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PubMed1997

Allelic variation at a hypervariable compound microsatellite locus in the ascomycete Ascochyta rabiei.

The genome of the fungal chickpea pathogen Ascochyta rabiei was screened for polymorphisms by microsatellite-primed PCR. While ethidium-bromide staining of electrophoretically separated amplification products showed only limited polymorphism among 24 Tunisian A. rabiei isolates, Southern hybridization of purified PCR fragments to restriction digests of fungal DNA revealed polymorphic DNA fingerprints. One particular probe that gave rise to a hypervariable single-locus hybridization signal was cloned from the Syrian isolate AA6 and sequenced. It contained a large compound microsatellite harbouring the penta- and decameric repeat units (CATTT)n, (CATTA)n, (CATATC-ATTT)n and (TATTT)n. We call this locus ArMS1 (Ascochyta rabiei microsatellite 1). Unique flanking sequences were used to design primer pairs for locus-specific microsatellite amplification and direct sequencing of additional ArMS1 alleles from Tunisian and Pakistani isolates. A high level of sequence variation was observed, suggesting that multiple mutational mechanisms have contribute to polymorphism. Hybridization and PCR analyses were performed on the parents and 62 monoascosporic F1 progeny derived from a cross between two different mating types of the fungus. Progeny alleles could be traced back to the parents, with one notable exception, where a longer than expected fragment was observed. Direct sequencing of this new length allele revealed an alteration in the copy number of the TATTT repeat [(TATTT)53 to (TATTT)65], while the remainder of the sequence was unchanged.

Ascomycota↗

PubMed1997

Characterization of three loci controlling resistance of Arabidopsis thaliana accession Ms-0 to two powdery mildew diseases.

Arabidopsis thaliana accession La-er was susceptible, and accession Ms-0 was resistant, to powdery mildew diseases caused by Erysiphe cruciferarum UEA1 and E. cichoracearum UCSC1. The resistance reaction phenotype of A. thaliana Ms-0 to both pathogens was characterized, and the resistance loci were genetically mapped. Growth of E. cruciferarum UEA1 on Ms-0 leaves was arrested after formation of the first appressorium: the underlying host epidermal cell collapsed, and occasionally there was necrosis of one or two host mesophyll cells. Growth of E. cichoracearum UCSC1 on Ms-0 leaves was arrested after emergence of several germ tubes from the conidium, and there was necrosis of host mesophyll cells at the sites of infection. Examination of F2 progeny of a cross La-er x Ms-0 indicated that two independently-segregating dominant loci were required for resistance to E. cruciferarum UEA1. One locus, named RPW6, was genetically mapped to chromosome 5, in a 5.6 cM interval flanked by pCITf16 and PI. The other locus, named RPW7, mapped to chromosome 3 in a 8.5 cM interval flanked by CDC2A and AFC1. Independent effects of RPW6 and RPW7 on E. cruciferarum UEA1 could be detected by quantitative measurements of growth of mycelium and production of conidia. Resistance to E. cichoracearum UCSC1 mapped to a single locus, named RPW8, at a location on chromosome 3 which we could not distinguish from RPW7. Evidently, RPW7 and RPW8 define either a complex resistance locus, or a common resistance gene with dual specificity.

Arabidopsis↗

PubMedDate not supplied

The relative roles of major and minor histocompatibility antigens in the induction of immunologic unresponsiveness by blood transfusion.

Renal allograft survival may be prolonged indefinitely in some strains of rats following preoperative transfusion with whole blood from the organ donor. Similarly donor-specific transfusion results in a reduction in the proliferative response of lymph node (LN) white cells (WBCs) to donor-specific stimulators in mixed-lymphocyte culture (MLC). To determine the relative roles of major and minor histocompatibility antigens in the depression of the proliferative response, in vitro lymphocyte proliferation assays were performed using congenic rat strains as blood donors. Unidirectional MLCs were set up between haplotype-disparate responder and stimulator LN cells, in cases in which the responding cells had been harvested from rats transfused with blood that shared either some, all, or none of the major histocompatibility complex genes with the stimulator strain. The proliferative response of LN cells harvested from rats transfused with blood sharing major (class I or II) or minor antigens, or both, with the in vitro stimulator cells was significantly less than the response of cells harvested from nontransfused controls. No single-locus product was more or less effective than whole blood in depressing cell proliferation. These data suggest that the beneficial effect of preoperative random blood transfusions observed in clinical transplantation may arise from the fortuitous sharing by the blood donor and the subsequent organ donor of not only a single major histocompatibility antigen but also of minor histocompatibility antigens.

