Mapping genome-genome epistasis: A high-dimensional model

Yuehua Cui, Rongling Wu

Research output: Contribution to journalArticlepeer-review

14 Scopus citations

Abstract

Motivation: The proper development of any organ or tissue requires the coordinated expression of its underlying genes that can be located on different genomes present in an organism. For instance, each step in the development of seed for a higher plant is the consequence of gene interactions from the maternal, embryo and endosperm genomes. Results: We present a multivariate statistical model for mapping quantitative trait loci (QTL) by incorporating two important aspects of seed development in plants - QTL interactions derived from different genomes, the maternal, embryo and endosperm, and genetic correlations among phenotypic traits expressed in different genome-specific tissues. This model, which has a high dimensionality, is constructed within the maximum-likelihood context based on a finite mixture model. The implementation of the expectation-maximization algorithm allows for the efficient estimation of QTL positions, their action and interaction effects and pleiotropic effects. The application of this high-dimensional model to a real rice dataset has validated its usefulness. Conclusions: Our model was derived for self-pollinated plants, but it can be extended to cross-pollinated plants and to animals. With the burgeoning of genetic and genomic data, this high-dimensional model will have many implications for agricultural and evolutionary genetic research.

Original languageEnglish (US)
Pages (from-to)2447-2455
Number of pages9
JournalBioinformatics
Volume21
Issue number10
DOIs
StatePublished - May 15 2005

All Science Journal Classification (ASJC) codes

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

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