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PubMed1985

Segregation and linkage analysis of alpha-N-acetyl-D-glucosaminidase (NAG) levels in a black family.

Alpha-N-acetyl-D-glucosaminidase (NAG) activities were evaluated on serum samples from 67 persons in a large black family. These data were analyzed in conjunction with those from 126 previously tested unrelated blacks [Vance et al, 1980]. After loge transformation, admixture analysis indicated a significantly better fit (P less than .01) of a mixture of 2 normal distributions for NAG activity versus a single normal distribution. Segregation analysis using the transmission probability model of Elston and Stewart [1971] demonstrated that a genetic model fits the data better than the random "environmental" model. Thus, the existence of a major gene is suggested in the family, although the possibility of polygenic or other familial effects cannot be ruled out. These results confirm the existence of a polymorphism for NAG reported earlier in a series of White half-sib twin families [Vance et al, 1980]. However, the estimates of the means of the three genotypes (AA, AA', A'A') appear to differ in the two racial groups. Thus, the data suggest either a racial polygenic effect and/or different alleles segregating in the two populations. In fact, thermal stability data [Vance et al, 1981a] suggest that at least two alleles are structurally distinct. Linkage analysis of the pedigree with 20 marker loci gave no clear indication of linkage. A lod score of 1.44 was found at 0 recombination with orosomucoid (ORM).

Acetylglucosaminidase↗
PubMed1993

Monte Carlo analysis on a large pedigree.

Monte Carlo methods for linkage and segregation analysis are applied to the HGAR1 pedigree. To address these data, the methods are extended in several ways. The results are compared with those provided by PAP.

Adolescent↗
PubMed1998

Measured haplotype analysis of the angiotensin-I converting enzyme gene.

Linkage and segregation analysis have shown that circulating angiotensin-I converting enzyme (ACE) levels are influenced by a major quantitative trait locus that maps within or close to the ACE gene. The D variant of a 287 bp insertion/deletion (I/D) polymorphism in intron 16 of the gene is associated with high ACE levels and may also be related to increased risk of cardiovascular disease. Multiple variants that are in linkage disequilibrium with the I/D polymorphism have been described, but it is unknown if any of these are directly implicated, alone or in combination with as yet undiscovered variants, in the determination of ACE levels. An analysis of 10 polymorphisms spanning 26 kb of the ACE gene revealed a limited number of haplotypes in Caucasian British families due to strong linkage disequilibrium operating over this small chromosomal region. A haplotype tree (cladogram) was constructed with three main branches (clades A-C) which account for 90% of the observed haplotypes. Clade C is most likely derived from clades A and B following an ancestral recombination event. This evolutionary information was then used to direct a series of nested, measured haplotype analyses that excluded upstream sequences, including the ACE promoter, from harbouring the major ACE-linked variant that explains 36% of the total trait variability. Residual familial correlations were highly significant, suggesting the influence of additional unlinked genes. Our results demonstrate that a combined cladistic/measured haplotype analysis of polymorphisms within a gene provides a powerful means to localize variants that directly influence a quantitative trait.

England↗
PubMed2007

Molecular mapping of resistance genes to tan spot [Pyrenophora tritici-repentis race 1] in synthetic wheat lines.

Synthetic wheat lines (2n = 6x = 42, AABBDD), which are amphiploids developed from the hybrid between tetraploid wheat (Triticum turgidum L., 2n = 4x = 28, AABB) and Aegilops tauschii Coss. (2n = 2x = 14, DD), are important sources of resistance against tan spot of wheat caused by Pyrenophora tritici-repentis. In the present study, inheritance, allelism and genetic linkage analysis in synthetic wheat lines have been carried out. Segregation analysis of the phenotypic and molecular data in F(2:3) populations of CS/XX41, CS/XX45, and CS/XX110 has revealed a 1:2:1 segregation ratio indicating that resistance of tan spot in these synthetic lines is controlled by a single gene. Allelism tests detected no segregation for susceptibility among F(1) and F(2) plants derived from intercrosses of the resistance lines XX41, XX45 and XX110 indicating that the genes are either allelic or tightly linked. Linkage analysis using SSR markers showed that all the three genes: tsn3a in XX41, Tsn3b in XX45 and tsn3c in XX110 are clustered in the region around Xgwm2a, located on the short arm of chromosome 3D. The linked markers and genetic relationship of these genes will greatly facilitate their use in wheat breeding and deployment of cultivars resistant to tan spot.