Animals↗

PubMed1999

Evolution of the fungal self-fertile reproductive life style from self-sterile ancestors.

In most fungal ascomycetes, mating is controlled by a single locus (MAT). Fungi requiring a partner to mate are heterothallic (self-sterile); those not requiring a partner are homothallic (self-fertile). Structural analyses of MAT sequences from homothallic and heterothallic Cochliobolus species support the hypothesis that heterothallism is ancestral. Homothallic species carry both MAT genes in a single nucleus, usually closely linked or fused, in contrast to heterothallic species, which have alternate MAT genes in different nuclei. The structural organization of MAT from all heterothallic species examined is highly conserved; in contrast, the organization of MAT in each homothallic species is unique. The mechanism of conversion from heterothallism to homothallism is a recombination event between islands of identity in otherwise dissimilar MAT sequences. Expression of a fused MAT gene from a homothallic species confers self-fertility on a MAT-null strain of a heterothallic species, suggesting that MAT alone is sufficient to change reproductive life style.

DNA-Binding Proteins↗

PubMed1996

The cloned gene, Xa21, confers resistance to multiple Xanthomonas oryzae pv. oryzae isolates in transgenic plants.

The cloned rice gene, Xa21, confers resistance to multiple pathogen isolates of Xanthomonas oryzae pv. oryzae in transgenic plants. The resistance phenotype was stably transmitted to T1 progeny and inherited as a single locus. The T1 progeny were tested for resistance to 32 X. oryzae pv. oryzae isolates from eight countries. Both the engineered line and the donor line showed resistance to 29 isolates and susceptibility to three isolates. The identical resistance spectrum of both lines indicates that the presence of a single member of a multigene family, Xa21, is sufficient to confer multi-isolate resistance. The results presented here have important implications for engineering disease resistance in crop plants.

Base Sequence↗

PubMed2000

A quantitative-trait locus controlling peripheral B-cell deficiency maps to mouse Chromosome 15.

Peripheral B-lymphocyte homeostasis is determined through incompletely defined positive and negative regulatory processes. The A/WySnJ mouse, but not the related A/J strain, has disturbed homeostasis leading to peripheral B-lymphocyte deficiency. B lymphopoeisis is normal in A/WySnJ mice, but the B cells apoptose rapidly in the periphery. This B cell-intrinsic defect segregated as a single locus, Bcmd, in (A/WySnJxA/J)F2 mice. Here we mapped a quantitative-trait locus (QTL) that contributes to the A/WySnJ B-cell deficiency by examining the F2 progeny of a cross between strains A/WySnJ and CAST/Ei. In this cross, minimally 1.9 QTLs controlling peripheral B lymphocyte deficiency segregated. The (A/WySnJxCAST/Ei)F2 mice were phenotyped for splenic B-cell percentage and the DNA from progeny with extreme phenotypes was used to map the QTL by the simple-sequence length polymorphism method. A genome scan showed linkage between peripheral B-cell deficiency and Chromosome (Chr) 15 markers. When closely spaced Chr 15 markers were analyzed, the 99% confidence interval for the QTL map position extended along the entire chromosome length. The peak lod scores >17 occurred between 30 and 45 cM. We conclude that a significant QTL segregating in (A/WySnJxCAST/Ei)F2 mice resides in this middle region of Chr 15.

Animals↗

PubMed1993

Somatic homologous recombination in planta: the recombination frequency is dependent on the allelic state of recombining sequences and may be influenced by genomic position effects.

We have previously described a non-selective method for scoring somatic recombination in the genome of whole plants. The recombination substrate consists of a defective partial dimer of Cauliflower Mosaic Virus (CaMV) sequences, which can code for production of viable virus only upon homologous recombination; this leads to disease symptoms on leaves. Brassica napus plants (rapeseed) harbouring the recombination substrate as a transgene were used to examine the time in plant development at which recombination takes place. The analysis of three transgene loci revealed recombination frequencies specific for each locus. Recombination frequencies were increased if more than one transgene locus was present per genome, either in allelic (homozygosity of the transgene locus) or in non-allelic positions. In both cases, the overall recombination frequency was found to be elevated to approximately the sum of the frequencies for the individual transgene loci or slightly higher, suggesting that the respective transgene loci behave largely independently of each other. For all plants tested (single locus, two or multiple loci) maximal recombination frequencies were of the order of 10(-6) events per cell division.

Alleles↗

PubMed2002

Molecular characterization of a mouse cDNA encoding Dicer, a ribonuclease III ortholog involved in RNA interference.

