Fact-checked by Grok 2 weeks ago

Additive genetic effects

Additive genetic effects refer to the linear and independent contributions of individual alleles to an individual's phenotypic value, where the effects of alleles at different loci sum cumulatively without interactions. The additive genetic value of an individual, known as the breeding value, is defined as the sum of the average effects of all the alleles it carries, which is transmitted to offspring through Mendelian inheritance.^[1] This value represents the expected deviation of an individual's progeny from the population mean, assuming random mating.^[1] At the population level, additive genetic effects manifest as additive genetic variance (V_A), which quantifies the variance in breeding values among individuals and arises from the segregation of alleles that influence quantitative traits.^[2] V_A is a key component of total phenotypic variance (V_P), alongside environmental variance (V_E) and non-additive genetic components like dominance (V_D) and epistasis (V_I), such that V_P = V_A + V_D + V_I + V_E.^[2] Unlike non-additive effects, which involve allele interactions within or across loci, additive effects assume no such dependencies and are modeled as the sum of allele substitution effects.^[3]^[4] The importance of additive genetic effects lies in their role in narrow-sense heritability (h² = V_A / V_P), which measures the proportion of phenotypic variance due to additive genetic variance and directly predicts a population's short-term response to natural or artificial selection (R = h² S, where S is the selection differential).^[1]^[5] Empirical studies across diverse traits and species consistently show that V_A accounts for over half of the total genetic variance in many cases, underscoring its dominance in evolutionary potential and breeding programs.^[6] For instance, in behavioral traits like extraversion, additive effects explain 20-23% of variation, often interacting with environmental factors but remaining heritable across generations.^[3] This framework is foundational in quantitative genetics for understanding adaptation and trait evolution.^[5]

Fundamentals

Definition

Additive genetic effects represent the portion of phenotypic variation attributable to the independent, linear contributions of individual alleles at different loci, without considering interactions such as dominance or epistasis. These effects are modeled as the cumulative sum of small, additive increments from each allele, allowing quantitative traits to exhibit continuous variation in populations. This conceptualization underpins the analysis of inheritance for complex traits influenced by many genes of minor effect each.^[7] The additive effect of an allele is quantified as the average change in phenotype resulting from substituting one allele for another, averaged across all possible genetic backgrounds in the population—a measure known as the average effect of allelic substitution. For instance, in a diploid locus with alleles A and a, where the homozygote AA has a genotypic value of +2, heterozygote Aa has +1, and homozygote aa has 0 (assuming no dominance), the additive effect of allele A is +1, calculated as half the difference between the homozygote values: (2 - 0)/2 = 1. This substitution effect reflects the allele's marginal contribution to the trait, independent of specific combinations with other alleles.^[7] This framework was pioneered by Ronald A. Fisher in his seminal 1918 work on reconciling Mendelian inheritance with continuous variation in quantitative traits, where he introduced the notion of average effects to explain correlations between relatives under polygenic control.^[8] Fisher's approach emphasized that, for traits governed by numerous loci, the heritable component arises primarily from these additive allelic effects, forming the foundation for estimating evolutionary responses to selection. In one sentence, these effects are central to narrow-sense heritability, which quantifies the transmissible genetic variance relative to total phenotypic variance.

Additive versus Non-Additive Effects

Non-additive genetic effects encompass interactions that deviate from the simple summation of individual allelic contributions to the phenotype, primarily including dominance and epistasis. Dominance refers to the interaction between alleles at the same locus, where the heterozygote phenotype does not represent the average of the two homozygotes.^[9] Epistasis involves interactions between alleles at different loci, where the effect of one locus on the phenotype depends on the genotype at another locus.^[10] A classic example of dominance is observed in a single locus with alleles A and a, where the heterozygote Aa exhibits a phenotype that deviates from the mid-parent value (the average of the AA and aa homozygotes), known as the dominance deviation.^[11] For epistasis, consider a scenario in plant breeding where the effect of a gene influencing flower color at one locus is masked or enhanced by the genotype at a second locus, altering pigmentation outcomes beyond what additive effects alone would predict.^[12] The key distinction between additive and non-additive effects lies in their predictability and transmission: additive effects are cumulative and transmitted independently to offspring, allowing reliable prediction of progeny phenotypes based on parental breeding values, whereas non-additive effects, such as dominance and epistasis, rely on specific allelic combinations that are disrupted during sexual reproduction and thus not independently heritable across generations.^[9] This makes additive effects the foundation for narrow-sense heritability estimates in breeding programs.^[11] To illustrate, in a two-locus model (A/a and B/b) with equal allele frequencies, additive effects contribute linearly to the phenotype by summing the average impacts of each allele across loci, yielding predictable genotypic values. However, epistasis introduces non-linear outcomes, such as overdominance (where the double heterozygote exceeds both parental types) or underdominance (where it falls below), resulting in phenotypic variances that cannot be decomposed solely into additive components.^[10]