Alleles↗
PubMed2025

Dual genetic loci and flavonoid metabolism orchestrate fruiting body coloration in Flammulina filiformis: a multi-omic roadmap for fungal pigmentation.

BACKGROUND: The fruiting bodies of macrofungi exhibit diverse coloration, traditionally attributed to melanin and carotenoid biosynthesis. This study is the first to reveal that flavonoids, rather than these classical pigments, are the predominant contributors to yellow pigmentation in the Flammulina filiformis. OBJECTIVE: To uncover the genetic basis and key regulatory genes involved in pigment formation in F. filiformis fruiting bodies, and to establish a model framework for studying color genetics in macrofungi. METHODS: Metabolomic profiling was conducted on yellow and white F. filiformis fruiting bodies to identify key pigment components. A segregating population was constructed, followed by integrated multi-omics analyses-including bulk segregant analysis (BSA), genome-wide association study (GWAS), and transcriptomics-to map regulatory loci and candidate genes. Functional roles were validated via genetic transformation and protein structural modeling. RESULTS: Flavonoid accumulation was identified as the biochemical hallmark of pigmented fruiting bodies. Genetic analysis revealed a dual regulatory mechanism: a qualitative locus governing pigmentation presence and a quantitative trait determining color intensity. Combined BSA and GWAS pinpointed a major locus, Ffcrs, within a recombination-suppressed region. Transcriptomic analysis identified two key regulators, Ffakr (a transcriptional activator) and Ffpal (encoding phenylalanine ammonia-lyase). Functional verification via transformation, structural modeling, and metabolite profiling in transgenic lines confirmed their essential roles in flavonoid biosynthesis and pigmentation. CONCLUSION: This study uncovers a flavonoid-based pigmentation mechanism in F. filiformis and elucidates a complex genetic architecture shaped by both qualitative and quantitative loci, providing a new paradigm for understanding pigment formation in macrofungi. The identified regulatory factors establish a molecular foundation for the precise manipulation of economically important pigmentation traits in edible mushroom.

Flavonoids↗
PubMed2001

Mutations in ABCR (ABCA4) in patients with Stargardt macular degeneration or cone-rod degeneration.

PURPOSE: To determine the spectrum of ABCR mutations associated with Stargardt macular degeneration and cone-rod degeneration (CRD). METHODS: One hundred eighteen unrelated patients with recessive Stargardt macular degeneration and eight with recessive CRD were screened for mutations in ABCR (ABCA4) by single-strand conformation polymorphism analysis. Variants were characterized by direct genomic sequencing. Segregation analysis was performed on the families of 20 patients in whom at least two or more likely pathogenic sequence changes were identified. RESULTS: The authors found 77 sequence changes likely to be pathogenic: 21 null mutations (15 novel), 55 missense changes (26 novel), and one deletion of a consensus glycosylation site (also novel). Fifty-two patients with Stargardt macular degeneration (44% of those screened) and five with CRD each had two of these sequence changes or were homozygous for one of them. Segregation analyses in the families of 19 of these patients were informative and revealed that the index cases and all available affected siblings were compound heterozygotes or homozygotes. The authors found one instance of an apparently de novo mutation, Ile824Thr, in a patient. Thirty-seven (31%) of the 118 patients with Stargardt disease and one with CRD had only one likely pathogenic sequence change. Twenty-nine patients with Stargardt disease (25%) and two with CRD had no identified sequence changes. CONCLUSIONS: This report of 42 novel mutations brings the growing number of identified likely pathogenic sequence changes in ABCR to approximately 250.

ATP-Binding Cassette Transporters↗
PubMed2001

Stickler syndrome and vitreoretinal degeneration: correlation between locus mutation and vitreous phenotype. Apropos of a case.

