A statistical model for QTL mapping in polysomic autotetraploids underlying double reduction

Brief Bioinform. 2014 Nov;15(6):1044-56. doi: 10.1093/bib/bbt073. Epub 2013 Oct 30.

Abstract

As a group of economically important species, linkage mapping of polysomic autotetraploids, including potato, sugarcane and rose, is difficult to conduct due to their unique meiotic property of double reduction that allows sister chromatids to enter into the same gamete. We describe and assess a statistical model for mapping quantitative trait loci (QTLs) in polysomic autotetraploids. The model incorporates double reduction, built in the mixture model-based framework and implemented with the expectation-maximization algorithm. It allows the simultaneous estimation of QTL positions, QTL effects and the degree of double reduction as well as the assessment of the estimation precision of these parameters. We performed computer simulation to examine the statistical properties of the method and validate its use through analyzing real data in tetraploid switchgrass.

Keywords: EM algorithm; polysomic autotetraploid; quantitative genetic model; quantitative trait loci.

Publication types

  • Research Support, Non-U.S. Gov't
  • Validation Study

MeSH terms

  • Algorithms
  • Chromosome Mapping / statistics & numerical data*
  • Computational Biology
  • Computer Simulation
  • Likelihood Functions
  • Models, Genetic*
  • Models, Statistical
  • Monte Carlo Method
  • Panicum / genetics
  • Plants / genetics
  • Polyribosomes / genetics
  • Quantitative Trait Loci*
  • Tetraploidy*