“Conversion” of epistatic into additive genetic variance in finite populations and possible impact on long-term selection response

AbstractThe ability of a population to adapt to changes in their living conditions, whether in nature or captivity, often depends on polymorphisms in multiple genes across the genome. In-depth studies of such polygenic adaptations are difficult in natural populations, but can be approached using the resources provided by artificial selection experiments. Here, we dissect the genetic mechanisms involved in long-term selection responses of the Virginia chicken lines, populations that after 40 generations of divergent selection for 56-day body weight display a nine-fold difference in the selected trait. In the F15 generation of an intercross between the divergent lines, 20 loci explained more than 60% of the additive genetic variance for the selected trait. We focused particularly on seven major QTL and found that only two fine-mapped to single, bi-allelic loci; the other five contained linked loci, multiple alleles or were epistatic. This detailed dissection of the polygenic adaptations in the Virginia lines provides a deeper understanding of genome-wide mechanisms involved in the long-term selection responses. The results illustrate that long-term selection responses, even from populations with a limited genetic diversity, can be polygenic and influenced by a range of genetic mechanisms.

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The Impact of Genomic and Traditional Selection on the Contribution of Mutational Variance to Long-Term Selection Response and Genetic Variance

Genetics ◽

10.1534/genetics.119.302336 ◽

2019 ◽

Vol 213 (2) ◽

pp. 361-378 ◽

Cited By ~ 1

Author(s):

Herman A. Mulder ◽

Sang Hong Lee ◽

Sam Clark ◽

Ben J. Hayes ◽

Julius H. J. van der Werf

Keyword(s):

Genetic Variance ◽

Selection Response ◽

Term Selection ◽

The Impact ◽

Mutational Variance

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THE SELECTION LIMIT DUE TO THE CONFLICT BETWEEN TRUNCATION AND STABILIZING SELECTION WITH MUTATION

Genetics ◽

10.1093/genetics/114.4.1313 ◽

1986 ◽

Vol 114 (4) ◽

pp. 1313-1328

Author(s):

Zhao-Bang Zeng ◽

William G Hill

Keyword(s):

Genetic Variation ◽

Genetic Variance ◽

Selection Response ◽

Stabilizing Selection ◽

Phenotypic Variance ◽

Selection Differential ◽

Term Selection ◽

Truncation Selection ◽

Infinite Population

ABSTRACT Long-term selection response could slow down from a decline in genetic variance or in selection differential or both. A model of conflict between truncation and stabilizing selection in infinite population size is analysed in terms of the reduction in selection differential. Under the assumption of a normal phenotypic distribution, the limit to selection is found to be a function of κ, the intensity of truncation selection, ω 2, a measure of the intensity of stabilizing selection, and σ 2, the phenotypic variance of the character. The maintenance of genetic variation at this limit is also analyzed in terms of mutation-selection balance by the use of the "House-of-cards" approximation. It is found that truncation selection can substantially reduce the equilibrium genetic variance below that when only stabilizing selection is acting, and the proportional reduction in variance is greatest when the selection is very weak. When truncation selection is strong, any further increase in the strength of selection has little further influence on the variance. It appears that this mutation-selection balance is insufficient to account for the high levels of genetic variation observed in many long-term selection experiments.

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Selection Response in Finite Populations

Genetics ◽

10.1093/genetics/144.4.1961 ◽

1996 ◽

Vol 144 (4) ◽

pp. 1961-1974 ◽

Cited By ~ 2

Author(s):

Ming Wei ◽

Armando Caballero ◽

William G Hill

Keyword(s):