Variance Decomposition

Components of Genetic Variance

The phenotypic variance V_P observed in a quantitative trait within a population arises from multiple sources and is fundamentally decomposed into genetic and non-genetic components. In quantitative genetics, this decomposition is expressed as V_P = V_G + V_E + V_{GE}, where V_G represents the total genetic variance attributable to differences in genotypes, V_E denotes the environmental variance due to non-heritable factors affecting trait expression, and V_{GE} captures the variance stemming from interactions between genotypes and environmental conditions.^[13] The total genetic variance V_G is itself partitioned into additive and non-additive components to reflect the different ways genes contribute to trait variation. Specifically, V_G = V_A + V_D + V_I, with V_A being the additive genetic variance, V_D the dominance variance arising from interactions between alleles at the same locus, and V_I the epistatic variance resulting from interactions among alleles at different loci.^[10] This breakdown allows researchers to distinguish the heritable portions of variation that can be predicted across generations from those that cannot. Combining these, the basic model for phenotypic variance simplifies to V_P = V_A + V_D + V_I + V_E when genotype-environment interactions are minimal or separately analyzed.^[13] Among these, the additive genetic variance V_A is particularly significant, as it quantifies the variance due to breeding values—the average effects of parental alleles on offspring phenotypes, assuming no dominance or epistasis.^[10] This component, rooted in the linear summation of individual gene effects, underpins predictions of response to selection in breeding programs.^[13]

Additive Genetic Variance

Additive genetic variance, denoted as V_A, represents the portion of phenotypic variance attributable to the additive effects of alleles and is formally defined as the variance in breeding values among individuals in a population. The breeding value A of an individual quantifies its expected contribution to the next generation and is calculated as A = 2 \times (mid-parent deviation from the population mean), where the mid-parent value is the average phenotype of its parents. This formulation arises because, under an additive genetic model, the expected mean of an individual's progeny is the population mean plus half its breeding value, making the breeding value twice the deviation of the progeny mean from the population mean; symmetrically, it equals twice the parental mid-point deviation assuming no non-additive effects. Consequently, V_A = 2 \times \mathrm{Cov}(\text{mid-parent value}, \text{[offspring](/page/Offspring) value}), reflecting the additive genetic component captured in parent-offspring resemblance across the population.^[10] A key property of V_A is its transmissibility across generations, as breeding values are linearly inherited and remain stable under random mating, enabling predictable resemblance between relatives. This heritability underpins the breeder's equation, R = h^2 S, where R is the response to selection, S is the selection differential, and h^2 = V_A / V_P (with V_P as total phenotypic variance) is the narrow-sense heritability, providing a brief theoretical link to evolutionary change. The magnitude of V_A is influenced by allele frequencies at contributing loci, as expressed in the formula V_A = \sum 2pq\alpha^2 (where p and q are allele frequencies, and \alpha is the average effect of allele substitution), which peaks at intermediate frequencies and diminishes under fixation. Linkage disequilibrium can also modulate V_A by altering allele associations, though it is minimal in randomly mating populations where independent assortment predominates.