Members of the ribonuclease III superfamily of double-stranded(ds)-RNA-specific endoribonucleases participate in diverse cellular RNA maturation and degradation pathways. A recently identified eukaryotic RNase III family member, named "Dicer", functions in the RNA interference (RNAi) pathway by producing 21--23 bp dsRNAs which target the selective destruction of homologous RNAs. RNAi is operative in animals, plants, and fungi, where it is proposed to inhibit viral reproduction and retroposon movement, as well as to participate in developmental pathways. RNAi functions in mammalian cells, including mouse oocytes and embryos. This article reports the cDNA sequence characterization and expression analysis of the mouse Dicer ortholog. On the basis of the cDNA sequence, the Dicer polypeptide is 1906 amino acids and has a predicted molecular mass of 215 kDa. Mouse Dicer contains a DExH/DEAH helicase motif; a PAZ domain; a tandem repeat of RNase III catalytic domain sequences; and a dsRNA-binding motif. The Dicer gene maps to a single locus on the distal portion of mouse Chromosome (Chr) 12. The Dicer transcript is expressed from the embryonic through adult stages of development. The Dicer transcript is also present in a wide variety of adult mouse organs. The highly conserved set of functional domains and the occurrence of a single-copy gene strongly indicate that the encoded protein is the RNase III ortholog responsible for dsRNA processing in the RNAi pathway.

Amino Acid Sequence↗

PubMed1989

Mutation of a Locus of Arabidopsis thaliana Confers Resistance to the Herbicide Isoxaben.

Mutants resistant to the herbicide N-(3-[1-ethyl-1-methylpropyl]-5-isoxazolyl)-2,6,dimethoxybenzamide (isoxaben) were recovered from an M2 population of Arabidopsis thaliana. Two of these mutants, DH47 and DH48, had a high level of resistance in the homozygous state. Crosses of these mutants to marker strains, and to each other, showed that each contained a mutation at a single locus tightly linked to lutescens, a marker on the fifth chromosome of A. thaliana. Growth curves of these mutants and of the F1 progeny of a cross with the wild type parent strain, in the presence of different concentrations of the herbicide, showed that both mutants display a semidominant phenotype. The two mutations differed in their degree of resistance, both as homozygotes and heterozygotes. This suggests that they are two different alleles. Callus cultures were established from plants homozygous, as well as heterozygous, for each of these mutations. Growth curves of these cultures in the presence of the herbicide mimicked the data obtained in vivo indicating that sensitivity to isoxaben is not dependent on a differentiated function.

Journal Article↗

PubMed2005

[Relationship between heterozygosity and quantitative traits: intralocus interactions and multiple-locus averaging].

The dependence of the expression of genotypic values (Y) on gene dosage (X) have been analyzed for four types of intralocus interactions (additivity, dominance, overdominance, and neutrality) using a linear model. Artificial numerical examples have been used to demonstrate that X and Y are positively associated with each other in the cases of additivity, dominance, and overdominance and are not associated in the case of neutrality. The averaging of single-locus genotypic values to obtain multiple-locus genotypes yields different results for different types of intralocus interactions. Genotypic values and individual heterozygosity are positively correlated with each other in the cases of dominance and overdominance and are negatively correlated in the case of additivity. In the case of neutrality, there is still no correlation after averaging. The results obtained and their interpretation suggest a new view on the experimental studies and generalizations on the relationship between heterozygosity and quantitative traits.

Heterozygote↗

PubMed2007

Explorative two-locus linkage analysis suggests a multiplicative interaction between the 7q32 and 16p13 myoclonic seizures-related photosensitivity loci.

In traits suspected to be governed by at least two loci, linkage analysis incorporating the joint action of both loci may improve the power to detect linkage, increase the precision of estimating locus positions and provide insight into the underlying etiological mechanism. Recently, we mapped two susceptibility loci for epilepsy-related photosensitivity (or photoparoxysmal response, PPR) at regions 7q32 (PPR1) and 16p13 (PPR2) in PPR families with prominent myoclonic seizures background (MS-related PPR). To follow-up these results and evaluate interaction effects between these regions, we conducted two-locus (2L) linkage analyses using parametric and non-parametric methods. The 2L linkage was calculated under a multiplicative (MULT) epistasis model, encompassing models where each locus is necessary but not sufficient for MS-related PPR and a heterogeneity (HET) model, encompassing models in which each locus is by itself sufficient but not necessary for MS-related PPR expression. We found maximal 2L linkage under the (MULT) model, which was significantly better than the 2L linkage under the (HET) model (P = 0.001). The 2L analyses gave no increase in power to detect linkage over the single-locus analyses nor did they improve location estimates at PPR1 and PPR2, as expected under a best-fit 2L (MULT) model in an affecteds-only analysis. Our findings suggest that the genes underlying the PPR1 and PPR2 susceptibility loci may have similar functions or act in the same biochemical pathway.

