Behavior Genetics

, Volume 28, Issue 1, pp 29–38 | Cite as

Effect of Within-Strain Sample Size on QTL Detection and Mapping Using Recombinant Inbred Mouse Strains

  • J. K. Belknap


Increasing the number of mice used to calculate recombinant inbred (RI) strain means increases the accuracy of determining the phenotype associated with each genotype (strain), which in turn enhances quantitative trait locus (QTL) detection and mapping. The purpose of this paper is to examine quantitatively the effect of within-strain sample size (n) on additive QTL mapping efficiency and to make comparisons with F2and backcross (BC) populations, where each genotype is represented by only a single mouse. When 25 RI strains are used, the estimated equivalent number of F2mice yielding the same power to detect QTLs varies inversely as a function of the heritability of the trait in the RI population \(h_{{\text{RI}}}^{\text{2}} \). For example, testing 25 strains with n= 10 per strain is approximately equivalent to 160 F2mice when \(h_{{\text{RI}}}^{\text{2}} \)= 0.2, but only 55 when \(h_{{\text{RI}}}^{\text{2}} \)= 0.6. While increasing nis always beneficial, the gain in power as nincreases is greatest when \(h_{{\text{RI}}}^{\text{2}} \)is low and is much diminished at high \(h_{{\text{RI}}}^{\text{2}} \)values. Thus, when \(h_{{\text{RI}}}^{\text{2}} \)is high, there is little advantage of large n, even when napproaches infinity. A cost analysis suggested that RI populations are more cost-effective than conventional selectively genotyped F2populations at \(h_{{\text{RI}}}^{\text{2}} \)values likely to be seen in behavioral studies. However, with DNA pooling, this advantage is greatly reduced and may be reversed depending on the values of \(h_{{\text{RI}}}^{\text{2}} \)and n.

Recombinant inbred strain quantitative trait locus chromosome mapping quantitative genetics mouse 


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© Plenum Publishing Corporation 1998

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  • J. K. Belknap

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