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Genetic Basis of Response to 50 Generations of Selection on Body Weight in Inbred Mice
Peter D. Keightleyaa Institute of Cell, Animal and Population Biology, University of Edinburgh, Edinburgh EH9 3JT, Scotland
Corresponding author: Peter D. Keightley, Institute of Cell, Animal and Population Biology, University of Edinburgh, West Mains Road, Edinburgh EH9 3JT, Scotland, p.keightley{at}edinburgh.ac.uk (E-mail).
Communicating editor: Z-B. ZENG
| ABSTRACT |
|---|
A long-established inbred strain of mice was divergently selected for body weight for 50 generations. Selection of new mutations affecting the trait eventually led to a divergence of approximately three phenotypic standard deviations between the high and low lines. Heritability for body weight increased at a rate between 0.23% and 0.57% per generation from new mutations, depending on the genetic model assumed. About two-thirds of the selection response was in the upward direction. The response was episodic, suggesting a substantial contribution from the selection of mutations with large effects on the trait. A maximum likelihood procedure was used to estimate the number of factors contributing to the response using data from line crosses, with models of n equivalent gene effects (i.e., to estimate the Wright-Castle index), or n genes with variable effects. The results of the analysis of data from a cross between the selected high line and an unselected control line indicated that two major factors were involved, with the suggestion of an additional minor factor.
THE rate of increase of genetic variance of quantitative traits from the accumulation of new mutations has been known for some time to be on the order of 0.1% of the environmental variance per generation (![]()
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, where N is the effective population size, i is the selection intensity, Vm is the increment in variance from one generation of mutation, and
p is the phenotypic standard deviation. At the opposite extreme, if mutational variation is contributed by a small number of mutations with large additive effects, the predicted asymptotic rate of response is the same as under the infinitesimal model, but the asymptotic rate is expected to be reached more quickly. For both models, the response reaches a rate proportional to the effective population size, and this is an argument for maintaining commercial selection lines at as large as possible population sizes. Response from mutations with large effects is expected to be highly variable, as it depends on their chance appearance and fixation, but the response is linearly related to population size because fixation probability is essentially independent of N, but the number of mutation events is proportional to N. Recessive mutant alleles are expected to make small contributions to initial selection response, as their initial rates of frequency change are slow.
Two experiments in Drosophila to measure the contribution of new mutations to selection response for bristle number using inbred or isogenic base populations have been carried out on a large enough scale to allow the evaluation of some of the theoretical predictions just described. ![]()
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Most of our knowledge of the potential for new mutations to contribute to artificial selection responses is restricted to Drosophila bristle number. In mice, there are a number of estimates of the rate of accumulation of variance for various morphological traits, based on rates of divergence between inbred sublines, which suggests that heritability increases at least an order of magnitude faster than is typical for Drosophila morphological traits (reviewed by ![]()
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| MATERIALS AND METHODS |
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Mouse selection line and mutational variance estimation:
The origin and maintenance of the lines and the methods used to estimate mutational variance have been described previously (![]()
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The increment of genetic variation per generation, Vm, was estimated in three different ways:
- By an animal-model restrictd maximum likelihood (REML) analysis that assumes the infinitesimal model of many unlinked genes with small additive effects and uses all the data in the pedigree (
MEYER 1989 ). The genetic variation in the inbred line was assumed to be 4Vm, as expected for a line at mutation-drift balance maintained by brother-sister mating (
LYNCH and HILL 1986 ). Previously (e.g.,
KEIGHTLEY and HILL 1992 ), the base population variance has been erroneously assumed to be 5Vm, which leads to marginally different estimates. A random litter effect and fixed effects of sex, generation number, and litter size were included in the model.
- By fitting the expected response under the infinitesimal model to the observed high-low, high-control, or control-low divergences by least squares using the equation of
HILL 1982B .