Chromosome Mapping↗

PubMed2002

Genetics of ethylene biosynthesis and restriction fragment length polymorphisms (RFLPs) of ACC oxidase and synthase genes in melon ( Cucumis melo L.).

We investigated the genetics of ethylene biosynthesis and its linkage to the RFLPs of the ACC oxidase and synthase genes in melon ( Cucumis melo L.). The results suggested that the A(0) and B(0) fragments of RFLP-MEL1 of the ACC oxidase gene were two alleles from a single locus, as were the B and C fragments of RFLP-MEACS1 of the ACC synthase gene. The B(0) allele seemed to be partially dominant over the A(0) allele, whereas B and C alleles appeared to map to quantitative trait loci (QTLs), which most likely contributed to ethylene production. Both RFLPs were linked to ethylene production rates, but they were not linked to each other. The interaction effects of the ACC oxidase and synthase genes on ethylene production were revealed by segregation of RFLP-MEL1 and RFLP-MEACS1. The results of single-copy-reconstruction assays suggested that the ACC oxidase gene is a single copy, whereas the ACC synthase gene is a component of a multigene family in the melon genome. The abscission phenotype appeared to be controlled by an independent locus, with the abscission (full-slip) allele dominant over the non-abscission (not full-slip) allele. These results may facilitate efforts toward mapping the quantitative trait loci (QTLs) of ethylene production. The RFLPs may be used in marker-assisted selection in developing melons with a more-desirable low ethylene production rate for enhancing postharvest storage life.

Journal Article↗

PubMed2006

An algorithm for model construction and its applications to pharmacogenomic studies.

A model depicts the relationship between clinical phenotypes and genotypes on a set of genetic polymorphisms. After the model is constructed and validated, it may be used to predict clinical phenotypes such as traits of complex diseases. A pharmacogenomic model is used to predict the efficacies or adverse drug reactions of a medication. The construction of a model is a challenging task. This is because a single-locus polymorphism does not contain enough information to stratify patients in general, given the complex biological mechanisms involved. An exhaustive search for the correct combination of genotypes across multiple loci is, however, computationally infeasible. We are, thus, motivated to propose a novel algorithm for the construction of models using the multiple single-nucleotide polymorphism (SNP) information in diplotype forms. This algorithm utilizes the techniques of genetic algorithms and Boolean algebra (GABA). The proposed algorithm is tested on simulated data, as well as real genotype datasets of chronic hepatitis C patients treated with interferon-combined therapy. A model for predicting the treatment efficacy is constructed and validated. The results showed that the proposed algorithm is very effective in deriving models comprising multiple SNPs.

Algorithms↗

PubMed1990

Genetic profile of cosmopolitan populations: effects of hidden subdivision.

Natural populations of many organisms exhibit excess of rare alleles in comparison with the predictions of the neutral mutation hypothesis. It has been shown before that either a population bottleneck or the presence of slightly deleterious mutations can explain this phenomenon. A third explanation is presented in this work, showing that hidden subdivision within a population can also lead to an excess of rare alleles in the total population when the expectations of the neutral model are based on the allele frequency profile of the entire population data. With two examples (mitochondrial DNA-morph distribution and isozyme allele frequency distributions), it is shown that most cosmopolitan human populations exhibit excess of rare as well as total allele counts, when these are compared with the expectations of the neutral mutation hypothesis. The mitochondrial data demonstrate that such excesses can be detected from genetic variation at a single locus as well, and this is not due to stochastic error of allele frequency distributions. Contrast of the present observations with the allele frequency profiles in agglomerated tribal populations from South and Central America shows that even when the neutral expectations hold for individual subpopulations, if all subpopulations are grouped into a single population, the pooled data exhibit an excess of total number of alleles that is mainly due to the excess of rare alleles. Therefore, a primary cause of the excess number of rare alleles could be the hidden subdivision, and the magnitude of the excess indicates the extent of substructuring. The two components of hidden subdivision are: 1) Number of subpopulations, and 2) the average genetic distance among them. The implications of this observation in estimating mutation rate are discussed indicating the difficulties of comparing mutation rates from different population surveys.

Alleles↗

PubMed2004

Multilocus analysis of hypertension: a hierarchical approach.

