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Trait Association (trait + association)
Selected AbstractsQuantitative trait association in parent offspring trios: Extension of case/pseudocontrol method and comparison of prospective and retrospective approachesGENETIC EPIDEMIOLOGY, Issue 8 2007Eleanor Wheeler Abstract The case/pseudocontrol method provides a convenient framework for family-based association analysis of case-parent trios, incorporating several previously proposed methods such as the transmission/disequilibrium test and log-linear modelling of parent-of-origin effects. The method allows genotype and haplotype analysis at an arbitrary number of linked and unlinked multiallelic loci, as well as modelling of more complex effects such as epistasis, parent-of-origin effects, maternal genotype and mother-child interaction effects, and gene-environment interactions. Here we extend the method for analysis of quantitative as opposed to dichotomous (e.g. disease) traits. The resulting method can be thought of as a retrospective approach, modelling genotype given trait value, in contrast to prospective approaches that model trait given genotype. Through simulations and analytical derivations, we examine the power and properties of our proposed approach, and compare it to several previously proposed single-locus methods for quantitative trait association analysis. We investigate the performance of the different methods when extended to allow analysis of haplotype, maternal genotype and parent-of-origin effects. With randomly ascertained families, with or without population stratification, the prospective approach (modeling trait value given genotype) is found to be generally most effective, although the retrospective approach has some advantages with regard to estimation and interpretability of parameter estimates when applied to selected samples. Genet. Epidemiol. 2007. © 2007 Wiley-Liss, Inc. [source] What does species richness tell us about functional trait diversity?GLOBAL ECOLOGY, Issue 4 2010Predictions, evidence for responses of species, functional trait diversity to land-use change ABSTRACT In the conservation literature on land-use change, it is often assumed that land-use intensification drives species loss, driving a loss of functional trait diversity and ecosystem function. Modern research, however, does not support this cascade of loss for all natural systems. In this paper we explore the errors in this assumption and present a conceptual model taking a more mechanistic approach to the species,functional trait association in a context of land-use change. We provide empirical support for our model's predictions demonstrating that the association of species and functional trait diversity follows various trajectories in response to land-use change. The central premise of our model is that land-use change impacts upon processes of community assembly, not species per se. From the model, it is clear that community context (i.e. type of disturbance, species pool size) will affect the response trajectory of the relationship between species and functional trait diversity in communities undergoing land-use change. The maintenance of ecosystem function and of species diversity in the face of increasing land-use change are complementary goals. The use of a more ecologically realistic model of responses of species and functional traits will improve our ability to make wise management decisions to achieve both aims in specific at-risk systems. [source] Fusarium head blight resistance derived from Lophopyrum elongatum chromosome 7E and its augmentation with Fhb1 in wheatPLANT BREEDING, Issue 5 2006X. Shen Abstract The objective of this study was to assess the effectiveness of Fusarium head blight (FHB) resistance derived from wheatgrass Lophopyrum elongatum chromosome 7E and to determine whether this resistance can augment resistance in combination with other FHB resistance quantitative trait loci (QTL) or genes in wheat. The ,Chinese Spring',Lophopyrum elongatum disomic substitution line 7E(7B) was crossed to three wheat lines: ,Ning 7840', L3, and L4. F2 populations were evaluated for type II resistance with the single-floret inoculation method in the greenhouse. Simple sequence repeat markers associated with Fhb1 in ,Ning 7840' and L4 and markers located on chromosome 7E were genotyped in each population. Marker,trait association was analysed with one-way or two-way analysis of variance. The research showed that, in the three populations, the average number of diseased spikelets (NDS) in plants with chromosome 7E is 1.2, 3.1 and 3.2, vs. NDS of 3.3, 7.2 and 9.1 in plants without 7E, a reduction in NDS of 2.1, 4.1 and 5.9 in the respective populations. The QTL on 7E and the Fhb1 gene augment disease resistance when combined. The effect of the QTL on 7E was greater than that on 3BS in this experiment. Data also suggest that the FHB resistance gene derived from L. elongatum is located on the long arm of 7E. [source] Association between the CHRM2 gene and intelligence in a sample of 304 Dutch familiesGENES, BRAIN AND BEHAVIOR, Issue 8 2006M. F. Gosso The CHRM2 gene is thought to be involved in neuronal excitability, synaptic plasticity and feedback regulation of acetylcholine release and has previously been implicated in higher cognitive processing. In a sample of 667 individuals from 304 families, we genotyped three single-nucleotide polymorphisms (SNPs) in the CHRM2 gene on 7q31,35. From all individuals, standardized intelligence measures were available. Using a test of within-family association, which controls for the possible effects of population stratification, a