Genetic Models and Heritability

Genetic architecture of traits

Genetic architecture refers to how many genes contribute to genetic variation in a trait and how genetics and environment influence phenotype. Quantitative genetics model: P = G + E + G*E where P = Phenotype, G = Genotype, and E = Environment. Simple-inherited traits are controlled by one/few loci, usually Mendelian and discrete with low environmental influence. Polygenic traits are controlled by many loci, often continuous, and strongly influenced by environment and G×E interactions. Examples of simply inherited traits: coat colour, polled/horned, genetic disorders, disease resistance, double muscling. Examples of polygenic traits: milk yield, butterfat, feed efficiency, longevity, carcass traits, growth performance, and meat quality.

Threshold trait

“A polygenic trait in which phenotypes are expressed in categories e.g. dystocia, disease and fertility in dairy and beef cattle.”

Infinitesimal model vs finitesimal model

Infinitesimal model: “Assumes that traits are determined by an infinite number of unlinked and additive loci/genes, each with an infinitesimally small effect.” This model is the foundation of animal breeding value estimation and has been highly successful in dairy and beef cattle. Finitesimal model: “Assumes there is a finite number of loci underlying the genetic variation in quantitative traits because of the existence of a finite (limited) number of genes on the genome.” Main idea: a few genes have large effects (QTL) while many genes have small effects.

QTL and QTL mapping

QTL = Quantitative Trait Loci. These are genes/genomic regions with distinguishable influence on quantitative traits. QTL mapping: “The process of identifying the genomic regions, genes or genetic variants associated with (or causing) the genetic variation in a trait of interest.”

Why quantitative traits are challenging

Most economically important traits are polygenic and heavily influenced by environmental conditions, making phenotype a combination of many genes plus environmental effects. This makes accurate estimation of breeding value difficult.

Myostatin gene (MSTN) example

MSTN is located on chromosome 2 and has 1887 bp with three exons and two introns. “A deletion of 11 bp nucleotides in the third exon causes a loss of 102 amino acids due to a frame-shift.” “Absence of functional myostatin increases in all muscles up to 40%, and the gene is incomplete autosomal dominance.” This causes double muscling in Belgian Blue and Piedmontese cattle and demonstrates that a quantitative trait may sometimes be strongly influenced by a major gene.

Incomplete autosomal dominance

A heterozygote shows an intermediate phenotype between the two homozygotes rather than complete dominance.

Genetic value equation

Genetic value = Additive + Dominance + Interaction.

Additive genetic component

Additive effects are the sum of allele effects across loci and represent the inheritable portion of genetic value. “Estimated Breeding Value (EBV): A measure of the sum of effects of individual alleles (‘genes working together’).” Additive effects are inherited due to independent assortment and allelic segregation and are the most important component for selection.

EPD and PTA

Expected Progeny Difference (EPD) = ½ EBV and is mainly used in beef cattle, swine, and equine industries. Predicted Transmitting Ability (PTA) = ½ EBV and is mainly used in dairy cattle. They equal half the EBV because offspring inherit half of the parent’s alleles.

Dominance and interaction components

“Dominance genetic component: A measure of the combined dominance effects of individual loci (not transmitted to progeny). It is a non-additive genetic effect.” “Interaction genetic component: A measure of the combined interactions between loci (e.g. epistasis) (not transmitted to progeny). It is a non-additive genetic effect.” These effects are less useful in selection because they are not predictably inherited.

Gene Combination Value (GCV)

GCV refers to combination effects unique to an individual that will not be inherited if bred. Includes dominance and interaction effects.

Additive and dominance calculation example

TT = 20, TC = 18, CC = 10. Additive effect of allele T = (20 − 10)/2 = +5. Additive effect of allele C = (10 − 20)/2 = −5. Dominance effect = 18 − ((20 + 10)/2) = +3. A positive dominance deviation means the heterozygote performs better than the midpoint of the homozygotes.

Genomic breeding value calculation

Calculated by summing additive effects across SNPs/genotypes using estimated allele effects from a reference population.

Comprehensive quantitative genetics model

P = BV + GCV + E + E*G where BV = Breeding Value, GCV = Gene Combination Value, E = Environment, and E*G = genotype-by-environment interaction.

Breeding Value (BV)

The value of an individual to a breeding program based on additive genetic merit. BV is the most important component for genetic improvement because additive effects are inherited.

