Logo of geneticsGeneticsCurrent IssueInformation for AuthorsEditorial BoardSubscribeSubmit a Manuscript
Genetics. 2004 Mar; 166(3): 1541–1551.
PMCID: PMC1470782

A general framework for analyzing the genetic architecture of developmental characteristics.

Abstract

The genetic architecture of growth traits plays a central role in shaping the growth, development, and evolution of organisms. While a limited number of models have been devised to estimate genetic effects on complex phenotypes, no model has been available to examine how gene actions and interactions alter the ontogenetic development of an organism and transform the altered ontogeny into descendants. In this article, we present a novel statistical model for mapping quantitative trait loci (QTL) determining the developmental process of complex traits. Our model is constructed within the traditional maximum-likelihood framework implemented with the EM algorithm. We employ biologically meaningful growth curve equations to model time-specific expected genetic values and the AR(1) model to structure the residual variance-covariance matrix among different time points. Because of a reduced number of parameters being estimated and the incorporation of biological principles, the new model displays increased statistical power to detect QTL exerting an effect on the shape of ontogenetic growth and development. The model allows for the tests of a number of biological hypotheses regarding the role of epistasis in determining biological growth, form, and shape and for the resolution of developmental problems at the interface with evolution. Using our newly developed model, we have successfully detected significant additive x additive epistatic effects on stem height growth trajectories in a forest tree.

Full Text

The Full Text of this article is available as a PDF (250K).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Arthur Wallace. The emerging conceptual framework of evolutionary developmental biology. Nature. 2002 Feb 14;415(6873):757–764. [PubMed]
  • Atchley WR, Zhu J. Developmental quantitative genetics, conditional epigenetic variability and growth in mice. Genetics. 1997 Oct;147(2):765–776. [PMC free article] [PubMed]
  • VON BERTALANFFY L. Quantitative laws in metabolism and growth. Q Rev Biol. 1957 Sep;32(3):217–231. [PubMed]
  • Carlborg Orjan, Kerje Susanne, Schütz Karin, Jacobsson Lina, Jensen Per, Andersson Leif. A global search reveals epistatic interaction between QTL for early growth in the chicken. Genome Res. 2003 Mar;13(3):413–421. [PMC free article] [PubMed]
  • Cheverud JM, Routman EJ. Epistasis and its contribution to genetic variance components. Genetics. 1995 Mar;139(3):1455–1461. [PMC free article] [PubMed]
  • Churchill GA, Doerge RW. Empirical threshold values for quantitative trait mapping. Genetics. 1994 Nov;138(3):963–971. [PMC free article] [PubMed]
  • Grattapaglia D, Sederoff R. Genetic linkage maps of Eucalyptus grandis and Eucalyptus urophylla using a pseudo-testcross: mapping strategy and RAPD markers. Genetics. 1994 Aug;137(4):1121–1137. [PMC free article] [PubMed]
  • Kirkpatrick M, Heckman N. A quantitative genetic model for growth, shape, reaction norms, and other infinite-dimensional characters. J Math Biol. 1989;27(4):429–450. [PubMed]
  • Kirkpatrick M, Lofsvold D, Bulmer M. Analysis of the inheritance, selection and evolution of growth trajectories. Genetics. 1990 Apr;124(4):979–993. [PMC free article] [PubMed]
  • Kirkpatrick M, Hill WG, Thompson R. Estimating the covariance structure of traits during growth and ageing, illustrated with lactation in dairy cattle. Genet Res. 1994 Aug;64(1):57–69. [PubMed]
  • Korol AB, Ronin YI, Itskovich AM, Peng J, Nevo E. Enhanced efficiency of quantitative trait loci mapping analysis based on multivariate complexes of quantitative traits. Genetics. 2001 Apr;157(4):1789–1803. [PMC free article] [PubMed]
  • Lander ES, Botstein D. Mapping mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics. 1989 Jan;121(1):185–199. [PMC free article] [PubMed]
  • Lin Min, Lou Xiang-Yang, Chang Myron, Wu Rongling. A general statistical framework for mapping quantitative trait loci in nonmodel systems: issue for characterizing linkage phases. Genetics. 2003 Oct;165(2):901–913. [PMC free article] [PubMed]
  • Lou Xiang-Yang, Casella George, Littell Ramon C, Yang Mark C K, Johnson Julie A, Wu Rongling. A haplotype-based algorithm for multilocus linkage disequilibrium mapping of quantitative trait loci with epistasis. Genetics. 2003 Apr;163(4):1533–1548. [PMC free article] [PubMed]
  • Ma Chang-Xing, Casella George, Wu Rongling. Functional mapping of quantitative trait loci underlying the character process: a theoretical framework. Genetics. 2002 Aug;161(4):1751–1762. [PMC free article] [PubMed]
  • Núez-Antón V, Zimmerman DL. Modeling nonstationary longitudinal data. Biometrics. 2000 Sep;56(3):699–705. [PubMed]
  • Pletcher SD, Geyer CJ. The genetic analysis of age-dependent traits: modeling the character process. Genetics. 1999 Oct;153(2):825–835. [PMC free article] [PubMed]
  • Raff RA. Evo-devo: the evolution of a new discipline. Nat Rev Genet. 2000 Oct;1(1):74–79. [PubMed]
  • Rice SH. The analysis of ontogenetic trajectories: when a change in size or shape is not heterochrony. Proc Natl Acad Sci U S A. 1997 Feb 4;94(3):907–912. [PMC free article] [PubMed]
  • Rougvie AE. Control of developmental timing in animals. Nat Rev Genet. 2001 Sep;2(9):690–701. [PubMed]
  • Vaughn TT, Pletscher LS, Peripato A, King-Ellison K, Adams E, Erikson C, Cheverud JM. Mapping quantitative trait loci for murine growth: a closer look at genetic architecture. Genet Res. 1999 Dec;74(3):313–322. [PubMed]
  • West GB, Brown JH, Enquist BJ. A general model for ontogenetic growth. Nature. 2001 Oct 11;413(6856):628–631. [PubMed]
  • Wu Rongling, Ma Chang-Xing, Zhao Wei, Casella George. Functional mapping for quantitative trait loci governing growth rates: a parametric model. Physiol Genomics. 2003 Aug 15;14(3):241–249. [PubMed]
  • Yin Tongming, Zhang Xinye, Huang Minren, Wang Minxiu, Zhuge Qiang, Tu Shengming, Zhu Li-Huang, Wu Rongling. Molecular linkage maps of the Populus genome. Genome. 2002 Jun;45(3):541–555. [PubMed]

Articles from Genetics are provided here courtesy of Genetics Society of America

Formats:

Save items

Related citations in PubMed

See reviews...See all...

Cited by other articles in PMC

See all...

Links

  • MedGen
    MedGen
    Related information in MedGen
  • PubMed
    PubMed
    PubMed citations for these articles

Recent Activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...