmembrane short tandem repeats in the populations reported here, and in other populations taken from published reports, suggest that South American Indians are more closely related to Asians than to Europeans.     

Mapping the human liver/islet glucose transporter (GLUT2) gene within a genetic linkage map of chromosome 3q using a (CA)n dinucleotide repeat polymorphism and characterization of the polymorphism in three racial groups.

The human liver/islet glucose transporter (GLUT2), a candidate gene for diabetes, has been incorporated into a genetic linkage map for chromosome 3q using a (CA)n dinucleotide repeat polymorphism adjacent to the 3'-end of exon 4a. We have found a total of nine alleles ranging in length from 153 to 169 nucleotides in three racial groups and have determined the precise structure of the variable region for four of the alleles by DNA sequencing. Five alleles were found to be common to the American Black, Caucasian, and Pima Indian racial groups studied. One allele (169 bp) was unique to American Blacks, and another rare allele (153 bp) was found only in the Caucasian population studied. Observed heterozygosity of the polymorphism in the Caucasian (CEPH) reference pedigree collection is 60%, for American Blacks 71%, and for Pima Indians 53%. An independent study recently identified the same dinucleotide repeat and found six alleles in a Caucasian population (Froguel et al., 1991), a result that we confirm; however, our sequencing data indicate a different molecular structure for the polymorphism for some of the alleles. We have constructed a new genetic linkage map of chromosome 3q uniquely placing the GLUT2 gene between flanking markers D3S26 and D3S43. The genetic map consists of 23 loci (25 RFLPs and 2 (CA)n dinucleotide repeat markers) with 14 markers uniquely localized with odds of at least 1000:1. Three genes (FTHL4, TF, GLUT2) are integrated into the map, which spans a sex-average distance of 147.3 cM, 103.8 cM in males and 227.0 cM in females.(ABSTRACT TRUNCATED AT 250 WORDS)     

Association of the DTNBP1 locus with schizophrenia in a U.S. population

Linkage and association studies have recently implicated dystrobrevin-binding protein 1 (DTNBP1) in the etiology of schizophrenia. We analyzed seven previously tested DTNBP1 single-nucleotide polymorphisms (SNPs) in a cohort of 524 individuals with schizophrenia or schizoaffective disorder and 573 control subjects. The minor alleles of three SNPs (P1578, P1763, and P1765) were positively associated with the diagnosis of schizophrenia or schizoaffective disorder in the white subset of the study cohort (258 cases, 467 controls), with P1578 showing the most significant association (odds ratio 1.76, P =.0026). The same three SNPs were also associated in a smaller Hispanic subset (51 cases, 32 controls). No association was observed in the African American subset (215 cases, 74 controls). A stratified analysis of the white and Hispanic subsets showed association with the minor alleles of four SNPs (P1578, P1763, P1320, and P1765). Again, the most significant association was observed for P1578 (P =.0006). Haplotype analysis supported these findings, with a single risk haplotype significantly overrepresented in the white sample (P =.005). Our study provides further evidence for a role of the DTNBP1 gene in the genetic etiology of schizophrenia.     

Snake relationships revealed by slow-evolving proteins: a preliminary survey

We present an initial evaluation of relationships among a diverse sample of 215 species of snakes (8% of the world snake fauna) representing nine of the 16 commonly-recognized families. Allelic variation at four slow-evolving. protein-coding loci, detected by starch-gel electrophoresis, was found to be informative for estimating relationships among these species at several levels. The numerous alleles detected at these loci [ Arp -2 (42 alleles). Ltlh -2 (43), Mdh -1 (29), Pgm (Z)] provided unexpected clarity in partitioning these taxa. Most congeneric species and several closely-related genera have the same allele at all four loci or differ at only a single locus. At thc other extreme are those species with three or four unique alleles; these taxa cannot be placed in this analysis. Species sharing two or three distinctive alleles are those most clearly separated into clades. Typhlopids, pythonids, viperids, and elapids were resolved into individual clades. whereas bods were separated into boincs and erycines, and colubrids appeared as scveral distinct clades (colubrines, natricines, psammophines, homalopsines, and xenodontines). Viperids were recognized as a major division containing three separate clades: Asian and American crotalines. Pabearctic and Oriental viperines, and Ethiopian causines. The typhlopids were found to be the basal clade, with the North American erycine boid Chrrrino and the West Indian woodsnakes Tropidophi, Y near the base. A number of species and some small clades were not allocated because of uninformative (common, unique, or conflicting) alleles. Of the 21 S species examined, five to eight appear to have been misplaced in the analysis of these electrophoretic data.     

