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At least 739 records · Page 41Linked to original sources
PubMed2000

Comparison of genetic variability and parentage in different ploidy classes of the Japanese oyster Crassostrea gigas.

Chemical treatments with cytochalasin B were used to induce triploidy in the progeny of a mass fertilization of 3 male and 7 female Crassostrea gigas parents. Triploids were produced either by retention of the first (meiosis I (MI) triploids) or the second (meiosis II (MII) triploids) polar bodies. These animals, together with their diploid siblings, were divided for two experiments. One set was used to compare physiological performance, and the other set deployed to compare growth in two different natural environments. For both experiments, genetic variability in different ploidy classes was estimated using three microsatellite loci and eight allozyme loci. The microsatellite loci were highly polymorphic, allowing independent confirmation of ploidy status and the unambiguous identification of parentage for each oyster. Significant differences in parentage were found between ploidy classes, despite the fact they originated from the same mass fertilization. This indicates that the assumptions of a common genetic background among random samples of animals taken from the same mass fertilization may not be generally valid. Knowledge of parentage also allowed the more accurate scoring of allozyme loci. As expected, triploids were found to be significantly more polymorphic than diploids. However, MI triploids were not significantly more polymorphic than MII triploids. MII triploid genotypes were used to estimate recombination rates between loci and their centromeres. These rates varied between 0.29 and 0.71, indicating only moderate chiasma interference.

Alleles↗
PubMed2001

Linkage disequilibrium mapping of the bolting gene in sea beet using AFLP markers.

The possibility of using linkage disequilibrium mapping in natural plant populations was assessed. In studying linkage disequilibrium among 137 mapped AFLP markers in four populations of sea beet (Beta vulgaris ssp. maritima (L.) Arcang.) it was shown that tightly linked loci could be detected by screening for associations. It was hypothesized that the short distances spanned by linkage disequilibrium enable markers that are very tightly linked to a target gene to be identified. The hypothesis was tested by whole-genome screening of AFLP markers for association with the gene for the annual growth habit, the B gene, in a sample of 106 sea beets. Despite the dominant nature of AFLP, two markers showing significant linkage disequilibrium with the B gene were detected. The results indicate the potential use of linkage disequilibrium for gene mapping in natural plant populations.

Alleles↗
PubMed2004

On the prediction of simultaneous inbreeding coefficients at multiple loci.

A new deterministic method for predicting simultaneous inbreeding coefficients at three and four loci is presented. The method involves calculating the conditional probability of IBD (identical by descent) at one locus given IBD at other loci, and multiplying this probability by the prior probability of the latter loci being simultaneously IBD. The conditional probability is obtained applying a novel regression model, and the prior probability from the theory of digenic measures of Weir and Cockerham. The model was validated for a finite monoecious population mating at random, with a constant effective population size, and with or without selfing, and also for an infinite population with a constant intermediate proportion of selfing. We assumed discrete generations. Deterministic predictions were very accurate when compared with simulation results, and robust to alternative forms of implementation. These simultaneous inbreeding coefficients were more sensitive to changes in effective population size than in marker spacing. Extensions to predict simultaneous inbreeding coefficients at more than four loci are now possible.

Data Interpretation, Statistical↗
PubMed2004

The effect of an imprecise map on interval mapping QTLs.

The statistical analysis of quantitative trait locus (QTL) experiments relies on the use of a linkage map of the markers genotyped. Such a map is, at best, a good estimate of the true map. Resources might be diverted into developing better marker maps or improved maps become available after the analysis, raising concerns over the original analysis. It is therefore important to understand the sensitivity of QTL analysis to map inaccuracy. We have used simulation methods to investigate the consequences of an incorrect map on the results of a QTL analysis using interval mapping. Backcross data sets were generated with a particular map and then analysed with both the correct map and incorrect maps. If the incorrect maps maintained the true linkage groups (i.e. no markers were incorrectly assigned to another linkage group), the accuracy of the map had little or no impact on the ability to detect QTLs, the true significance levels of the tests or the relative placement of QTLs. When a marker was incorrectly placed on another linkage group, there was a small increase in the level of the test. After adjusting for this increase, there was a decrease in power to detect a QTL near the misplaced marker. This decrease was of a similar magnitude to that found when using a single-marker analysis compared with interval mapping. These results mean that QTL analyses can proceed without the need for very accurate marker maps, and that estimated QTL positions can be translated onto updated maps without the need for reanalysis.

