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  • Hou, Wei  (11)
  • Biodiversity Research  (11)
  • 1
    Online Resource
    Online Resource
    Estimation of Multilocus Linkage Disequilibria in Diploid Populations With Dominant Markers
    Oxford University Press (OUP) ; 2007
    In:  Genetics Vol. 176, No. 3 ( 2007-07-01), p. 1811-1821
    Details
    In: Genetics, Oxford University Press (OUP), Vol. 176, No. 3 ( 2007-07-01), p. 1811-1821
    Abstract: Analysis of population structure and organization with DNA-based markers can provide important information regarding the history and evolution of a species. Linkage disequilibrium (LD) analysis based on allelic associations between different loci is emerging as a viable tool to unravel the genetic basis of population differentiation. In this article, we derive the EM algorithm to obtain the maximum-likelihood estimates of the linkage disequilibria between dominant markers, to study the patterns of genetic diversity for a diploid species. The algorithm was expanded to estimate and test linkage disequilibria of different orders among three dominant markers and can be technically extended to manipulate an arbitrary number of dominant markers. The feasibility of the proposed algorithm is validated by an example of population genetic studies of hickory trees, native to southeastern China, using dominant random amplified polymorphic DNA markers. Extensive simulation studies were performed to investigate the statistical properties of this algorithm. The precision of the estimates of linkage disequilibrium between dominant markers was compared with that between codominant markers. Results from simulation studies suggest that three-locus LD analysis displays increased power of LD detection relative to two-locus LD analysis. This algorithm is useful for studying the pattern and amount of genetic variation within and among populations.
    Type of Medium: Online Resource
    ISSN: 1943-2631
    URL: Article
    DOI: 10.1534/genetics.106.068890
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2007
    detail.hit.zdb_id: 1477228-0
    SSG: 12
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  • 2
    Online Resource
    Online Resource
    Genetic linkage map construction and QTL identification of juvenile growth traits in Torreya grandis
    Springer Science and Business Media LLC ; 2014
    In:  BMC Genetics Vol. 15, No. Suppl 1 ( 2014), p. S2-
    Details
    In: BMC Genetics, Springer Science and Business Media LLC, Vol. 15, No. Suppl 1 ( 2014), p. S2-
    Type of Medium: Online Resource
    ISSN: 1471-2156
    URL: Article
    DOI: 10.1186/1471-2156-15-S1-S2
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2014
    detail.hit.zdb_id: 2041497-3
    detail.hit.zdb_id: 3058779-7
    SSG: 12
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  • 3
    Online Resource
    Online Resource
    A model for computing genes governing marital dissolution through sentimental dynamics
    Elsevier BV ; 2014
    In:  Journal of Theoretical Biology Vol. 353 ( 2014-07), p. 24-33
    Details
    In: Journal of Theoretical Biology, Elsevier BV, Vol. 353 ( 2014-07), p. 24-33
    Type of Medium: Online Resource
    ISSN: 0022-5193
    URL: Article
    DOI: 10.1016/j.jtbi.2014.02.010
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2014
    detail.hit.zdb_id: 1470953-3
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  • 4
    Online Resource
    Online Resource
    A Hyperspace Model to Decipher the Genetic Architecture of Developmental Processes: Allometry Meets Ontogeny
    Oxford University Press (OUP) ; 2006
    In:  Genetics Vol. 172, No. 1 ( 2006-01-01), p. 627-637
    Details
    In: Genetics, Oxford University Press (OUP), Vol. 172, No. 1 ( 2006-01-01), p. 627-637
    Abstract: To better utilize limited resources for their survival and reproduction, all organisms undergo developmental changes in both body size and shape during ontogeny. The genetic analysis of size change with increasing age, i.e., growth, has received considerable attention in quantitative developmental genetic studies, but the genetic architecture of ontogenetic changes in body shape and its associated allometry have been poorly understood partly due to the lack of analytical tools. In this article, we attempt to construct a multivariate statistical framework for studying the genetic regulation of ontogenetic growth and shape. We have integrated biologically meaningful mathematical functions of growth curves and developmental allometry into the estimation process of genetic mapping aimed at identifying individual quantitative trait loci (QTL) for phenotypic variation. This model defined with high dimensions can characterize the ontogenetic patterns of genetic effects of QTL over the lifetime of an organism and assess the interplay between genetic actions/interactions and phenotypic integration. The closed forms for the residual covariance matrix and its determinant and inverse were derived to overcome the computational complexity typical of our high-dimensional model. We used a worked example to validate the utility of this model. The implications of this model for genetic research of evo–devo are discussed.
