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  • Online-Ressource  (11)
  • Hindawi Limited  (11)
  • Biodiversitätsforschung  (11)
Materialart
  • Online-Ressource  (11)
Verlag/Herausgeber
  • Hindawi Limited  (11)
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  • Biodiversitätsforschung  (11)
Fachgebiete(RVK)
  • 1
    Online-Ressource
    Online-Ressource
    Functional mapping of reaction norms to multiple environmental signals
    Hindawi Limited ; 2007
    In:  Genetical Research Vol. 89, No. 1 ( 2007-02), p. 27-38
    Details
    In: Genetical Research, Hindawi Limited, Vol. 89, No. 1 ( 2007-02), p. 27-38
    Kurzfassung: Whether there are different genes involved in response to different environmental signals and how these genes interact to determine the final expression of the trait are of fundamental importance in agricultural and biological research. We present a statistical framework for mapping environment-induced genes (or quantitative trait loci, QTLs) of major effects on the expression of a trait that respond to changing environments. This framework is constructed with a maximum-likelihood-based mixture model, in which the mean and covariance structure of environment-induced responses is modelled. The means for responses to continuous environmental states, referred to as reaction norms, are approximated for different QTL genotypes by mathematical equations that were derived from fundamental biological principles or based on statistical goodness-of-fit to observational data. The residual covariance between different environmental states was modelled by autoregressive processes. Such an approach to studying the genetic control of reaction norms can be expected to be advantageous over traditional mapping approaches in which no biological principles and statistical structures are considered. We demonstrate the analytical procedure and power of this approach by modelling the photosynthetic rate process as a function of temperature and light irradiance. Our approach allows for testing how a QTL affects the reaction norm of photosynthetic rate to a specific environment and whether there exist different QTLs to mediate photosynthetic responses to temperature and light irradiance, respectively.
    Materialart: Online-Ressource
    ISSN: 0016-6723 , 1469-5073
    URL: Article
    DOI: 10.1017/S0016672307008622
    RVK:
    WA 15000
    Sprache: Englisch
    Verlag: Hindawi Limited
    Publikationsdatum: 2007
    ZDB Id: 2412684-6
    ZDB Id: 1472156-9
    SSG: 12
    Standort Signatur Einschränkungen Verfügbarkeit
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    Online-Ressource
  • 2
    Online-Ressource
    Online-Ressource
    A logistic mixture model for characterizing genetic determinants causing differentiation in growth trajectories
    Hindawi Limited ; 2002
    In:  Genetical Research Vol. 79, No. 3 ( 2002-06), p. 235-245
    Details
    In: Genetical Research, Hindawi Limited, Vol. 79, No. 3 ( 2002-06), p. 235-245
    Kurzfassung: The logistic or S-shaped curve of growth is one of the few universal laws in biology. It is certain that there exist specific genes affecting growth curves, but, due to a lack of statistical models, it is unclear how these genes cause phenotypic differentiation in growth and developmental trajectories. In this paper we present a statistical model for detecting major genes responsible for growth trajectories. This model is incorporated with pervasive logistic growth curves under the maximum likelihood framework and, thus, is expected to improve over previous models in both parameter estimation and inference. The power of this model is demonstrated by an example using forest tree data, in which evidence of major genes affecting stem growth processes is successfully detected. The implications for this model and its extensions are discussed.
