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Gene Action (gene + action)
Selected AbstractsLogistic Regression Models for Polymorphic and Antagonistic Pleiotropic Gene Action on Human Aging and LongevityANNALS OF HUMAN GENETICS, Issue 6 2003Qihua Tan Summary In this paper, we apply logistic regression models to measure genetic association with human survival for highly polymorphic and pleiotropic genes. By modelling genotype frequency as a function of age, we introduce a logistic regression model with polytomous responses to handle the polymorphic situation. Genotype and allele-based parameterization can be used to investigate the modes of gene action and to reduce the number of parameters, so that the power is increased while the amount of multiple testing minimized. A binomial logistic regression model with fractional polynomials is used to capture the age-dependent or antagonistic pleiotropic effects. The models are applied to HFE genotype data to assess the effects on human longevity by different alleles and to detect if an age-dependent effect exists. Application has shown that these methods can serve as useful tools in searching for important gene variations that contribute to human aging and longevity. [source] EPISTASIS AND THE TEMPORAL CHANGE IN THE ADDITIVE VARIANCE-COVARIANCE MATRIX INDUCED BY DRIFTEVOLUTION, Issue 8 2004Carlos López-Fanjul Abstract The effect of population bottlenecks on the components of the genetic covariance generated by two neutral independent epistatic loci has been studied theoretically (additive, covA; dominance, covD; additive-by-additive, covAA; additive-by-dominance, covAD; and dominance-by-dominance, covDD). The additive-by-additive model and a more general model covering all possible types of marginal gene action at the single-locus level (additive/dominance epistatic model) were considered. The covariance components in an infinitely large panmictic population (ancestral components) were compared with their expected values at equilibrium over replicates randomly derived from the base population, after t consecutive bottlenecks of equal size N (derived components). Formulae were obtained in terms of the allele frequencies and effects at each locus, the corresponding epistatic effects and the inbreeding coefficient Ft. These expressions show that the contribution of nonadditive loci to the derived additive covariance (covAt) does not linearly decrease with inbreeding, as in the pure additive case, and may initially increase or even change sign in specific situations. Numerical examples were also analyzed, restricted for simplicity to the case of all covariance components being positive. For additive-by-additive epistasis, the condition covAt > covA only holds for high frequencies of the allele decreasing the metric traits at each locus (negative allele) if epistasis is weak, or for intermediate allele frequencies if it is strong. For the additive/dominance epistatic model, however, covAt > covA applies for low frequencies of the negative alleles at one or both loci and mild epistasis, but this result can be progressively extended to intermediate frequencies as epistasis becomes stronger. Without epistasis the same qualitative results were found, indicating that marginal dominance induced by epistasis can be considered as the primary cause of an increase of the additive covariance after bottlenecks. For all models, the magnitude of the ratio covAt/covA was inversely related to N and t. [source] THE EFFECT OF EPISTASIS ON THE EXCESS OF THE ADDITIVE AND NONADDITIVE VARIANCES AFTER POPULATION BOTTLENECKSEVOLUTION, Issue 5 2002Carlos López-Fanjul Abstract The effect of population bottlenecks on the components of the genetic variance generated by two neutral independent epistatic loci has been studied theoretically (VA, additive; VD, dominant; VAA, additive × additive; VAD, additive × dominant; VDD; dominant × dominant components of variance). Nonoverdominance and overdominance models were considered, covering all possible types of marginal gene action at the single locus level. The variance components in an infinitely large panmictic population (ancestral components) were compared with their expected values at equilibrium, after t consecutive bottlenecks of equal size N (derived components). Formulae were obtained in terms of allele frequencies and effects at each locus and the corresponding epistatic value. An excess of VA after bottlenecks can be assigned to two sources: (1) the spatiotemporal changes in the marginal average effects of gene substitution ai, which are equal to zero only for additive gene action within and between loci; and (2) the covariance between a2i and the heterozygosity at the loci involved, which is generated by dominance, with or without epistasis. Numerical examples were analyzed, indicating that an increase in VA after bottlenecks will only occur if its ancestral value is minimal or very small. For the nonoverdominance model with weak reinforcing epistasis, that increase has been detected only for extreme frequencies of the negative allele at one or both loci. With