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Note to the Reader Text file started Sept 1, 1998. This version updated July 3, 2000.
Please refer to: Williams RW (1999) A targeted screen to detect recessive mutations that have quantitative effects. Mammalian Genome 10:734–738.

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A Targeted Screen to Detect Recessive Mutations that have Quantitative Effects

Robert W. Williams
Center for Neuroscience and the Department of Anatomy and Neurobiology, University of Tennessee, Memphis TN 38163

        Materials and Methods
        Figure 1: The Mutagenesis Breeding Plan
            Consomic Strains
            Generating Mutations
            Generating and Genotyping G2 Females
            Genotyping G3 Progeny
            Phenotyping G4 Progeny
            Are Mutations On-Target?
            Detecting Recessive Mutations in QTLs
            Genotyping and Colony Costs of the Screen
            Objections to a Targeted Screen
            Starting with Congenic Strains
            Precedents: Other Targeted Mutagenesis Tactics

           Related Links on Mutatgenesis
           Related Articles in PubMed

Abstract.  Chromosome substitution strains have been used for more than four decades to isolate, map, and characterize recessive mutations in Drosophila. This paper describes an experimental cross in mice that can be used to define and map induced germ-line mutations that map to a single chromosome. The cross is a modification and extension of a conventional three-generation recessive mutagenesis screen. It begins with an inbred consomic strain that carries the desired target chromosome. Consomic males are mutated and bred back to the background strain. G1 heterozygous males are also crossed to the background strain. Second generation male and female progeny that inherited non-recombinant target chromosomes are identified by genotyping and are bred. The third generation progeny are genotyped for multiple markers on the target chromosome, but the aim in this generation is to identify males and females that are homozygous for the same short interval of the target chromosome (5 to 25 cM). These near-congenic pairs are bred. Multiple litters of fourth generation animals that are homozygous for known segments of the target chromosome are phenotyped. Mutations with relatively small and somewhat variable effects can be detected and then mapped to a precision as high as 5–10 cM.



The genome is a robust code. Not only do diploid organisms have two copies of most genes, but many genes also have closely related variants, or paralogs that serve similar functions (Nadeau and Sankoff, 1997). Even when both alleles of a given gene are mutated, the phenotypic repercussions can be subtle. This is what Sewall Wright (1977) had in mind when he commented that sets of related genes may be "maintained by selection for quantitative effects, while protected from drastic effects of inactivation or loss." It follows that an important problem in a systematic screen for mutations is to devise protocols capable of detecting more subtle variants. Without sufficient sensitivity, mutant alleles in a significant fraction of genes may never be detected. Screens will lack power. In contrast, mutations in genes that lack backup may be detected many times. To cite an extreme example, a mutagenesis screen in C. elegans recently produced 63 novel mutations in a single mechanoreceptor gene (Chalfie and Au, 1989; García-Añoveros and Corey, 1997). In contrast, mutations and knockouts of numerous important genes, for example, the retinoic acid receptors, often have surprisingly modest effects that would elude most screens (Luo et al., 1995; Mendelsohn et al., 1994; Zhou et al., 1998). In this paper I describe a promising technique designed with this problem in mind. The technique relies on a novel type of mouse called a consomic mouse and on a four-generation breeding protocol (Fig. 1).
      A consomic mouse is a fully inbred animal in which a single intact pair of homologous chromosomes from an inbred donor strain has been transferred into the genome of a fully inbred recipient strain (Fig. 1, top; Hudgins et al., 1985). If chromosome 7 from donor strain A is introgressed into recipient strain B, the resulting animals are designated B-7A consomic mice. Several consomic strains have been generated by Jean-Louis Guénet and Maria Rosa Arnau (PWK and SPRET chromosomes introgressed into C57BL/6). We are using the C57BL/6-19PWK strain to begin a mutagenesis screen of Chr 19 (RW Williams, JL Guénet, D Goldowitz, in progress). A complete set of consomic strains in which chromosomes from A/J have been transferred to C57BL/6J are now being generated by J Nadeau, J Singer, and E Lander (personal communication). With this set of strains any chromosome can become the focus of a recessive screen. Although, the particular screen outlined here is just now being tested in mice, chromosomal substitution lines of Drosophila with similar properties have been used very effectively to isolate mutations with quantitative effects on viability, sensory bristle number, behavior, and body weight (e.g., Lyman et al., 1996; Anholt et al., 1996; Currie et al., 1998).