Microsatellite analysis of relationships among North American plums (Prunus sect. Prunocerasus, Rosaceae)

Fifteen microsatellite primer pairs developed in sweet cherry and peach were used to explore genetic relationships among North American plums (Prunus section Prunocerasus). In all, 186 putative alleles were detected with a mean value of 12.4 per locus. The Jaccard coefficient of similarity was calculated between all pairs of accessions and their genetic similarities represented by a UPGMA dendrogram. Despite the apparent closeness among native American plums as evidenced by their ability to hybridize freely and their very similar ITS and trnL-trnF nucleotide sequences, all pairs of accessions among the North American plums shared fewer than half of their alleles. Some of the relationships suggested by the UPGMA dendrogram are congruent with current taxonomic hypotheses, but others are difficult to interpret. Further resolution of relationships among American plums will require molecular markers more variable than ITS yet less variable than microsatellites.     

Identification and characterization of nine polymorphic microsatellite loci in the North American pika,Ochotona princeps

Nine polymorphic microsatellite loci were developed for the North American pika (Ochotona princeps) from di‐ and tetranucleotide repeat‐enriched genomic libraries. Polymorphism was assessed for 165 individuals from eight geographical locations in the western United States. All loci were polymorphic. The number of alleles per locus ranged from three to 14, with observed heterozygosity between 0.189 and 0.822. All loci were in Hardy–Weinberg equilibrium (< 0.05). Regional differences were evident with unique alleles at multiple loci in six of eight populations.     

Structure and inheritance of ribosomal DNA variants in cultivated and wild hop, Humulus lupulus L.

Genetic variation was assessed among cultivated and wild hop, Humulus lupulus, by restriction fragment length polymorphisms (RFLPs) of the ribosomal RNA genes (rDNA). Two rDNA length variants of 10.3 and 9.3 kbp represented by three phenotypes designated A, B and C were detected with XhoI. Restriction-site mapping showed that hop rDNA is structurally similar to those of most higher plants. A high level of homogeneity existed in rDNA repeat lengths among the diverse hop genotypes. Generally, phenotype A was predominant in wild and cultivated European and Asian genotypes; phenotype B in North American cultivars; while phenotype C was present only in native North American hop, providing a potential molecular marker for the identification of this germ plasm. The rDNA data provided genetic evidence for the separation of native and cultivated American genotypes and supports the hypothesis that North American hop cultivars are of hybrid origin from European and native American genotypes. The segregation of rDNA phenotypes in four F₁ families suggests that a single locus with two co-dominant alleles controls genetic variability for rDNA variants in hop.     

FMR1 in global populations.

Fragile X syndrome, a frequent form of inherited mental retardation, results from the unstable expansion of a cryptic CGG repeat within the 5' UTR region of the FMR1 gene. The CGG repeat is normally polymorphic in length, and the content is frequently interrupted by AGG triplets. These interruptions are believed to stabilize the repeat, and their absence, leading to long tracts of perfect CGG repeats, may give rise to predisposed alleles. In order to examine the stability of normal FMR1 alleles, the repeat length of 345 chromosomes from nine global populations was examined with the content also determined from 114 chromosomes as assessed by automated DNA sequencing. The FMR1 alleles, defined by the CGG repeat, as well as by the haplotypes of nearby polymorphic loci, were very heterogeneous, although the level of variation correlated with the age and/or genetic history of a particular population. Native American alleles, interrupted by three AGG repeats, exhibited marked stability over 7,000 years. However, in older African populations, parsimony analysis predicts the occasional loss of an AGG, leading to more perfect CGG repeats. These data therefore support the suggestion that AGG interruptions enhance the stability of the FMR1 repeat and indicate that the rare loss of these interruptions leads to alleles with longer perfect CGG-repeat tracts.     

