Usually, null-mutant mice generated using gene targeting are recombinants of two inbred parental strains (e.g. 129 and C57BL/6 strains). These mice contain a chromosomal region surrounding the locus of the targeted gene that is exclusively 129 type in the mutant but C57BL/6 (B6) type in the control, a problem known as the ‘flanking allele’ confound. Many consider this to be a serious problem because it makes the interpretation of gene-targeting studies ambiguous: one can never tell what caused the phenotypical alteration in the mutant, the null mutation or the 129-type alleles flanking it. In a recent paper, however, Bolivar et al.1xMapping of quantitative trait loci with knockout/congenic strains. Bolivar, V.J. et al. Genome Res. 2001; 11: 1549–1552Crossref | PubMed | Scopus (66)See all References1 have shown that flanking alleles might be used to our advantage.Numerous null-mutant strains have been backcrossed to B6 mice to reduce the presence of 129 alleles in their genome. These backcrossed lines are genetically identical in all regions of their genome (containing B6 alleles), except for the flanking region, where the mutants have 129-type alleles, and the wild-type controls have B6-type alleles. In essence, these strains are congenic. Congenic lines have been used in quantitative trait locus (QTL) mapping because they allow one to examine the phenotypical effects of genetic differences localized to short regions of a chromosome. Hence, the suggestion by Bolivar et al. that we should use the ever increasing number of null-mutant strains as congenic lines to look for novel genetic loci that influence brain function and behavior. The suggestion has merit. B6 and 129 strains are genetically distinct; this distinction is manifested as robust differences in brain function and behavior. Thus, B6 congenic lines carrying chromosomal regions of 129-type alleles flanking different targeted loci are expected to have idiosyncratic phenotypical characteristics, which will facilitate the mapping and identification of the gene(s) responsible for the phenotypical differences.First, Bolivar et al. suggest a multi-step breeding and testing scheme, which, they claim, will allow one to decide whether the phenotypical alterations of the mutant are due to the effects of the flanking genes or the targeted gene. The scheme is ingenious yet simple. It has some weaknesses, however, and it might not allow one always to pinpoint the genetic source of phenotypical differences unambiguously. Nevertheless, Bolivar et al. used it successfully.Focussing mainly on behavioral characteristics that were not found previously to be influenced by the targeted disruption of the genes of interest, Bolivar et al. identified a null-mutant strain, the B6-IL10−/− mouse, as being different in open-field behavior from B6 mice. They confirmed that the alteration was not due to targeted disruption of the gene encoding interleukin-10 (IL-10) but to the 129-type chromosomal region flanking the target locus. Employing numerous genetic markers, they revealed that the locus of the targeted gene was on chromosome 1 and a putative QTL resided within a 33 centi-Morgan chromosomal segment surrounding the target locus that contains 129-type alleles in the mutants. The results agreed with finer mapping data obtained previously with classical QTL analyses, and confirmed that a (set of) gene(s) associated with emotionality and open-field behavior might reside within this region of chromosome 1. The results demonstrate clearly a new use for null-mutant mice! These mice, together with the increasing amount of mouse DNA-sequence information, will facilitate identification of novel genes that might, perhaps, play key roles in human neuropsychiatric diseases associated with abnormal fear, anxiety, emotionality, cognition and many other behavioral phenomena.