Key features of this method are:

  1. Entire litters of homozygotes are examined, not isolated individuals within litters. A large number of mutants can be generated in the first round of analysis. Animals with recessive mutations can be studied at several ages or can be sent to multiple investigators. The analysis of entire litters increases the power of the screen.

  2. Mutations are screened on a relatively homogeneous genetic background. This increases the sensitivity of the screen. Control lines for comparative analysis are easily generated.

  3. Only individuals known to be non-recombinant on defined intervals of a target chromosome are bred, and only homozygous progeny are phenotyped. This increases the overall efficiency of phenotyping. This selectivity relies on highly efficient genotype assays.

  4. Mutations are mapped to specific intervals of a target chromosome without extensive genotyping or additional rounds of breeding and phenotyping. Resolution of 5–20 cM is achieved in the first pass. This increases the efficiency with which mutations are mapped and, ultimately, cloned.

  5. Embryonic lethal alleles are readily detected and simultaneously mapped in the form of “missing homozygotes.” Lethal alleles can be recovered and studied by crossing heterozygotes.


 Figure 1: Design of a Consomic Recessive Screen

Figure 1

Figure 1. Download a color high-resolution PDF version of this figure.

Consomic mutagenesis cross. The upper-left box represents the genome of a fully inbred consomic male mouse (4 of 19 autosome pairs are illustrated). Three of the consomic male's chromosomes are identical to those of the recipient strain female (upper-right box). The exceptional chromosome (black target chromosome) is derived from a donor strain that is not illustrated. The original male (G0) is mutagenized with ENU and is crossed to a recipient strain female. The small box (center-left) represent a single gamete of the mutagenized male. Eight mutations are indicated using small open circles, two of which are on-target, six of which are off-target. The G1 male (A) is also crossed to a recipient strain female. G2 progeny are genotyped and non-recombinant individuals (e.g., animal B) are identified and bred. Note that the number of off-target mutations carried by the G2 male (B), is half that carried by the G1 male (labeled A). The diagonal line marked backcross dilution represents an optional step that can be used one or more times to sequentially dilute off-target mutations. G3 progeny are genotyped and pairs of animals that are homozygous on common intervals of the target chromosome are mated. In this example, the G3 breeders share a homozygous interval that extends from approximately 15 to 40 cM. A set of litters of G4 animals that have a comparatively uniform genome are phenotyped to identify and map recessive mutations on the target chromosome. Note that the figure only illustrates one of a potentially large number of such G4 test litters; each homozygous on different parts of the target chromosome.


Methods and Materials

Consomic Strain

The key starting material for a targeted recessive screen is one or more consomic strains of mice. These strains are produced by introgressing entire chromosomes derived from an inbred donor into an inbred recipient strain (Hudgins et al., 1985). Consomic lines are also referred substitution lines or insertion lines because an exogenous pair of homologous chromosomes is substituted for the usual pair. Several consomic strains have been successfully generated by Jean-Louis Guénet and colleagues (SPRET/Ei chromosomes moved onto a C57BL/6 background; JL Guénet, personal communication). A complete set of consomic strains in which A/J chromosomes have been transferred to a C57BL/6J background are now being generated by Joseph Nadeau, Jonathan Singer, and Eric Lander (1998). Consomic mice in which Chr 7 is derived from A/J have the formal designation C57BL/6J-7A/J (B.A7 for short). I will use the B.A7 strain for illustration in this paper, but any consomic or chromosome substitution strain can be used.  


Generating Mutations

Consomic males are mutagenized with N-ethyl-N-nitrosourea (ENU) or another mutagen (Fig. 1, top left). Those animals that regain fertility are mated with several females belonging to the recipient strain used to make the consomic line (inbred females, top right). ENU is a potent mutagen of spermatogonia. Each sperm will carry a load of mutations. Tests of specific gene loci suggest that the right dose of ENU can mutagenize up to one gene in a thousand (Russell et al., 1979; 1982; Rinchik et al., 1990). Chr 7 makes up roughly 5% of the mouse genome, and single gametes produced by a B.A7 male will harbor an average of five of the approximately 100 mutations generated randomly across the genome. The great majority of mutations (>90%) carried by the G1 male will be recessives (Kacser and Burns, 1981; Lynch and Walsh, 1998, pp. 63–65).  


