scholarly journals Accounting for genetic interactions improves modeling of individual quantitative trait phenotypes in yeast

2016 ◽  
Author(s):  
Simon K. G. Forsberg ◽  
Joshua S. Bloom ◽  
Meru J. Sadhu ◽  
Leonid Kruglyak ◽  
Örjan Carlborg

Experiments in model organisms report abundant genetic interactions underlying biologically important traits, whereas quantitative genetics theory predicts, and data support, that most genetic variance in populations is additive. Here we describe networks of capacitating genetic interactions that contribute to quantitative trait variation in a large yeast intercross population. The additive variance explained by individual loci in a network is highly dependent on the allele frequencies of the interacting loci. Modeling of phenotypes for multi-locus genotype classes in the epistatic networks is often improved by accounting for the interactions. We discuss the implications of these results for attempts to dissect genetic architectures and to predict individual phenotypes and long-term responses to selection.

Genetics ◽  
1992 ◽  
Vol 132 (2) ◽  
pp. 603-618 ◽  
Author(s):  
A S Kondrashov ◽  
M Turelli

Abstract Apparent stabilizing selection on a quantitative trait that is not causally connected to fitness can result from the pleiotropic effects of unconditionally deleterious mutations, because as N. Barton noted, "...individuals with extreme values of the trait will tend to carry more deleterious alleles...." We use a simple model to investigate the dependence of this apparent selection on the genomic deleterious mutation rate, U; the equilibrium distribution of K, the number of deleterious mutations per genome; and the parameters describing directional selection against deleterious mutations. Unlike previous analyses, we allow for epistatic selection against deleterious alleles. For various selection functions and realistic parameter values, the distribution of K, the distribution of breeding values for a pleiotropically affected trait, and the apparent stabilizing selection function are all nearly Gaussian. The additive genetic variance for the quantitative trait is kQa2, where k is the average number of deleterious mutations per genome, Q is the proportion of deleterious mutations that affect the trait, and a2 is the variance of pleiotropic effects for individual mutations that do affect the trait. In contrast, when the trait is measured in units of its additive standard deviation, the apparent fitness function is essentially independent of Q and a2; and beta, the intensity of selection, measured as the ratio of additive genetic variance to the "variance" of the fitness curve, is very close to s = U/k, the selection coefficient against individual deleterious mutations at equilibrium. Therefore, this model predicts appreciable apparent stabilizing selection if s exceeds about 0.03, which is consistent with various data. However, the model also predicts that beta must equal Vm/VG, the ratio of new additive variance for the trait introduced each generation by mutation to the standing additive variance. Most, although not all, estimates of this ratio imply apparent stabilizing selection weaker than generally observed. A qualitative argument suggests that even when direct selection is responsible for most of the selection observed on a character, it may be essentially irrelevant to the maintenance of variation for the character by mutation-selection balance. Simple experiments can indicate the fraction of observed stabilizing selection attributable to the pleiotropic effects of deleterious mutations.


Author(s):  
Bruce Walsh ◽  
Michael Lynch

In a finite population, drift is often more important than selection in removing any initial additive variance. This chapter examines the joint impact of selection, drift, and mutation on the long-term response in a quantitative trait. One key result is the remarkable finding of Robertson that the expected long-term response from any initial additive variance is bounded above by the product of twice the effective population size times the initial response. This result implies that the optimal selection intensity for long-term response it to save half of the population in each generation.


2015 ◽  
Vol 6 (1) ◽  
Author(s):  
Joshua S. Bloom ◽  
Iulia Kotenko ◽  
Meru J. Sadhu ◽  
Sebastian Treusch ◽  
Frank W. Albert ◽  
...  

Author(s):  
Bruce Walsh ◽  
Michael Lynch

Selection changes the additive-genetic variance (and hence the response in the mean) by both changing allele frequencies and by generating correlations among alleles at different loci (linkage disequilibrium). Such selection-induced correlations can be generated even between unlinked loci, and (generally) are negative, such that alleles increasing trait values tend to become increasingly negative correlated under direction or stabilizing selection, and positively correlated under disruptive selection. Such changes in the additive-genetic variance from disequilibrium is called the Bulmer effects. For a large number of loci, the amount of change can be predicted from the Bulmer equation, the analog of the breeder's equation, but now for the change in the variance. Upon cessation of selection, any disequilibrium decays away, and the variances revert back to their additive-genic variances (the additive variance in the absence of disequilibrium). Assortative mating also generates such disequilibrium.