Population quantitative genetics model

Pindividual = μ + deviation from average. μ (mu) represents the population average phenotype. Deviations may come from breeding value, gene combination value, or environmental effects.

Basic quantitative trait model

Pindividual = μ + Genetic value + E.

Characteristics of the basic model

1. “The model represents the genetic and environmental contributions to a single performance record on one animal.” 2. “The values (G1, G2, Gn) are trait specific.” 3. “Because Gn and En are expressed as deviations from a mean, average of G and E = 0.” 4. “If G and E are considered independent, the genotype has no influence on the environmental effect and vice versa.”

Main goal of quantitative genetics

Estimate breeding value accurately to select the best animals and increase the frequency of favorable alleles in populations.

Variance form of quantitative genetics model

VP = VG + VE where VP = phenotypic variance, VG = genetic variance, and VE = environmental variance.

Expanded variance model

σ²P = σ²A + σ²D + σ²I + σ²Ep + σ²Et where additive, dominance, interaction, permanent environmental, and temporary environmental variances all contribute to phenotypic variance.

Importance of genetic variance

“The main component in genetic change or improvement is the existence of the genetic variance.”

Broad sense heritability

“The proportion of variation that is explained by genetics.” and “The proportion of total variance that is genetic variance.” Equation: h² = σ²G / σ²P. Broad sense heritability includes additive, dominance, and epistatic variance.

Narrow sense heritability

“The proportion of total variance that is additive genetic.” Also: “Describe the degree to which variation BV explains the variation in phenotypes.” Equation: h² = σ²A / σ²P = σ²BV / σ²P. Narrow sense heritability is most important in breeding because additive effects are inherited.

Relationship between heritability and environment

“when h² is high, σ²E is low and vice versa.” Heritability is population specific because environmental variance differs among populations.

Heritability ranges

High heritability = 0.4–0.8 (structure traits, stature, height). Medium heritability = 0.2–0.4 (average daily gain, feed efficiency, marbling score, somatic cell score). Low heritability = 0.01–0.2 (fertility, disease, behavior traits).

Important interpretation of h² = 0.4

“h² = 0.4 does not mean 40% of the trait is determined by genetics but 40% of all the phenotypic variation for that trait is due to variation in genotypes for that trait.”

Why heritability matters

Heritability allows prediction of how strongly parents genetically influence offspring and helps estimate breeding values. Higher heritability leads to faster genetic progress through selection, while low heritability traits respond slowly because environmental effects mask genotype.

Misconceptions about heritability

Misconception 1: “A heritability of 0.4 indicates that 40 % of the trait is determined by genetics.” FALSE. Misconception 2: “A low heritability means that traits are not determined by genes.” FALSE. Genetic variance may simply be small relative to phenotypic variance. Misconception 3: “low heritability means that genetic differences are small.” FALSE. Environmental/error variance may instead be large. Misconception 4: “A heritability is a fixed value.” FALSE. Heritability changes among populations because environmental variance changes.

True/False high-yield concepts

Additive genetic effects are transmitted to offspring = TRUE. Dominance effects are reliably inherited = FALSE. Polygenic traits are often affected by environment = TRUE. High heritability means environment is unimportant = FALSE. Heritability applies to populations, not individuals = TRUE. Low heritability means traits are not genetically controlled = FALSE. QTL mapping identifies genomic regions associated with trait variation = TRUE. Breeding value mainly refers to additive effects = TRUE.

Most important variance component for selection

Additive genetic variance (σ²A) because additive effects are predictably inherited by offspring.

Why polygenic traits are continuous

Many genes each contribute small effects, creating a continuous distribution of phenotypes.

Why Mendelian traits are discrete

One or few genes produce distinct phenotype categories.

Broad vs narrow sense heritability

Broad sense heritability includes all genetic variance (additive + dominance + epistasis). Narrow sense heritability includes only additive variance and is therefore more useful in animal breeding.

Effect of environmental variance on heritability

If environmental variance increases, heritability decreases because phenotypic variance increases.

Relationship between phenotype and breeding value

Phenotype includes genetic and environmental effects, while breeding value represents only the additive inherited genetic portion.

Why phenotype is not a perfect measure of genotype

Environmental effects and non-additive genetic effects also influence phenotype.

Purpose of animal selection programs

Increase frequency of favorable alleles in populations through selection of animals with superior breeding values.