Generating and Genotyping G2 Females

Four chromosomes are depicted in Figure 1—the target and three other chromosomes. The G1 male is a heterozygote at all mutant loci and at all Chr 7 loci that are polymorphic between A/J and C57BL/6J (left margin). Like his father, he is mated to the recipient or background strain (C57BL/6J, in this case) to generate a set of G2 progeny. A majority of his progeny will inherit recombinant Chr 7s, but a significiant fraction will inherit a non-recombinant A/J-type chromosome 7 that traces its descent from a single gamete of the mutated G0 male (e.g., left-most G2 female). For short chromosomes (50 cM) subject to a single obligatory recombination event during meiosis, two of the four chromatids will usually be non-recombinant (Lawrie et al., 1995). However, for longer chromosomes the fraction of non-recombinant chromatids is approximately 0.5L/50, where L is the length of the chromosome in centimorgans. For Chr 7, with a length of approximately 75 cM, the estimated fraction of non-recombinant chromosome is 0.35, of which half will be derived from the consomic parental strain. This equation gives estimates that are biased upward because it fails to account for the non-independence of recombination events within the tetrad. Interference extends over approximately 60 Mb (Lawrie et al., 1995) and results in a more uniform distribution of second crossover events. To sort mice with recombinant and non-recombinant target chromosomes, all G2 mice are genotyped. The number of G2 progeny that are genotyped will depend on the length of the target chromosome, but an average of 30 to 60 G2 animals will typically need to be tested. To reduce this effort a two step procedure can be employed. All animals are initially genotyped for markers near proximal and distal ends of the target chromosome. Mice that are heterozygotes for both markers are subsequently genotyped at five to ten internal markers spaced at approximately 10 cM intervals to determine whether or not they inherited an intact A/J chromosome 7 from their G1 sire. Only those G2 males and females that are non-recombinant across the entire target chromosome are retained for breeding.
      To generate sufficient numbers of non-recombinant G2 progeny, the G1 male is bred to five or more C57BL/6J females, generating 40 or more offspring. The probability that any one G2 offspring carries a nonrecombinant A/J chromosome is about 0.25 for small chromosomes (~50 cM) and 0.125 for long chromosomes (~100 cM). In the case of Chr 7 (75 cM), about 1 in 6 G2 animals are expected to carry an intact A/J chromosome bearing a set of mutations. We expect 3 nonrecombinant mice in 20, and the probability of finding at least 1 nonrecombinant of each sex in 40 is close to 95%. It will be necessary to identify enough nonrecombinant females to ensure that 50 or more G3 progeny can be generated quickly.
      The G2 females are bred to G2 males, and are not backcrossed to the G1 male as in a standard G3 recessive screen. The key difference between G1 and G2 males is that G2 progeny carry half the load of extraneous mutations (mutations on non-target chromosomes) as does the G1 male. As described below, it is important to reduce the load of these extraneous mutations.  


Genotyping and Breeding G3 progeny

Nonrecombinant G2 females are crossed to one or more G2 nonrecombinant males to generate G3 progeny (Fig. 1). All G3s are genotyped at moderate resolution on the target chromosome (makers spaced at 10 cM). Individuals homozygous for segments of the target chromosome longer than 5–10 cM are retained for phenotyping and breeding. An average of one-fourth of G3 progeny will be homozygous for a given part of the target chromosome.
      G3 males and females that are homozygous for shared segments of the target chromosome are paired. The goal is to ensure that the target chromosome is fully represented by overlapping and nested sets of breeding pairs. In this way the load of mutations carried on the target chromosome is effectively split apart and mapped in one process. The larger the number of breeding pairs with overlapping homozygous intervals, the better the resolution and assurance with which mutations can be mapped. Assuming that a line does not carry lethal alleles, it should be possible to screen all of Chr 7 for recessive mutations using only a few breeding pairs, each homozygous over matched a 30 to 40 cM interval. In subsequent cycles of breeding, different G3 males and females sharing progressively smaller common intervals can be paired to refine intervals that harbor mutations.



Detecting Lethal Mutations

Recessive lethal alleles can make up a large fraction of induced mutations—up to 90% in some screens of Drosophila (Wright, 1977). Unless visible markers are incorporated into a screen these recessive lethals can be difficult to detect. However, in a consomic screen it is easy to recognize and even map recessive lethal mutations. G3 progeny are genotyped at a set of markers that span the target chromosome, and if few or no G3 individuals are homozygous for a particular interval, then this is good evidence that a recessive embryonic lethal mutation has been generated and detected. Similarly, alleles that compromise prenatal and early postnatal viability should lead to segregation distortion of genotypes assayed at weaning. It should subsequently be possible to choose appropriate G3 animals that are heterozygotes across these missing intervals and breed them to confirm, recover, and characterize lethal mutations. Assessing the frequency of missing homozygous intervals among G3 progeny may be an effective way to estimate the efficacy of mutagen dosage.  