Heritability Measures

Broad-Sense Heritability

Broad-sense heritability, denoted as H^2, is defined as the proportion of phenotypic variance in a population that is attributable to total genetic variance, expressed as H^2 = \frac{V_G}{V_P}, where V_G represents all genetic contributions including additive, dominance, and epistatic effects, and V_P is the total phenotypic variance. This measure quantifies the overall genetic influence on a trait without distinguishing between types of genetic effects. The value of H^2 ranges from 0 to 1, with 0 indicating no genetic contribution to phenotypic variation and 1 indicating that genetics account for all observed differences in the trait. A high H^2 implies that genetic factors predominantly explain phenotypic differences within the studied population, but this does not guarantee reliable prediction of the trait across generations, as non-additive genetic effects may not be consistently inherited. Broad-sense heritability is commonly estimated using twin studies, which leverage the genetic similarity between monozygotic and dizygotic twins to partition variance into genetic and environmental components via structural equation modeling; this captures total genetic variance (additive plus dominance) as H² = (V_A + V_D)/V_P, often assuming minimal shared environmental effects. In experimental designs, such as those in plant or animal breeding, it can also be derived from analyses of variance among clonal or full-sib families that reflect total genotypic effects.^[14] One limitation of broad-sense heritability is that it overestimates the heritable variation that can be transmitted predictably to offspring, since non-additive components like dominance and epistasis do not follow simple Mendelian inheritance patterns and thus contribute less to response in selection programs. The total genetic variance V_G encompasses additive genetic variance as a subset, but H^2 includes these non-transmissible elements, potentially misleading applications focused on breeding value.

Narrow-Sense Heritability

Narrow-sense heritability, denoted as h^2, is defined as the ratio of additive genetic variance (V_A) to total phenotypic variance (V_P), quantifying the proportion of observed trait variation attributable solely to the additive effects of alleles.^[15] This measure focuses exclusively on the linear contributions of individual genes, excluding interactions or dominance effects that do not transmit predictably across generations.^[16] The concept was formalized by Ronald A. Fisher in his 1918 paper on correlations between relatives, where he partitioned genetic variance into additive components relevant to inheritance. A primary advantage of narrow-sense heritability lies in its utility for predicting parent-offspring resemblance and the response to selection in quantitative genetics, as it captures only the heritable portion of variation that can be reliably passed on.^[17] This makes h^2 particularly valuable in breeding programs, where selecting for additive traits maximizes genetic gain over generations.^[18] In contrast to broad-sense heritability, which encompasses all genetic variance including dominance (V_D) and epistatic (V_I) effects, narrow-sense heritability is typically lower because it isolates transmissible additive components, rendering it more applicable to evolutionary and selective contexts.^[19] Falconer's formula, h^2 = 2(r_{MZ} - r_{DZ}), provides a simple estimate from twin studies by doubling the difference in phenotypic correlations between monozygotic (r_MZ) and dizygotic (r_DZ) twins, assuming equal environmental influences. For instance, in human height—a classic polygenic trait—narrow-sense heritability is estimated at approximately 0.8, underscoring a strong additive genetic basis that explains much of the variation in stature across populations.^[20]

Theoretical Foundations

Fisher's Fundamental Theorem

Ronald Fisher introduced the Fundamental Theorem of Natural Selection in his 1930 book The Genetical Theory of Natural Selection, where he formalized the relationship between genetic variation and evolutionary change.^[21] The theorem posits that the rate of increase in the mean fitness of a population at any time ascribable to natural selection equals the additive genetic variance in fitness at that time.^[21]^[22] Mathematically, the theorem is expressed as

\Delta \bar{w} = \frac{V_A(w)}{\bar{w}},

where \Delta \bar{w} is the change in mean fitness due to natural selection, V_A(w) is the additive genetic variance in fitness, and \bar{w} is the mean fitness.^[22] This formulation highlights that the additive component of genetic variance in fitness directly determines the short-term rate of evolutionary improvement in fitness under selection.^[22] The theorem relies on several key assumptions, including random mating within the population to ensure that genotypic frequencies align with Hardy-Weinberg expectations, and no changes in the environment that would alter the selective values of genotypes.^[22] Additionally, it treats fitness itself as the focal trait, with non-additive genetic effects such as dominance and epistasis considered part of the environmental component rather than heritable variance.^[22] These conditions allow the theorem to isolate the deterministic effects of natural selection on additive genetic variation.^[21] At its core, the theorem underscores that evolutionary change occurs through alterations in gene frequencies, with natural selection acting primarily on the additive effects of genes that contribute to variance in fitness.^[21] This additive focus emphasizes the heritable portion of phenotypic variation that can be transmitted across generations and respond predictably to selection pressures.^[22]