    Type of Medium: Online Resource
    ISSN: 1943-2631
    URL: Article
    DOI: 10.1534/genetics.105.045310
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2006
    detail.hit.zdb_id: 1477228-0
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  • 5
    Online Resource
    Online Resource
    Multilocus genomics of outcrossing plant populations
    Elsevier BV ; 2009
    In:  Theoretical Population Biology Vol. 76, No. 1 ( 2009-8), p. 68-76
    Details
    In: Theoretical Population Biology, Elsevier BV, Vol. 76, No. 1 ( 2009-8), p. 68-76
    Type of Medium: Online Resource
    ISSN: 0040-5809
    URL: Article
    DOI: 10.1016/j.tpb.2009.04.005
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2009
    detail.hit.zdb_id: 1471916-2
    SSG: 12
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  • 6
    Online Resource
    Online Resource
    Systems mapping of HIV-1 infection
    Springer Science and Business Media LLC ; 2012
    In:  BMC Genetics Vol. 13, No. 1 ( 2012-12)
    Details
    In: BMC Genetics, Springer Science and Business Media LLC, Vol. 13, No. 1 ( 2012-12)
    Abstract: Mathematical models of viral dynamics in vivo provide incredible insights into the mechanisms for the nonlinear interaction between virus and host cell populations, the dynamics of viral drug resistance, and the way to eliminate virus infection from individual patients by drug treatment. The integration of these mathematical models with high-throughput genetic and genomic data within a statistical framework will raise a hope for effective treatment of infections with HIV virus through developing potent antiviral drugs based on individual patients’ genetic makeup. In this opinion article, we will show a conceptual model for mapping and dictating a comprehensive picture of genetic control mechanisms for viral dynamics through incorporating a group of differential equations that quantify the emergent properties of a system.
    Type of Medium: Online Resource
    ISSN: 1471-2156
    URL: Article
    DOI: 10.1186/1471-2156-13-91
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2012
    detail.hit.zdb_id: 2041497-3
    detail.hit.zdb_id: 3058779-7
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  • 7
    Online Resource
    Online Resource
    Wavelet-Based Parametric Functional Mapping of Developmental Trajectories With High-Dimensional Data
    Oxford University Press (OUP) ; 2007
    In:  Genetics Vol. 176, No. 3 ( 2007-07-01), p. 1879-1892
    Details
    In: Genetics, Oxford University Press (OUP), Vol. 176, No. 3 ( 2007-07-01), p. 1879-1892
    Abstract: The biological and statistical advantages of functional mapping result from joint modeling of the mean-covariance structures for developmental trajectories of a complex trait measured at a series of time points. While an increased number of time points can better describe the dynamic pattern of trait development, significant difficulties in performing functional mapping arise from prohibitive computational times required as well as from modeling the structure of a high-dimensional covariance matrix. In this article, we develop a statistical model for functional mapping of quantitative trait loci (QTL) that govern the developmental process of a quantitative trait on the basis of wavelet dimension reduction. By breaking an original signal down into a spectrum by taking its averages (smooth coefficients) and differences (detail coefficients), we used the discrete Haar wavelet shrinkage technique to transform an inherently high-dimensional biological problem into its tractable low-dimensional representation within the framework of functional mapping constructed by a Gaussian mixture model. Unlike conventional nonparametric modeling of wavelet shrinkage, we incorporate mathematical aspects of developmental trajectories into the smooth coefficients used for QTL mapping, thus preserving the biological relevance of functional mapping in formulating a number of hypothesis tests at the interplay between gene actions/interactions and developmental patterns for complex phenotypes. This wavelet-based parametric functional mapping has been statistically examined and compared with full-dimensional functional mapping through simulation studies. It holds great promise as a powerful statistical tool to unravel the genetic machinery of developmental trajectories with large-scale high-dimensional data.