Phenotyping G4 progeny

Matched G3 animals are bred and entire litters of G4 individuals are phenotyped. All are homozygous across large segments of the target chromosome. If a segment harbors a recessive mutation, then there should be a consistent abnormality within a G4 litter. Litters of G4 progeny can be compared to the original consomic strain and to other litters with overlapping and non-overlapping regions of homozygosity.
      G3 parents will share mutations with their G4 offspring and it may initially be puzzling that G4 animals are generated prior to an extensive analysis of their G3 parents. The main reason is that if G3 animals appear normal, then by allowing the G3 pair to produce one or more G4 litters we can get enough test class animals to search for mutations with subtle qualitative and quantitative effects. A related reasons is that in a recessive screen a factor that often limits progress is the number of test class animals that can be generated. If a pair of G3 animals is fertile, then large numbers of test class animals that are homozygous on defined intervals can be generated efficiently. They can be sent to several investigators for analysis. Third, if G3 animals are obviously mutants, then mating these animals allows us to determine the impact that mutations have on reproduction.

How isogenic are G4 test class animals? G4 animals are similar in genetic composition to both the consomic parental strain and to the original inbred recipient strain (Fig. 1). However, even G4 littermates produced from interval-matched G3 parents are not isogenic. First, they carry a variable set of segregating mutations on otherwise inbred non-target chromosomes (Fig. 1). Second, the G4 progeny are genetically heterogeneous in the variable length intervals that flank the homozygous interval of the target chromosome (Fig. 1, bottom). G4 progeny from single litters will therefore have some residual genetic variance. Variance due to off-target mutations can be reduced significantly using an intervening backcross to the wildtype recipient strain (see next section on Collateral Damage). However, the genetic variance within G4 litters should not prevent the detection of mutations. If a mutation maps to the chosen interval of the target chromosome, then other G4 litters that share this interval but that were produced by mating different G3 mice should have the same aberrant phenotype. It is therefore possible to confirm that a mutation maps to the target chromosome and simultaneously refine the position of mutations by comparing several litters from different G3 parents. [Furthermore, by crossing G4 animals to mice carrying small deletions in selected homozygous intervals (Schimenti and Bucan, 1998), it should also be possible to quickly refine the location of a mutation by complementation analysis.]

If G4 animals are used to generated additional generations of progeny, a significant number of these mutations will become fixed.
      In both G2 and G3 generations animals that do not meet the genotype criteria are never mated. This filtering can be done before weaning and reduces the size of the colony and number of individuals that need to be phenotyped. -->  




Collateral Damage: Are Mutations On-Target?

Selective breeding of G2 and G3 progeny enriches for homozygotes on defined intervals of the target chromosome. However, there will still be many non-target segments of the genome that harbor mutant alleles (see G3 and G4 progeny in Fig. 1). Mutations that are off-target in G2 progeny are diluted twofold relative to mutations on the target (compare the mutation load in the G1 male to that in G2 progeny in figure 1). For this reason, the probability that a single G3 parent is homozygous for an off-target mutation originally carried by the G1 male is about 1 in 8. The probability that two randomly chosen G3 animals will both be homozygous mutants for off-target intervals is 1 in 64. However, the non-targeted part of the genome is on average about 20 times larger than the target. The approximate likelihood that a mutation is off target is therefore about 1 in 3 (1:64 times 20:1).To compute a more precise estimate would require information on several factors, including the relative size of the target chromosome and the homozygous target interval, the relative gene density of the particular interval, and the relative abundance of lethal alleles that are off-target. A practical way to assess whether a mutation is on- or off-target is to examine litters generated from different sets of G3 parents that share common homozygous intervals. If enough G3 mating pairs are bred, every part of the target should be represented by two or more G4 litters. The likelihood that two G4 litters from different parents will have mutations associated with the same recessive allele on a non-target chromosome is low—on the order of ~0.005. If three or more independently derived litters have the same aberration then the mutation is highly likely to be on-target.
       One other factor adds some complexity to the analysis of G4 progeny. Numerous mutations that are off-target will be carried in a heterozygous state by the G3 progeny. Phenotypes that appear on average in one-quarter or one half of mice in one G4 litters, but not another, will for the most part be caused by segregation at these mutated loci. An example is shown on the third pair of chromosomes at the bottom of Figure 1 in which the male G3 parent is –/+ and the female G3 parent is –/– for an off-target mutation. The source of this variability can be rapidly assessed using the same method mentioned above; namely, to compare phenotypes of sets of litters with matched or overlapping homozygous intervals. However, there is an alternative method that may be useful, depending on the sensitivity of the screen to this collateral genetic damage. By backcrossing G2 nonrecombinant males to parental strain females the off-target mutations can be diluted twofold per generation. This step is shown in Figure 1 by an oblique line labeled dilution backcross. With each generation of backcrossing to the recipient strain, the load of residual off-target mutations is halved.