- By fitting the expected response under a model of additive genes with large effects fixed rapidly by selection to the observed divergences by least squares, again using the equation of
HILL 1982B .
Both infinitesimal and large-gene-effects models assume that mutations affect fitness only through their effects on the artificially selected trait. In fitting the expected divergences to the observed high-low divergence, a nonzero intercept was fitted to account for a response induced by a maternal effect. With data from the high-control or control-low divergences, a zero intercept had to be assumed, as there were no data in the initial generations to reliably estimate the intercept. The mutational variance is scaled relative to the environmental variance between and within letters and is expressed as the mutational heritability, h2m =
Relaxed selection lines and crosses between them:
At generation 43, sublines were split from the high and low selection lines and maintained without selection for two generations with 10-pair matings. The control line was also maintained at 10-pair matings in generations 44 and 45. To investigate the genetic basis of the upward selection response that had occurred by this time, the progeny of the relaxed high line from generations 44 and 45 were crossed to the control line, and 6-wk body weights of large populations of F1 and F2 mice were recorded.
ML estimation of Wright's effective number of loci:
The number of loci, n, contributing to the difference, R, between divergently selected lines can be estimated using Wright's formula, which relates R to the genetic variance when the lines are crossed (![]()
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(1) |
2b , yij is the observed trait value of individual j from litter i, freqc(g) is the frequency of the multilocus genotype g from line c from the states = 3n possible genotypes for the n genes, µ is the population mean, ag and dg are additive and dominance effects, respectively, for genotype g (the sum of the additive or dominance effects of each locus), xij is the design matrix for fixed effects and the covariate for individual ij, f is the vector of fixed and covariate effects and
2w is the residual variance. The parental lines are assumed to be fixed for opposite alleles acting in the same direction at all the loci at which they differ, and the F1 is assumed to be heterozygous at all loci, so for these subpopulations there is only one nonzero freqc(g), which takes the value one. For the F2, the values of freqc(g) were obtained from a binomial expansion. For a given n, likelihood was computed by evaluating Equation 1 using Simpson's rule to numerically integrate for the litter effects. Maximization as a function of the parameter values was performed using the simplex algorithm (
Variable gene effects:
The classic model to estimate the number of loci explaining fixed differences between selection lines assumes equal gene effects for all the n loci affecting the trait. By ML, is is also possible to compare the fit of the model for cases of small numbers of loci, each with different additive and dominance effects, by evaluating Equation 1. Each additional variable locus introduces two extra parameters, compared with the model with equal effects. The models therefore have large numbers of parameters, so the multidimensional likelihood surfaces were explored extensively to check for local maxima, but none were found for cases of one, two, or three variable loci. With four variable loci, difficulty was encountered in locating the global maximum, as there appeared to be a local maximum. The likelihood space was explored from 12 widely differing combinations of starting parameter values and was found in all cases to converge either to the one local or to the putative global maximum. Likelihood maximization was also attempted with the Metropolis algorithm with simulated annealing (![]()
| RESULTS |
|---|
Response to selection and estimates of mutational variance:
Mean 6-wk body weights for the selection and control lines are plotted against generation number in Figure 1. The selection response was episodic, suggesting the appearance and fixation of a small number of major mutations. The bursts of response are more obvious in the plot of the high-low divergence (Figure 2), which also shows that there was little response in the last 12 generations. About two-thirds of the response was upward and possibly associated with a jump between generations 3540 (Figure 2), although the lack of control line data before generation 37 makes it difficult to tell whether the jump occurred in the low or high line. The greater upward than downward response is surprising, because in mice, very many more mutations are known that reduce growth than increase it (![]()