Linkage Disequilibrium ◽

Inbreeding Depression ◽

Genetic Variance ◽

Relative Rate ◽

Selection Response ◽

Rate Of Change ◽

Effective Population ◽

Short Term ◽

Model Account

Formulae were derived to predict genetic response under various selection schemes assuming an infinitesimal model. Account was taken of genetic drift, gametic (linkage) disequilibrium (Bulmer effect), inbreeding depression, common environmental variance, and both initial segregating variance within families (σAW02) and mutational (σM2) variance. The cumulative response to selection until generation t(CRt) can be approximated asCRt≈R0[t−β(1−σAW∞2σAW02)t24Ne]−Dt2Ne,where Ne is the effective population size, σAW∞2=NeσM2 is the genetic variance within families at the steady state (or one-half the genic variance, which is unaffected by selection), and D is the inbreeding depression per unit of inbreeding. R 0 is the selection response at generation 0 assuming preselection so that the linkage disequilibrium effect has stabilized. β is the derivative of the logarithm of the asymptotic response with respect to the logarithm of the within-family genetic variance, i.e., their relative rate of change. R 0 is the major determinant of the short term selection response, but σM2, Ne and β are also important for the long term. A selection method of high accuracy using family information gives a small Ne and will lead to a larger response in the short term and a smaller response in the long term, utilizing mutation less efficiently.

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LONG-TERM SELECTION RESPONSE FOR 12-DAY LITTER WEIGHT IN MICE

Genetics ◽

10.1093/genetics/72.1.129 ◽

1972 ◽

Vol 72 (1) ◽

pp. 129-142

Author(s):

E J Eisen

Keyword(s):

Body Weight ◽

Genetic Correlation ◽

Half Life ◽

Selection Process ◽

Selection Response ◽

Exponential Model ◽

Correlated Response ◽

Term Selection ◽

Litter Weight

ABSTRACT Long-term selection for increased 12-day litter weight in two replicate lines (W2, W3) of mice resulted in an apparent selection limit at about 17 generations. Quadratic polynomial and exponential models were fitted to the data in order to estimate the plateaued response and half-life of the selection process. Using the polynomial results, the half-life estimates were 4.5 and 8.6 generations for W2 and W3, respectively. The plateaued responses were 5.1 and 5.8 g which, when expressed in phenotypic standard deviation units, became 1.1 and 1.3. The exponential model provides similar estimates. A negative association between 12-day litter weight and fitness was not considered to be an adequate explanation for the plateau since there was no decrease in fertility of the selected lines. Evidence that exhaustion of genetic variability was not the cause of the plateau came from the immediate response to reverse selection. It was proposed that the plateau may be due to a negative genetic correlation between direct and maternal genetic effects, which would be expected to occur after many generations of selection. There were positive correlated responses in both replicates for adult body weight, which was in agreement with the positive genetic correlation between preweaning and postweaning body weight. The expected positive correlated response for number born was realized in only one of the replicates.

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Accumulation of mutations affecting body weight in inbred mouse lines

Genetics Research ◽

10.1017/s0016672300033152 ◽

1995 ◽

Vol 65 (2) ◽

pp. 145-149 ◽

Cited By ~ 11

Author(s):

Armando Caballero ◽

Peter D. Keightley ◽

William G. Hill

Keyword(s):

Body Weight ◽

Maximum Likelihood ◽

Genetic Variance ◽

Inbred Mouse ◽

Additive Genetic Variance ◽

Selection Response ◽

Spontaneous Mutations ◽

Line Selection ◽

Divergence Estimates ◽

Mouse Lines

SummaryThe variation from spontaneous mutations for 6-week body weight in the mouse was estimated by selection from a cross of two inbred sublines, C57BL/6 and C57BL/10, separated about 50 years previously from the same inbred line. Selection was practised high and low for 12 generations from theF2, followed by one generation of relaxation. The lines diverged by approximately 1·7 g or 0·7 sd. The additive genetic variance was estimated in theF2by restricted maximum likelihood and from the selection response, and from this variance the mutational heritabilityhM2was estimated using the number of generations since divergence. Estimates ofhM2range from 0·08 to 0·10% depending on the method of analysis. These estimates are similar to those found for other species, but lower than other estimates for the mouse. It is concluded that substantial natural and, perhaps, artificial selection operated during the maintenance of the sublines.

