CHAPTER 3:

QUANTITATIVE INHERITANCE
IN PLANT BREEDING
NUR FAEZAH BINTI OMAR
1
 AT THE END OF THIS LECTURE,
STUDENTS ARE ABLE TO :

• Define a population.
• Discuss the concept of a gene pool.
• Discuss the changes in gene frequencies in
populations.
• Discuss the Hardy–Weinberg law.

2
 DEFINITION
• Population is a group of sexually interbreeding
individuals.

• Gene pool is the total number and variety of

genes and alleles in a sexually reproducing
population that are available for transmission to
the next generation.

• Population genetics is concerned with how the

frequencies of alleles in a gene pool change over
time.
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 Hardy Weinberg Equilibrium

Gregor Mendel (1822-1884) G. H. Hardy (1877 - 1947) Wilhem Weinberg

(1862 – 1937)
 Recall
Darwin’s Observation

Evolution acts through changes in

allele frequency at each generation

Leads to average change in

characteristic of the population

However, Darwin did not understand

how genetic variation was passed
on from generation to generation
 Gregor Mendel, “Father of Modern Genetics”

• Mendel presented a mechanism Gregor Mendel

for how traits got passed on

“Individuals pass alleles on to

their offspring intact”

(the idea of particulate (genes)

inheritance)

(1822-1884)
 Gregor Mendel, “Father of Modern Genetics”

Mendel’s Laws of Inheritance

Gregor Mendel
• Law of Segregation
– only one allele passes from each
parent on to an offspring
• Law of Independent Assortment
– different pairs of alleles are passed to
offspring independently of each other

(1822-1884)
 Using 29,000 pea plants, Mendel discovered the 1:3 ratio of
phenotypes, due to dominant vs. recessive alleles

• In cross-pollinating plants with either yellow or green peas,

Mendel found that the first generation (f1) always had yellow
seeds (dominance). However, the following generation (f2)
consistently had a 3:1 ratio of yellow to green.
Hardy-Weinberg Principle

• Mathematical description of Mendelian

inheritance

Godfrey Hardy
(1877-1947) Wilhem Weinberg
(1862 – 1937)
Testing for Hardy-Weinberg equilibrium can
be used to assess whether a population is
evolving
 The Hardy-Weinberg Principle

• A population that is not evolving shows allele and

genotypic frequencies that are in Hardy Weinberg
equilibrium

• If a population is not in Hardy-Weinberg

equilibrium, it can be concluded that the
population is evolving
 Hardy-Weinberg Equilibrium

• According to the Hardy-Weinberg principle,

frequencies of alleles and genotypes in a
population remain constant from generation to
generation

• Also, the genotype frequencies you see in a

population should be the Hardy-Weinberg
expectations, given the allele frequencies
 Requirements of Hardy Weinberg
Evolution
Large population size Genetic drift

Random Mating Inbreeding & other

No Mutations Violation
Mutations

No Natural Selection Natural Selection

No Migration
Migration

An evolving population is one that violates

Hardy-Weinberg Assumptions
Large population size 14
Random Mating 15
No Natural Selection
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• No Migration

No Migration 17
No Mutations
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In the absence of evolution…
Patterns of inheritance should always be in
“Hardy Weinberg Equilibrium”

Following the transmission rules of Mendel

 “Null Model”
• No Evolution: Null Model to test if no
evolution is happening should simply be a
population in Hardy-Weinberg Equilibrium

• No Selection: Null Model to test whether

Natural Selection is occurring should have no
selection, but should include Genetic Drift
– This is because Genetic Drift is operating even
when there is no Natural Selection
 Think !!

• Does Hardy Weinberg

equilibrium apply to the human
population?

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 Gene pool
• consists of all the copies of all the genes in
that population

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 Allele frequency
• refers to how common an allele is in a
population.
• It is determined by counting how many times
the allele appears in the population then
dividing by the total number of copies of the
gene

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 Allele frequency
• If all the alleles in a population of pea plants were purple
alleles, W, the allele frequency of W would be 100%, or 1.0.

• However, if half the alleles were W and half were w, each

allele would have an allele frequency of 50%, or 0.5.

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Finding allele frequency
W copies = 13
w copies = 5
The total number of gene copies in the whole
population is 13 + 5 = 18.

Frequency are given the symbols p and q

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 Genotype frequency
• Allele frequency is different from genotype
frequency or phenotype frequency.
• Genotype and phenotype frequencies can also
be calculated and are important for
understanding how populations evolve,
• but they are not the same thing as allele
frequency.

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There has been a change in allele frequencies in the population over generations, so—
by the definition of microevolution—we can say that the population has evolved.

If we were actually doing research, we might want to use a statistical test to confirm that
these proportions were really different.
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Evolution & Population Genetics

• Limitations of evolution
• Selection can only act on existing variations.
• Genes, alleles, phenotypes (anatomy and
physiology) are limited by historical &
developmental constraints.
• Adaptations are compromises.
• Better adaptations can be imagined, designed by
engineers, but the genes or alleles don’t exist.
• Chance, natural selection, and environment
interact.
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Hardy-Weinberg Theorem
In a non-evolving population,
frequency of alleles and genotypes
remain constant over generations

You should be able to

predict the genotype
frequencies, given the
allele frequencies
Fig. 23-6

Alleles in the population

Frequencies of alleles
Gametes produced
p = frequency of
Each egg: Each sperm:
CR allele = 0.8

q = frequency of
CW allele = 0.2 80% 20% 80% 20%
chance chance chance chance

Hardy-Weinberg proportions indicate the

expected allele and genotype frequencies,
given the starting frequencies
• By convention, if there are 2 alleles at a locus, p and
q are used to represent their frequencies

• The frequency of all alleles in a population will add

up to 1

– For example, p + q = 1
If p and q represent the relative frequencies of the
only two possible alleles in a population at a
particular locus, then for a diploid organism (2
chromosomes),
(p + q) 2 = 1

= p2 + 2pq + q2 = 1
– where p2 and q2 represent the frequencies of the
homozygous genotypes and 2pq represents the
frequency of the heterozygous genotype
 Hardy Weinberg Theorem
ALLELES
Probability of A = p p+q=1
Probability of a = q

GENOTYPES
AA: p x p = p2
Aa: p x q + q x p = 2pq
aa: q x q = q2

p2 + 2pq + q2 =1
In a certain population of 1000 fruit flies, 640
have red eyes while the remainder have sepia
eyes. The sepia eye trait is recessive to red eyes.
How many individuals would you expect to be
homozygous for red eye color?

