Originally published as Genetics Published Articles Ahead of Print on May 27, 2008.

Genetics, Vol. 179, 1069-1078, June 2008, Copyright © 2008
doi:10.1534/genetics.107.083873

Breeding Designs for Recombinant Inbred Advanced Intercross Lines

Matthew V. Rockman1 and Leonid Kruglyak

Lewis-Sigler Institute for Integrative Genomics and Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey 08544

1 Corresponding author: 110 Carl Icahn Laboratory, Princeton University, Princeton, NJ 08544.
E-mail: mrockman{at}princeton.edu

Recombinant inbred lines derived from an advanced intercross, in which multiple generations of mating have increased the density of recombination breakpoints, are powerful tools for mapping the loci underlying complex traits. We investigated the effects of intercross breeding designs on the utility of such lines for mapping. The simplest design, random pair mating with each pair contributing exactly two offspring to the next generation, performed as well as the most extreme inbreeding avoidance scheme at expanding the genetic map, increasing fine-mapping resolution, and controlling genetic drift. Circular mating designs offer negligible advantages for controlling drift and exhibit greatly reduced map expansion. Random-mating designs with variance in offspring number are also poor at increasing mapping resolution. Given equal contributions of each parent to the next generation, the constraint of monogamy has no impact on the qualities of the final population of inbred lines. We find that the easiest crosses to perform are well suited to the task of generating populations of highly recombinant inbred lines.