Chromosome Mapping↗
PubMed2004

Power calculations for selective genotyping in QTL mapping in backcross mice.

Selective genotyping concerns the genotyping of a portion of individuals chosen on the basis of their phenotypic values. Often individuals are selected for genotyping from the high and low extremes of the phenotypic distribution. This procedure yields savings in cost and time by decreasing the total number of individuals genotyped. Previous work by Darvasi et al. (1993) has shown that the power to detect a QTL by genotyping 40-50 % of a population is roughly equivalent to genotyping the entire sample. However, these power studies have not accounted for different strategies of analysing the data when phenotypes of individuals in the middle are excluded, nor have they investigated the genome-wide type I error rate under these different strategies or different selection percentages. Further, these simulation studies have not considered markers over the entire genome. In this paper, we present simulation studies of power for the maximum likelihood approach to QTL mapping by Lander & Botstein (1989) in the context of selective genotyping. We calculate the power of selectively genotyping the individuals from the middle of the phenotypic distribution when performing QTL mapping over the whole mouse genome.

Animals↗
PubMed2005

The detection of shared and ancestral polymorphisms.

There is increasing evidence that closely related species contain many polymorphisms that were present in their common ancestral species. Use of a more distant relative as an outgroup increases the ability to detect such ancestral polymorphisms. We describe a method for further improving estimates of the fraction of polymorphisms that are ancestral, and illustrate this with reference to data on Drosophila pseudoobscura and D. miranda. We also derive formulae for the proportion of fixations arising from ancestral polymorphisms and new mutations, respectively. The results should be useful for tests of selection based on the levels of expected and observed ancestral polymorphisms.

Alleles↗
PubMed2002

Acylglycerol and fatty acid components of pulp, seed, and whole olive fruit oils. Their use to characterize fruit variety by chemometrics.

The contents of triacylglycerols and diacylglycerols in three kinds of olive fruit oils (pulp, seed, and whole fruit) were determined. The fatty acid composition and the quality ratios 1,2-diacylglycerols/1,3-diacylglycerols and 1,2-diacylglycerols/total diacylglycerols were also assessed. Seven major Italian olive varieties were considered. Results of univariate statistical analyses indicated that the above analytical parameters (glyceridic ratios excepted) were effective in discriminating between pulp and seed oils. The seed oil fraction did not determine any change in the glyceridic indices and the acylglycerol or fatty acid composition concerning the whole fruit oil (mixture of pulp and seed oil fractions), the weight (%) of seed ( approximately 2%) being by far lower than the weight (%) of pulp ( approximately 85%) (fruit weight basis). Based on the data of triacylglycerol or fatty acid composition, and using appropriate parametric or nonparametric multivariate statistics, the genetic origins (olive variety) of the three fruit oil kinds were characterized.

Diglycerides↗
PubMed2003

Variation in cell wall composition among forage maize (Zea mays L.) inbred lines and its impact on digestibility: analysis of neutral detergent fiber composition by pyrolysis-gas chromatography-mass spectrometry.

Cell wall digestibility is an important determinant of forage quality, but the relationship between cell wall composition and digestibility is poorly understood. We analyzed the neutral detergent fiber (NDF) fraction of nine maize inbred lines and one brown midrib3 mutant with pyrolysis-gas chromatography-mass spectrometry (Py-GC-MS). Among 29 pyrolysis fragments that were quantified, two carbohydrate-derived and six lignin-derived fragments showed statistically significant genetic variation. The pyrolysis products 4-vinyl phenol and 2,6-dimethoxy-4-vinyl phenol were negatively correlated with digestibility, whereas furfural and 3-(4-hydroxyphenyl)-3-oxopropanal showed a positive correlation with digestibility. Linear discriminant analysis of the pyrolysis data resulted in the resolution of groups of inbred lines with different digestibility properties based on their chemical composition. These analyses reveal that digestibility is governed by complex interactions between different cell wall compounds, but that several pyrolysis fragments can be used as markers to distinguish between maize lines with different digestibility.