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A Gene-assumed Model to Predict the Long- term Selection Response Taking Account of the Change in Genetic Properties from Parents to Offspring

Nihon Chikusan Gakkaiho ◽

10.2508/chikusan.59.554 ◽

1988 ◽

Vol 59 (6) ◽

pp. 554-559 ◽

Cited By ~ 1

Author(s):

H. TAKEDA ◽

A. NISHIDA ◽

A. TAKEBE

Keyword(s):

Selection Response ◽

Term Selection

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A guide to using a multiple-matrix animal model to disentangle genetic and nongenetic causes of phenotypic variance

10.1101/318451 ◽

2018 ◽

Cited By ~ 3

Author(s):

Caroline E. Thomson ◽

Isabel S. Winney ◽

Oceane C. Salles ◽

Benoit Pujol

Keyword(s):

Animal Model ◽

Genetic Variance ◽

Genetic Relatedness ◽

Additive Genetic Variance ◽

Phenotypic Traits ◽

Phenotypic Variance ◽

Data Types ◽

Evolutionary Potential ◽

Recent Developments

AbstractNon-genetic influences on phenotypic traits can affect our interpretation of genetic variance and the evolutionary potential of populations to respond to selection, with consequences for our ability to predict the outcomes of selection. Long-term population surveys and experiments have shown that quantitative genetic estimates are influenced by nongenetic effects, including shared environmental effects, epigenetic effects, and social interactions. Recent developments to the “animal model” of quantitative genetics can now allow us to calculate precise individual-based measures of non-genetic phenotypic variance. These models can be applied to a much broader range of contexts and data types than used previously, with the potential to greatly expand our understanding of nongenetic effects on evolutionary potential. Here, we provide the first practical guide for researchers interested in distinguishing between genetic and nongenetic causes of phenotypic variation in the animal model. The methods use matrices describing individual similarity in nongenetic effects, analogous to the additive genetic relatedness matrix. In a simulation of various phenotypic traits, accounting for environmental, epigenetic, or cultural resemblance between individuals reduced estimates of additive genetic variance, changing the interpretation of evolutionary potential. These variances were estimable for both direct and parental nongenetic variances. Our tutorial outlines an easy way to account for these effects in both wild and experimental populations. These models have the potential to add to our understanding of the effects of genetic and nongenetic effects on evolutionary potential. This should be of interest both to those studying heritability, and those who wish to understand nongenetic variance.

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Elite populations for conifer breeding and gene conservation

Canadian Journal of Forest Research ◽

10.1139/x26-051 ◽

1996 ◽

Vol 26 (3) ◽

pp. 453-461 ◽

Cited By ~ 21

Author(s):

Claire G. Williams ◽

J.L. Hamrick

Keyword(s):

Tree Breeding ◽

Forest Tree ◽

Selection Response ◽

Gene Conservation ◽

Forest Tree Breeding ◽

Short Term ◽

Term Selection ◽

Loss Of Genetic Diversity ◽

Advanced Generation

Elite populations managed for short-term gain have received increasing attention as advanced-generation breeding strategies have taken shape for forest tree species. They are prevalent for two reasons: (1) their short-term gains provide justification for the rising costs of recurrent forest tree breeding and (2) the advent of control-pollinated seed production has reduced the requirement for a large number of unrelated selections. This paper addresses the concept of an elite population, its potential for compressed generation intervals, its predicted long-term selection response, as well as the concomitant risks of severe inbreeding depression and loss of genetic diversity.

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Long-term animal research in genetic improvement of livestock and poultry

Canadian Journal of Plant Science ◽

10.4141/cjps96-105 ◽

1996 ◽

Vol 76 (4) ◽

pp. 581-585

Author(s):

E. B. Burnside

Keyword(s):

Animal Species ◽

Genetic Variance ◽

Genetic Selection ◽

Selection Response ◽

Animal Experimentation ◽

Private Industry ◽

Animal Products ◽

Selection Experiments ◽

Long Term Studies

In animal experimentation, long-term studies have contributed substantially to our knowledge of genetics in particular, and of nutrition, physiology, and reproduction, to lesser extents. Long-term genetic selection experiments have yielded information on selection limits, dissipation of genetic variance over time, and created unique lines which may be utilized as consumer demands shift. Costs of long-term experimentation are not inordinately high in comparison to other experimentation, if economic animal species are used and returns from animal products are recovered to help finance the experiment. Government finance is, however, required for long-term experimentation, as private industry has little motivation for this work. The paper outlines recent significant contributions of long-term experimentation, and provides guidelines for planning experiments. Key words: Selection response, animal genetics, long-term experimentation, experimental design

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