Calculation:
q2 for this population is 360/1000 = 0.36
q = √0.36 = 0.6
p = 1 − q = 1 − 0.6 = 0.4
The homozygous dominant frequency = p2 = (0.4)(0.4) = 0.16.
Therefore, you can expect 16% of 1000, or 160 individuals, to be
homozygous dominant.
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 ALLELE Frequencies
Frequency of A = p = 0.8
Frequency of a = q = 0.2
p+q=1

Expected GENOTYPE Frequencies

AA: p x p = p2 = 0.8 x 0.8 = 0.64
Aa: p x q + q x p = 2pq
= 2 x (0.8 x 0.2) = 0.32
aa: q x q = q2 = 0.2 x 0.2 = 0.04

p2 + 2pq + q2
Allele frequencies remain the same at
next generation = 0.64 + 0.32 + 0.04 = 1
Expected Allele Frequencies at 2nd Generation
p = AA + Aa/2 = 0.64 + (0.32/2) = 0.8
q = aa + Aa/2 = 0.04 + (0.32/2) = 0.2
 Hardy Weinberg Theorem
ALLELE Frequency
Frequency of A = p = 0.8 p+q=1
Frequency of a = q = 0.2

Expected GENOTYPE Frequency

AA: p x p = p2 = 0.8 x 0.8 = 0.64
Aa: p x q + q x p = 2pq = 2 x (0.8 x 0.2) = 0.32
aa : q x q = q2 = 0.2 x 0.2 = 0.04

p2 + 2pq + q2 = 0.64 + 0.32 + 0.04 = 1

Expected Allele Frequency at 2nd Generation
p = AA + Aa/2 = 0.64 + (0.32/2) = 0.8
q = aa + Aa/2 = 0.04 + (0.32/2) = 0.2
Similar example,
But with different starting allele frequencies

p q
 p2
2pq
q2
Fig. 23-7-4
80% CR ( p = 0.8) 20% CW (q = 0.2)

Sperm
CR CW
(80%) (20%)

Perform the same

64% ( p2) 16% ( pq) calculations using
CR CR CR CW
16% (qp)
percentages
4% (q2)
CR CW CW CW

64% CR CR, 32% CR CW, and 4% CW CW

Gametes of this generation:

64% CR + 16% CR = 80% CR = 0.8 = p
4% CW + 16% CW = 20% CW = 0.2 = q
Genotypes in the next generation:

64% CR CR, 32% CR CW, and 4% CW CW plants

Fig. 23-7-1
80% CR (p = 0.8) 20% CW (q = 0.2)

Sperm
CR CW
(80%) (20%)

64% (p2) 16% (pq)

CRCR CRCW

16% (qp) 4% (q2)

CRCW CW CW
Fig. 23-7-2

64% CRCR, 32% CRCW, and 4% CWCW

Gametes of this generation:

64% CR + 16% CR = 80% CR = 0.8 = p

4% CW + 16% CW = 20% CW = 0.2 = q

Fig. 23-7-3

64% CRCR, 32% CRCW, and 4% CWCW

Gametes of this generation:

64% CR + 16% CR = 80% CR = 0.8 = p

4% CW + 16% CW = 20% CW = 0.2 = q

Genotypes in the next generation:

64% CRCR, 32% CRCW, and 4% CWCW plants

 What about for a triploid organism?

• (p + q)3 = 1

= p3 + 3p2q + 3pq2 + q3 = 1

Potential offspring: ppp, ppq, pqp, qpp, qqp,

pqq, qpq, qqq

How about tetraploid? You work it out.

QUANTITATIVE GENETICS

46
 AT THE END OF THIS LECTURE,
STUDENTS ARE ABLE TO :
1. Define quantitative inheritance and its
measurement .
2. Identify multiple alleles.
3. Discuss type of gene action.
4. Discuss the concept of heritability of traits.
5. Discuss selection and define the “breeders’
equation”.
6. Discuss combining ability
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 Quality vs Quantity
Quality:
• Appearance of
fruit/plant/seed
– size, colour
– flavour, taste, texture
– shelflife (transport)

• Composition
– fiber, starch, oil & protein as food/
industrial ingredients
– recovery and processing
– valorization of by-products

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Quality vs Quantity

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 Quality vs Quantity
Breeding for Quality: a moving field (1)

What are the driving forces?

Consumer/society Technology
Flavour (taste, odour)  breeding strategies
Convenience  insight plant processes
Product appearance
Personal health  new processing techniques (e.g.
high pressure)
Food safety
Awareness environment  better understanding structure-
function relationships biomolecules

 improved analytics 50
 Quality vs Quantity

Quantity: Yield

Biotic (disease) resistance

Abiotic resistance
 Drought resistance
 Lodging
 Salt/Salinity
 Bad soil etc

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QUANTITATIVE GENETIC
• Population genetics and quantitative genetics - closely related
fields,
• both dealing with the genetic basis of phenotypic variation
among the individuals in a population.

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 POPULATION GENETIC vs
QUANTITATIVE GENETIC

• focuses on linking
• focuses on

quantitative genetics
phenotypic variation of
Population genetics

frequencies of complex traits to its

alleles and underlying genetic basis to
enable researchers better
genotypes, understand and predict
genetic architecture and
long term change in
populations

• (to predict the response to

selection given data on the
phenotype and
relationships of individuals
in the population). 53
 QUANTITATIVE GENETIC
• The modern molecular view of quantitative genetics
focuses on the use of molecular genetics tools

• (genomics, bioinformatics, computational biology,

etc.)

• to reveal links between genes and complex

phenotypes (quantitative traits).

• Genes that control quantitative traits are called

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quantitative trait loci (QTLs).
55
 Qualitative and Quantitative traits
Qualitative traits:
• Phenotypes with discrete and easy to
measure values.
• Individuals can be correctly classified
according to phenotype.
• Show mendelian inheritance (monogene)
• Little environmental effect
• Molecular markers are qualitative traits
• Examples:
Quantitative traits:
• Individuals cannot be classified by discrete
values
• Quantitative trait distribution show a
continuous range of variation and phenotypes
can take any value
• Complex mode of inheritance (controlled by
multiple genes or polygenes)
• Moderate to great environmental effect)
• Examples: Plant height, yield, disease severity,
grain weight, etc

% of plants

20 30 40

Plant Height (in)

 Polygene
• a gene whose individual effect on a phenotype is too small to be observed,
but which can act together with others to produce observable variation.
• 2 or more genes affect 1 phenotype

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58
 Multiple alleles
• Just as a single gene may have multiple alleles that produce
different forms of one enzyme, there can be more than one gene
for the same enzyme.