highly significant association was found between the CHRM2 gene and intelligence. The strongest association was between rs324650 and performance IQ (PIQ), where the T allele was associated with an increase of 4.6 PIQ points. In parallel with a large family-based association, we observed an attenuated , although still significant , population-based association, illustrating that population stratification may decrease our chances of detecting allele,trait associations. Such a mechanism has been predicted earlier, and this article is one of the first to empirically show that family-based association methods are not only needed to guard against false positives, but are also invaluable in guarding against false negatives. [source] Comparison of two plant functional approaches to evaluate natural restoration along an old-field , deciduous forest chronosequenceJOURNAL OF VEGETATION SCIENCE, Issue 2 2009Isabelle Aubin Abstract Question: Are direct and indirect trait-based approaches similar in their usefulness to synthesize species responses to successional stages? Location: Northern hardwood forests, Québec, Canada (45°01,,45°08,N; 73°58,,74°21,W). Methods: Two different trait-based approaches were used to relate plant functional traits to succession on an old-field , deciduous forest chronosequence: (i) a frequently used approach based on co-occurrence of traits (emergent groups), and (ii) a new version of a direct functional approach at the trait level (the fourth-corner method). Additionally, we selected two different cut-off levels for the herb subset of the emergent group classification in order to test its robustness and ecological relevance. Results: Clear patterns of trait associations with stand developmental stages emerged from both the emergent group and the direct approach at the trait level. However, the emergent group classification was found to hide some trait-level differences such as a shift in seed size, light requirement and plant form along the chronosequence. Contrasting results were obtained for the seven or nine group classification of the herbaceous subset, illustrating how critical is the number of groups for emergent group classification. Conclusion: The simultaneous use of two different trait-based approaches provided a robust and comprehensive characterization of vegetation responses in the old-field , deciduous forest chronosequence. It also underlines the different goals as well as the limitations and benefits of these two approaches. Both approaches indicated that abandoned pastures of the northern hardwood biome have good potential for natural recovery. Conversion of these lands to other functions may lead to irremediable loss of biodiversity. [source] Association analysis of fibre traits in Gossypium arboreum accessionsPLANT BREEDING, Issue 2 2008S. K. Kantartzi Abstract Advances in the use of diploid Asiatic species in cotton breeding require an understanding of the relatedness and ancestry of diploid cotton accessions, and identification of simple sequence repeat (SSR) markers associated with agronomically important phenotypic traits, for example, fibre quality. Fifty-six Gossypium arboreum germplasm accessions introduced from nine regions of Africa, Asia and Europe were evaluated for eight fibre characters (lint percentage, lint colour, elongation, micronaire, strength, 50% span length, 2.5% span length and maturity%) and genotyped with 98 SSR markers. When viewed across all accessions most of the SSR markers were polymorphic. Population structure analysis identified six main clusters for the accessions which corresponded to different geographic regions, indicating agreement between genetic and predefined populations. The general linear model method was used to disclose marker,trait associations. Marker,trait associations were investigated by fitting single marker regression models for phenotypic traits on marker band intensities with correction for population structure. This paper illustrates the potential of association mapping in diploid cotton, because existing phenotypic data, a modest number of SSR markers, and a pioneering statistical analysis, identified interesting associations. [source] The Impact of Incomplete Linkage Disequilibrium and Genetic Model Choice on the Analysis and Interpretation of Genome-wide Association StudiesANNALS OF HUMAN GENETICS, Issue 4 2010Mark M. Iles Summary When conducting a genetic association study, it has previously been observed that a multiplicative risk model tends to fit better at a disease-associated marker locus than at the ungenotyped causative locus. This suggests that, while overall risk decreases as linkage disequilibrium breaks down, non-multiplicative components are more affected. This effect is investigated here, in particular the practical consequences it has on testing for trait/marker associations and the estimation of mode of inheritance and risk once an associated locus has been found. The extreme significance levels required for genome-wide association studies define a restricted range of detectable allele frequencies and effect sizes. For such parameters there is little to be gained by using a test that models the correct mode of inheritance rather than the multiplicative; thus the Cochran-Armitage trend test, which assumes a multiplicative model, is preferable to a more general model as it uses fewer degrees of freedom. Equally when estimating risk, it is likely that a multiplicative risk model will provide a good fit to the data, regardless of the underlying mode of inheritance at the true susceptibility locus. This may lead to problems in interpreting risk estimates. [source] | ||||||||||