strong epistasis, however, this result can be extended to a broad range of intermediate frequencies. With no epistasis, the same qualitative results were found, indicating that dominance can be considered as the primary cause of an increase in VA following bottlenecks. In parallel, the derived total nonadditive variance exceeded its ancestral value (VNA= VD+ VAA+VAD+ VDD) for a range of combinations of allele frequencies covering those for an excess of VA and for very large frequencies of the negative allele at both loci. For the overdominance model, an increase in VA and VNA was respectively observed for equilibrium (intermediate) frequencies at one or both loci or for extreme frequencies at both loci. For all models, the magnitude of the change of VA and VNA was inversely related to N and t. At low levels of inbreeding, the between-line variance was not affected by the type of gene action. For the models considered, the results indicate that it is unlikely that the rate of evolution may be accelerated after population bottlenecks, in spite of occasional increments of the derived VA over its ancestral value. [source] A unified framework for transmission-disequilibrium test analysis of discrete and continuous traitsGENETIC EPIDEMIOLOGY, Issue 1 2002Ying Liu Abstract This paper presents a unified framework for transmission-disequilibrium tests for discrete and continuous traits. A conditional score test is derived that maximizes power to detect small effects for any exponential family distribution, which includes binary and normal distributions, and distributions that are skewed or have non-normal kurtosis. The specific distributional form need not be specified, and the method applies to sibships of arbitrary size. Formulas for the distribution of the test statistic are given for models including complex genetic effects (additive, dominant, and recessive gene action), covariates, multiple gene models including gene-gene interactions or heterogeneity, and gene-environment interactions. We develop refinements of our method for trait-based sampling designs and multiple siblings that can have dramatic effects on power. Genet. Epidemiol. 22:26,40, 2002. © 2002 Wiley-Liss, Inc. [source] Epigenetic gambling and epigenetic drift as an antagonistic pleiotropic mechanism of agingAGING CELL, Issue 6 2009George M. Martin Summary Generations of biogerontologists have been puzzled by the marked intraspecific variations in lifespan of their experimental model organisms despite all efforts to control both genotype and environment. The most cogent example comes from life table studies of wild-type Caenorhabditis elegans when grown in suspension cultures using axenic media. While nuclear and mitochondrial somatic mutations and ,thermodynamic noise' likely contribute to such lifespan variegations, I raise an additional hypothetical mechanism, one that may have evolved as a mechanism of phenotypic variation which could have preceded the evolution of meiotic recombination. I suggest that random changes in cellular gene expression (cellular epigenetic gambling or bet hedging) evolved as an adaptive mechanism to ensure survival of members of a group in the face of unpredictable environmental challenges. Once activated, it could lead to progressive epigenetic variegation (epigenetic drift) amongst all members of the group. Thus, while particular patterns of gene expression would be adaptive for a subset of reproductive individuals within a population early in life, once initiated, I predict that continued epigenetic drift will result in variable onsets and patterns of pathophysiology , perhaps yet another example of antagonistic pleiotropic gene action in the genesis of senescent phenotypes. The weakness of this hypothesis is that we do not currently have a plausible molecular mechanism for the putative genetic ,randomizer' of epigenetic expression, particularly one whose ,setting' may be responsive to the ecology in which a given species evolves. I offer experimental approaches, however, to search for the elusive epigenetic gambler(s). [source] Genetic Analysis of Tolerance to Rice Tungro Bacilliform Virus in Rice (Oryza sativa L.) Through AgroinoculationJOURNAL OF PHYTOPATHOLOGY, Issue 4 2006N. S. Zenna Abstract Balimau Putih [an Indonesian cultivar tolerant to rice tungro bacilliform virus (RTBV)] was crossed with IR64 (RTBV, susceptible variety) to produce the three filial generations F1, F2 and F3. Agroinoculation was used to introduce RTBV into the test plants. RTBV tolerance was based on the RTBV level in plants by analysis of coat protein using enzyme-linked immunosorbent assay. The level of RTBV in cv. Balimau Putih was significantly lower than that of IR64 and the susceptible control, Taichung Native 1. Mean RTBV levels of the F1, F2 and F3 populations were comparable with one another and with the average of the parents. Results indicate that there was no dominance and an additive gene action may control the expression of tolerance to RTBV. Tolerance based on the level of RTBV coat protein was highly heritable (0.67) as estimated using the mean values