• The same enzymes produced by different genes are called

isozymes. Isozymes are common in plants.

• For example, the enzyme phosphoglucomutase in Helianthus debilis

is controlled by two nuclear genes and two chloroplast genes.

• Isozymes and allozymes were the first molecular markers

developed for use in plant and animal genetic research.

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60
 Inheritance of Quantitative traits

P1 P2
PARENT 1: PARENT 2:
• pure line, completely • pure line,
homozygote completely
• 40 inches homozygote
× • 20 inches

% of plants
F1: range of height distribution F1
but no type of segregation

20 30 40
Plant Height (in)

Plant Height (in)

F2: wider range of height
% of plants

F2
distribution but no type of
segregation
20 30 40
Plant Height (in)
 Inheritance of Quantitative traits
In 1903 the Danish botanist Wilhelm Johannsen measured the weight of seeds in the
Princess variety of bean. This variety is a pure line since beans are self-fertilizing .

From a seed lot he measured and classified the beans by weight and obtained the range of
distribution for that variety.

% of plants
Then he selected 19 beans of different weights
and self-pollinated them several generations

Doing this he got 19 pure lines (completely homozygous)

250 400 550
in case they were not at the beginning of the experiment Weight (gr)

He found that:
The weight of the 5,494 beans he obtained followed a normal distribution
All lines within each of the 19 groups were genetically identical but showed also a
range of variation in weights.
The average and distribution of weight in each pure line were similar to those of
the original population
 Inheritance of Quantitative traits
The Experiment of Johannsen

% of plants
250 400 550
Weight (gr)
% of plants

% of plants

% of plants
250 400 550 250 400 550 250 400 550
Weight (gr) Weight (gr) Weight (gr)
Conclusions:
•There is a genetic control that keeps the same average weight and distribution
•However not all genetically identical seeds have the same weight.
•The phenotype of each individual must be determined by the genotype and the
environmental conditions
•Without genetic variability, genetic improvement is not possible
 Inheritance of Quantitative traits

Johannsen showed that quantitative traits are determined by genes. However he did not
find any type of Mendelian segregation.
This was studied in 1909 by Swedish Herman Nilsson-Ehle who studied kernel color in wheat
He had several pure lines of red and white colored kernels. When crossing red x white he
got always red F1, but different proportions of red and white kernels depending on the
cross:
a) 3 red : 1 white
b) 15 red : 1 White
c) 63 red : 1 white

He deduced that the color was controlled by three loci. Only individuals with recessive
homozygous alleles at the three loci showed the white phenotype. When a single dominant
allele (A, B or C) is present at any of the three loci the red phenotype shows up.
 Inheritance of Quantitative traits
a) 3 red : 1 white For case a), allelic variation between the
b) 15 red : 1 White two parents was present only at one locus
c) 63 red : 1 white

P1 (red) P2 (white)
AAbbcc X aabbcc

F1(red) Aabbcc

F2 ¼ AAbbcc : ½ Aabbcc : ¼ aabbcc

(only one locus (red) (red) (white)
segregating)
Segregation 3 red : 1 white

Only individuals with recessive homozygous alleles at the three loci showed the
white phenotype.
 Inheritance of Quantitative traits
a) 3 red : 1 white
b) 15 red : 1 White
c) 63 red : 1 white

P1 (red) P2 (white)
AABBcc X aabbcc

F1(red) AaBbcc

1/16 AABBcc (red)

2/16 AABbcc (red)
1/16 AAbbcc (red)
F2
2/16 AaBBcc (red) Segregation 15 red : 1 white
(two loci
4/16 AaBbcc (red)
segregating)
2/16 Aabbcc (red)
1/16 aaBBcc (red)
2/16 aaBbcc (red)
1/16 aabbcc (white)
 Inheritance of Quantitative traits
a) 3 red : 1 white
b) 15 red : 1 White
c) 63 red : 1 white

P1 (red) P2 (white)
AABBCC X aabbcc

F2 F1(red) AaBbCc
(three loci
segregating) Segregation 63 red : 1 white

1/64 AABBCC (red) 2/64 AABBCc (red) 1/64 AABBcc (red)

2/64 AABbCC (red) 4/64 AABbCc (red) 2/64 AABbcc (red)
1/64 AabbCC (red) 2/64 AabbCc (red) 1/64 Aabbcc (red)
2/64AaBBCC (red) 4/64 AaBBCc (red) 2/64 AaBBcc (red)
4/64 AaBbCC (red) 8/64 AaBbCc (red) 4/64 AaBbcc (red)
2/64 AabbCC (red) 4/64 AabbCc (red) 2/64 Aabbcc (red)
1/64 aaBBCC (red) 2/64 aaBBCc (red) 1/64 aaBBcc (red)
2/64 aaBbCC (red) 4/64 aaBbCc (red) 2/64 aaBbcc (red)
1/64 aabbCC (red) 2/64 aabbCc (red) 1/64 aabbcc (white)
 Inheritance of Quantitative traits
However, Nilsson-Ehle not only classified the seeds by color. He also classified them by color
intensity and saw that color intensity also had a defined segregation pattern

P1 (purple, X P2 (white) P1 (purple, P2 (white)

very dark red) very dark red)
AABB X aabb
He proposed that for this cross,
F1(red) color intensity was determined
by two loci with two alleles each: F1(red) AaBb
one that produced red pigment
(A and B) and other with no
pigment (a and b).
1/16 AABB (Purple)
2/16 AABb (dark-red)
He determined that the effects of
1/16 AAbb (red)
the alleles were additive and
2/16 AaBB (dark-red)
contributed equally to the
4/16 AaBb (red)
1/16 : purple phenotype, which depended on
2/16 Aabb (light-red)
4/16: dark-red the number of alleles for
1/16 aaBB (red)
6/16: red pigment present
2/16 aaBb (light-red)
4/16: light-red 1/16 aabb (white)
1/16: white
 Inheritance of Quantitative traits

P1 (purple, X P2 (white)
very dark red) Going one step further, He saw that within
each of the groups there was also some
variation
F1(red)

Frequency
+ purple - white
Color intensity

1/16 : purple
4/16: dark-red
6/16: red
4/16: light-red
1/16: white
 Inheritance of Quantitative traits
The inheritance of quantitative traits also explains the phenomenon of transgressive
segregation: In the progeny of a cross we can get phenotypes out of the range of the parents

Frequency
P1 P2

0 10
Cold tolerance

Let’s assume 5 loci with additive effects control the trait

P1 P2
aabbccddEE X AABBCCDDee

F1 AaBbCcDdEe

F2 All possible combinations of alleles at 5 loci.