    Materialart: Online-Ressource
    ISSN: 0016-6723 , 1469-5073
    URL: Article
    DOI: 10.1017/S0016672302005633
    RVK:
    WA 15000
    Sprache: Englisch
    Verlag: Hindawi Limited
    Publikationsdatum: 2002
    ZDB Id: 2412684-6
    ZDB Id: 1472156-9
    SSG: 12
    Standort Signatur Einschränkungen Verfügbarkeit
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    Online-Ressource
  • 3
    Online-Ressource
    Online-Ressource
    An algorithmic model for constructing a linkage and linkage disequilibrium map in outcrossing plant populations
    Hindawi Limited ; 2009
    In:  Genetics Research Vol. 91, No. 1 ( 2009-02), p. 9-21
    Details
    In: Genetics Research, Hindawi Limited, Vol. 91, No. 1 ( 2009-02), p. 9-21
    Kurzfassung: A linkage–linkage disequilibrium map that describes the pattern and extent of linkage dis-equilibrium (LD) decay with genomic distance has now emerged as a viable tool to unravel the genetic structure of population differentiation and fine-map genes for complex traits. The prerequisite for constructing such a map is the simultaneous estimation of the linkage and LD between different loci. Here, we develop a computational algorithm for simultaneously estimating the recombination fraction and LD in a natural outcrossing population with multilocus marker data, which are often estimated separately in most molecular genetic studies. The algorithm is founded on a commonly used progeny test with open-pollinated offspring sampled from a natural population. The information about LD is reflected in the co-segregation of alleles at different loci among parents in the population. Open mating of parents will reveal the genetic linkage of alleles during meiosis. The algorithm was constructed within the polynomial-based mixture framework and implemented with the Expectation–Maximization (EM) algorithm. The by-product of the derivation of this algorithm is the estimation of outcrossing rate, a parameter useful to explore the genetic diversity of the population. We performed computer simulation to investigate the influences of different sampling strategies and different values of parameters on parameter estimation. By providing a number of testable hypotheses about population genetic parameters, this algorithmic model will open a broad gateway to understand the genetic structure and dynamics of an outcrossing population under natural selection.
    Materialart: Online-Ressource
    ISSN: 0016-6723 , 1469-5073
    URL: Article
    DOI: 10.1017/S0016672308009932
    RVK:
    WA 15000
    Sprache: Englisch
    Verlag: Hindawi Limited
    Publikationsdatum: 2009
    ZDB Id: 2412684-6
    ZDB Id: 1472156-9
    SSG: 12
    Standort Signatur Einschränkungen Verfügbarkeit
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    Online-Ressource
  • 4
    Online-Ressource
    Online-Ressource
    Quantitative trait loci for growth trajectories in Populus
    Hindawi Limited ; 2003
    In:  Genetical Research Vol. 81, No. 1 ( 2003-2), p. 51-64
    Details
    In: Genetical Research, Hindawi Limited, Vol. 81, No. 1 ( 2003-2), p. 51-64
    Materialart: Online-Ressource
    ISSN: 0016-6723 , 1469-5073
    URL: Article
    DOI: 10.1017/S0016672302005980
    RVK:
    WA 15000
    Sprache: Unbekannt
    Verlag: Hindawi Limited
    Publikationsdatum: 2003
    ZDB Id: 2412684-6
    ZDB Id: 1472156-9
    SSG: 12
    Standort Signatur Einschränkungen Verfügbarkeit
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    Online-Ressource
  • 5
    Online-Ressource
    Online-Ressource
    Linkage mapping of sex-specific differences
    Hindawi Limited ; 2002
    In:  Genetical Research Vol. 79, No. 1 ( 2002-02), p. 85-96
    Details
    In: Genetical Research, Hindawi Limited, Vol. 79, No. 1 ( 2002-02), p. 85-96
    Kurzfassung: Most current linkage analyses assume identical fractions of meiotic recombination between homologous marker loci of the two sexes. This assumption is not realistic, because considerable sex-related differences have been observed in recombination fraction. In this paper, a general EM-based algorithm is presented to estimate sex-specific recombination fractions for a mixed set of molecular markers segregating differently in a full-sib family derived from two heterozygous parents. The asymptotic variances of the estimates of linkage specifically for each of the parents are evaluated using a numerical analysis based on information functions. This approach will have important implications for precise gene mapping based on sex-specific linkage maps.