of F3 lines, suggesting that selection for tolerance to RTBV can be performed in the early selfing generations using the technique employed in this study. The RTBV level had a negative correlation with plant height, but positive relationship with disease index value. [source] Quantitative trait loci analysis of mineral element concentrations in an Arabidopsis halleri × Arabidopsis lyrata petraea F2 progeny grown on cadmium-contaminated soilNEW PHYTOLOGIST, Issue 2 2010Glenda Willems Summary ,This study describes the quantitative trait locus (QTL) analysis of cadmium (Cd), zinc (Zn), iron (Fe), potassium (K), magnesium (Mg) and calcium (Ca) accumulation in the pseudometallophyte Arabidopsis halleri under conditions of Cd excess using an interspecific A. halleri × Arabidopsis lyrata F2 population. ,Our data provide evidence for the implication of one major QTL in Cd hyperaccumulation in A. halleri, and suggests that Cd tolerance and accumulation are not independent in A. halleri. Moreover, the major loci responsible for Zn hyperaccumulation in the absence of Cd appear to be the same when Cd is present at high concentrations. ,More than twofold higher Fe concentrations were measured in A. halleri shoots than in A. lyrata, suggesting a different regulation of Fe accumulation in the hyperaccumulator. ,With the exception of Ca, the accumulation of Cd was significantly correlated with the accumulation of all elements measured in the F2 progeny, suggesting pleiotropic gene action. However, QTL analysis identified pleiotropic QTLs only for Cd, Zn and Fe. Mg accumulation was negatively correlated with Cd accumulation, as well as with dry shoot biomass, suggesting that it might indicate cellular damage. [source] Identification of sources and inheritance of resistance of Chinese Brassica vegetables to white blisterPLANT BREEDING, Issue 6 2009M. R. Santos Abstract There is no information in the literature about the variability of resistance of Chinese Brassica vegetables, pak choi and Chinese cabbage, to the white blister disease caused by Albugo candida (Pers.) Kuntze. A collection of 43 accessions of pak choi and 19 accessions of Chinese cabbage was screened for resistance to the Portuguese A. candida isolate Ac 506 at the cotyledon stage. Different levels of resistance were found among the germplasm tested, ranging from complete resistance to full susceptibility. Most of the accessions were highly susceptible with less than 10% of resistant seedlings, and only four accessions of pak choi, presenting more than 50% resistant seedlings, were considered as new sources or resistance to white blister. Inheritance of resistance at the cotyledon stage was studied in two crosses between the most resistant pak choi accession, BRA 117, and the highly susceptible rapid cycling Brassica rapa line CrGC 1.19. It was proposed that resistance to white blister in pak choi BRA 117 is controlled by two nuclear genes with dominant recessive epistatic gene action. [source] Inheritance of heading time in spring barley evaluated in multiple environmentsPLANT BREEDING, Issue 3 2001L. W. Gallagher Abstract The inheritance of heading time of spring barley was studied in three extremely early genotypes IB, RL and ,Mona' (M), which is homozygous recessive for the early maturity ea8 (=eak) gene conferring extreme earliness under short daylengths and is relatively photoperiod insensitive, and five (GP, MA, PS, NU and BA) spring genotypes that are early to intermediate for heading time. Frequency distributions of F2 generations grown at Ouled Gnaou, Morocco (32°15, N), an environment which maximizes differences between photoperiod-insensitive and photoperiod-sensitive genotypes, indicated that across populations many loci were segregating in a complex Mendelian manner. IB and RL were both homozygous recessive for the ea8 gene, which conferred an early heading time. RL had partially dominant alleles at second locus (Enea8), which enhanced its earliness. Recovery of only progeny within the parental range of genotypes for heading time from the crosses of RL/M and IB/M suggests that numerous loci remained suppressed, perhaps latent, given their diverse parentage. The ea8 recessive homozygote in RL suppressed another unidentified locus which, when homozygous recessive in the absence of the ea8 recessive homozygote, conferred extreme earliness in one short daylength environment (Ouled Gnaou, Morocco) but was undetected in another environment (Davis, CA, USA). Epistatic gene action and genotype × environment effects strongly influenced heading time. In addition to a genetic system consisting of single-locus recessive homozygotes conferring photoperiod insensitivity, a second genetic system, based on dominant alleles at one or a few loci, derived from the early heading Finnish landrace ,Olli', also confers extremely early heading time under short daylengths and relative photoperiod insensitivity in the genotype GP. [source] Heterotic effects for yield and tuber solids and type of gene action for five traits in 4x potato families derived from interploid (4x-2x) crossesPLANT BREEDING, Issue 