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At least 361 records · Page 20Linked to original sources
PubMed2001

Deleterious mutations and genetic variation for flower size in Mimulus guttatus.

Mimulus guttatus is a wildflower that exhibits substantial genetic variation in flower size. Here, we test the hypothesis that this variation is caused by deleterious mutations maintained through mutation-selection balance. The deleterious-mutation model predicts that rare, partially recessive alleles will be the primary source of variation. We test this prediction by measuring the change in the mean flower size (deltaM) and the directional dominance of flower size (deltaB) within a selection experiment. If variation is due to rare (partially) recessive alleles, deltaB/deltaM is expected to be positive and exceed one. However, we obtain negative values for deltaB/deltaM from three independent selection lines. This result is statistically inconsistent with the deleterious-mutation model.

Alleles↗
PubMed1997

HIV genetic variation is directed and restricted by DNA precursor availability.

The effects of deoxynucleoside triphosphate (dNTP) imbalances on the fidelity of human immunodeficiency virus type 1 (HIV-1) replication were investigated. Using detergent permeabilized virions and biased dNTP concentrations different types of hypermutants were readily produced. However, the mutant spectrum was different from naturally occurring hypermutants demonstrating that the host cell may restrict variation. Using a genetic screen based on the blue/white beta-galactosidase complementation assay, G --> A hypermutants were recovered from HIV-infected thymidine treated U937 cells. Furthermore, hypermutants were recovered from 1 to 2% of resting or activated peripheral blood mononuclear cells indicating that small proportions of primary cells had distorted intracellular [dTTP] and [dCTP]. Such imbalances may underlie a proportion of somatic and germline point mutations and shape to some extent the evolution of mammalian and viral genomes.

Base Sequence↗
PubMed1994

Genetic variation in lactation means of somatic cell scores for six breeds of dairy cattle.

Lactation means of somatic cell scores from sample days were used to estimate the components of variation for additive genetic, permanent environmental, and herd-sire interaction effects. Data included records of 4314 Ayrshire, 7845 Brown Swiss, 18,115 Guernsey, 1,135,752 Holstein, 67,862 Jersey, and 787 Milking Shorthorn cows from across the US. Records were preadjusted for length of lactation. Fixed effects of herd-year, calving age, and calving month were included in animal models for estimation of variance components. Additive genetic estimates from REML relative to a phenotypic variance of 1.00 were .07 for Ayrshires, .07 for Brown Swiss, .11 for Guernseys, .09 for Holsteins, .09 for Jerseys, and .08 for Milking Shorthorns; permanent environmental estimates were .25, .26, .22, .21, .20, and .35; and herdsire interaction estimates were .04, .02, .00, .02, .02, and .01. Effects of calving age were similar for all regions of the US but differed for Jerseys and Holsteins. Effects of calving month were similar for all breeds. Cows calving during summer had the highest lactation means for somatic cell score from sample days. Impact of calving month was greatest in the Southeast.

Animals↗
PubMed2000

New genetic variation in European hares, Lepus granatensis and L. europaeus.

Six genetic polymorphisms for the Iberian hare (Lepus granatensis) and four for the brown hare (L. europaeus) are newly described. The genetic variation of peptidases B (PEPB) and C (PEPC), hemoglobin alpha chain (HBA), hemopexin (HPX), vitamin D binding protein (GC), and properdin factor B (BF) was assessed by conventional electrophoresis and isoelectric focusing in carrier ampholytes and hybrid pH gradients. Six alleles were detected in PEPB, three in PEPC, four in HBA, six in GC, five in HPX, and six in BF. At least one allele was shared between species at all loci except HBA. The allelic overlap between the two species was medium to high in PEPB, GC, and HPX and small in PEPC and BF.

Alleles↗
PubMed2006

Genetic variation in thyroid hormone pathway genes; polymorphisms in the TSH receptor and the iodothyronine deiodinases.

Serum thyroid parameters show substantial inter-individual variability, in which genetic variation is a major factor. Findings in patients with subclinical hyper- and hypothyroidism illustrate that even minor alterations in serum thyroid function tests can have important consequences for a variety of thyroid hormone-related clinical endpoints, such as atherosclerosis, bone mineral density, obesity, and heart rate. In the last few years, several studies described polymorphisms in thyroid hormone pathway genes that alter serum thyroid function tests. In this review, we discuss the genetic variation in the TSH receptor and iodothyronine deiodinases. We discuss the possible consequences of these studies for the individual patient and also the new insights in thyroid hormone action that can be obtained from these data.