Between them: AABBCCDDEE (all favorable alleles)
aabbccddee (all unfavorable alleles)
 Inheritance of Quantitative traits
Quantitative traits are usually controlled by several genes with small
additive effects and influenced by the environment

Heritability h2 measures the proportion of phenotypic variation (variance)

that is due to genetic causes

P = G + E; VP = VG + VE
VG
h2 
VP

A heritability of 40% for cold tolerance means that within that population,
genetic differences among individuals are responsible of 40% of the variation.

Therefore, 60% is due to environmental causes.

However, that does not mean that the cold tolerance of a certain individual
is due 40% to genetic causes and 60% to environmental causes.
h2 is a property of the population and not of individuals
 Inheritance of Quantitative traits
Heritability h2 measures the proportion of phenotypic variation (variance)
that is due to genetic causes

P = G + E; VP = VG + VE
VG
h 
2

VP

h2 ranges between 0 and 1

If h2 is 0 means :

a) The trait is not genetically controlled. All the variation we see is

due to environmental factors, or
b) The trait is genetically controlled but all individuals have the
same genotype

h2 is very useful because it allows us to predict the response to artificial selection

 Inheritance of Quantitative traits
Heritability h2 measures the proportion of phenotypic variation (variance)
that is due to genetic causes
VG
h2 
P = G + E; VP = VG + VE VP
h2 is very useful because it allows us to predict the response to artificial selection.
In plant breeding, the starting point is a segregating population (with genetic
variability). The best individuals are selected to be the progenitors of the next
generation
μ0
Frequency

Selection differential (S) = μS – μ0

μS
Response to selection (R) = μR – μ0

0 Grain yield 6000 Realized heritability:

R
(lb/A)
h2 
μ 0 μR S
Frequency

Is the ratio of the single-generation progress of

selection to the selection differential of the
parents. The higher h2, the higher the progress
of selection in each generation
0 Grain yield 6000
(lb/A)
 Analysis of Quantitative traits

The analysis of quantitative traits is based on the identification of the individual

loci (QTL) controlling the trait, their location, effects and interactions

A quantitative trait locus/loci (QTL) is the location of individual locus or multiple

loci that affects a trait that is measured on a quantitative (linear) scale.

These traits are typically affected by more than one gene, and also by the
environment.

Thus, mapping QTL is not as simple as mapping a single gene that affects a
qualitative trait (such as flower color).
 Analysis of Quantitative traits

There are two main approaches for QTL analysis:

a) QTL analysis in mapping populations

b) Association mapping

Both approaches share a set of common elements:

a) A population (array of individuals) that show variability for the trait of

study
b) Phenotypic information: We need to design an experiment to
estimate the phenotypic value of each individual
c) Genotypic information: A set of molecular markers that have been
running all the individuals of the population
d) A statistical method to estimate QTL position, effects and interactions
 Analysis of Quantitative traits
QTL analysis in mapping populations

We need to develop a population from a single cross between two individuals

that show contrasting phenotypes for the trait of study.

For example, if we want to study quantitative resistance to Barley Stripe Rust

(Puccinia striiformis f. sp. Hordei) we will develop a population from the cross
between a susceptible line and a resistant line.

The offspring of that cross will show recombination between the two parents
and therefore, some individuals will be resistant and other will be susceptible

Different types of mapping populations can be used:

Doubled haploids (DH), Recombinant inbred lines (RIL), F2, Back cross (BC), etc.

Always all individuals trace back to a single cross

 Analysis of Quantitative traits
QTL analysis in mapping populations

The first step is getting genotypic information for all the individuals of the
population: molecular markers