    Materialart: Online-Ressource
    ISSN: 0016-6723 , 1469-5073
    URL: Article
    DOI: 10.1017/S0016672301005389
    RVK:
    WA 15000
    Sprache: Englisch
    Verlag: Hindawi Limited
    Publikationsdatum: 2002
    ZDB Id: 2412684-6
    ZDB Id: 1472156-9
    SSG: 12
    Standort Signatur Einschränkungen Verfügbarkeit
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    Online-Ressource
  • 6
    Online-Ressource
    Online-Ressource
    Modelling epistatic effects of embryo and endosperm QTL on seed quality traits
    Hindawi Limited ; 2006
    In:  Genetical Research Vol. 87, No. 1 ( 2006-02), p. 61-71
    Details
    In: Genetical Research, Hindawi Limited, Vol. 87, No. 1 ( 2006-02), p. 61-71
    Kurzfassung: Coordinated expression of embryo and endosperm tissues is required for proper seed development. The coordination among these two tissues is controlled by the interaction between multiple genes expressed in the embryo and endosperm genomes. In this article, we present a statistical model for testing whether quantitative trait loci (QTL) active in different genomes, diploid embryo and triploid endosperm, epistatically affect a trait expressed on the endosperm tissue. The maximum likelihood approach, implemented with the EM algorithm, was derived to provide the maximum likelihood estimates of the locations of embryo- and endosperm-specific QTL and their main effects and epistatic effects. This model was used in a real example for rice in which two QTL, one from the embryo genome and the other from the endosperm genome, exert a significant interaction effect on gel consistency on the endosperm. Our model has successfully detected Waxy , a candidate gene in the embryo genome known to regulate one of the major steps of amylose biosynthesis in the endosperm. This model will have great implications for agricultural and evolutionary genetic research.
    Materialart: Online-Ressource
    ISSN: 0016-6723 , 1469-5073
    URL: Article
    DOI: 10.1017/S0016672306007956
    RVK:
    WA 15000
    Sprache: Englisch
    Verlag: Hindawi Limited
    Publikationsdatum: 2006
    ZDB Id: 2412684-6
    ZDB Id: 1472156-9
    SSG: 12
    Standort Signatur Einschränkungen Verfügbarkeit
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    Online-Ressource
  • 7
    Online-Ressource
    Online-Ressource
    An optimal strategy for functional mapping of dynamic trait loci
    Hindawi Limited ; 2010
    In:  Genetics Research Vol. 92, No. 1 ( 2010-02), p. 55-62
    Details
    In: Genetics Research, Hindawi Limited, Vol. 92, No. 1 ( 2010-02), p. 55-62
    Kurzfassung: As an emerging powerful approach for mapping quantitative trait loci (QTLs) responsible for dynamic traits, functional mapping models the time-dependent mean vector with biologically meaningful equations and are likely to generate biologically relevant and interpretable results. Given the autocorrelation nature of a dynamic trait, functional mapping needs the implementation of the models for the structure of the covariance matrix. In this article, we have provided a comprehensive set of approaches for modelling the covariance structure and incorporated each of these approaches into the framework of functional mapping. The Bayesian information criterion (BIC) values are used as a model selection criterion to choose the optimal combination of the submodels for the mean vector and covariance structure. In an example for leaf age growth from a rice molecular genetic project, the best submodel combination was found between the Gaussian model for the correlation structure, power equation of order 1 for the variance and the power curve for the mean vector. Under this combination, several significant QTLs for leaf age growth trajectories were detected on different chromosomes. Our model can be well used to study the genetic architecture of dynamic traits of agricultural values.
    Materialart: Online-Ressource
    ISSN: 0016-6723 , 1469-5073
    URL: Article
    DOI: 10.1017/S0016672310000030
    RVK:
    WA 15000
    Sprache: Englisch
    Verlag: Hindawi Limited
    Publikationsdatum: 2010
    ZDB Id: 2412684-6
    ZDB Id: 1472156-9
    SSG: 12
    Standort Signatur Einschränkungen Verfügbarkeit
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    Online-Ressource
  • 8
    Online-Ressource
    Online-Ressource
    Genetic mapping of allometric scaling laws
    Hindawi Limited ; 2006
    In:  Genetical Research Vol. 87, No. 3 ( 2006-06), p. 207-216
    Details
    In: Genetical Research, Hindawi Limited, Vol. 87, No. 3 ( 2006-06), p. 207-216
    Kurzfassung: Many biological processes, from cellular metabolism to population dynamics, are characterized by particular allometric scaling relationships between rate and size (power laws). A statistical model for mapping specific quantitative trait loci (QTLs) that are responsible for allometric scaling laws has been developed. We present an improved model for allometric mapping of QTLs based on a more general allometry equation. This improved model includes two steps: (1) use model II regression analysis to estimate the parameters underlying universal allometric scaling laws, and (2) substitute the estimated allometric parameters in the mixture-based mapping model to obtain the estimation of QTL position and effects. This model has been validated by a real example for a mouse F 2 progeny, in which two QTLs were detected on different chromosomes that determine the allometric relationship between growth rate and body weight.