Breeding↗
PubMed2000

Fitness effect analysis of a heterochromatic supernumerary segment in the grasshopper Eyprepocnemis plorans.

Several components of fitness were analysed in relation to the presence of a supernumerary chromosome segment (SCS) in two natural populations of the grasshopper Eyprepocnemis plorans, including clutch size, egg fertility, egg and embryo productivity and survivability from embryo to adult, and SCS transmission through males. The results have shown the absence of a significant relationship between SCS presence and these fitness components, with the single exception of egg fertility which decreases significantly in SCS females with mating shortage. This fertility decrease is thus expected to be relevant for the population dynamics of the SCS only in low-density populations, those in which it is difficult for females to find a male to copulate with before each egg-batch is ready to be laid. The analysis of the SCS transmission through males showed no significant differences between expected and observed SCS frequencies. The SCS polymorphism seems to be at a status close to neutrality in respect to fitness, but its slight disadvantage in transmission through females carrying B chromosomes predicts that the polymorphism should tend to disappear, unless SCS recurrent amplification, or another undiscovered force, counteracts this tendency.

Analysis of Variance↗
PubMed2003

Prevalence of IL-1A and IL-1B polymorphisms in a Greek population.

OBJECTIVES: Given the possible ethnic diversity in distribution of genetic variants, aim of the present study was to estimate the prevalence of the polymorphisms of IL-1A+4845 and IL-1B+3954 in a Greek population of unknown periodontal status and to compare this prevalence with one from a group of patients with chronic (adult) periodontitis. MATERIAL AND METHODS: 110 healthy subjects of unknown periodontal status and 45 patients with chronic periodontitis were genotyped, using a PCR-based method and primers described in the literature. The differences in genotype, allele frequencies, allele carriage rate and presence of positive composite genotype as described by Kornman et al. (1997) were analyzed using Fisher's exact test and calculating two-sided p-value, odds ratios and confidence intervals. RESULTS: No differences were observed in any of the parameters tested between the two groups. CONCLUSIONS: Given the high prevalences of these polymorphisms observed in the general population,findings of the present study do not support a possible predictive value of the presence of allele 2 at IL-1A+4845 and IL-1B+3954 or the positive composite genotype for presence or absence of periodontal disease,in a Greek population.

Adult↗
PubMed2002

The increase in the frequency of MICA gene A6 allele in oral squamous cell carcinoma.

BACKGROUND: Oral squamous cell carcinoma (OSCC) was reported to be associated with immune function. The MICA (MHC class I chain-related gene A) is expressed by keratinocytes and other epithelial cells, and its encoded protein interacts with gamma/delta T cells localized in submucosa. The MICA also influences the heat shock protein function. We speculated that the alterations of MICA might influence the pathogenesis of OSCC through the aberration in presenting tumor antigens or heat shock protein. MICA gene has a triplet repeat (GCT) polymorphism in the transmembrane domain, resulting in five distinctive allelic patterns. METHODS: We analysed this MICA polymorphism in 67 OSCC patients and 351 randomly selected unrelated controls. By using the ABI Prism 377-18 DNA sequencer (Applied Biosystems, Foster City, CA, USA) to analyse the sample DNA PCR products. The number of micro-satellite repeats was estimated with Genescan 672 software (Applied Biosystems) with a standard size marker of GS-350 TAMRA (N,N,N,N-tetramethyl-6-carbohydroxyl rhodamine; Applied Biosystems). RESULTS: The phenotype frequency of allele A6 of MICA in subjects with OSCC was significantly higher than that in controls (RR = 3.46, 95% CI = 1.73-6.94, P = 0.0002), as was the frequency of allele (RR = 2.64, 95% CI = 1.39-5.02, P = 0.002). CONCLUSION: The results suggest that allele A6 in MICA might confer the risk of OSCC.

Adult↗