Introduction to

Quantitative Genetics
 Quantitative
Characteristics
Many organisms traits are genetically influenced, but do
not show single-gene (Mendelian) patterns of
inheritance.
They are influenced by the combined action of many
genes and are characterized by continuous variation.
These are called polygenic traits.
Continuously variable characteristics that are both
polygenic and influenced by environmental factors are
called multifactorial traits. Examples of quantitative
characteristics are height, weight.
 Types of Quantitative Traits
1. a continues measurement (quantity).
2. a countable meristic (measured in whole numbers). It can
take on integer values only: For example, litter size.
3. a threshold characteristic which is either present or absent
depending on the cumulative effect of a number of additive
factors (diseases are often this type). It has an underlying
quantitative distribution, but the trait only appears only if a
threshold is crossed.
Types of Quantitative Trait
In general, the distribution of quantitative traits values in a population
follows the normal distribution (also known as Gaussian distribution or
bell curve). These curves are characterized by the mean (mid-point)
and by the variance (width). Often standard deviation, the square root
of variance, is used as a measure of the curves width.
 Principles of Quantitative
Inheritance
Quantitative traits are influenced by the combined effects
of numerous genes. These are called polygenic or
multifactorial traits.
The genes follow Mendelian laws of inheritance; however,
multifactorial traits have numerous possible phenotypic
categories.
Environmental influences blur the phenotypic differences
between adjacent genotypes.
As the number of loci affecting
the trait increases, the #
phenotypic categories
increases.

Number of phenotypic
categories =
(# gene pairs 2) +1

Connecting the points of a

frequency distribution creates a
bell-shaped curve called a
normal distribution.
 Normal Distribution

Standard
Deviation

Mean
(average -
center of
distribution)

-5 -4 -3 -2 -1 0 1 2 3 4 5

Mean +/- 1s = 66% of values; +/- 2s = over 95% of values

 Quantitative Genetics
not discrete

Continuous phenotypic variation within populations

Whole organism level
Causes of variation
Genes vs. environment
Interactions between genes and environment
Components of genetic variation
Components of environmental variation
 Why is quantitative genetics
important?

Fisheries
Economically important traits =
quantitative traits
Quantitative genetics theory -> basis
for breeding programs
Environmental variation reduces
efficiency of selection
 Why is quantitative genetics
important?
Consequences of inbreeding and out-crossing
Fisheries inbred lines, hybrids, F1s
Conservation endangered species, captive
breeding programs
Why is quantitative genetics
important?
Evolution
Natural selection requires heritable variation for
traits
 History
Around 1900, there were two camps:
Biometricians
Continuous traits
Mendelians
Discrete traits

Are discrete traits inherited in

the same way as quantitative
traits?
 History
Reconciliation:
Multiple loci (genes)
contribute to variation!

Is variation caused by a few loci

of large effects or many loci with
small effects?
 Mathematical Basis of
Quantitative Genetics
The basic premise of quantitative genetics: phenotype =
genetics plus environment.

P=G+E
In fact we are looking at variation in the traits, which is
measured by the width of the Gaussian distribution curve.
This width is the variance (or its square root, the standard
deviation).
Variance is a useful property, because variances from
different sources can be added together to get total
variance.
 Mathematical Basis of
Quantitative Genetics
Quantitative traits can thus be expressed as:
VT = VG + VE
where VT = total variance, VG - variance due to
genetics, and VE = variance due to environmental
(non-inherited) causes.
This equation is often written with an additional
covariance term: the degree to which genetic and
environmental variance depend on each other. We
are just going to assume this term equals zero in
our discussions.
 Heritability
Measured using resemblance between relatives

h2 = genetic variation
phenotypic variation

Genetic + environmental + interaction

 Heritability
One property of interest is heritability, the proportion of a traits variation that
is due to genetics (with the rest of it due to environmental factors). This
seems like a simple concept, but it is loaded with problems.

The broad-sense heritability, symbolized as H (sometimes H2 to indicate that

the units of variance are squared). H is a simple translation of the statement
from above into mathematics:
H = VG / VT

This measure, the broad-sense heritability, is fairly easy to measure,

especially in human populations where identical twins are available.
However, different studies show wide variations in H values for the same
traits, and plant breeders have found that it doesnt accurately reflect the
results of selection experiments. Thus, H is generally only used in social
science work.
 Heritability
(broad-sense)

Heritability (broad-sense) is the proportion of a

populations phenotypic variance that is attributable
to genetic differences
 Genetic Variance
The biggest problem with broad sense heritability comes from
lumping all genetic phenomena into a single Vg factor.
Paradoxically, not all variation due to genetic differences can be
directly inherited by an offspring from the parents.

Genetic variance can be split into 2 main components, additive

genetic variance (VA) and dominance genetic variance (VD).
VG = VA + VD

Additive variance is the variance in a trait that is due to the effects

of each individual allele being added together, without any
interactions with other alleles or genes.
Additive vs. Dominance Genetic Variance

Dominance variance is the variance that is due to interactions

between alleles: synergy, effects due to two alleles interacting to
make the trait greater (or lesser) than the sum of the two alleles
acting alone. We are using dominance variance to include both
interactions between alleles of the same gene and interactions
between difference genes, which is sometimes a separate
component called epistasis variance.

