A general mixture model approach for mapping quantitative trait loci from diverse cross designs involving
multiple inbred lines

YUEFU LIU and ZHAO-BANG ZENG
Program in Statistical Genetics, Department of Statistics, North Carolina State University, Raleigh,
NC 27695-8203, USA

(Received March 19, 1999; Revised September 27, 1999; Revised November 8, 1999)

Abstract

Most current statistical methods developed for mapping quantitative trait loci (QTL) based on inbred
line designs apply to crosses from two inbred lines. Analysis of QTL in these crosses is restricted by
the parental genetic differences between lines. Crosses from multiple inbred lines or multiple families
are common in plant and animal breeding programmes, and can be used to increase the efficiency of a
QTL mapping study. A general statistical method using mixture model procedures and the EM
algorithm is developed for mapping QTL from various cross designs of multiple inbred lines. The
general procedure features three cross design matrices, W, that define the contribution of parental lines
to a particular cross and a genetic design matrix, D, that specifies the genetic model used in multiple
line crosses. By appropriately specifying W matrices, the statistical method can be applied to various
cross designs, such as diallel, factorial, cyclic, parallel or arbitrary-pattern cross designs with two or
multiple parental lines. Also, with appropriate specification for the D matrix, the method can be used to
analyse different kinds of cross populations, such as F2 backcross, four-way cross and mixed crosses
(e.g. combining backcross and F2). Simulation studies were conducted to explore the properties of the
method, and confirmed its applicability to diverse experimental designs.

Article Text (PDF) (296 Kb)