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1
Define a population.
Discuss the concept of a gene pool.
Discuss the changes in gene frequencies
in populations.
Discuss the Hardy–Weinberg law.
2
Population is a group of sexually interbreeding
individuals. The capacity to interbreed implies that
every gene within the group is accessible to all
members through the sexual process.
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.
3
Hardy Weinberg
Equilibrium
Gregor Mendel
Wilhem Weinberg
(1822-1884) (1862 – 1937)
G. H. Hardy
(1877 - 1947)
Recall
Darwin’s Observation
(1822-1884)
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
Godfrey Hardy
(1877-1947) Wilhem Weinberg
(1862 – 1937)
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
Evolutionary Mechanisms
Genetic Drift
Natural Selection
Mutation
Migration
*Epigenetic modifications change expression of alleles but not
the frequency of alleles themselves, so they won’t affect the
actual inheritance of alleles
However, if you count the phenotype frequencies, and not the
genotype frequencies , you might see phenotypic frequencies
out of HW Equilibrium due to epigenetic silencing of alleles.
(epigenetic modifications can change phenotype, not genotype)
Large population size Genetic drift
Random Mating
Inbreeding & other
No Mutations Violation
Mutations
No Natural Selection Natural Selection
No Migration
Migration
Also,
the genotype frequencies you see in a
population should be the Hardy-Weinberg
expectations, given the allele frequencies
NoEvolution: Null Model to test if no
evolution is happening should simply be a
population in Hardy-Weinberg Equilibrium
19
Sources of variation
• Sex and Recombination
• Crossing-over, independent assortment,
fertilization
Alters expression
Produces new combinations in genotypes
Produces new combinations of phenotypes
20
A group of organisms of the same
species that are found in the same area
and can interbreed. A population is the
smallest unit that can evolve—in other
words, an individual can’t evolve.
21
isthe field of biology that studies allele
frequencies in populations and how they
change over time.
22
consistsof all the copies of all the genes
in that population
23
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
24
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.
25
W copies = 13
w copies = 5
The total number of gene copies in the
whole population is 13 + 5 = 18.
26
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.
27
28
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.
30
Hardy-Weinberg Theorem
In a non-evolving population,
frequency of alleles and genotypes
remain constant over generations
q = frequency of
CW allele = 0.2 80% 20% 80% 20%
chance chance chance chance
• 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
(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.
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
One locus three alleles: (p + q + r)2 = p2 + q2 + r2 + 2pq
+2pr + 2qr
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
ALLELE Frequency
Frequency of A = p = 0.8 p+q=1
Frequency of a = q = 0.2
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
calculations using
64% ( p2) 16% ( pq) percentages
CR CR CR CW
16% (qp) 4% (q2)
CR CW CW CW
Sperm
CR CW
(80%) (20%)
• Composition
– fiber, starch, oil & protein as food/
industrial ingredients
– recovery and processing
– valorization of by-products
50
51
Breeding for Quality: a moving field (1)
Consumer/society Technology
Flavour (taste, odour) breeding strategies
Convenience insight plant processes
Product appearance
Personal health new processing techni-ques (e.g.
high pressure)
Food safety
Awareness environment better understanding structure-
function re-lationships biomolecules
improved analytics 52
Quantity: Yield
Abiotic resistance
Drought resistance
Lodging
Salt/Salinity
Bad soil etc
53
Population genetics and quantitative genetics - closely
related fields,
both dealing with the genetic basis of phenotypic
variation among the individuals in a population.
54
• focuses on frequencies of alleles • focuses on linking phenotypic
Population genetics
quantitative genetics
and genotypes, variation of complex traits to its
underlying genetic basis to
enable researchers better
understand and predict genetic
architecture and long term
change in populations
55
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 quantitative trait
loci (QTLs).
Molecular-basedQTL analyses are being used to evaluate the
coupling associations of the polymorphic DNA sites with
phenotypic variations of quantitative and complex traits and
analyzing their genetic architecture.
There is evidence of a paradigm shift in the field of quantitative
genetics.
56
57
Qualitative and Quantitative traits
Qualitative traits: Quantitative traits:
% of plants
20 30 40
59
60
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.
61
62
Inheritance of Quantitative traits
The study of quantitative trait inheritance followed the same steps as for Mendelian traits.
At the beginning they were thought to not follow Mendel’s laws. But it is not true
PARENT 1: P1 P2
• pure line, completely homozygote
• 40 inches
PARENT 2:
• pure line, completely homozygote
×
• 20 inches
% of plants
F1: range of height distribution F1
but no type of segregation
20 30 40
Plant Height (in)
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
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
P1 (red) P2 (white)
AABBcc X aabbcc
F1(red) AaBbcc
P1 (red) P2 (white)
AABBCC X aabbcc
F2 F1(red) AaBbCc
(three loci
segregating) Segregation 63 red : 1 white
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
He deduced that many loci were involved (not only two) in the trait and taking
into account Johanssen’s findings:
Phenotype=Genotype+Environment
3 2
+ purple
1 - white
Color intensity
Frequency
P1 P2
0
Cold tolerance 10
F1 AaBbCcDdEe
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.
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
If h2 is 0 means :
μ0 μR S
Frequency
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
b) Association mapping
The offspring of that cross will show recombination between the two
parents and therefore, some individuals will be resistant and other will be
susceptible
The first step is getting genotypic information for all the individuals of the
population: molecular markers
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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
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
QTL analysis in mapping populations
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
Association mapping
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
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
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
Statistical test are performed at the position of each marker.
6H-55.94-1_0513
6H-60.23-1_0270
6H-65.03-1_1261
6H-74.55-3_1088
6H-90.15-1_0202
6H-112.32-1_0239
If differences between genotypic classes are statistically different,
6H-126.18-3_1498
7H-14.96-1_0841
7H-37.55-2_0126
7H-54.37-1_0772
The average phenotype of individuals with one genotypic class (with a
7H-68.46-3_0639
7H-77.85-2_0879
7H-79.6-1_0370
certain allele) is tested against the average phenotype of individuals with
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