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Comparison of the genetic diversity of wild and captive groups of Microcebus murinus using the random amplified polymorphic DNA method.

Continued survival of most animal species depends on population management and active protection. It is generally agreed that, in order to avoid extinction of endangered species, ex situ and in situ conservation must be developed in tandem. However, even though many recommendations have been put forward to promote the survival of captive populations, some rapidly become extinct due to loss of genetic diversity (drift effect). Genetic markers, such as random amplified polymorphic DNA (RAPD) markers, can be applied to rapid testing of many individuals. They also permit analysis of very small amounts of DNA, when small species such as mouse lemurs (Microcebus) are to be tested. Using RAPD markers, we compare genetic diversity in four captive groups of Microcebus murinus to that in a sample of 70 wild mouse lemurs. Following the principles of Mendelian inheritance, each amplified fragment of DNA may be considered as a 'locus' (or an amplifying site). The series of bands amplified by a particular primer in any individual is referred to as the individual's 'profile'. We tested 5 primers, or, in the above terms, we studied 98 different 'loci'. Results showed that the captive groups had lost genetic information with respect to the wild sample. Among the four captive groups, the loss of genetic diversity varied according to their number of founders and/or the management of their captive reproduction. Our study of polymorphism permitted us to establish tools for the genetic management of captive breeding, and for the determination of paternity which frequently give better results than behavioural studies; and simulation of introductions or departures of individuals in one very monomorphic group permitted estimation of future increases in its genetic diversity.

Amino Acid Sequence↗

Segregation analysis of body mass index in an unselected French-Canadian sample: the Québec Family Study.

Interest in a single gene etiology for obesity, as assessed by the body mass index (BMI), has been spurred recently by reports of a putative recessive major gene for extreme values, which accounts for as much as 40% of the variance. The major gene hypothesis was evaluated here in the Québec Family Study, a random sample of 375 French-Canadian volunteer families. This report represents one component in a more complete investigation of obesity in these families. In contrast to the recent studies, a major gene hypothesis for BMI was not verified here. Although there was a major effect, it did not conform to a Mendelian pattern of transmission. A multifactorial component (i.e., polygenic and/or common environmental factors) accounted for 42% of the phenotypic variance. In addition, evidence of heterogeneity between the generations was found. The heterogeneity was traced to the major non-Mendelian component (which accounted for 0.01% of the variance in parents and over 40% in offspring) rather than to the multifactorial one. These results would suggest that a simple recessive gene mixed model may not be sufficient to explain the familial distribution of the BMI. Several factors which may have contributed to these results include temporal trends and surrogate effects such as those related to variation in body composition and energy balance components.

Adipose Tissue↗

Genetic exchange in trypanosomes.

The process of genetic exchange in trypanosomes was first described 10 years ago, when Jenni and colleagues obtained hybrid trypanosomes after cotransmitting 2 Trypanosoma brucei ssp. clones through the tsetse fly. The process is a non-obligatory part of the trypanosome life cycle and takes place in the fly, probably during development in the salivary glands. Nuclear DNA markers are inherited for the most-part in a mendelian fashion, indicating that meiosis is involved. However, there is no evidence for haploid gametes. Analysis of the inheritance of kinetoplast DNA, the trypanosome's mitochondrial DNA, indicates that trypanosome mitochondria fuse during genetic exchange, allowing parental kDNAs to mix. Population genetics analysis of natural T. brucei ssp. provides little support for random or widespread mating in the wild. However, even very rate mating events, by mobilising genes for drug resistance, virulence or human infectivity into other genetic backgrounds, could have implications for the generation of epidemics.

Animals↗

Chromosomal regions associated with segregation distortion in maize.

Segregation distortion skews the genotypic frequencies from their Mendelian expectations. Our objectives in this study were to assess the frequency of occurrence of segregation distortion in maize, identify chromosomal regions consistently associated with segregation distortion, and examine the effects of gametophytic factors on linkage mapping. We constructed a simple sequence repeat (SSR) linkage map for a LH200/LH216 F(2)Syn3 (i.e., random-mated three times) population, and compared the segregation distortion in this map with the segregation distortion in three published linkage maps. Among 1,820 codominant markers across the four mapping populations, 301 (17%) showed segregation distortion ( P < 0.05). The frequency of markers showing segregation distortion ranged from 19% in the Tx303/CO159 mapping population to 36% in the B73/Mo17 mapping population. A positive relationship was found between the number of meioses and the frequency of segregation distortion detected in a population. On a given chromosome, nearly all of the markers showing segregation distortion favored the allele from the same parent. A total of 18 chromosomal regions on the ten maize chromosomes were associated with segregation distortion. The consistent location of these chromosomal regions in four populations suggested the presence of segregation distortion regions (SDRs). Three known gametophytic factors are possible genetic causes of these SDRs. As shown in previous research, segregation distortion does not affect the estimate of map distance when only one gametophytic factor is present in an SDR.