The important point: dominance variance is not directly inherited

from parent to offspring. It is due to the interaction of genes from
both parents within the individual, and of course only one allele is
passed from each parent to the offspring.
 Heritability
(narrow sense)
Heritability (narrow sense) is the proportion of a
populations phenotypic variance that is attributable to
additive genetic variance as opposed to dominance
genetic variance (interaction between alleles at the same
locus).

Additive genetic variance responds to selection

 Narrow Sense Heritability
For a practical breeder, dominance
variance cant be predicted, and it
doesnt affect the mean or variance
of the offspring of a selection cross in
a systematic fashion. Thus, only
additive genetic variance is useful.
Breeders and other scientists use
narrow sense heritability, h, as a
measure of heritability.
h = VA / VT

Narrow sense heritability can also be

calculated directly from breeding
experiments. For this reason it is
also called realized heritability.
 The genetic Correlation

Traits are not inherited as independent unit, but the several

traits tend to be associated with each other

This phenomenon can arise in 2 ways:

1. A subset of the genes that influence one trait may also influence
another trait (pleiotropy)
2. The genes may act independently on the two traits, but due to non
random mating, selection, or drift, they may be associated (linkage
disequilibrium)
 Basic formula:

rG = covXY / (varX varY)0.5

rG often used both for additive (rA)

and genotypic (rG) correlation!

Phenotypic correlation:
A combination of genetic and environmental (incl. nonadd gen
effects) corr:
rP = hX hY rG + (1-h2X)0.5 (1-h2Y)0.5 rE
rP = hX hY rG + eX eY rE

The magnitude and even the sign of rG cannot be determined from rP

alone!
 The use of genetic correlations

1. Trait-trait correlation
Relation between different traits.
For studies of how the improvement of one trait will affect another trait.
2. Age-age correlation
Relation between a trait at young and mature age. Gives info about when
reliable estimations can be achieved.
3. Site-site correlation
Relation between genotype and environment. For deliniation of breeding and
seed zones and for optimization of number of trials per zone

Another basic use of rG is prediction of genetic gain.

Two basic estimations of
rG
Burdon correlation, type A:
Both traits are measured on the same individual (true
genetic corr.). Trait-trait and age-age correlations

Burdon correlation, type B:

Two traits are measured on different individuals
(approximated genetic corr.). One trait expressed at
two sites are considered as two different traits. Site-site
correlations.
 Some features of
genetic correlations

rG = covXY / (varX varY)0.5

1) The three components are hard to estimate with any precision, i.e.
large materials are needed.

2) Strongly influenced by gene frequencies, i.e. it is valid for a certain

population only. Genetic correlations are easily changed by selection.

.
Type B correlations are routinely made
by univariate methods

Problems:
1) Correlation estimates are biased for unbalanced data and when
variances across environments are heterogenous.

2) The estimates are frequently out of the theoretical parameter space due
to sampling errors of genetic variances and covariances (rG > 1.0).

3) The correlations are seldom normally distributed unless the test

population is large. Standard error of genetic correlations are difficult to
estimate and are often approximated! Estimates of standard error
should be interpreted with caution. However they indicate the relatively
reliability
 Correlated response
If we select for character X, what will be the change of the correlated
character Y?

CRY = i hX hY rG PY

CRY = the correlated response in trait Y,

i = the intensity of selection,
hX and hY = the square root of the h2
rG = the genetic correlation between traits X and Y
PY = the phenotypic standard deviation for trait Y.

The CRY can be expressed in percent by relating it to the phenotypic

mean of variable Y.
 Indirect selection
When character X will be improved, but select for another character
(Y) and achieve progress due to the correlated response.

CRX / RX = (iY rA hY) / (iX hX)

Presumptions:
HY > HX and strong CR or iY > iX.
Usable when difficult to apply selection directly to the desired
character:
1) Hard to measure with any precision, which reduces h2
2) The desired trait is costly to measure. Then it would be better to
select for an easily measurable, correlated trait.
 G x E interaction
Parallell and
1 2
no reaction norm

Scale effects
1 2

True interaction
1 2

Both scale and

true interaction
1 2
 G x E interaction
It is the true interactions that should affect breeding strategies.
Scale effects can be handled by transformation prior to analysis to
ensure homogenity of among-genotype variances in environments.
The question is whether breeding should be producing genotypes
suitable for specific environments or genotypes adapted to a wide
range of environments?
G x E can be used in practice when interactions and the specific
environments are well defined.
The smaller G x E, the fewer test sites are needed.
 Calculations of G x E

1. ANOVA according to the simple model: Y=G+E

+ G E.

The model assumes homogenous variances between

sites. Scale effects (not true interactions) will generate
an interaction!
Not independent of whether environment is a fixed or
random effect.
2. G x E as genetic correlations:
I. Yamada: r G= varG / (varG + varI)
varG = genetic variance component from ANOVA involving data from two
environments and varI = G x E variance component from ANOVA.

II. Burdon: rG = rXY / (hX hY)

rXY = phenotypic correlation between family means in environment X and Y
hX hY = square roots of heritabilities of the genetic family means in
environment X and Y.

III. GCA-approach: rG = r / (rax ray)

r = Pearson correlation between BLUP-values in environment X and Y
rax ray = estimated relation between the true and the predicted breeding
values calculated as (h2 k) / (1+h2(k-1)) where k is the harmonic mean of the
number of replications per family.