Animals↗
PubMed2004

Influence of dominance, leptokurtosis and pleiotropy of deleterious mutations on quantitative genetic variation at mutation-selection balance.

In models of maintenance of genetic variance (V (G)) it has often been assumed that mutant alleles act additively. However, experimental data show that the dominance coefficient varies among mutant alleles and those of large effect tend to be recessive. On the basis of empirical knowledge of mutations, a joint-effect model of pleiotropic and real stabilizing selection that includes dominance is constructed and analyzed. It is shown that dominance can dramatically alter the prediction of equilibrium V (G). Analysis indicates that for the situations where mutations are more recessive for fitness than for a quantitative trait, as supported by the available data, the joint-effect model predicts a significantly higher V (G) than does an additive model. Importantly, for what seem to be realistic distributions of mutational effects (i.e., many mutants may not affect the quantitative trait substantially but are likely to affect fitness), the observed high levels of genetic variation in the quantitative trait under strong apparent stabilizing selection can be generated. This investigation supports the hypothesis that most V (G) comes from the alleles nearly neutral for fitness in heterozygotes while apparent stabilizing selection is contributed mainly by the alleles of large effect on the quantitative trait. Thus considerations of dominance coefficients of mutations lend further support to our previous conclusion that mutation-selection balance is a plausible mechanism of the maintenance of the genetic variance in natural populations.

Genes, Dominant↗
PubMed2000

Patterns of genetic variation in Gymnadenia conopsea, the fragrant orchid.

Gymnadenia conopsea (L.) R. Br., or the fragrant orchid, is one of many plant species negatively influenced by new practices in agriculture and forestry during the last decades. This study describes the level of microsatellite variation within and among 10 Swedish populations of this species. It was not possible to detect strong effects of small population size or fragmentation. In general, the species had high genetic variation within and low genetic divergence among populations, although the correlation between population size and number of alleles was close to significance at the 95% level. Also, a significant isolation by distance effect was observed, indicating the presence of modest restrictions in gene dispersal between the investigated populations.

DNA, Plant↗
PubMed1990

Genetic variation for gas exchange rates in grain sorghum.

Carbon assimilation rate (A) and stomatal conductance (g) are highly correlated. However, the slope of the A versus g relationship differs among species and environments resulting in differences in gas exchange efficiency which should reflect water use efficiency. The objective of this research was to determine the genetic variation for A and g in grain sorghum (Sorghum bicolor [L.] Moench.). Field experiments were conducted using 30 sorghum hybrids with four water supply treatments. A, g, and leaf water potential (Psi(w)) of individual leaves were monitored every 15 to 20 days. Significant genetic variation existed among the hybrids for A and g. Plant age and water supply also affected A and g as expected. When A was regressed on g for each hybrid, large and significant differences existed among the slopes, implying differences in intrinsic gas exchange efficiency. The regression analysis of A and g versus Psi(w) suggested that A was more sensitive than g to increasing water stress. Genetic differences in the rate of change in A as water stress increased were observed. Regression analysis was used to evaluate the individual hybrid response relative to other hybrids. Twofold difference in slopes existed for A. These results provide evidence for genetic variation in gas exchange rates which might directly contribute to whole plant water use efficiency and productivity.

Journal Article↗
PubMed1994

Identification of genetic variation in the human serotonin 1D beta receptor gene.

Disturbances of serotonergic pathways have been implicated in a wide variety of neuropsychiatric disorders such as depression, anxiety, migraine, and substance abuse. Genetic variation in genes coding for serotonin receptor proteins might well be involved in the genetic predisposition to these diseases and/or of pharmacogenetic relevance. Genomic samples from 46 unrelated healthy subjects were investigated by single-strand conformation analysis (SSCA) to screen for genetic variation in the human serotonin 1D beta (5-HT1D beta) receptor gene. Overlapping PCR (polymerase chain reaction) fragments covered the whole coding sequence as well as 5' untranslated regions of the 5-HT1D beta gene. Four nucleotide sequence variants were found: a coding mutation in nucleotide position 371 which leads to an amino acid exchange (Phe-->Cys) in position 124 of the receptor protein and three mutations in the 5' flanking region. For all mutations specific PCR-based assays were developed which allow rapid genotyping in populations and families. To our knowledge, the Phe-124-Cys substitution is the first natural occurring molecular variant which has been identified for the 5-HT1D beta receptor so far.

Alleles↗
PubMed1999

Low genetic variation in muskoxen (Ovibos moschatus) from western Greenland using microsatellites.