    Materialart: Online-Ressource
    ISSN: 0016-6723 , 1469-5073
    URL: Article
    DOI: 10.1017/S0016672306008172
    RVK:
    WA 15000
    Sprache: Englisch
    Verlag: Hindawi Limited
    Publikationsdatum: 2006
    ZDB Id: 2412684-6
    ZDB Id: 1472156-9
    SSG: 12
    Standort Signatur Einschränkungen Verfügbarkeit
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    Online-Ressource
  • 9
    Online-Ressource
    Online-Ressource
    A Bayesian Framework for Functional Mapping through Joint Modeling of Longitudinal and Time-to-Event Data
    Hindawi Limited ; 2012
    In:  International Journal of Plant Genomics Vol. 2012 ( 2012-05-22), p. 1-12
    Details
    In: International Journal of Plant Genomics, Hindawi Limited, Vol. 2012 ( 2012-05-22), p. 1-12
    Kurzfassung: The most powerful and comprehensive approach of study in modern biology is to understand the whole process of development and all events of importance to development which occur in the process. As a consequence, joint modeling of developmental processes and events has become one of the most demanding tasks in statistical research. Here, we propose a joint modeling framework for functional mapping of specific quantitative trait loci (QTLs) which controls developmental processes and the timing of development and their causal correlation over time. The joint model contains two submodels, one for a developmental process, known as a longitudinal trait, and the other for a developmental event, known as the time to event, which are connected through a QTL mapping framework. A nonparametric approach is used to model the mean and covariance function of the longitudinal trait while the traditional Cox proportional hazard (PH) model is used to model the event time. The joint model is applied to map QTLs that control whole-plant vegetative biomass growth and time to first flower in soybeans. Results show that this model should be broadly useful for detecting genes controlling physiological and pathological processes and other events of interest in biomedicine.
    Materialart: Online-Ressource
    ISSN: 1687-5370 , 1687-5389
    URL: Article
    DOI: 10.1155/2012/680634
    Sprache: Englisch
    Verlag: Hindawi Limited
    Publikationsdatum: 2012
    ZDB Id: 2401017-0
    Standort Signatur Einschränkungen Verfügbarkeit
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    Online-Ressource
  • 10
    Online-Ressource
    Online-Ressource
    EM Algorithm for Mapping Quantitative Trait Loci in Multivalent Tetraploids
    Hindawi Limited ; 2010
    In:  International Journal of Plant Genomics Vol. 2010 ( 2010-01-05), p. 1-10
    Details
    In: International Journal of Plant Genomics, Hindawi Limited, Vol. 2010 ( 2010-01-05), p. 1-10
    Kurzfassung: Multivalent tetraploids that include many plant species, such as potato, sugarcane, and rose, are of paramount importance to agricultural production and biological research. Quantitative trait locus (QTL) mapping in multivalent tetraploids is challenged by their unique cytogenetic properties, such as double reduction. We develop a statistical method for mapping multivalent tetraploid QTLs by considering these cytogenetic properties. This method is built in the mixture model-based framework and implemented with the EM algorithm. The method allows the simultaneous estimation of QTL positions, QTL effects, the chromosomal pairing factor, and the degree of double reduction as well as the assessment of the estimation precision of these parameters. We used simulated data to examine the statistical properties of the method and validate its utilization. The new method and its software will provide a useful tool for QTL mapping in multivalent tetraploids that undergo double reduction.
    Materialart: Online-Ressource
    ISSN: 1687-5370 , 1687-5389
    URL: Article
    DOI: 10.1155/2010/216547
    Sprache: Englisch
    Verlag: Hindawi Limited
    Publikationsdatum: 2010
    ZDB Id: 2401017-0
    Standort Signatur Einschränkungen Verfügbarkeit
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    Online-Ressource
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