Detecting Recessive Mutations in Quantitative Trait Loci

A key issue in a mutagenesis screen is to have sufficiently sensitive and economical assays to detect altered traits. Minimizing extraneous genetic variance is critical. Mackay and colleagues (Anholt et al., 1996) have used a chromosome substitution protocol and they have been able to detect and map numerous mutations in Drosophila that affect behavioral responses to volatile organic compounds. In a consomic screen the final analysis of deviant phenotypes is based on a comparison between several litters of G4 progeny and three possible control populations: (1) the consomic strain, (2) the recipient inbred strain, and (3) non-mutagenized G4 control lines generated in the same way as the experimental G4 litters and homozygous for the same interval.
       For phenotypes that are inherently noisy, such as many behavioral and disease-susceptibility traits, entire litters of homozygotes can be screened, and the litter's mean, variance, or incidence becomes the key measure. As is true of recombinant inbred lines, the precision and reliability of results can be assessed and improved by examining numerous offspring from multiple litters. Unusual phenotypes in the G4 should be found in at least several members of each litter. Ultimately, the phenotype should also be noted in G3 parents. The G4 screen is robust in the sense that episodic, but unfortunately common, non-heritable abnormalities (developmental phenocopies) should not become a distraction. For this reason exhaustive assessment of G4 animals may be warranted. For example, quantitative histological analysis might reveal reliable differences between G4 litters and control lines. Extensive quantitative serological, complex expression assays, and extensive behavioral and neurological testing might be justified.
      How small an effect can one expect to detect with a consomic design? The statistical power depends primarily on the number of G4 animals and litters that one has the patience to phenotype. A reasonable expectation is that for any part of the target chromosome one will have at least two homozygous litters available for analysis (x2 coverage). The mean phenotypes of G4 animals should be compared with those of a G4 litter that is homozyogus on the same interval but generated from a non-mutagenized consomic stock. The statistical power of the comparison is that of a conventional t test (Snedecor and Cochran, 1980, p. 70). For example, with 12 animals in the mutagenized G4 group, the power to detect a mutation at the p = 0.05 level with an effect that shifts the mean +/- 1 SD is approximately 0.94. With 25 animals (4–5 litters) one should have a 50% chance of detecting mutations with an effect size of only 0.4 SD. In some cases the power will be less because the appropriate n for traits sensitive to maternal effects will be litter number. The power of a search for a mutation with an effect of +/- 1 SD is approximately 0.50 using four litters.


Genotyping and Colony Costs of the Screen

Genotyping Costs.  A targeted screen using consomic strains relies on efficient genotyping. Approximately 100 to 200 G2 and G3 animals will need to be genotyped to characterize on-target mutations carried each G1 male. If 10 markers were typed per individual, a maximum of 2000 reactions would be required. A more typical estimate is 500 to 1000 reactions. Thanks to the high density of MIT microsatellite markers (Dietrich et al., 1992), simple DNA extraction procedures, and streamlined PCR protocols (Williams and Strom, <>), the time, effort, and expense of genotyping is now comparatively low (~$1/genotype).
      Colony Costs.  While the G4 design is somewhat complicated, this does not mean that the colony size needs to be large or that the screening will be slow. Each G1 male is initially bred to 5 to 8 inbred females in one large cage. G2 animals can be culled shortly after they have been genotyped and just before weaning. The G1 male is retired and a son and several daughters that all have nonrecombinant target chromosomes (Fig. 2, middle) are left in the cage. The G3 progeny will need to be marked, genotyped, culled, or retained prior to weaning. At this point, pairs of matched G3 progeny can be moved to smaller breeding cages. As few as 3 pairs, or as many as 20 pairs, could be used to cover the entire target chromosome. Additional heterozygote mating cages may need to be set up to characterize intervals harboring putative recessive lethal mutations. Approximately four months after the initial G1 matings, the G2 mating cage will have been supplanted by 3 to 15 small breeding cages of G3 parents and their G4 offspring. Each cage will probably need to be retained in the colony for a minimum of two months to allow enough time to phenotype each litter. The average colony requirement associated with a single G1 lineage is approximately 1 large cage for a duration of 4 months followed by 10 small cages for a duration of 3 months. The frequency with which mutations are identified will determine the cost of success—those costs associated with characterizing, archiving, and distributing mutant lines.