P1 P2 Back Cross population

P1 P2
Parent 1
Parent 2

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SNP
1_0002 G A G A G G G G G A G G A A G A G A G G A G G G A A A G G A A A G A A G A A G A A G G A A G A G G G G A A A G G A G A G G A A A G G G A
1_0004 T A T T T T A A T A T T T T A T T A A T A A T A T A A T A T T A A A A T A A A T A A A T A A A A A A T T A A T A T A T A A T A A A A T T
1_0011 A T T A T T A T A T T A T T T T T A A T A A A A A A A T T T T T A A T A A T A T T A A T T A A T T T A T A A A A T A A T A A T A A T T T
1_0014 G T T T T T T T G T T G T T G G T T T G T G T G G T T T G T G T T T G G G G G G T T G G T T T T G T G G G G G T T T G G G T T T T G T T
1_0020 C G C C C C G C G C G G C C C C C G G C C C G G G G G C C C G C G C G C G C G C C C G C C C G G G G G C G G C G C C C C C G C G C C C C
1_0023 A T A T A A A A T T A T T T T T A A A A T A A T T T T A T T A A T T A T A T A A A T A A A T A T A T T T T A T A T A A T A A A T A A A A
1_0024 T A A A T A T T T A A A T T T T A A T T A T T A T A A A T A T A T A T A A A A T T A A T T A T A A T T T A A A T A A T T A A A A T A A T
1_0026 G C G G C G G C C C C G G C C C G G G C G G G G G C G G C C G C G G G G G G G G C G G G C G G C C C C C G G G C C G G C G C C G G G G G
1_0031 G C G C G G C C G G G G C C G C G C C C G C C C G G G G C G G G C C C G G C G A A G G C C G G C G C C C C C G C C C G G G C G C C C G C
1_0036 G T G T G G T T T G G G T G T T G G T G T T G G G G G G G T G T G T G G G G A T A A G G G G T T T T G T G T G G G G T T G G T T G T G G
1_0041 G T G T T G T T G T T T T G T T G T T G T G T G T T T G T T T T T T T G G G A T T A G T T G G G T T T T T T G T T G T T T G T T T G G G
1_0047 T A A T A A T A A A A T A T A A A T T A A T T A T T A A A T T A T T A T T A G G T T T A T T T A A A T A T T T T A A T A A A A T T A A A
1_0048 T A T A T T A A T T T T A A T A T A A A T A A A T A A T T T T T A A A A T A G C C C T A A T T A T A A A T A A A A A T T T A T T A A T A
1_0050 A T A A A A T T T T T T T A A T T T T T T A A T A A A A A T A T A A T A A T A A A T T T T T A T T T T T A A A T T A T A T T T T A T A A
1_0051 T A A T A A T A T A T T A T A T T T T A A A T T A A A A A A A T A A A T T A A T T A T T A A T A A A T T T A T T T T A T A T T T T T A T
1_0052 A T A T A A A T A A T A A T T T T T A T A A T T T T T A A A A A T T T T T T G G C G A A T T T T A T T T A A T T T A A A A T A A T T A T
1_0053 A T A T A A A T A A T A A T T T T T A T A A T T T T T A A A A A T T T T T T G A A G A A T T T T A T T T A A T T T A A A A T A A T T A T
1_0055 G C G C G G C C G C G G C G G G C C C C G C G C G G G G G C G C G G C G G C A T A A G G C G G C C G C G G G G C C G C G C C C C G C G G
1_0061 T G T G T T T G G G T T G G T T T T T T G T T G G G G T T T G G T G T G T G A T T A G T T T T T T G G T G T G T T T T G T T G G G T T G
1_0063 T A T A T T A A T T T T A A T A T A A A T A A A T A A T T T T T A A A A T A G G T T T A A T T A T A A A T A A A A A T T T A T A A A T A
1_0064 T C T C T T T T C C T C C C C C T T T T C T T C C C C T C C T T C C T C T C G C C C T T T C T C T C T C C T C T C T T C T T T C T T T T
1_0065 T G G T T G G G G T G T T G T G G G G G T G G T T T G G T G T G T G G G G G A A A T T T T G G G G G G G G G G T G T G G G T G G T T G T
1_0071 G C C G C C G C G C G G C G C G G G G C C C G G C C C C C C C G C C C G G C A T T A G G C C G C C C G G G C G G G G C G C G G G G G C G
1_0073 G C G C G G C C G C G G C G G G C C C C G C G C G G G G G C G C G G C G G C G G C G G G C G G C C G C G G G G C C G C G C C C C G C G G
1_0080 T G T T T T G G T G T T T T G T T G G T G G T G T G G T G T T G G G G T G G G A A G G T G G G G G G T T G G T G T G T G G T G G G G T T
1_0081 T A T T A T T A A A A T T A A A T T T A T T T T T T T T A A A A T T T T T T A T A A T T A T T A A A A A T T T T A T T A T A A T T T T T
1_0083 G C G C G G C C G C G G C G G G C C C C G C G C G G G G G C G C G G C G G C A T T A C G C G G C C G C G G G G C C G C G C C C C G C G G
1_0084 C G G G C G C C G G G G C G G G C C C G C C G G C G G G G G G G C C C G C C G G T T C G G C C C C C C G C G G C G G C C G G G C G G G G

High Throughput genotyping platform (SNP)

 Analysis of Quantitative traits
QTL analysis in mapping populations

If molecular markers are polymorphic, we can construct a linkage map based on

recombination frequencies:
1H 2H 3H 4H 5H 6H 7H

0 MWG634
21 MWG077
24 HVM40 0 ABG704
0 BCD1434 29 DsT-29 0 scssr02306 14 Bmag0007
7 DsT-66 0 DsT-1 0 BCD907 6 MWG618 0 MWG620
5 ABG058 30 CDO542 Bmac0316 20 scind00694
12 Act8A 31 CDO122 8 DsT-6 4 29 AW982580
18 RbgMD 7 scind02622 11 ABC483 scssr09398
35 hvknox3 31 MWG652A 36 MWG089
22 MWG837B 17 ABG008 39 Dhn6 12 ABG610 CDO475
25 scind00046 26 ABC171A 35 MWG602B
30 GBM1074 ABC303 42 scind60002 38 ABG380
26 ABC165C 36 scssr10226 41 44 BE602073
39 scssr07759 33 scssr10559 scssr20569 37 ABG395 45 JS10A
29 Bmac0399 44 CDO795 57 scssr07970
30 GBM1007 42 GBM1066 36 MWG798B 44 scssr02503 51 GBM1021
39 Dst-27 49 HVM3 45 scssr18076 61 GBM1068 66 scsnp00460
36 BCD098 45 Pox 68 ABC255
56 scssr03381 42 BCD706 DST-46 53 Bmac0096 65 BG299297
48 GBM1042 50 scind03751 69 ABC165D
54 BG367013 scssr12344 58 DsT-39 55 NRG045A 68 HVM31
scssr18005 56 scsnp04260 70 rob 73 HvVRT2
58 Bmag0211 63 scssr02236 61 alm 82 scssr15864
Ebmac0684 52 Tef2 58 Ale Bmag0009
61 BG369940 66 Bmac0209 60 GBM1020 71 86 GBM1030
68 GBM1051 65 BCD1434.2 69 ABC325 scssr02093
62 Bmag0353 81 ABG474 scsnp22290
73 ABC160 68 ABG356 73 DsT-67 79 ABC302 MWG808
71 GBM1023 67 scind10455 88 Bmac0218C 89
86 JS10C 74 DsT-79 82 scind16991 DAK642
87 Bmac0144A 83 scsnp03343 87 scssr25691 85 scssr15334 92 ABG388
89 ABG377 scssr14079 99 scsnp21226 scind00149
96 MWG706A 88 vrs1 80 90 scsnp06144 scsnp00703
94 Bmag0125 ABG472 101 MWG820 97
101 KFP170 98 Bmag0225 83 GBM1059 100 srh MWG2031
111 Blp 97 DsT-41 122 GBM1008
92 KFP221 123 scssr05599 98 RSB001C
119 ABC261 102 MWG503 103 nud
103 GBM1062 94 Ebmac0701 111 scssr05939 126 MWG934
121 MWG2028 95 MWG652B 115 lks2
122 KFP257B 104 KFP203 121 Act8C 120 RSB001A 132 scind04312b
124 ABG499 101 GBM1048 scssr00103 117 ABC1024
130 WMC1E8 108 MWG882A 135 125 Bmag0120
117 ABG1032 125 GBM1043 111 Hsh 128 scsnp00177 GBM1022
133 MWG912 112 HVM67 126 DsT-30
ABG387A 124 ABG072 134 0SU-STS1 143 Bmac0040
116 KFP241.1 145 DsT-18 127 WG380B
136 scssr04163 137 Ebmc0415 141 ABG003B 137 ABC310B
139 cnx1 124 ABG601 146 DsT-32B
scssr08238 139 Ris44
149 Zeo1 151 scsnp23255 157 scssr10148 152 DsT-22
161 GBM1019 155 ABG004 166 Tef3 159 DsT-28
163 Aglu5F3R2 169 MWG877 160 scind60001
165 MWG720 166 scind02281 DsT-74 167 ABG461A
170 BE456118A 171 WG380A
170 GBM1012 172 MWG883 179 ABG496 162 MWG514
173 wst7 scsnp02109 163 MWG798A 178 GBM1065
181 DsT-24 193 167 DsT-71
179 scssr08447 E10757A
180 MWG949A 190 HVM62 197 ABG391 196 HVM5
198 JS10B 197 scssr04056
199 DsT-40 KFP255
205 ABC622
ABC172 207 DsT-33 199 ThA1
212 scssr25538 215 Bmag0113C
218 DsT-35 223 MWG602A
224 scssr03907
225 scssr03906
 Analysis of Quantitative traits