While hypertension is a complex disease with a well-documented genetic component, genetic studies often fail to replicate findings. One possibility for such inconsistency is that the underlying genetics of hypertension is not based on single genes of major effect, but on interactions among genes. To test this hypothesis, we studied both single locus and multilocus effects, using a case-control design of subjects from Ghana. Thirteen polymorphisms in eight candidate genes were studied. Each candidate gene has been shown to play a physiological role in blood pressure regulation and affects one of four pathways that modulate blood pressure: vasoconstriction (angiotensinogen, angiotensin converting enzyme - ACE, angiotensin II receptor), nitric oxide (NO) dependent and NO independent vasodilation pathways and sodium balance (G protein-coupled receptor kinase, GRK4). We evaluated single site allelic and genotypic associations, multilocus genotype equilibrium and multilocus genotype associations, using multifactor dimensionality reduction (MDR). For MDR, we performed systematic reanalysis of the data to address the role of various physiological pathways. We found no significant single site associations, but the hypertensive class deviated significantly from genotype equilibrium in more than 25% of all multilocus comparisons (2,162 of 8,178), whereas the normotensive class rarely did (11 of 8,178). The MDR analysis identified a two-locus model including ACE and GRK4 that successfully predicted blood pressure phenotype 70.5% of the time. Thus, our data indicate epistatic interactions play a major role in hypertension susceptibility. Our data also support a model where multiple pathways need to be affected in order to predispose to hypertension.

Alleles↗

PubMed1989

The beta subunit locus of the human fibronectin receptor: DNA restriction fragment length polymorphism and linkage mapping studies.

The beta subunit of the human fibronectin receptor (FNRB) is a transmembrane protein belonging to the VLA (very late antigens of activation) family. Using pGEM-32, a 2.5-kb partial cDNA clone corresponding to the 3' portion of the human FNRB locus, multiple restriction fragment length polymorphisms (RFLPs) were revealed on DNAs from unrelated Caucasians. RFLPs detected by five enzymes, BanII, HinfI, KpnI, BglII, and SacI, are of the simple two-allele form, and pairwise linkage analyses of these RFLPs with numerous known DNA markers from the chromosome-10 pericentromeric region not only confirmed the chromosome-10 assignment of the functional FNRB gene but also supported its localization at p11.2 suggested by in situ hybridization. An infrequent MspI RFLP was detected by pB/R2, a 4.6-kb genomic clone from the FNRB locus. Another type of DNA polymorphism was also revealed by the cDNA clone and it was visualized on the Southern blot analyses as the presence or absence of an extra band (or a set of extra bands). It seems to stem from a stretch of DNA sequence present in some individuals at one single locus but absent in others, and is of non-chromosome-10 origin based on linkage analyses with known chromosome 10 markers. This "presence/absence" type of polymorphism could be revealed by all of the 25 restriction enzymes tested and is similar in nature to that previously reported with one of the human dihydrofolate reductase pseudogenes, DHFRP1. Dissection of the pGEM-32 clone demonstrated that the region revealing the non-chromosome-10 sequences is within a fragment about 1.7 kb in length extending from about 600 nucleotides preceding the stop codon down to the end of the cloned FNRB 3' untranslated region. Due to its high polymorphism information content (PIC) value (0.71 for haplotypes of BanII, HinfI, and KpnI RFLPs) and proximity to the centromere. FNRB will prove to be a highly useful marker for genetic linkage studies of multiple endocrine neoplasia type 2A (MEN2A) as well as for chromosome-10 linkage studies in general.

Chromosome Mapping↗

PubMed1980

Enhanced responses to opiates produced by a single gene substitution in the mouse.

Adult male mice of the C57Bl/6J strain, or mice differing at a single locus from the above, pallid mice (C57Bl/6J-pa), were treated with morphine or vehicle and two responses associated with opiate receptor stimulation were examined. In comparison with vehicle treatment, morphine produced stereotyped running and reduced core temperature in the parent C57Bl/6J line. These responses were significantly enhanced in the coisogenic pallid line. Thus, a single gene may enhance normal sensitivity to opiates. This suggests the existence of discrete and identified biochemical influences upon sensitivity to opiates through genetic means, and offers a novel model of naturally occurring permanently altered opiate sensitivity.

Animals↗

PubMed2006

The stationary distribution of allele frequencies when selection acts at unlinked loci.

We consider population genetics models where selection acts at a set of unlinked loci. It is known that if the fitness of an individual is multiplicative across loci, then these loci are independent. We consider general selection models, but assume parent-independent mutation at each locus. For such a model, the joint stationary distribution of allele frequencies is proportional to the stationary distribution under neutrality multiplied by a known function of the mean fitness of the population. We further show how knowledge of this stationary distribution enables direct simulation of the genealogy of a sample at a single-locus. For a specific selection model appropriate for complex disease genes, we use simulation to determine what features of the genealogy differ between our general selection model and a multiplicative model.

Analysis of Variance↗