2 2000J. A. Buso Abstract The degree of heterosis for total tuber yield (TTY) and total solids (TS) in 4x-2x crosses was estimated by comparing the performance of 12 families with their respective parents in two locations in Wisconsin (USA). The parental 2x clones were Phureja-haploid Tuberosum hybrids with 2n -pollen production by first-division restitution. The general combining ability (GCA) and specific combining ability (SCA) were estimated for TTY, TS, vine maturity (VM), length of tuber sprout dormancy (LD), and tuber eye depth (ED). Family performance for TTY ranged from 74 to 146% at Hancock (E#1) and from 77 to 287 at Rhinelander (E#2) when compared with that of the 4x parent group. For VM, the families were late maturing, but a few precocious ones were identified. For TS, the families had heterosis of 5.1% over the 4x parent group. The families had slightly higher ED values than the 4x parents, but families with values within the commercial range were identified. The family average for LD (54 days) was closer to the 2x group (51 days) than to the 4x group (88 days). The direction and magnitude of the parent-family relationships were variable. The 4x parent TTY was correlated with progeny in E#1 but not E#2. The 2x parent VM had correlation with the offspring at E#2 but not at E#1. The type of gene action had a trait-specific expression. Significant SCA and GCA variances were observed, suggesting that additive as well as non-additive genetic effects were operating. The 4x-2x crosses were able to generate heterotic families for TTY and TS in combination with other useful traits. However, no promising results were found for LD because of the apparent dominance of the short-dormancy phenotype. This result indicates the need of additional selection and breeding efforts for some specific traits when using S. phureja -derived germplasm. [source] Logistic Regression Models for Polymorphic and Antagonistic Pleiotropic Gene Action on Human Aging and LongevityANNALS OF HUMAN GENETICS, Issue 6 2003Qihua Tan Summary In this paper, we apply logistic regression models to measure genetic association with human survival for highly polymorphic and pleiotropic genes. By modelling genotype frequency as a function of age, we introduce a logistic regression model with polytomous responses to handle the polymorphic situation. Genotype and allele-based parameterization can be used to investigate the modes of gene action and to reduce the number of parameters, so that the power is increased while the amount of multiple testing minimized. A binomial logistic regression model with fractional polynomials is used to capture the age-dependent or antagonistic pleiotropic effects. The models are applied to HFE genotype data to assess the effects on human longevity by different alleles and to detect if an age-dependent effect exists. Application has shown that these methods can serve as useful tools in searching for important gene variations that contribute to human aging and longevity. [source] Sex-Specific Aggression and Antipredator Behaviour in Young Brown TroutETHOLOGY, Issue 7 2001Jörgen I. Johnsson Sex differences in adult behaviour are often interpreted as consequences of sexual selection and/or different reproductive roles in males and females. Sex-specific juvenile behaviour, however, has received less attention. Adult brown trout males are more aggressive than females during spawning and juvenile aggression may be genetically correlated with adult aggression in fish. We therefore tested the prediction that immature brown trout males are more aggressive and bolder than immature females. Because previous work has suggested that precocious maturation increases dominance in salmonids, we included precocious males in the study to test the prediction that early sexual maturation increase male aggression and boldness. Aggression and dominance relations were estimated in dyadic contests, whereas boldness was measured as a response to simulated predation risk using a model heron. Independent of maturity state, males initiated more than twice as many agonistic interactions as females in intersexual contests. However, males were not significantly more likely to win these contests than females. The response to a first predator attack did not differ between sex categories, but males reacted less to a second predator attack than females. Sexual maturity did not affect the antipredator response in males. Since there is no evidence from field studies that stream-living immature male and female salmonids differ in growth rate, it appears unlikely that the sex differences demonstrated are behavioural consequences of sex-specific investment in growth. It seems more likely that sex-specific behaviour arises as a correlated response to sexually selected gene actions promoting differential behaviour in adult males and females during reproduction. Alternatively, sex differences may develop gradually during juvenile life, because a gradual developmental program should be less costly than a sudden behavioural change at the onset of sexual maturity. [source] | ||||||||||