Comparison of genetic and morphological methods to detect the presence of American lobsters, <Emphasis Type="Italic">Homarus americanus</Emphasis> H. Milne Edwards, 1837 (Astacidea: Nephropidae) in Norwegian waters

American lobsters (Homarus americanus H. Milne Edwards, 1837) are imported live to Europe and should according regulations be kept in land-based tanks until sold. In spite of the strict regulations aimed specifically at preventing the introduction of this species into the NE Atlantic, several specimens of H. americanus have been captured in the wild, especially in Oslofjord, Norway since 1999. One of the great concerns is interbreeding between the introduced American species and the local European lobster, H. gammarus (Linnaeus, 1758). For this reason an awareness campaign was launched in 2000 focusing on morphologically “unusual” lobsters caught in local waters. Morphological characters have been based on colour and sub-ventral spines on the rostrum. Two samples of H. americanus were used for comparisons, as well as samples of European lobster from Oslofjord collected in 1992. Previous genetic analyses (allozymes, mtDNA and microsatellite DNA) have demonstrated that the American lobster is distinct from its European counterpart, with several additional alleles at many loci in addition to different allelic frequency distribution of alleles of “shared” alleles. During the present study, thirteen microsatellite loci were tested in the initial screening, and the three most discriminating loci (Hgam98, Hgam197b and Hgam47b) were used in a detailed comparison between the two species. A total of 45 unusual lobsters were reported captured from Ålesund (west) to Oslofjord (southeast) from 2001 to 2005 and these were analysed for the three microsatellite loci. Nine specimens were identified as American lobsters. Comparisons between morphological and genetic characteristics revealed that morphological differences are not reliable in discrimination the two species, or to identify hybrids. Further, some loci display almost no overlapping in allele frequency distribution for the reference samples analysed, thus providing a reliable tool to identify hybrids.     

广西融水苗族3个STR基因座的群体遗传学研究

为了解广西融水苗族人群无关个体的3个短串联重复序列(short tandem repeat,STR):HUMCSF1PO,HUMTPOX,HUMTH01遗传多态性分布情况,本文用枸橼酸钠抗凝法采集血样,酚—氯仿抽提法提取DNA,应用复合扩增技术对血样DNA的3个STR基因座进行扩增和检测。结果显示:在三个STR位点共检测出19种等位基因,48种基因型,频率分布分别在0.0024—0.4663和0.0048—0.3173之间;基因型的分布符合Hardy-Weinberg平衡定律(P>0.05)。计算种族、民族之间的遗传距离,并对之进行比较得出:广西融水苗族与美国高加索人及美国非洲人存在显著差异,且与美国非洲人之间的差异大于与美国高加索人之间的差异;广西融水苗族与广西侗族的关系近于与其他少数民族的关系。     

Prevalence and phenotype consequence of FRAXA and FRAXE alleles in a large,ethnically diverse,special education-needs population.

We conducted a large population-based survey of fragile X (FRAXA) syndrome in ethnically diverse metropolitan Atlanta. The eligible study population consisted of public school children, aged 7-10 years, in special education-needs (SEN) classes. The purpose of the study was to estimate the prevalence among whites and, for the first time, African Americans, among a non-clinically referred population. At present, 5 males with FRAXA syndrome (4 whites and 1 African American), among 1,979 tested males, and no females, among 872 tested females, were identified. All males with FRAXA syndrome were mentally retarded and had been diagnosed previously. The prevalence for FRAXA syndrome was estimated to be 1/3,460 (confidence interval [CI] 1/7,143-1/1,742) for the general white male population and 1/4, 048 (CI 1/16,260-1/1,244) for the general African American male population. We also compared the frequency of intermediate and premutation FRAXA alleles (41-199 repeats) and fragile XE syndrome alleles (31-199 repeats) in the SEN population with that in a control population, to determine if there was a possible phenotype consequence of such high-repeat alleles, as has been reported previously. No difference was observed between our case and control populations, and no difference was observed between populations when the probands were grouped by a rough estimate of IQ based on class placement. These results suggest that there is no phenotype consequence of larger alleles that would cause carriers to be placed in an SEN class.     

Evidence for multiple introductions of Centaurea stoebe micranthos (spotted knapweed,Asteraceae) to North America

Invasive species’ success may depend strongly on the genetic resources they maintain through the invasion process. We ask how many introductions have occurred in the North American weed Centaurea stoebe micranthos (Asteraceae), and explore whether genetic diversity and population structure have changed as a result of introduction. We surveyed individuals from 15 European native range sites and 11 North American introduced range sites at six polymorphic microsatellite loci. No significant difference existed in the total number of alleles or in the number of private alleles found in each range. Shannon–Weaver diversity of phenotype frequencies was also not significantly different between the ranges, while expected heterozygosity was significantly higher in the invasive range. Population structure was similar between the native range and the invasive range, and isolation by distance was not significant in either range. Traditional assignment methods did not allocate any North American individuals to the sampled European populations, while Bayesian assignment methods grouped individuals into nine genetic clusters, with three of them shared between North America and Europe. Invasive individuals tended to have genetically admixed profiles, while natives tended to assign more strongly to a single cluster. Many North American individuals share assignment with Romania and Bulgaria, suggesting two separate invasions that have undergone gene flow in North America. Samples from three other invasive range sites were genetically distinct, possibly representing three other unique introductions. Multiple introductions and the maintenance of high genetic diversity through the introduction process may be partially responsible for the invasive success of C. stoebe micranthos.     