    Type of Medium: Online Resource
    ISSN: 1943-2631
    URL: Article
    DOI: 10.1534/genetics.107.070920
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2007
    detail.hit.zdb_id: 1477228-0
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  • 8
    Online Resource
    Online Resource
    Functional Mapping of Quantitative Trait Loci That Interact With the hg Mutation to Regulate Growth Trajectories in Mice
    Oxford University Press (OUP) ; 2005
    In:  Genetics Vol. 171, No. 1 ( 2005-09-01), p. 239-249
    Details
    In: Genetics, Oxford University Press (OUP), Vol. 171, No. 1 ( 2005-09-01), p. 239-249
    Abstract: The high growth (hg) mutation increases body size in mice by 30–50%. Given the complexity of the genetic regulation of animal growth, it is likely that the effect of this major locus is mediated by other quantitative trait loci (QTL) with smaller effects within a web of gene interactions. In this article, we extend our functional mapping model to characterize modifier QTL that interact with the hg locus during ontogenetic growth. Our model is derived within the maximum-likelihood context, incorporated by mathematical aspects of growth laws and implemented with the EM algorithm. In an F2 population founded by a congenic high growth (HG) line and non-HG line, a highly additive effect due to the hg gene was detected on growth trajectories. Three QTL located on chromosomes 2 and X were identified to trigger significant additive and/or dominant effects on the process of growth. The most significant finding made from our model is that these QTL interact with the hg locus to affect the shapes of the growth process. Our model provides a powerful means for understanding the genetic architecture and regulation of growth rate and body size in mammals.
    Type of Medium: Online Resource
    ISSN: 1943-2631
    URL: Article
    DOI: 10.1534/genetics.104.040162
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2005
    detail.hit.zdb_id: 1477228-0
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  • 9
    Online Resource
    Online Resource
    Structured Antedependence Models for Functional Mapping of Multiple Longitudinal Traits
    Walter de Gruyter GmbH ; 2005
    In:  Statistical Applications in Genetics and Molecular Biology Vol. 4, No. 1 ( 2005-01-16)
    Details
    In: Statistical Applications in Genetics and Molecular Biology, Walter de Gruyter GmbH, Vol. 4, No. 1 ( 2005-01-16)
    Abstract: In this article, we present a statistical model for mapping quantitative trait loci (QTL) that determine growth trajectories of two correlated traits during ontogenetic development. This model is derived within the maximum likelihood context, incorporated by mathematical aspects of growth processes to model the mean vector and by structured antedependence (SAD) models to approximate time-dependent covariance matrices for longitudinal traits. It provides a quantitative framework for testing the relative importance of two mechanisms, pleiotropy and linkage, in contributing to genetic correlations during ontogeny. This model has been employed to map QTL affecting stem height and diameter growth trajectories in an interspecific hybrid progeny of Populus, leading to the successful discovery of three pleiotropic QTL on different linkage groups. The implications of this model for genetic mapping within a broader context are discussed.
    Type of Medium: Online Resource
    ISSN: 1544-6115 , 2194-6302
    URL: Article
    DOI: 10.2202/1544-6115.1136
    Language: Unknown
    Publisher: Walter de Gruyter GmbH
    Publication Date: 2005
    detail.hit.zdb_id: 2115012-6
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  • 10
    Online Resource
    Online Resource
    A model for linkage analysis with apomixis
    Springer Science and Business Media LLC ; 2011
    In:  Theoretical and Applied Genetics Vol. 123, No. 5 ( 2011-9), p. 681-691
    Details
    In: Theoretical and Applied Genetics, Springer Science and Business Media LLC, Vol. 123, No. 5 ( 2011-9), p. 681-691
    Type of Medium: Online Resource
    ISSN: 0040-5752 , 1432-2242
    URL: Article
    DOI: 10.1007/s00122-011-1618-4
    RVK:
    WA 15000
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2011
    detail.hit.zdb_id: 1478966-8
    SSG: 12
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