Implications for Evolution

Additive genetic variance plays a central role in enabling evolutionary responses to selection, as it represents the heritable portion of phenotypic variation that can be transmitted across generations, allowing populations to adapt predictably to changing environments. The breeder's equation quantifies this relationship, stating that the response to selection (R) equals the product of narrow-sense heritability (h², or V_A / V_P) and the selection differential (S), thereby linking additive effects directly to the rate of evolutionary change. Without sufficient V_A, adaptation is limited, as non-additive components like dominance and epistasis do not contribute reliably to offspring resemblance. Over long-term selection, depletion of V_A can constrain further evolution unless replenished by mechanisms such as mutation. Modern interpretations of Fisher's fundamental theorem extend its scope beyond fitness to any trait under selection, via the secondary theorem of natural selection, which posits that the rate of change in a trait equals its additive genetic covariance with fitness. This framework highlights how additive effects drive multivariate evolution, interacting with genetic drift—which can erode V_A in finite populations—and mutation, which introduces new variation to sustain long-term adaptability. These interactions underscore that while selection exploits existing V_A, other forces modulate its availability, influencing overall evolutionary dynamics. Critiques of the original theorem note its omission of non-additive effects and environmental changes, which can alter total fitness trajectories despite selection on additive variance. Extensions, such as the Price equation, address this by decomposing evolutionary change into partial effects due to selection (captured by Fisher's theorem) and transmission or environmental components, providing a more comprehensive model. For instance, Price clarified that the theorem describes only the selective component of change, resolving ambiguities in dynamic environments. A prominent example is the adaptation in Darwin's finches (Geospiza spp.), where shifts in beak size during droughts are driven by natural selection on additive polygenic effects, with narrow-sense heritabilities for beak traits estimated at 0.65–0.79, enabling rapid intergenerational responses.^[23]

Estimation and Applications

Methods of Estimation

One primary method for estimating additive genetic effects involves parent-offspring regression, which assesses the resemblance between parental and offspring phenotypes to infer narrow-sense heritability, defined as twice the slope of the regression of offspring phenotype on the mid-parent value.^[24] This approach assumes random mating and no environmental covariance between parents and offspring, allowing the regression coefficient b to relate directly to the additive genetic variance component V_A through the formula h^2 = 2b, where h^2 = V_A / V_P and V_P is the total phenotypic variance.^[24] Sib analysis, particularly using half-sib designs common in animal breeding, partitions phenotypic variance by comparing covariances within and between half-sib groups, which share one parent.^[25] In this design, the between-sire (or between-dam) variance component \sigma^2_F captures a quarter of the additive genetic variance due to shared additive effects, yielding the estimate V_A = 4 \sigma^2_F, often analyzed via analysis of variance (ANOVA) or mixed models to separate V_A from dominance variance V_D.^[26] Full-sib analyses extend this by incorporating both additive and dominance components but require adjustments to isolate V_A.^[24] Modern genomic methods leverage single nucleotide polymorphism (SNP) markers to construct a genomic relationship matrix (GRM), as in genomic best linear unbiased prediction (GBLUP), which replaces traditional pedigree-based matrices with marker-derived ones to estimate breeding values and V_A.^[27] In GBLUP models, the additive genetic covariance is modeled as \mathbf{G} \sigma^2_g, where \mathbf{G} is the GRM scaled by allele frequencies and \sigma^2_g approximates V_A, enabling estimation even in populations with complex relatedness via mixed linear models integrated with genome-wide association studies (GWAS).^[27] These methods face challenges, including assumptions of negligible epistasis, linkage disequilibrium, and genotype-environment interactions, which can bias V_A estimates if violated.^[24] Restricted maximum likelihood (REML) addresses some biases inherent in maximum likelihood estimation by accounting for uncertainty in fixed effects, providing more reliable variance components through iterative optimization of the restricted likelihood function.^[28]