QTL analysis in mapping populations

The basic QTL analysis method consists in walking trough the

chromosomes performing statistical test at the positions of the
markers in order to test whether there is a marker-trait association
or not
 Disease Analysis of
severity (%) DsT-66 1H
Parent 1(Resistant) 5 A
Quantitative traits
Parent 2 (Susceptible) 90 B
Line1 56 B
Line2 30 A
Line3 59 A 0 BCD1434
Line4 95 A 7 DsT-66
12 Act8A
Line5 31 A 18 RbgMD
Line6 42 A Average Disease severy of 22 MWG837B
Line7 94 A 25 scind00046
Line8 42 A plants with allele “A” (Inherited 26
29
ABC165C
Bmac0399
Line9 15 B from Resistant parent) = 49.8 30 GBM1007
36 BCD098
Line10 3 B 48 GBM1042
Line11 84 B 54 BG367013
Line12 82 B 58 Bmag0211
61 BG369940
Line13 30 B 68 GBM1051
Line14 60 A 73 ABC160
86 JS10C
Line15 26 B Average Disease severity of 87 Bmac0144A
Line16 57 B 96 MWG706A
Line17 12 A plants with allele “B” (Inherited 101 KFP170
111 Blp
Line18 68 A from Susceptible parent) = 50.3 119 ABC261
Line19 53 B 121 MWG2028
122 KFP257B
Line20 69 B 130 WMC1E8
Line21 43 B 133 MWG912
Line22 42 A ABG387A
136 scssr04163
Line23 67 B 49.8 and 50.3 are not scssr08238
Line24 64 B statistically different. Therefore,
Line25 46 A
Line26 28 A marker DsT-66 is not associated
Line27 41 B with resitance/susceptibility to
Line28 50 B
Line29 91 B the disease
Line30 25 B
 Disease Analysis of
severity (%) ABC261 1H
Parent 1(Resistant) 5 A
Quantitative traits
Parent 2 (Susceptible) 90 B
Line1 56 B
Line2 30 A
Line3 59 B Average Disease severy of 0 BCD1434
Line4 95 B plants with allele “A” (Inherited 7 DsT-66
12 Act8A
Line5 31 A 18 RbgMD
Line6 42 A from Resistant parent) = 30.4 22 MWG837B
Line7 94 B 25 scind00046
26 ABC165C
Line8 42 A 29 Bmac0399
Line9 15 A 30 GBM1007
36 BCD098
Line10 3 A 48 GBM1042
Line11 84 B 54 BG367013
Line12 82 B Average Disease severity of 58
61
Bmag0211
BG369940
Line13 30 A plants with allele “B” (Inherited 68 GBM1051
Line14 60 B 73 ABC160
Line15 26 A from Susceptible parent) = 69.8 86
87
JS10C
Bmac0144A
Line16 57 B 96 MWG706A
Line17 12 A 101 KFP170
111 Blp
Line18 68 B 119 ABC261
Line19 53 B 30.4 and 69.8 are statistically 121 MWG2028
122 KFP257B
Line20 69 B 130 WMC1E8
Line21 43 A different. Therefore, marker 133 MWG912
Line22 42 A ABG387A
ABC261 is linked with a 136 scssr04163
Line23 67 B scssr08238
Line24 64 B resitance/susceptibility QTL.
Line25 46 A
Line26 28 A
Line27 41 A The additive effect of the QTL is:
Line28 50 B a = (69.8-30.4)/2 = 14.7
Line29 91 B
Line30 25 A
 0 MWG634
21 MWG077
24 HVM40
29 DsT-29 0 scssr02306
CD907 6 MWG618 0
30 CDO542
31 CDO122 8 DsT-6 4
35 hvknox3 11 ABC483
12 ABG610 31
39 Dhn6
Most likely position of the QTL

BC171A 35
BM1074 41 ABC303 42
scssr20569
Analysis of Quantitative traits

ssr10559 37 ABG395 45
WG798B 44 CDO795 44 scssr02503 51
st-27 49 HVM3 45 scssr18076 61
CD706 DST-46 53 Bmac0096 65
50 scind03751 55 NRG045A 68
sT-39 scssr18005
m 56 scsnp04260 70
52 Tef2 58 Ale
mac0209 60 GBM1020 71
BC325 62 Bmag0353
sT-67 79 ABC302 81
67 scind10455 88
74 DsT-79 82 scind16991
ssr25691 85 scssr15334 92
BG377 80 scssr14079 99
ABG472 90 scsnp06144
mag0225 101
83 GBM1059 100 srh 122
92 KFP221 123
94 Ebmac0701 111 scssr05939 126
ct8C 95 MWG652B 132
101 GBM1048 120 RSB001A
BG499
135
QTL analysis in mapping populations