Screening for Late-Onset Mutations. It should be practical to retain small numbers of G3 and G4 animals in the colony to study the long-term consequences of novel recessive alleles. The original G3 mating pairs will often be 100-days-old before the analysis of their first litter of G4 progeny is complete. If no interesting phenotypes are initially detected in the G4 animals, then it may nonetheless be useful to hold several sets of G3 or G4 breeders in anticipation of possible late-onset traits. It may often be possible to test an entire chromosome by retaining only animals with long congenic intervals. In the absence of recessive lethal alleles, as few as one to five pairs of mice could cover an entire chromosome. Periodic test matings may be useful to ensure that mutations with late lethal effects are not lost.  


Targeted Screens—Disadvantages and Advantages

A targeted screen ignores mutations generated across most of the genome—19 out of 20 mutations will be rejected in a typical consomic screen. For this reason, a targeted approach may not be appropriate (1) if the screening procedure is tightly focused, reliable, rapid, and inexpensive; (2) if there is good evidence that traits of interest are known to be controlled by small numbers of loci; and (3) if mapping mutations is a low priority and one that can be more conveniently done after mutations have been identified. One particular potential problem with a targeted approach is the possibility that a narrow chromosomal focus will be coupled with a low yield of mutations (Schimenti and Bucan, 1998). The consomic approach enriches for homozygotes and this does increase the efficiency and sensitivity of the screen. However, even after selectively breeding G2 and G3 individuals, some mutations that do not map on the target chromosome will be detected among G4 progeny. In order to retain focus on mutations that can be rapidly mapped and for which a list of candidate genes can be identified, these off-target mutations will generally need to be ignored. Whether this focused approach yields a sufficiently high output of novel recessive alleles will depend in part on the ingenuity, sensitivity, and number of tests that can be performed on G4 litters.
      One potential problem with a targeted approach is the possibility that a narrow focus will be coupled with a low yield of mutations (Schimenti and Bucan, 1998). On the one hand, the consomic targeted approach enriches for homozygotes, increasing the efficiency and sensitivity of the screen and this method also simplifies subsequent high-resolution mapping. On the other hand, even after genotyping G2 and G3 individuals, some mutations that are off-target are likely to be detected. In order to retain focus on those mutant phenotypes that can be rapidly mapped and for which a list of candidate genes can be identified, off-target mutations will generally need to be ignored. Whether this focused approach yields a sufficiently high output of novel recessive alleles will depend in part on the ingenuity, sensitivity, and number of tests that can be performed on G4 litters.
      Although a consomic recessive screen targets particular chromosomes, there is no reason why it would not be possible to systematically target each chromosome in turn. In this respect, a targeted approach could be as comprehensive in scope as a random whole-genome screen. One possible advantage of the targeted approach is that it is more practical to assess when a particular part of the genome has been saturated with mutations (Rinchik et al., 1990). It should be possible to fine-tune the relative intensity of mutagenesis and screening to reflect the large regional differences in gene density. Furthermore, if the consomic target chromosome were derived from the particular strain of mouse whose genome is soon be sequenced (C57BL/6J), then once a set of candidate genes have been identified in a given homozygous interval, it will be straightforward to sequence candidates as a first step in identifying the responsible mutation.
      [Because the G4 progeny are homozygous on well-defined intervals, one may want to finetune the particular type of phenotype screen to detect novel mutations in well mapped genes and quantitative trait loci. For instance, if a particular interval is known to contains a family of voltage-gated potassium channels or a QTL that specifically affects organ weights, then selected litters might be subjected to special functional or morphometric tests.]
      Two other issues associated with the G4 consomic design deserve mention. (1) The ENU dosages appropriate for this design has not yet been established. Given the likelihood of generating numerous recessive lethal alleles, it may be difficult to determine a suitable dosage for a given set of consomic strains. (2) In other targeted recessive designs it is often possible to take advantage of visible markers and inversions to simplify the generation and categorization of homozygous animals. This completely avoids the somewhat onerous genotyping that is vital to a G4 consomic screen. Except in Drosophila, it is generally not possible to use visible markers or inversions as part of a consomic design. However, to give one example in which this will be possible, the B-7A consomic strain will be a white albino. The interval around the tyrosinase locus could in principle be targeted with minimal genotyping.