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The episodic nature of the response implies that the infinitesimal model of many additive, unlinked mutations contributing to the response is inappropriate. An alternative model, the "large-gene-effects model," assumes unlinked, additive mutations of large effect, which become fixed in a short time scale relative to the duration of the experiment, but this also has the drawback of assuming additive mutation effects. Nonetheless, these two models are standard benchmarks for quantifying the mutational input for quantitative traits. Estimated rates of increase of heritability from mutation per generation, (h2m) , based only on information from the divergence between the high and low lines or between the selection lines and control line, assuming either the infinitesimal or large-gene-effects model, are compared to an estimate from the animal-model REML analysis in Table 1. The animal-model REML analysis assumes the infinitesimal model, with mutational variation incorporated in the numerator relationship matrix (![]()
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Relaxed selection:
During the first 20 generations of the experiment, the high and low lines differed, on average, by 1.0 g (Figure 2), a likely consequence of a maternal effect induced by selection. A maternal effect is expected because high (low) selected mothers will tend to have larger (smaller) offspring than average. This effect is expected to disappear rapidly if unselected parents are used (![]()
Means and variances in a cross between high and control lines and calculation of effective number of loci:
Means and variance components from REML analysis (GENSTAT 5 COMMITTEE 1993) of data from generations 4445 of the relaxed selection lines, the control line, and their F1 and F2 are compared in Table 2. The difference between the relaxed high and control lines was 3.46 g (more than two phenotypic SD), while the difference between the control and relaxed low line was only 0.3 g, but the latter difference is somewhat increased if the data are corrected for litter size (Figure 2). The F1 is closer in body weight to the high line, suggesting dominance of high-line mutant alleles. By generation 44, the response appeared to have reached a plateau, so it is reasonable to assume that mutant alleles are fixed in the high line and that the difference in within-litter variance between the F2 and the F1 can be equated to the genetic variance, Vg. The effective number of loci, n, assuming equal additive and dominance effects for each locus, is related to the high-control difference, R, and the deviation from the F1 from the mean of its parents, D, according to n =
. Substitution of the observed R (3.46 g), D (0.61 g) and Vg (0.98 g2) values (Table 2) gives an estimate for n of 1.6. This estimate is consistent with the pattern of selection response, which suggests that one or two major loci were involved.
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Estimation of number of loci differentiating the lines:
The ML procedure detailed in MATERIALS AND METHODS was applied to the complete, untransformed data set from the high and control lines and to their F1 and F2 from generations 44 and 45. Natural log likelihood of the data as a function of the number of loci, under a model of equal additive and dominance effects, is shown in Figure 3. A two-locus model gives the best fit to the data, with a considerably higher likelihood than the one-locus model (the likelihood ratio is e 6.3 = 545). A significance test is not possible, however, as the constraint of equal additive and dominance effects implies that the definition of the parameters changes as extra loci are added to the model. To allow such tests, models in which loci have variable additive and dominance effects were also investigated (Table 3). Likelihood must increase as extra loci are added to the model. Likelihood for two variable loci turned out to be the same as for two equivalent loci: two equal loci maximize the variance for a given difference between the line means, and this is presumably the major factor determining the fit. The addition of one locus with an additive and a dominance parameter implies that the change in twice log likelihood follows a chi-square distribution with two degrees of freedom, so the change in log likelihood of 6.3 between the one- and two-locus models is significant (P < 0.01). Somewhat surprisingly, the addition of a third variable locus also resulted in a significant increase in log likelihood (P < 0.01). The best fitting three-locus model was two major dominant loci and one minor, underdominant locus (Table 3), a result which is difficult to explain intuitively. With four variable loci, there were two maxima in the likelihood surface, the first with three dominant loci and an underdominant locus, and the second with two dominant loci and two underdominants, and maximization to one or the other of these occurred, depending on the initial parameter values. The four-locus model with two underdominant loci gave a higher likelihood, however, but not significantly higher than the three-locus model (Table 3).