Journal Article↗

Distinguishing the effects of maternal and offspring genes through studies of "case-parent triads".

A gene variant that increases disease risk will be overrepresented among diseased persons, even compared with their own biologic parents. This insight has led to tests based solely on the asymmetric distribution of a variant allele among cases and their parents (e.g., the transmission/disequilibrium test). Existing methods focus on effects of alleles that operate through the offspring genotype. Alleles can also operate through the mother's genotype, particularly for conditions such as birth defects that have their origins in fetal life. An allele working through the mother would have higher frequency in case-mothers than in case-fathers. The authors develop a log-linear method for estimating relative risks for alleles in the context of case-parent triads. This method is able to detect the effects of genes working through the offspring, the mother, or both. The authors assume Mendelian inheritance, but Hardy-Weinberg equilibrium is unnecessary. Their approach uses standard software, and simulations demonstrate satisfactory power and confidence interval coverage. This method is valid with a self-selected or hospital-based series of cases and helps to protect against misleading inference that can result when cases and controls are randomly sampled from a population not in Hardy-Weinberg equilibrium.

5,10-Methylenetetrahydrofolate Reductase (FADH2)↗

Testing for association with a case-parents design in the presence of genotyping errors.

Genotyping errors can create a problem for the analysis of case-parents data because some families will exhibit genotypes that are inconsistent with Mendelian inheritance. The problem with correcting Mendelian inconsistent genotype errors by regenotyping or removing families in which they occur is that the remaining unidentified genotype errors can produce excess type I (false positive) error for some family-based tests for association. We address this problem by developing a likelihood ratio test (LRT) for association in a case-parents design that incorporates nuisance parameters for a general genotype error model. We extend the likelihood approach for a single SNP to include short haplotypes consisting of 2 or 3 SNPs. The extension to haplotypes is based on assumptions of random mating, multiplicative penetrances, and at most a single genotype error per family. For a single SNP, we found, using Monte Carlo simulation, that type I error rate can be controlled for a number of genotype error models at different error rates. Simulation results suggest the same is true for 2 and 3 SNPs. In all cases, power declined with increasing genotyping error rates. In the absence of genotyping errors, power was similar whether nuisance parameters for genotype error were included in the LRT or not. The LRT developed here does not require prior specification of a particular model for genotype errors and it can be readily computed using the EM algorithm. Consequently, this test may be generally useful as a test of association with case-parents data in which Mendelian inconsistent families are observed.

Adult↗

Competition between phenotypes.

We present two models for phenotypic-dependent interspecific competition. In both cases the survivorship of individuals of one population depends on the entire phenotypic distribution of the other species. The first model considers a continuously varying metric trait, with assortative or random mating; the second model examines a character controlled by two alleles at a single locus. Pursuing the notion that each population maximizes its mean fitness we define a vector-optimum strategy using the concepts of cooperative and competitive optima. It is found that the dynamical constraints placed on the equations of motion by Mendelian genetics often prevent a population from evolving to a strategic optimum. However, for the single locus case with complete dominance, the competitive optimum always coincides with some dynamical equilibrium on the Hardy-Weinberg manifold.

Alleles↗

The causes of essential hypertension.

1. Confusion between the criteria for defining and diagnosing hypertension may have misled the search for the causes of hypertension. 2. The systematic approach of molecular genetics appears to offer the best chance of explaining hypertension, but the attractions are partly offset by the large numbers required, and unproven record of the genetic techniques in finding functional mutations in complex human disorders. 3. Part of the evidence for the polygenic nature of essential hypertension derives from the variable response to a large number of different anti-hypertensive agents. Systematic investigation of this variability may provide a basis for dividing patients into genetically more homogeneous sub-groups, within which smaller numbers will be required to detect the genes responsible for the susceptibility to hypertension. 4. The proportion of hypertensive patients with affected siblings has been studied in 6000 patients from Addenbrookes Hospital and local general practices. A recurrence risk for hypertension of approximately 3.5 was found. 5. Approximately two-thirds of patients have no known affected siblings. The next largest group, about one third, is patients whose siblings are all hypertensive. In a small group, < 10% of all patients, half the siblings are hypertensive. 6. We conclude from these surprising findings that hypertension is not a continuous, multifactorial part of the normal blood pressure distribution. They suggest that several more single-gene disorders causing hypertension will be found. The sibships where all members are hypertensive are inconsistent with the segregation of Mendelian genetics and suggest the selection of some genes linked to hypertension at the time of gamete maturation.