BACKGROUND: Autosomal dominant vitreoretinopathies are characterized by genetic heterogeneity. Structural mutations in COL2A1 are the most frequent cause of Stickler syndrome with ocular involvement. The affected patients have a characteristic vitreous alteration, so-called membranous vitreous, or type 1 vitreous phenotype. Recently a novel mutation in the gene encoding the alpha 1 chain of type XI collagen (COL11A1) was reported in rare Stickler pedigrees, with a different, so-called beaded or type 2 vitreous phenotype. METHODS: Five patients of an Italian family affected by high myopia, high frequency of retinal detachment, and other systemic stigmata evocative of Stickler syndrome (flat midface, depressed nasal bridge, short nose, spondyloepiphyseal dysplasia and osteoarthritis) were studied. Genetic investigations were also performed, considering three candidate loci for Stickler syndrome and Wagner syndrome (COL2A1, COL11A1, WGN1). RESULTS: Segregation analysis was performed utilizing polymorphic markers. COL2A1 and WGN1 segregations were excluded; COL11A1 showed concordance with the disease. The vitreous phenotype of the family was a typical type 1 or "membranous" vitreous, although all the previously reported COL11A1-related Stickler syndromes had always shown the type 2 or "beaded" vitreous phenotype. CONCLUSIONS: The clear presence of the type 1 or "membranous" vitreous phenotype in our family, despite the probable mutation in the COL11A1 gene, suggests greater phenotypical heterogeneity and a more extensive mutation spectrum, even of the COL11A1 gene, than previously thought, explaining the basis for the different vitreous phenotypes seen in Stickler syndrome.

Child↗
PubMed1993

Testing genomic imprinting in Wilm's tumor.

Data from 511 cases of Wilms' tumor in France (including 12 familial cases) and 8 pedigrees from the literature were analyzed to test three modifications of Knudson's classical bimutational theory, based on genomic imprinting in Wilms' tumor carcinogenesis. Analysis of data of age at diagnosis and segregation analysis were performed to determine the number of independent events for Wilms' tumor development and to search for a differential role of paternal and maternal alleles. Unexpectedly, we show that only one rare event is required for tumor development in isolated unilateral cases which are considered to be mainly nonhereditary. In familial cases, we observe no effect of the sex of the transmitting parent on either hge at diagnosis or segregation ratio. We show that this could be explained by models of genomic imprinting which assume two nonindependent events, or only one rare genetic event. In bilateral cases we show a bimodality for age at diagnosis which could be due to a mixture of hereditary and nonhereditary cases. This result completely questions the classical assumption according to which all bilateral cases would be hereditary. These findings support the hypothesis that this childhood cancer arises from a variety of etiological pathways and might be useful to find strategies for further molecular investigations.

Adolescent↗
PubMed1995

Segregation and linkage analysis of serum angiotensin I-converting enzyme levels: evidence for two quantitative-trait loci.

Human serum angiotensin I-converting enzyme (ACE) levels vary substantially between individuals and are highly heritable. Segregation analysis in European families has shown that more than half of the total variability in ACE levels is influenced by quantitative-trait loci (QTL). One of these QTLs is located within or close to the ACE locus itself. Combined segregation/linkage analysis in a series of African Caribbean families from Jamaica shows that the ACE insertion-deletion polymorphism is in moderate linkage disequilibrium with an ACE-linked QTL. Linkage analysis with a highly informative polymorphism at the neighboring growth-hormone gene (GH) shows surprisingly little support for linkage (LOD score [Z] = 0.12). An extended analysis with a two-QTL model, where an ACE-linked QTL interacts additively with an unlinked QTL, significantly improves both the fit of the model (P = .002) and the support for linkage between the ACe-linked QTL interacts additively with an unlinked QTL, significantly improves both the fit of the model (P = .002) and the support for linkage between the ACe-linked QTL and GH polymorphism (Z = 5.0). We conclude that two QTLs jointly influence serum ACE levels in this population. One QTL is located within or close to the ACE locus and explains 27% of the total variability; the second QTL is unlinked to the ACE locus and explains 52% of the variability. The identification of the molecular mechanisms underlying both QTLs is necessary in order to interpret the role of ACE in cardiovascular disease.

Analysis of Variance↗
PubMed1980

Genetic analysis of von Willebrand's disease in two large pedigrees: a multivariate approach.