Uses in Breeding and Selection

The breeder's equation, R = h^2 S, quantifies the expected response to selection (R) in a population as the product of narrow-sense heritability (h^2) and the selection differential (S), which is the difference between the mean phenotype of selected parents and the population mean. This equation arises from the regression of offspring phenotype on parental phenotype, where the covariance between parent and offspring equals the additive genetic variance V_A, leading to an expected offspring deviation of (V_A / V_P) \times S = h^2 S, assuming selection on both parents and no environmental covariance.^[29]^[30] In animal breeding, estimated breeding values (EBVs) leverage additive genetic effects to predict an individual's genetic merit for economically important traits, enabling precise selection of superior sires and dams. For instance, in dairy cattle, EBVs for milk yield are calculated from pedigree and performance data, allowing breeders to select bulls whose progeny are expected to produce 500–1,000 kg more milk per lactation than the population average, thereby accelerating genetic progress without direct progeny testing.^[31]^[32] In plant breeding, selection indices incorporate estimates of additive genetic variance to simultaneously improve multiple traits, assigning economic weights to balance gains in yield against disease resistance. These indices, such as those used in wheat or maize programs, maximize response by prioritizing genotypes with high V_A-based predictions for grain yield while maintaining resistance to pathogens like rust.^[33]^[34] Genomic selection enhances the exploitation of additive effects by using whole-genome marker data to predict breeding values across the genome, often via methods like genomic best linear unbiased prediction (GBLUP), which reduces generation intervals from years to months in crops and livestock. This approach has doubled annual genetic gains for traits like maize yield by enabling early selection of seedlings based on predicted additive contributions from thousands of loci, without waiting for field performance.^[35]^[36]