Genetic Predisposition to Disease↗

A gene trap approach in Xenopus.

The frog transgenesis technique ultimately promises to make mutagenesis possible through random insertion of plasmid DNA into the genome. This study was undertaken to evaluate whether a gene trap approach combined with transgenesis would be appropriate for performing insertional mutagenesis in Xenopus embryos. Firstly, we confirmed that the transgenic technique results in stable integration into the genome and that transmission through the germline occurs in the expected Mendelian fashion. Secondly, we developed several gene trap vectors, using the green fluorescent protein (GFP) as a marker. Using these vectors, we trapped several genes in Xenopus laevis that are expressed in a spatially restricted manner, including expression in the epiphysis, the olfactory bulb and placodes, the eyes, ear, brain, muscles, tail and intestine. Finally, we cloned one of the trapped genes using 5' rapid amplification of cDNA ends polymerase chain reaction (RACE PCR). These results suggest that the transgenic technique combined with a gene trap approach might provide a powerful method for generating mutations in endogenous genes in Xenopus.

Amino Acid Sequence↗

Multilocus analysis of atopy in Korean children using multifactor-dimensionality reduction.

BACKGROUND: Atopy is considered to be a complex genetic trait and does not follow a simple mendelian pattern of inheritance. It is now well recognised that gene-gene interactions are important in complex genetic disease. AIM: To analyse the influence of gene-gene interactions in the development of atopy. METHODS: A total of 2055 ethnically identical participants aged 10-18 years living in rural areas on Jeju Island, Korea, were randomly recruited. Atopy was defined as a positive skin prick test response to one or more common inhalant allergens. Gene-gene interactions among 12 polymorphic loci were analysed in the seven candidate genes of atopy using the multidimensionality-reduction method. RESULTS: A significant interaction was found between V297I in the gene coding vascular endothelial growth factor receptor 2 (KDR) and -308G-->A in the gene coding tumour necrosis factor (TNF)alpha on the risk of atopy, with a cross-validation consistency of 10 out of 10 and a prediction error of 35.9% (p = 0.001). Conventional logistic regression also revealed significant interactions between KDR and TNF for atopy. Individuals with the variant allele of -308G-->A in TNF (GA or AA) and V297I in KDR (VI or II) had a significantly higher risk of atopy (OR 2.23; 95% CI 1.48 to 3.57). CONCLUSION: KDR and TNF may synergistically influence the development of atopy through gene-gene interaction in Korean children and adolescents.

Adolescent↗

Genetic polymorphism of the sixth component of complement (C6) in the rhesus monkey.

With isoelectric focusing, the complement protein C6 has been shown to be genetically polymorphic in the rhesus monkey. Three codominant alleles of a single autosomal locus, Rh C6, have been recognized: C6A, C6B, and C6R, with gene frequencies of 0.592, 0.354, and 0.053 in a random rhesus monkey population. Hardy-Weinberg analysis of the phenotypic frequencies in this population yielded observed values very close to those expected. Both natural mating between individuals carrying the various alleles and artificial combinations of sera of the different C6 types demonstrate patterns consistent with this model. Analysis of several families of monkeys confirmed the Mendelian autosomal codominant inheritance with numbers of offspring very close to expected values and no offspring types inconsistent with the mating pair types.

Animals↗

Association of IL12RB1 polymorphisms with pulmonary tuberculosis in adults in Morocco.

Five disease-causing genes, including the IL12RB1 gene that encodes the beta 1 chain of the receptor for interleukin (IL)-12 (IL-12R beta 1), are known to be associated with the syndrome of Mendelian susceptibility to mycobacterial diseases. Some IL-12R beta 1-deficient patients present with tuberculosis as the only clinical phenotype. A comprehensive genetic study of IL12RB1 was conducted among 101 Moroccan families, including 157 offspring (age, >15 years) who had culture-positive pulmonary tuberculosis (PTB). The promoter, exons, and flanking intron regions of IL12RB1 in 40 randomly selected patients with PTB were entirely sequenced, leading to the detection of 19 variants (including 10 novel mutations). Blood cells obtained from individuals who were homozygous for any of the 13 most common variants responded to IL-12, indicating that these polymorphisms were not loss-of-function mutations. By use of a family-based study, 2 promoter polymorphisms that were in strong linkage disequilibrium were found to be associated with PTB, especially -2C-->T (odds ratio for CT or TT vs. CC, 2.69 [95% confidence interval, 1.19-6.09]). This result suggests that IL12RB1 polymorphisms might influence the risk of development of PTB in adults.