Clinical and laboratory data, including polymorphic marker traits for linkage analysis, were collected from two large multigenerational families segregating for von Willebrand disease. A new approach to the identification of gene carriers in these families, combining pedigree segregation analysis with multivariate discriminant analysis, is applied. Whereas individually the clinical symptoms and the factor VIII related activities could not distinguish between hypotheses, it was possible to find a discriminant function-showing consistency of the data with a dominant gene hypothesis, but not with a recessive gene or an environmental hypothesis. This function is estimated to lead to 3.2% and 5.5% minimum misclassification of the genotypes, respectively, in the two families. The discriminant function could be used for other families, but is should be calibrated for the specific population in which it is used. Among the markers investigated, GPT is the most likely to be linked to von Willbrand's disease, with a maximum lod score of about unity at 15% recombination.

Factor VIII↗
PubMed2005

Inheritance of resistance to Xylella fastidiosa within a Vitis rupestris x Vitis arizonica hybrid population.

The inheritance of resistance to Xylella fastidiosa (Xf), the bacterium which causes Pierce's disease (PD) in grapevines, was evaluated within a factorial mating design consisting of 16 full-sib families with resistance derived from Vitis arizonica interspecific hybrids. Measurements of disease progression under greenhouse conditions were based on quantitative assessment of Xf populations in stem tissues and on three phenotypic scores: leaf scorch, a cane maturation index (CMI) and an index that incorporated shoot stunting into the cane maturation index (CMSSI). Measurement of bacterial populations yielded the highest broad-sense heritability for resistance on a genotype mean basis (0.97), indicating that this measure of resistance was the least effected by environmental variation. Narrow-sense heritability of PD resistance was moderately high and measured 0.52, 0.60, 0.63 and 0.37 for Xf populations, CMI scores, CMSSI scores and leaf scorch values, respectively. Complex segregation analysis using the computer program Statistical Analysis for Genetic Epidemiology (SAGE: ) strongly indicated the existence of a major gene for PD resistance, which accounted for 91% of the total genetic variance. Conversion of the quantitative data into qualitative resistance levels and evaluation via a chi-square analysis showed that 15 of the 16 families segregated in accordance with a single gene hypothesis with a dominant allele controlling PD resistance. These data indicate that the trait should be relatively easy to pass on from parents to progeny in a breeding program for the development of PD-resistant grape cultivars, particularly when selection is based on cane maturation scores or stem Xf populations.

Breeding↗
PubMed1987

The outlook for linkage research in psychiatric disorders.

Analysis of the distribution of diagnoses in families (segregation analysis) has not, so far, advanced us toward the goal of resolving the inheritance of the major psychiatric disorders. Recent advances in genetics, particularly the development of new molecular genetic linkage methods, have made it, at least theoretically, feasible to scan the entire human genome, so that in a properly designed and executed set of studies it will be possible to demonstrate whether there exists single locus transmission for a particular disorder, and to map the locus. We present here an analysis of feasibility of moderate-sized pedigrees (approximately 15 persons, two generations) and affected-sib-pair sets in such studies. Eight to ten moderate-sized pedigrees are sufficient to perform definitive mapping under the tested conditions, of recessive or additive inheritance, low penetrance of the heterozygote, and a genetically homogeneous disorder. The affected-sib-pair method required 25 pairs of sibs to detect linkage under such conditions in a recessive model, and 45 in a dominant model. When there is genetic heterogeneity, moderate-sized pedigrees are much less useful, but the affected-sib-pair method retains considerable power.

Genetic Linkage↗
PubMed2002

Two new recursive likelihood calculation methods for genetic analysis.

Recursive likelihood calculations for genetic analysis with ungenotyped pedigree data employ variations of the Elston-Stewart (ES) or the Lander-Green (LG) algorithms. With the ES algorithm, the number of loci may be limited but not the pedigree size. With the LG algorithm, the reverse is the case. We introduce two new algorithms for the computation of regressive likelihoods for pedigrees with multivariate traits. The first is an alternative formulation of our existing model, which leads to a simpler form in the binary trait, polygenic and mixed model cases. The second is an approximation model, which is computationally efficient. These methods apply to both continuous and binary traits, in the oligogenic and polygenic cases. Both methods coincide in the binary case. We considered these methods for cases in which all the traits are controlled by a single locus, with each trait controlled by one locus independent to the others. Simulation studies and analysis of a real data are presented for segregation analysis as illustrations. These methods can also be used in other model-based analyses. These methods are implemented in G.E.M.S., the genetic epidemiology models software.