Characterization of polymorphic microsatellite markers for Microcyclus ulei,causal agent of South American leaf blight of rubber trees

South American leaf blight caused by the ascomycete Microcyclus ulei is the most harmful disease of the rubber tree in Latin America and a potential threat to Asiatic and African natural rubber production. Until now, the variability of this fungus was assessed through observation of pathogenicity of isolates on a range of rubber tree clones with known resistance reactions. The present study describes the process used to design 11 microsatellite markers and evaluates their usefulness in detecting genetic polymorphism. Nine of these markers were polymorphic among six isolates from Brazil (with two to three alleles per locus) and five markers were polymorphic among four isolates from French Guiana (with two to four alleles per locus).     

Invasion genetics of the Eurasian spiny waterflea: evidence for bottlenecks and gene flow using microsatellites

The Eurasian spiny waterflea (Bythotrephes longimanus) is a predacious zooplankter that has increased its range in Europe and is rapidly invading inland water-bodies throughout North America's Great Lakes region. To examine the genetics of these invasions, we isolated five microsatellite DNA loci with between 5 and 19 alleles per locus. We sampled three populations where B. longimanus has been historically present (Switzerland, Italy, and Finland) as well as an introduced European population (the Netherlands) and three North American populations (Lakes Erie, Superior, Shebandowan). Consistent with a bottleneck during colonization (i.e. founder effect), average heterozygosities of the four European populations ranged from 0.310 to 0.599, and were higher than that of three North American populations (0.151-0.220). Pairwise F(ST) estimates among North American populations (0.002-0.063) were not significantly different from zero and were much lower than among European populations (0.208-0.474). This is consistent with a scenario of high gene flow among North American populations relative to that of European ones. Contrary to an invasion bottleneck, however, Erie and Superior populations contained similar numbers of rare alleles as European populations. Assignment tests identified several migrant genotypes in all introduced populations (the Netherlands, Erie, Superior, Shebandowan), but rarely in native ones (Switzerland, Italy and Finland). A large number of genotypes from North America were assigned to our Italian population suggesting a second, previously unidentified, invasion source somewhere in the region of northern Italy. Together, our results support an invasion bottleneck for North American populations that has been largely offset by gene flow from multiple native sources, as well as gene flow among introduced populations.     

Genetic studies of low-abundance human plasma proteins. V. Evidence for a second orosomucoid structural locus (ORM2) expressed in plasma.

Orosomucoid (ORM) or alpha-1-acid glycoprotein is an acute-phase protein of human plasma whose function is suggested to be the competitive inhibition of cellular recognition by infective agents. Genetically determined variation in ORM has been reported, with two major alleles segregating in all populations studied to date. Isoelectric focusing-immunoblotting studies of ORM revealed the presence of isoprotein species that did not segregate with the predominant alleles at the ORM locus and suggested the expression of a second structural gene locus for orosomucoid (ORM2). Genetically independent variation consistent with expression of the ORM2 locus was observed in plasma samples from American blacks but was not observed in U.S. whites or sampled populations of North- and South-American Indians, Eskimos, Aleuts, or New Guinea Highlanders. The population allele frequencies for this locus were .958, .025, .006, and .011 for alleles ORM*1, ORM2*2, ORM2*3, and ORM2*4, respectively. Family studies confirm the autosomal codominant inheritance of the observed phenotypes.     

Equine markers genes. Polymorphism for group-specific component (Gc).

Polymorphism of equine Gc protein was demonstrated by immunofixation electrophoresis with a goat anti-human Gc antibody. Three different phenotypes, F, FS and S, were found. Family data supported the genetic theory of two autosomal codominant alleles, GcF and GcS. Both alleles occurred in Standardbred, Thoroughbred and Arabian horses and in Shetland ponies. A frequency of 0.23 for GcS in the American Standardbred horse indicates the system should be useful for problems of identification and parentage.