Adolescent↗

A unique pollen wall mutation in the family Compositae: ultrastructure and genetics.

During a routine screening of pollen fertility in the n = 2 chromosome race of Haplopappus gracilis, a spineless pollen wall mutation was discovered that renders the otherwise functional pollen grains completely unrecognizable as Compositae pollen. Normal Haplopappus pollen is characterized by an outer layer, the ektexine, consisting of large spines supported by a roof (tectum), which in turn is supported by collumellae that are joined basally. A large cavity (cavea) stretches from aperture to aperture and separates columellae bases from the final ektexine unit, the foot layer. The spines, tectum, columellae, and columellae bases are filled with perforations (internal foramina), while the foot layer is without them. Immediately underlying the foot layer is a thickened, lamellate, disrupted, internal foramina-free second exine layer, the endexine. In contrast, the mutant pollen ektexine is a jumble of components with randomly dispersed spines as the only clearly definable unit. The endexine layer is similar to the endexine in normal pollen. The mutation apparently disrupts only the organization of ektexine units, and mutant pollen appears to be without the caveae and foot layer characteristic of normal pollen. In genetic tests, the mutant allele is recessive. There is a simple Mendelian pattern of inheritance of the mutant gene, and its phenotype is under sporophytic control.

Journal Article↗

Classification principles and genetics of chronic gastritis.

Two family samples, (i) a sample considered to represent the population at large (431 subjects) and (ii) a sample of first-degree relatives of index subjects (IS) with overt pernicious anaemia (183 subjects) were analyzed in order to evaluate the onset and course of chronic gastritis (CG) and the pathogenetic factors involved with special reference to the effects of genetic variation. The analysis was based on data obtained from two generations: first generation (sibs of the IS) and second (children of the IS). Formulae derived from Poisson process were used for age-correction of the gastritic changes. Otherwise, conventional statistical methods were used in the genetic analysis and the calculation of prevalences of CG. This approach enabled us to achieve a classification of gastritis into more specific subgroups and to evaluate the natural course of the disease. The progression of gastritis in the second generation (children; mean age 35 years) was roughly similar in antrum and body, indicating that gastritis starts as a diffuse process affecting both areas of the stomach to a rather similar degree. The start of CG and its progression is at least to some degree influenced by genetic factors and probably regulated by the male sex. Thus nearly all children of male IS's with a non-atrophic mucosa (normal mucosa or superficial gastritis) showed a normal mucosa suggesting the existence of a particular sex-bound, genetic mechanisms. These mechanisms may prevent or delay the progression of gastritis up to middle age, when a change in dynamics occurs leading to formation of more specific subtypes of CG. In the first generation (mean age 60 years) CG dispersed into more specific subtypes (corresponding to types A and B of Strickland and McKay and type AB of Glass) and to more advanced stages, which were connected with a higher than expected prevalence of advanced stages also in the relatives. The families of IS's with type A atrophic gastritis (AG) (severe AG in the body but no AG in antrum), type B (AG in antrum but no AG in body) and type AB AG (AG in both antrum and body) showed typical dynamic patterns of the age-specific prevalences of AG. Genetic calculations showed that the type A of AG found in pernicious anaemia patients and their relatives is inherited by a simple dominant gene, while this type of inheritance is statistically unlikely in the type B of AG. The type B, on the other hand, exhibited characteristics that indicate a recessive Mendelian inheritance.(ABSTRACT TRUNCATED AT 400 WORDS)

Adolescent↗

Tetrahymena macronuclear genome mapping: colinearity Of macronuclear coassortment groups and the micronuclear map on chromosome 1l.

The genetics of the ciliate Tetrahymena thermophila are richer than for most other eukaryotic cells, because Tetrahymena possesses two genomes: a germline (micronuclear) genome that follows a Mendelian model of genetic transmission and a somatic (macronuclear) genome, derived from the micronuclear genome by fragmentation, which follows a different genetic transmission model called phenotypic assortment. While genetic markers in the micronucleus fall into classical linkage groups under meiotic recombination and segregation, the same markers in the macronucleus fall into coassortment groups (CAGs) under phenotypic assortment by the random distribution of MAC chromosome pieces. We set out to determine whether genomic mapping in the macronucleus by genetic means is feasible. To investigate the relationship between the micronuclear map and coassortment groups, we systematically placed into CAGs all of the markers lying on chromosome 1L that are also found in the macronucleus. Sixteen CAGs were identified, 7 of which contain at least two loci. We have concluded that CAGs represent a fundamental genetic feature of the MAC. The MIC and MAC maps on 1L are colinear; that is, CAGs consist exclusively of markers that map to a continuous segment in a given region of the micronuclear map, with no intervening markers from other CAGs. These findings provide a solid foundation for exploiting the MAC chromosome pieces to build a physical map of the Tetrahymena genome.