BM1043 111 Hsh 128 scsnp00177

112 HVM67 134 0SU-STS1 143
116 KFP241.1 141 ABG003B 145
124 ABG601 146
snp23255 152
Significance threshold

157 scssr10148
BG004 166 Tef3 159
ind02281 169 MWG877 160
170 BE456118A
WG883 179 ABG496 162
scsnp02109 163
sT-24 193 167
E10757A
VM62 197 ABG391
sT-40 198 JS10B
205 ABC622
BC172 207 DsT-33
ssr25538 215 Bmag0113C
sT-35 223 MWG602A
224 scssr03907
225 scssr03906
Probability
 Analysis of Quantitative traits
1H 2H 3H 4H 5H 6H 7H

0 MWG634
21 MWG077
24 HVM40 0 ABG704
0 BCD1434 29 DsT-29 0 scssr02306 14 Bmag0007
7 DsT-66 0 DsT-1 0 BCD907 6 MWG618 0 MWG620
5 ABG058 30 CDO542 Bmac0316 20 scind00694
12 Act8A 31 CDO122 8 DsT-6 4 29 AW982580
18 RbgMD 7 scind02622 11 ABC483 scssr09398
35 hvknox3 31 MWG652A 36 MWG089
22 MWG837B 17 ABG008 39 Dhn6 12 ABG610 CDO475
25 scind00046 26 ABC171A 35 MWG602B
30 GBM1074 ABC303 42 scind60002 38 ABG380
26 ABC165C 36 scssr10226 41 44 BE602073
39 scssr07759 33 scssr10559 scssr20569 37 ABG395 45 JS10A
29 Bmac0399 44 CDO795 57 scssr07970
30 GBM1007 42 GBM1066 36 MWG798B 44 scssr02503 51 GBM1021
39 Dst-27 49 HVM3 45 scssr18076 61 GBM1068 66 scsnp00460
36 BCD098 45 Pox 68 ABC255
56 scssr03381 42 BCD706 DST-46 53 Bmac0096 65 BG299297
48 GBM1042 50 scind03751 69 ABC165D
54 BG367013 scssr12344 58 DsT-39 55 NRG045A 68 HVM31
scssr18005 56 scsnp04260 70 rob 73 HvVRT2
58 Bmag0211 63 scssr02236 61 alm 82 scssr15864
Ebmac0684 52 Tef2 58 Ale Bmag0009
61 BG369940 66 Bmac0209 60 GBM1020 71 86 GBM1030
68 GBM1051 65 BCD1434.2 69 ABC325 scssr02093
62 Bmag0353 81 ABG474 scsnp22290
73 ABC160 68 ABG356 73 DsT-67 79 ABC302 MWG808
71 GBM1023 67 scind10455 88 Bmac0218C 89
86 JS10C 74 DsT-79 82 scind16991 DAK642
87 Bmac0144A 83 scsnp03343 87 scssr25691 85 scssr15334 92 ABG388
89 ABG377 scssr14079 99 scsnp21226 scind00149
96 MWG706A 88 vrs1 80 90 scsnp06144 scsnp00703
94 Bmag0125 ABG472 101 MWG820 97
101 KFP170 98 Bmag0225 83 GBM1059 100 srh MWG2031
111 Blp 97 DsT-41 122 GBM1008
92 KFP221 123 scssr05599 98 RSB001C
119 ABC261 102 MWG503 103 nud
103 GBM1062 94 Ebmac0701 111 scssr05939 126 MWG934
121 MWG2028 95 MWG652B 115 lks2
122 KFP257B 104 KFP203 121 Act8C 120 RSB001A 132 scind04312b
124 ABG499 101 GBM1048 scssr00103 117 ABC1024
130 WMC1E8 108 MWG882A 135 125 Bmag0120
117 ABG1032 125 GBM1043 111 Hsh 128 scsnp00177 GBM1022
133 MWG912 112 HVM67 126 DsT-30
ABG387A 124 ABG072 134 0SU-STS1 143 Bmac0040
116 KFP241.1 145 DsT-18 127 WG380B
136 scssr04163 137 Ebmc0415 141 ABG003B 137 ABC310B
139 cnx1 124 ABG601 146 DsT-32B
scssr08238 139 Ris44
149 Zeo1 151 scsnp23255 157 scssr10148 152 DsT-22
161 GBM1019 155 ABG004 166 Tef3 159 DsT-28
163 Aglu5F3R2 169 MWG877 160 scind60001
165 MWG720 166 scind02281 DsT-74 167 ABG461A
170 BE456118A 171 WG380A
170 GBM1012 172 MWG883 179 ABG496 162 MWG514
173 wst7 scsnp02109 163 MWG798A 178 GBM1065
181 DsT-24 193 167 DsT-71
179 scssr08447 E10757A
180 MWG949A 190 HVM62 197 ABG391 196 HVM5
198 JS10B 197 scssr04056
199 DsT-40 KFP255
205 ABC622
ABC172 207 DsT-33 199 ThA1
212 scssr25538 215 Bmag0113C
218 DsT-35 223 MWG602A
224 scssr03907
225 scssr03906

We identify the location of the QTL, the molecular markers

flanking them, their effect and their interactions
 Analysis of Quantitative traits
Association mapping

Also called Linkage Disequilibrium mapping

No need to develop populations from a single cross. Analysis is performed

on arrays of related or unrelated individuals.

Association between markers and QTL in mapping populations are based

only on linkage. However, in Association mapping these association can be
due to multiple factors: linkage, selection, mutation, genetic drift,
population structure, etc.

Unlike mapping populations, where only alleles from the two parents are
studied, multiple alleles may be present at any single locus.
 Analysis of Quantitative traits

The analysis is based on the same principles as QTL analysis in mapping

populations.