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Realized selection differential:
The pattern of the selection response, particularly the divergence between the high and low lines (Figure 2), suggests that the response had reached a plateau after generation 40. Natural selection opposing artificial selection because of selection of alleles with deleterious pleiotropic effects on fitness is one common explanation for selection limits (![]()
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Age-specific effects on body weight:
To test for age-specific differences in body weight between the lines, additional measurements were taken at 3 and 10 wk of age at generation 47 (Figure 5). Absolute differences between the high and control lines increase with age, but the relative differences are highest at 3 wk (35%, dropping to 20% at 6 and 10 wk).
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Checks on contamination of selection lines:
With the exception of a phaeomelanin-deficient mutant rimy (![]()
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| DISCUSSION |
|---|
Genetic variation for body weight from new mutations:
The mutational heritability estimate reported here of 0.53% from the animal-model REML analysis is about half the value reported from this experiment at generation 24 (![]()
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The extent of the response seen in the present experiment lends support to HILL's (1982a,b) suggestion that new mutations can make large contributions to responses in breeding programs. There are several examples of jumps in selection responses in mouse selection experiments for body size involving outbred lines (![]()
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Number of mutations differentiating the lines:
It has been emphasized repeatedly in the literature that estimates of the effective number of factors, n, tend to be biased downward because the basic method assumes unlinked genes with equivalent effects fixed for favorable alleles in the two lines (see, e.g., ![]()
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The results from analysis of the line-cross data by ML point to the response in the high line having been caused by two major mutations, possibly with additional minor mutations. However, the pattern of the selection response seems to show a rapid divergence between the lines at about generation 38, suggesting the fixation of one mutation with a very large effect. Simultaneous fixation of two mutations at about generation 35 seems unlikely. A possible explanation for the discrepancy between the statistical analysis and the response pattern is that segregation analysis methods are known not to be robust to departures from a normal distribution (![]()
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Nature of mutational variability for body weight:
Most information on the nature of spontaneous mutational variation comes from experiments involving selection or random accumulation of mutations in inbred lines of Drosophila, and it is relevant to consider these experiments in relation to the present one. There are large-scale selection experiments for abdominal or sternopleural bristle number in inbred Drosophila, typically resulting in the selection of mutations with large effects on the trait, but very often these mutations are recessive lethals or have detrimental effects on fitness. The mutation effects have been analyzed by chromosome extraction to test for lethals with effect on bristles in the heterozygote (![]()
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- Artificial selection was weak, corresponding to a within-family selection intensity of only 0.4 standard deviations, so lethal or highly deleterious alleles would be quickly eliminated unless they also had a very large effect on the trait. The weakness of the artificial selection was due to the small family size of the inbred strain.
- During most of the experiment, half the matings were between full sibs and the remainder between random nonfull sibs. This would have the effect of exposing deleterious recessives to selection and would lead to their rapid elimination. A bristle-number selection experiment in Drosophila with a similar mating scheme gave a substantially lower rate of accumulation of deleterious mutations affecting the trait than a parallel experiment with random mating (
MERCHANTE et al. 1995 ).
The general pattern of the selection response was very similar to patterns seen in selection experiments for bristle number in inbred Drosophila, which tend to show periods of apparent stasis punctuated by jumps. In the present experiment, most of the response was for increased body weight and was probably caused by a small number of mutations with large effects, but between generations 38 and 50, little subsequent selection response occurred. There is little evidence that this plateau was caused by a loss of selection intensity because of segregation of deleterious alleles with effects on the trait. A lack of variation in the lines seems to be the more likely explanation for the plateau. Under the infinitesimal model, application of the formula for response from new mutations of ![]()
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| ACKNOWLEDGMENTS |
|---|
I thank BILL HILL for continued interest and encouragement over the period of this experiment, FIONA OLIVER for technical assistance, SARA KNOTT for helpful advice on the analysis, PHILIPPE BARET and two anonymous reviewers for helpful comments on the manuscript, and the Biotechnology and Biological Sciences Research Council and the Royal Society for support.
Manuscript received September 18, 1997; Accepted for publication December 11, 1997.
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