Animals↗

Use of random amplified polymorphic DNA (RAPD) technique in inheritance studies of Plasmodium falciparum.

Effectiveness of random amplified polymorphic DNA (RAPD), a technique using 1 10-base primer to amplify random segments of genomic DNA, and some of its possible uses were tested in the A + T-rich genome of Plasmodium falciparum. The best concentrations of MgCl2, 60% G + C primer, and DNA were determined to be 4.0 mM, 0.4 microM, and 90-180 ng/15 microliters reaction, respectively. Use of 30% G + C primers did not allow amplification to occur. Application of RAPD to DNA of parent and progeny clones from a P. falciparum cross showed that polymorphisms identified in the parentals and tracked in the progeny were inherited in a Mendelian fashion and that RAPD-identified polymorphisms could be used as genetic markers. Some of these polymorphic markers were located on more than 1 chromosome, whereas others were specific for a single chromosome. Two of these markers, each located on chromosome 3 of 1 of the parental parasites, were missing from 2 of the 18 progeny, suggesting that deletions, or crossover events had occurred. RAPD markers also identified a higher number of nonparental-type progeny than expected, thus confirming previous observations for high genetic variability in malaria parasites.

Animals↗

Precise mapping of a locus affecting grain protein content in durum wheat.

Grain protein content (GPC) is an important factor in pasta and breadmaking quality, and in human nutrition. It is also an important trait for wheat growers because premium prices are frequently paid for wheat with high GPC. A promising source for alleles to increase GPC was detected on chromosome 6B of Triticum turgidum var. dicoccoides accession FA-15-3 (DIC). Two previous quantitative trait locus (QTL) studies found that the positive effect of DIC-6B was associated to a single locus located between the centromere and the Nor-B2 locus on the short arm of chromosome 6B. Microsatellite markers Xgwm508 and Xgwm193 flanking the QTL region were used in this study to develop 20 new homozygous recombinant substitution lines (RSLs) with crossovers between these markers. These 20 RSLs, plus nine RSLs developed in previous studies were characterized with four new RFLP markers located within this chromosome segment. Grain protein content was determined in three field experiments organized as randomized complete block designs with ten replications each. The QTL peaks for protein content were located in the central region of a 2.7-cM interval between RFLP markers Xcdo365 and Xucw67 in the three experiments. Statistical analyses showed that almost all lines could be classified unequivocally within low- and high- protein groups, facilitating the mapping of this trait as a single Mendelian locus designated Gpc-6B1. The Gpc-6B1 locus was mapped 1.5-cM proximal to Xcdo365 and 1.2-cM distal to Xucw67. These new markers can be used to reduce the size of the DIC chromosome segment selected in marker-assisted selection programs. Markers Nor-B2 and Xucw66 flanking the previous two markers can be used to select against the DIC segment and reduce the linkage drag during the transfer of Gpc-6B1 into commercial bread and pasta wheat varieties. The precise mapping of the high GPC gene, the high frequency of recombinants recovered in the targeted region, and the recent development of a tetraploid BAC library including the Gpc-6B1 DIC allele are the first steps towards the map-based cloning of this gene.

Alleles↗

Identification and inheritance of (GA/TC)n and (AC/GT)n repeats in the European flat oyster Ostrea edulis (L.).

Twelve microsatellites were isolated from a partial genomic library of Ostrea edulis using (GA/TC)n and (AC/GT)n probes and were subsequently sequenced. We estimate that, on average, 12,700 (GA/TC)n and 3900 (AC/GT)n microsatellites could be found in the genome assuming a random distribution. These estimates are high enough for the construction of a saturated genetic map. Primers were designed for three microsatellite loci, and analyses of polymorphism in a wild cohort revealed that one was suitable for population genetics studies (5 alleles), while the other two were highly polymorphic (between 17 and 48 alleles) and thus were more useful for paternity testing. Mendelian inheritance was tested on two full-sib families, and significant distortions of genotypic frequencies were found, although the gametic distributions seemed to be in agreement with Mendelian expectations. We interpret this as evidence for zygotic selection.

Animals↗