References

[1]
Estimating Trait Heritability | Learn Science at Scitable - Nature
The additive genetic value of an individual, called the breeding value, is the sum of the average effects of all the alleles the individual carries (Falconer & ...
[2]
Phenotypic Variance | Learn Science at Scitable
### Summary of Additive Genetic Effects/Variance
[3]
Non-additive and Additive Genetic Effects on Extraversion in 3314 ...
Additive genetic influence (A) describes the effect of multiple genes that exert influence in a linear or additive fashion. Non-additive genetic factors (NA), ...
[4]
Robust modeling of additive and nonadditive variation with intuitive ...
Additive variation is defined as variation of additive values, which are sums of allele substitution effects over the unobserved genotypes of causal loci.
[5]
Data and Theory Point to Mainly Additive Genetic Variance for ...
Feb 29, 2008 · ... additive genetic effects. Conversely, r MZ<2r DZ implies that common ... Falconer DS, Mackay TFC. Introduction to Quantitative Genetics ...
[6]
Data and theory point to mainly additive genetic variance ... - PubMed
We evaluate the evidence from empirical studies of genetic variance components and find that additive variance typically accounts for over half, and often close ...
[7]
Modeling Quantitative Trait Loci and Interpretation of Models - PMC
Recall that the additive effect a is defined as half of the difference between the homozygote genotypic values (G2 and G0) and that the dominance effect d is ...
[8]
The Correlation between Relatives on the Supposition of Mendelian ...
Genetically the heterozygote is inter- mediate between the dominant and the recessive, somatically it differs from their https://doi.org/10.1017/ ...
[9]
Unraveling Additive from Nonadditive Effects Using Genomic ... - NIH
Overall, our study supports the hypothesis that additive effects can capture a large proportion of the genetic variance from dominance and epistasis. This ...
[10]
Chapter 6: Components of Variance – Quantitative Genetics for ...
Additive gene action: There is no dominance (a>0, d=0). In this case, the genetic variance is additive, and it is greatest when p=q=0.5. Complete Dominance.Genetic Components Of... · Deriving Variance Components · Influence Of Epistasis
[11]
Additive Genetic Effects - an overview | ScienceDirect Topics
Average additive effect of allele Ai. Expectation over a population of the effect on phenotype of a substitution of one allele at locus A by allele Ai.
[12]
Modeling additive and non-additive effects in a hybrid population ...
Sep 2, 2015 · Introduction. Quantitative genetic models partition genetic variance into additive, dominance and epistatic components (Falconer and Mackay, ...Genetic Model · Pedigree And Marker... · Modeling Genetic Variance In...
[13]
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2842708/
[14]
Assessing the Heritability of Complex Traits in Humans - NIH
Broad sense heritability (H2) is the ratio of total genetic variance (A and D) divided by the total phenotypic variance. It explains the amount of phenotypic ...
[15]
Estimating Broad‐Sense Heritability with Unbalanced Data from ...
Mar 1, 2019 · Broad-sense heritability is defined as the proportion of phenotypic variance that is attributable to an overall variance for the genotype.<|control11|><|separator|>
[16]
Quantitative Genetics - David King
By definition, "narrow sense" heritability h2 is the proportion of phenotypic variance which is additive genetic variance, h2 = VA / VP. Additive genetic ...
[17]
[PDF] Quantitative characters II: heritability - The University of Utah
Here x is the midparent value (parental mean), y is the offspring value (see Gillespie, Table 6.2). The higher the slope, the better offspring resemble their ...
[18]
[PDF] Heritability: What's the point? What is it not for? A human genetics ...
Mar 5, 2022 · Thus, the narrow-sense heritability measures the resemblance between relatives, and hence is also a way to predict the response to selection.
[19]
CKgroup | Heritability
Narrow sense heribatiliby is important for selection and breeding, because additive variance has close relationship with how much one trait mean in the next ...
[20]
Effect of Regulatory Architecture on Broad versus Narrow Sense ...
May 9, 2013 · The broad-sense heritability of a trait is the proportion of phenotypic variance attributable to genetic causes, while the narrow-sense ...
[21]
From Galton to GWAS: quantitative genetics of human height
Mar 23, 2011 · Nevertheless, if the inference that the narrow-sense heritability of human height is ~80% is correct then there is not much room for non- ...From Galton To Gwas... · 5. Genome-Wide Association... · 10. Conclusions And The Way...
[22]
[PDF] OU_ 162958 - Gwern
The present book, with all the limitations of a first attempt, is at least an attempt to consider the theory of Natural Selection on its own merits. Whenthe ...
[23]
[PDF] Fisher's 'fundamental theorem' made clear - UBC Zoology
It has long been a mystery how Fisher (1930, 1941, 1958) derived his famous 'fundamental theorem of Natural Selection' and exactly what he meant by it.
[24]
Estimation of Variance Components of Quantitative Traits in Inbred ...
Commonly used methods for estimation of components of variance of quantitative traits include parent-offspring regression, analysis of variance (ANOVA) applied ...
[25]
[PDF] Analysis of Half-sib Progeny Tests in Forestry - Faculty Sites
Additive genetic variance, phenotypic variance, heritability and genetic gains are calculated based on variance components. Here is an example on estimation of ...
[26]
[PDF] 7. Estimation of Genetic Parameters - Woolwise
For example, the (paternal) half-sib variance is due to differences between sires. The variance component represents the sire variance, which is a quarter of ...
[27]
[PDF] Restricted Maximum Likelihood - GitHub Pages
Sep 27, 2022 · REML is based on linear mixed model methodology and use a restricted likelihood approach for estimating genetic parameters. 2 Estimation of ...
[28]
The Breeder's Equation | Learn Science at Scitable - Nature
The breeder's equation is used for a diversity of purposes in evolutionary biology. The most direct application is to predict evolutionary change.
[29]
8: The Response to Phenotypic Selection - Biology LibreTexts
Jan 7, 2023 · A simple model for the response to directional selection on a phenotype is given by the breeder's equation. The expected response to selection ...
[30]
What Is An EBV And How Can It Help You? - The Dairy Site
An EBV is a value which expresses the difference (+ or -) between an individual animal and the herd or breed benchmark to which the animal is being compared.
[31]
Genomic Estimated Breeding Value of Milk Performance and Fertility ...
The reliability of the estimated breeding value (EBV) for genotyped bulls ranged from 89 to 93% for the milk performance traits and 85 to 90% for the fertility ...
[32]
Estimating optimum and base selection indices in plant and animal ...
Nov 3, 2023 · The selection index method is the most useful method to choose superior genotypes based on using simultaneous several traits. The optimum and ...
[33]
Evaluating the effectiveness of selection indices and their genomic ...
Breeders often deal with traits that have antagonistic relationships, such as yield and disease resistance. A well-constructed index should achieve gains in all ...
[34]
Genomic selection in plant breeding: Key factors shaping two ...
Apr 1, 2024 · This article provides a holistic overview of key factors that have influenced GP in plant breeding during this period.
[35]
Genomic selection: Essence, applications, and prospects - ACSESS
Jun 1, 2025 · GS is a breeding strategy to predict the genotypic values of individuals for selection using their genotypic data and a trained model.Genomic Selection: Essence... · 1 Genomic Selection In Plant... · 2 Essence Of Genomic...