Using Congenic Strains?

A screen could in principle be adapted to exploit smaller target intervals that have been isolated in congenic, rather than consomic, strains of mice. In congenic strains the length of the donor interval is a function of the number of backcrosses, but even after ten backcross generations, the donor interval is typically 20 cM in length (~200/n cM, where n is the number of generations of successive backcrosses). One disadvantage of using congenic strains is that a significant fraction of mutations will occur in linked intervals that flank the congenic segment. These adjoining intervals will be larger than the congenic interval itself. This will make mapping mutations generated in congenic strains somewhat more unpredicable than those generated using consomic strains.



Precedents: Other Targeted Methods

Targeted screens for recessive mutations have been carried out for many years and it is important to compare the consomic design with well known alternatives. One of the first and best protocols to screen for recessive mutations takes advantage of hemizygous lines that are missing all or part of particular chromosomes (Muller, 1927; Justice et al., 1997, Schimenti and Bucan, 1998). Muller's classic mutagenesis experiments exploited the hemizygosity of the X chromosome of male fruit flies. But artificial hemizygous intervals can now be generated in mice of both sexes by deleting a short segments from one autosome. Mice from which 5 to 15 cM has been deleted are usually viable (Justice et al., 1997; Schimenti and Bucan, 1998). Recessive alleles that are in trans to the deletions are unmasked and mice have phenotypes similar, if not identical, to those of homozygote mutants. To expose a recessive mutation involves breeding G1 heterozygote carriers like those in Figure 1 to deletion stock. An average of one in four progeny of such a cross will be a hemizygous mutant. Rinchik and colleagues used mice from which the interval on chromosome 7 extending from tyrosinase to shaker 1 had been deleted (Rinchik et al. 1990; Rinchik, 1991). G1 females carrying mutations inherited from ENU-mutagenized sires were crossed to males hemizygous for the deletion. By a clever choice of coat-color mutations, they were able to restrict their main analysis to the hemizygous G2 test class animals. Schimenti and Bucan (1998) review a G2 screen in which recombination in a deletion interval is suppressed by using a stock that carries a large inversion and a coat-color mutation. This refinement simplifies the analysis by forcing a more nearly perfect concordance between visible markers and genotype (see their figure 3).
       In order to use a G2 screen of this type, deletions need to be generated and hemizygotes must be viable. Until recently, making deletion stocks would have been a serious technical impediment, but Schimenti and colleagues (You et al., 1997; <>) are now systematically generating embryonic stem cells that can be used to generate mice with deletions quickly. A set of 500 lines, each with a unique pair of thymidine kinase tags embedded 5 cM apart, are being generated. The interval between tags is deleted and the stem cells are then used as starting material to generate deletion stock. By combining deletions with visible markers and chromosomal inversions that suppress recombination—genetic tricks first perfected in Drosophila—it is possible to have a nearly perfect concordance between visible markers and genotypes (Schimenti and Bucan, 1998). This can greatly simplifies the analysis because only a particular and easily recognized class of G2 offspring are phenotyped. Generating the highly specialized lines of mice that are required to this type of screen is still difficult.
      There are significant advantages of using deletion stock in a mutagenesis screen that counterbalance the difficulties of generating mice. The major advantage is that recessive mutations can be detected in the second generation (Rinchik et al., 1990). The reduction in breeding costs relative to G3 and G4 designs is a major advantage. No other regions of the genome, except the male's X and Y chromosomes, are “homozygous” for off-target mutations, so mutational variance due to recessive alleles is restricted to the target interval. One minor disadvantage is that the genetic background of the G2 progeny will be a mixture of the genomes of the mutagenized male and the genome of the deletion stock. The DELBank Project deletions are carried on a (129/SvJae x C57BL/6J)F1 background. The G2 progeny will therefore combine alleles from 129 and C57BL/6 with whatever strains are used to generate heterozygous carriers of mutations. The high genetic variance of this type of G2 can be viewed as a positive feature—mutations that are detected will probably have good penetrance on a variety of genetic backgrounds. But the downside of this genetic complexity is that subtle effects of recessive mutations will be much more difficult to detect.
      Another factor to consider in comparing consomic and deletion methods is the relative intensity of mutagenesis that must be employed to compensate for the length of the target interval. Targeting a 5 cM interval typically involves using a relatively high mutagen dosage. Strains that tolerate high doses or ENU are therefore preferred. In a consomic screen in which the target is 10 to 20 times longer, a lower dose may be employed. As a result, even a strain such as C57BL/6 that is extremely sensitive to ENU may be useful.