Animals↗
PubMed1987

[Genetic analysis of the polyauxotrophy of the early mitotic progeny of Saccharomyces cerevisiae zygotes. III. The behavior of the chromosome-III markers in polyauxotrophic clones and their mitotic and meiotic segregants].

Cloning and segregation analysis of polyauxotrophic (PA) progeny, as well as the study of diploid segregants, revealed an unusual state of the diploid genome in these strains. Analysis of linkage markers of chromosome III in all crosses may be expected to illuminate relationships between the homologous chromosomes. All PA strains were assigned to two major classes. In the class of PA strains with recombinant chromosome III, the effect of approachment of third linkage markers was noted. In other strains, transposition of genetic marker metA1 to chromosome III and its linkage to leu2 were discovered. The present study has demonstrated that the unusual state of the diploid genome of PA strains induces multiple nonspecific alterations in chromosome relationship and structure. It is likely that these alterations are the consequence of disturbance in mitotic apparatus of cell.

Chromosomes↗
PubMed1988

Pedigree analysis of HDL cholesterol concentration in baboons on two diets.

Using complex segregation analysis, we examined the effects of genetic factors and diet on serum concentrations of high-density-lipoprotein cholesterol (HDL-C) in baboons. In analyses of 710 baboons in 23 sire families, we found evidence for a major gene as well as a polygenic contribution to HDL-C concentration in baboons fed a basal (chow) diet and also in the same animals after challenge with a high-cholesterol, saturated-fat diet. There was evidence for a polygenic contribution to the change in HDL-C concentration in response to the dietary challenge, but there was no evidence for a major gene effect.

Animals↗
PubMed1981

Segregation and linkage analysis of 40 multiplex multiple sclerosis families.

40 multiplex multiple sclerosis (MS) families were analyzed for evidence of an MS susceptibility gene linked to the HLA region of the sixth chromosome. We assumed that population associations between specific HLA alleles and MS are due to linkage disequilibrium, so preference was given to hypotheses compatible with tight linkage, and explanations were sought for conflicting evidence. The analyses proceeded in two steps: (1) segregation analysis using the computer program POINTER, and (2) linkage analysis using LINKAS, first assuming linkage equilibrium and then allowing for linkage disequilibrium and etiological heterogeneity. The results of the segregation analyses were indeterminate. The results of the linkage analyses suggest that analyses that do not allow for disequilibrium lose substantial evidence on linkage. Of the models that were investigated under linkage disequilibrium, the best fit is with a model of complete linkage (theta= 0.0) in 75% of the pedigrees and no linkage in the remaining pedigrees. We were unable, however, to statistically reject another model involving loose linkage and no heterogeneity.

Chromosomes, Human, 6-12 and X↗
PubMed1993

In situ analysis of centromere segregation in C57BL/6 x Mus spretus interspecific backcrosses.

The analysis of major satellite sequence differences between Mus spretus and laboratory mice provides a robust method for analyzing the centromere location for the genetic maps of each mouse chromosome. Fluorescence in situ hybridization (FISH) of a genomic probe, pMR196, for the laboratory mouse major satellite sequences was used to identify C57BL/6Ros (B6) pericentromeric heterochromatin in progeny of reciprocal backcross matings. These included 80 (B6 x M. spretus)F1 x M. spretus progeny (BSS) and 70 (B6 x M. spretus)F1 x B6 (BSB) progeny. FISH analysis of pericentromeric heterochromatin was conducted on the same metaphase spreads that were karyotypically analyzed for chromosome-specific banding patterns. Analysis of chromosomal segregation suggested that there was not primary deviation from random assortment during meiosis in the interspecific hybrid female, because nearly all of the 190 pair-wise comparisons did not deviate from expected and because there was no consistent pattern of deviation of the same chromosomes in the reciprocal backcross progeny from similar (C57BL/6 x M. spretus)F1 hybrid females. These results affirm the value of using the major satellite to genetically mark pericentromeric heterochromatin in the analysis of the segregation and assortment of centromeres in Mus interspecific crosses.

Animals↗