2016 ◽  
Author(s):  
Johan Hallin ◽  
Kaspar Martens ◽  
Alexander Young ◽  
Martin Zackrisson ◽  
Francisco Salinas ◽  
...  

Explaining trait differences between individuals is a core but challenging aim of life sciences. Here, we introduce a powerful framework for complete decomposition of trait variation into its underlying genetic causes in diploid model organisms. We intercross two natural genomes over many sexual generations, sequence and systematically pair the recombinant gametes into a large array of diploid hybrids with fully assembled and phased genomes, termed Phased Outbred Lines (POLs). We demonstrate the capacity of the framework by partitioning fitness traits of 7310 yeast POLs across many environments, achieving near complete trait heritability (mean H2 = 91%) and precisely estimating additive (74%), dominance (8%), second (9%) and third (1.8%) order epistasis components. We found nonadditive quantitative trait loci (QTLs) to outnumber (3:1) but to be weaker than additive loci; dominant contributions to heterosis to outnumber overdominant (3:1); and pleiotropy to be the rule rather than the exception. The POL approach presented here offers the most complete decomposition of diploid traits to date and can be adapted to most model organisms.


1999 ◽  
Vol 73 (3) ◽  
pp. 263-273 ◽  
Author(s):  
JOHN K. KELLY

Unconditionally deleterious mutations could be an important source of variation in quantitative traits. Deleterious mutations should be rare (segregating at low frequency in the population) and at least partially recessive. In this paper, I suggest that the contribution of rare, partially recessive alleles to quantitative trait variation can be assessed by comparing the relative magnitudes of two genetic variance components: the covariance of additive and homozygous dominance effects (Cad) and the additive genetic variance (Va). If genetic variation is due to rare recessives, then the ratio of Cad to Va should be equal to or greater than 1. In contrast, Cad/Va should be close to zero or even negative if variation is caused by alleles at intermediate frequencies. The ratio of Cad to Va can be estimated from phenotypic comparisons between inbred and outbred relatives, but such estimates are likely to be highly imprecise. Selection experiments provide an alternative estimator for Cad/Va, one with favourable statistical properties. When combined with other biometrical analyses, the ratio test can provide an incisive test of the deleterious mutation model.


2021 ◽  
Author(s):  
Yvonne C.J. Wientjes ◽  
Piter Bijma ◽  
Mario P.L. Calus ◽  
Bas J. Zwaan ◽  
Zulma G. Vitezica ◽  
...  

ABSTRACTGenomic selection has revolutionized genetic improvement in animals and plants, but little is known of its long term effects. Here we investigate the long-term effects of genomic selection on the change in the genetic architecture of traits over generations. We defined the genetic architecture as the subset, allele frequencies and statistical additive effects of causal loci. We simulated a livestock population under 50 generations of phenotypic, pedigree, or genomic selection for a single trait, controlled by either only additive, additive and dominance, or additive, dominance and epistatic effects. The simulated epistasis was based on yeast data. The observed change in genetic architecture over generations was similar for genomic and pedigree selection, and slightly smaller for phenotypic selection. Short-term response was highest with genomic selection, while long-term response was highest with phenotypic selection, especially when non-additive effects were present. This was mainly because the loss in genetic variance and in segregating loci was much greater with genomic selection. Compared to pedigree selection, genomic selection lost a similar amount of the genetic variance but maintained more segregating loci, which on average had lower minor allele frequencies. For all selection methods, the presence of epistasis limited the changes in allele frequency and the fixation of causal loci, and substantially changed the statistical additive effects over generations. Our results show that non-additive effects can have a substantial impact on the change in genetic architecture. Therefore, non-additive effects can substantially impact the accuracy and future genetic gain of genomic selection.


1971 ◽  
Vol 13 (3) ◽  
pp. 515-521 ◽  
Author(s):  
R. Watkins ◽  
L. P. S. Spangelo

It is predicted chat satisfactory estimates of genetic variance parameters could be obtained from quarter diallels at a considerable reduction in the cost compared to obtaining similar information from full diallels. It is also predicted that, for breeding procedures designed to exploit all the genetic variance, estimates of genetic progress obtained from half and quarter diallels would be almost identical to those obtained from full diallels.No genetic progress was indicated for strawberry yield for any reasonable selection intensity when only the additive variance was exploited.It is suggested that long-term genetic progress for an economic complex of characters may be obtained by exploiting major gene differences following classical Mendelian principles and using the resulting selections as one source of parents for crosses designed to exploit all the genetic variance – additive, dominant and epistatic.


Sign in / Sign up

Export Citation Format

Share Document