Drosophila Precedents. The consomic procedure outline here also has precedents that trace back to a series of experiments by Dobzhansky and colleagues (e.g., Dobzhansky et al., 1959) in which single chromosomes of wild populations of fruit flies were introgressed into special laboratory strains to examine the load of recessive lethal alleles carried by natural populations. Recombination in fruit flies can be suppressed, and given a laboratory strain with the right visible markers it is relatively simple to follow the assortment of chromosomes in a three generation cross. In several impressive studies, Mackay and colleagues (Mackay et al., 1992; Lyman et al. 1996; Anholt et al., 1996) have exploited chromosome substitution techniques to study effects of induced mutations. Mutated chromosomes were introgressed into isogenic backgrounds and the effects on fecundity, sensory bristle number, and olfactory behavior were assayed. In these studies a complex breeding scheme exploiting visible markers and tagged P-elements (Fig. 1 of Lyman et al., 1996) was used to filter progeny and generate test class animals (G4 through G6). They then examined large numbers of nearly isogenic mutants to detect subtle QTL-like effects. P-elements were subsequently mapped at high-resolution by in situ hybridization. In a consomic screen using mice, visible markers are replaced by molecular markers made visible using simple PCR protocols. There are many specific differences between the Drosophila substitution mutagenesis screen (see Fig. 1 of Lyman et al., 1996) and the consomic procedure described here, but the key goals are sharedÑminimize extraneous genetic variance while maximizing the efficiency with which induced mutations can be mapped. As in Drosophila, there is still extraneous mutational variance in the mouse consomic screen. The source of this variance in flies is not yet clearly understood (Lyman et al., 1996), but in consomic mice most of this variance will be associated with the potentially large load of off-target mutations. These mutations can only be removed by repeatedly backcrossing G2 non-recombinants to the inbred recipient strain.
      In comparing the merits of targeted approaches that rely either on consomic strains or deletion lines it will be critical to assess the likely yield of mutants as a function of effort and cost. In general, the smaller the interval that is targeted, the lower the yield. In a consomic screen, the target is an entire chromosome, and the yield will be relatively high. However, this design does require four generations; a negative when compared to a simple two-generation design. The yield of mutations is also a function of the sensitivity of tests. Here the advantage of screening entire litters of homozygotes on a relatively uniform genetic background may be a persuasive advantage of the consomic G4 design.



This research was supported by grant RO1 EY06627 from the National Eye Institute and RO1 NS35485 from the National Institute of Neurological Disorders and Stroke. I thank Kathryn Graehl for helpful discussion and for editing the text and Figure 1. My thank to Drs. Rosemary Elliott, Lorraine A. Flaherty, Jean-Louis Guénet, Eugene Rinchik, John Schimenti, Benjamin Taylor, and David W. Threadgill for comments and corrections.




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Related Links

  1. The MRC Mutagenesis Programme, Harwell, England. <>

  2. The German Human Genome Project Mouse ENU Mutagenesis Program. <>

  3. The DELBank Project. Links to the DELBank project and John Schimenti's Joy of Cloning protocol manual. <>

  4. Maja Bucan's Lab at the University of Pennsylvania. A short description of mutagenesis screens for behavioral abnormalities. <>

  5. Tennessee Genomics Consortium. Links to genomics and mutagenesis programs in Tennessee (Oak Ridge National Laboratory, Vanderbilt University, University of Tennessee, Meharry Medical School, and St. Jude Children's Research Hospital). <>

  6. A really quick way to get sufficient DNA for a few PCR reactions.


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