Muskoxen are large herbivores living in Arctic environments. Lack of genetic variation in allozymes has made it difficult to study the social and genetic structure of this species. In this study, we have tried to find polymorphic microsatellite loci using both cattle-derived microsatellite primers and primers developed from a genomic plasmid library of muskoxen. Only limited variation was found for both sets of microsatellite loci. We conclude that this consistent low genetic variation is probably due to demographic features of the muskoxen populations rather than to methodological constraints caused by the transfer of microsatellites between species.

Animals↗
PubMed2002

Genetic variation in proinflammatory and anti-inflammatory cytokine production in multiple organ dysfunction syndrome.

OBJECTIVES: The objectives of this study were to examine the prevalence of genetic variation for cytokine production (tumor necrosis factor [TNF]-alpha, interleukin-10, transforming growth factor-beta1) in patients with multiple organ dysfunction syndrome, to measure circulating cytokine levels and relate these to genotype, and to identify the relationship between genetic variation and outcome. DESIGN: Prospective analysis. SETTING: Intensive care unit of a university teaching hospital. PATIENTS: Eighty-eight critically ill patients with multiple organ dysfunction syndrome. MEASUREMENTS AND MAIN RESULTS: The frequency of the different interleukin-10 genotypes (corresponding to high, intermediate, and low interleukin-10 production ) were significantly different between controls and multiple organ dysfunction syndrome patients. High interleukin-10 producers were under-represented in the multiple organ dysfunction syndrome group: This genotype occurred in 30% of controls but in only 6% of patients ( <.001). There was no relationship between interleukin-10 genotype and mortality. The frequency of TNF-alpha genotypes was also significantly different between patients and controls. Intermediate TNF-alpha producers were under-represented (5.7% vs. 23%) and high TNF-alpha producers over-represented (35.2% vs. 16%) in the patient group (p <.001). TNF-alpha genotype was not related to mortality. The distribution of TNF-beta genotypes (homozygous B1, homozygous B2, and heterozygotes) was also different between controls and patients (p =.008). The B2/B2 genotype (associated with high TNF-alpha production) tended to occur less frequently in the intensive care unit population (31% vs. 50%) and was associated with a higher mortality rate than either the B1/B1 or B1/B2 genotypes (48% vs. 11% and 33% respectively, p=.115). The combination of proinflammatory (TNF-alpha/TNF-beta) and anti-inflammatory (interleukin-10/transforming growth factor-beta1) cytokine genotypes was associated with prolonged patient survival time. Patients predisposed to produce a balanced cytokine response (e.g., intermediate interleukin-10/TNF-alpha producers) demonstrated the longest survival times, although overall mortality was no different. CONCLUSION: A genetic predisposition to high interleukin-10 production or intermediate TNF-alpha production may be protective of admission to the intensive care unit, although once admitted, any protection provided by these genotypes seems to be lost. TNF-beta genotype conferred no advantage to patients with multiple organ dysfunction syndrome, the TNFB2 allele being associated with increased mortality. The combination of proinflammatory and anti-inflammatory cytokine genotypes supports the idea that a balanced cytokine response is favorable and was associated with prolonged patient survival time.

Adolescent↗
PubMed2005

Genetic variations and haplotypes of UGT1A4 in a Japanese population.

Nineteen genetic variations, including 11 novel ones, were found in exon 1 and its flanking region of the UDP-glucuronosyltransferase (UGT) 1A4 gene from 256 Japanese subjects, consisting of 60 healthy volunteers, 88 cancer patients and 108 arrhythmic patients. These variations include -217T>G and -36G>A in the 5'-flanking region, 30G>A (P10P), 127delA (43fsX22; frame-shift from codon 43 resulting in the termination at the 22nd codon, codon 65), 175delG (59fsX6), 271C>T (R91C), 325A>G (R109G), and 357T>C (N119N) in exon 1, and IVS1+1G>T, IVS1+98A>G and IVS1+101G>T in the following intron. Among them, 127delA and 175delG can confer early termination of translation, resulting in an immature protein that probably lacks enzymatic activity. Variation IVS1+1G>T is located at a splice donor site and thus may lead to aberrant splicing. Since we did not find any significant differences in the frequencies of all the variations among the three subject groups, the data were analyzed as one group. The allele frequencies of the novel variations were 0.006 for IVS1+101G>T, 0.004 for 30G>A (P10P) and 357T>C (N119N), and 0.002 for the 8 other variations. In addition, the two known nonsynonymous single nucleotide polymorphisms (SNPs), 31C>T (R11W) and 142T>G (L48V), were found at 0.012 and 0.129 frequencies, respectively. The SNP 70C>A (P24T), mostly linked with 142T>G (L48V) in German Caucasians, was not detected in this study. Sixteen haplotypes were identified or inferred, and some haplotypes were confirmed by cloning and sequencing. It was shown that most of 142T>G (L48V) was linked with -219C>T, -163G>A, 448T>C (L150L), 804G>A (P268P), and IVS1+43C>T, comprising haplotype *3a; haplotype *4a harbors 31C>T (R11W); 127delA (43fsX22) and 142T>G (L48V) were linked (haplotype *5a); 175delG (59fsX6) was linked with 325A>G (R109G) (*6a haplotype); and -219C>T, -163G>A, 142T>G (L48V), 271C>T (R91C), 448T>C (L150L), 804G>A (P268P), and IVS1+43C>T comprised haplotype *7a. Our results provide fundamental and useful information for genotyping UGT1A4 in the Japanese and probably Asian populations.

