Faculty Collaboration Database

Quantitative trait mapping in a diallel cross of recombinant inbred lines. Mamm Genome 2005 May;16(5):344-55

Date

08/18/2005

Pubmed ID

16104382

DOI

10.1007/s00335-004-2466-1

Scopus ID

2-s2.0-23844467156 (requires institutional sign-in at Scopus site)   19 Citations

Abstract

A recombinant inbred intercross (RIX) is created by generating diallel F1 progeny from one or more panels of recombinant inbred (RI) strains. This design was originally introduced to extend the power of small RI panels for the confirmation of quantitative trait loci (QTL) provisionally detected in a parental RI set. For example, the set of 13 C x B (C57BL/6ByJ x BALB/cByJ) RI strains can, in principle, be supplemented with 156 isogenic F1s. We describe and test a method of analysis, based on a linear mixed model, that accounts for the correlation structure of RIX populations. This model suggests a novel permutation algorithm that is needed to obtain appropriate threshold values for genome-wide scans of an RIX population. Despite the combinational multiplication of unique genotypes that can be generated using an RIX design, the effective sample size of the RIX population is limited by the number of progenitor RI genomes that are combined. When using small RI panels such as the C x B there appears to be only modest advantage of the RIX design when compared with the original RI panel for detecting QTLs with additive effects. The RIX, however, does have an inherent ability to detect dominance effects, and, unlike RI strains, the RIX progeny are genetically reproducible but are not fully inbred, providing somewhat more natural genetic context. We suggest a breeding strategy, the balanced partial RIX, that balances the advantage of RI and RIX designs. This involves the use of a partial RIX population derived from a large RI panel in which the available information is maximized by minimizing correlations among RIX progeny.

Author List

Tsaih SW, Lu L, Airey DC, Williams RW, Churchill GA

Author

Shirng-Wern Tsaih Research Scientist II in the Obstetrics and Gynecology department at Medical College of Wisconsin

MESH terms used to index this publication - Major topics in bold

Animals
Chromosome Mapping
Computer Simulation
Crosses, Genetic
Female
Male
Mice
Models, Genetic
Phenotype
Quantitative Trait Loci
Recombination, Genetic