Linkage maps are not needed

A higher density of markers is required

Line10
Line11
Line12
Line13
Line14
Line15
Line16
Line17
Line18
Line19
Line20
Line21
Line22
Line23
Line24
Line25
Line26
Line27
Line28
Line29
Line30
Line30
Line31
Line32
Line33
Line29
Line30
Line30
Line31
Line32
Line33
Line34
Line35
Line36
Line37
Line38
Line39
Line40
Line41
Line42
Line43
Line44
Line45
Line1
Line2
Line3
Line4
Line5
Line6
Line7
Line8
Line9

SNP
1_0002 G A G G G G G A G G A A G A G A G G A G G G A A A G G A A A G A A G A A G A A G G A A G A G G G G A A A
1_0004 T T T T A A T A T T T T A T T A A T A A T A T A A T A T T A A A A T A A A T A A A T A A A A A A T T A A
1_0011 T A T T A T A T T A T T T T T A A T A A A A A A A T T T T T A A T A A T A T T A A T T A A T T T A T A A
1_0014 T T T T T T G T T G T T G G T T T G T G T G G T T T G T G T T T G G G G G G T T G G T T T T G T G G G G
1_0020 C C C C G C G C G G C C C C C G G C C C G G G G G C C C G C G C G C G C G C C C G C C C G G G G G C G G
1_0023 A T A A A A T T A T T T T T A A A A T A A T T T T A T T A A T T A T A T A A A T A A A T A T A T T T T A
1_0024 A A T A T T T A A A T T T T A A T T A T T A T A A A T A T A T A T A A A A T T A A T T A T A A T T T A A
1_0026 G G C G G C C C C G G C C C G G G C G G G G G C G G C C G C G G G G G G G G C G G G C G G C C C C C G G
1_0031 G C G G C C G G G G C C G C G C C C G C C C G G G G C G G G C C C G G C G A A G G C C G G C G C C C C C
1_0036 G T G G T T T G G G T G T T G G T G T T G G G G G G G T G T G T G G G G A T A A G G G G T T T T G T G T
1_0041 G T T G T T G T T T T G T T G T T G T G T G T T T G T T T T T T T G G G A T T A G T T G G G T T T T T T
1_0047 A T A A T A A A A T A T A A A T T A A T T A T T A A A T T A T T A T T A G G T T T A T T T A A A T A T T
1_0048 T A T T A A T T T T A A T A T A A A T A A A T A A T T T T T A A A A T A G C C C T A A T T A T A A A T A
1_0050 A A A A T T T T T T T A A T T T T T T A A T A A A A A T A T A A T A A T A A A T T T T T A T T T T T A A
1_0051 A T A A T A T A T T A T A T T T T A A A T T A A A A A A A T A A A T T A A T T A T T A A T A A A T T T A
1_0052 A T A A A T A A T A A T T T T T A T A A T T T T T A A A A A T T T T T T G G C G A A T T T T A T T T A A
1_0053 A T A A A T A A T A A T T T T T A T A A T T T T T A A A A A T T T T T T G A A G A A T T T T A T T T A A
1_0055 G C G G C C G C G G C G G G C C C C G C G C G G G G G C G C G G C G G C A T A A G G C G G C C G C G G G
1_0061 T G T T T G G G T T G G T T T T T T G T T G G G G T T T G G T G T G T G A T T A G T T T T T T G G T G T
1_0063 T A T T A A T T T T A A T A T A A A T A A A T A A T T T T T A A A A T A G G T T T A A T T A T A A A T A
1_0064 T C T T T T C C T C C C C C T T T T C T T C C C C T C C T T C C T C T C G C C C T T T C T C T C T C C T
1_0065 G T T G G G G T G T T G T G G G G G T G G T T T G G T G T G T G G G G G A A A T T T T G G G G G G G G G
1_0071 C G C C G C G C G G C G C G G G G C C C G G C C C C C C C G C C C G G C A T T A G G C C G C C C G G G C
1_0073 G C G G C C G C G G C G G G C C C C G C G C G G G G G C G C G G C G G C G G C G G G C G G C C G C G G G
1_0080 T T T T G G T G T T T T G T T G G T G G T G T G G T G T T G G G G T G G G A A G G T G G G G G G T T G G
1_0081 T T A T T A A A A T T A A A T T T A T T T T T T T T A A A A T T T T T T A T A A T T A T T A A A A A T T
1_0083 G C G G C C G C G G C G G G C C C C G C G C G G G G G C G C G G C G G C A T T A C G C G G C C G C G G G
1_0084 G G C G C C G G G G C G G G C C C G C C G G C G G G G G G G C C C G C C G G T T C G G C C C C C C G C G
 0
1
2
3
4
5
6
1H-0-3_0969
1H-27.35-3_1276
1H-49.7-1_0159
1H-51.23-1_1484
1H-55.49-2_0798
1H-61.53-1_0798
1H-73.94-2_1126
1H-95.42-2_1373
1H-121.12-2_0908
1H-137.83-2_0138
2H-27.29-2_1015
2H-45.55-3_0363
2H-63.53-1_0191
2H-81.33-1_0859
2H-90.1-1_0969
2H-113.48-3_1402
2H-127.64-3_0310
2H-139.65-1_0551
3H-2.9-2_0159
3H-41-3_0953
3H-51.73-1_1313
3H-54.4-3_1008
3H-56.4-2_1062
3H-59.89-1_0373
3H-69.6-3_1242
3H-76.98-3_1346
3H-91.25-2_0659
3H-109.14-2_1513
3H-130.19-1_0280
3H-142.32-3_0137
3H-168.4-2_1267
4H-18.01-3_0150
4H-28.4-2_1374
4H-48.5-1_0577
4H-52.75-1_0946
4H-65.05-2_0906
4H-68.21-3_1536
4H-93.13-3_0142

other genotypic class (other allele)

4H-113.92-1_1066
5H-2.09-2_0226

then there is marker-QTL association

5H-37.11-3_0410
5H-50.27-2_1308
5H-51-2_1011
5H-51.6-2_1260
5H-59.4-2_0961
5H-60.74-3_1280
Significance threshold

5H-84.51-2_0096
5H-103.92-2_0327
5H-117.47-1_1200
5H-132.63-2_0259
5H-142.2-3_1366
5H-159.09-1_0820
5H-179.06-1_0254
6H-1.34-2_0881
6H-24.36-1_0868
6H-42.36-3_0783
6H-49.4-2_0291
Analysis of Quantitative traits

6H-54.6-1_0962
6H-55.94-1_0513
Statistical test are performed at the position of each marker.

6H-60.23-1_0270
6H-65.03-1_1261
6H-74.55-3_1088
6H-90.15-1_0202
If differences between genotypic classes are statistically different,

6H-112.32-1_0239
6H-126.18-3_1498
7H-14.96-1_0841
7H-37.55-2_0126
The average phenotype of individuals with one genotypic class (with a

7H-54.37-1_0772
7H-68.46-3_0639
certain allele) is tested against the average phenotype of individuals with

7H-77.85-2_0879
7H-79.6-1_0370
7H-79.6-3_0835
7H-87.97-1_0143
7H-110.99-2_0385
7H-133.79-2_1104
7H-144.45-1_0843
END….

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