Arrhythmias, Cardiac↗
PubMed2004

Natural genetic variation caused by transposable elements in humans.

Transposons and transposon-like repetitive elements collectively occupy 44% of the human genome sequence. In an effort to measure the levels of genetic variation that are caused by human transposons, we have developed a new method to broadly detect transposon insertion polymorphisms of all kinds in humans. We began by identifying 606,093 insertion and deletion (indel) polymorphisms in the genomes of diverse humans. We then screened these polymorphisms to detect indels that were caused by de novo transposon insertions. Our method was highly efficient and led to the identification of 605 nonredundant transposon insertion polymorphisms in 36 diverse humans. We estimate that this represents 25-35% of approximately 2075 common transposon polymorphisms in human populations. Because we identified all transposon insertion polymorphisms with a single method, we could evaluate the relative levels of variation that were caused by each transposon class. The average human in our study was estimated to harbor 1283 Alu insertion polymorphisms, 180 L1 polymorphisms, 56 SVA polymorphisms, and 17 polymorphisms related to other forms of mobilized DNA. Overall, our study provides significant steps toward (i) measuring the genetic variation that is caused by transposon insertions in humans and (ii) identifying the transposon copies that produce this variation.

DNA Transposable Elements↗
PubMed2005

Genetic variation, occurrence of mating types and different forms of Pyrenophora teres causing net blotch of barley in Finland.

The amplified fragment length polymorphism (AFLP) was used to study genetic variation in Pyrenophora teres causing net blotch of barley in Finland. The mean similarity was 93% between all isolates and a bit higher within two distinct populations based on 175 AFLP markers. Despite the high genetic similarity, 70 unique AFLP genotypes were identified among 72 isolates. Most of the genetic variation (68.5%) was observed within a field population and a smaller portion (30.3%) between them. Significant genetic differentiation (Fst = 0.308, P < 0.001) was identified between field populations. However only 1.2% of the variation was observed between mating types within a field and a lack of genetic differentiation (Fsc = 0.017, P = 0.087) was observed. The occurrence of the form of blotch (spot type, f. sp. maculata, or net type, P. teres f. sp. teres) was identified with specific PCR. All isolates were found to be of the net type. The existence of both mating types (MAT1 and MAT2) was identified for the first time in Finland and the ratio of the two mating types was almost 1:1 in both locations. The evolutionary potential and the possibility of sexual reproduction of P. teres occurring in Finland are discussed.

Ascomycota↗
PubMed1995

The expression of additive and nonadditive genetic variation under stress.

Experimental lines of Drosophila melanogaster derived from a natural population, which had been isolated in the laboratory for approximately 70 generations, were crossed to determine if the expression of additive, dominance and epistatic genetic variation in development time and viability was associated with the environment. No association was found between the level of additive genetic effects and environmental value for either trait, but nonadditive genetic effects increased at both extremes of the environmental range for development time. The expression of high levels of dominance and epistatic genetic variation at environmental extremes may be a general expectation for some traits. The disruption of the epistatic gene complexes in the parental lines resulted in hybrid breakdown toward faster development and there was some indication of hybrid breakdown toward higher viability. A combination of genetic drift and natural selection had therefore resulted in different epistatic gene complexes being selected after approximately 70 generations from a common genetic base. After crossing, the hybrid populations were observed for 10 generations. Epistasis contributed on average 12 hr in development time. Fluctuating asymmetry in sternopleural bristle number also evolved in the hybrid populations, decreasing by > 18% in the first seven generations after hybridization.

Animals↗