1/9/971 PHENOTYPIC SELECTION THEORY AND APPLICATION PHENOTYPIC SELECTION THEORY AND APPLICATION...
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Transcript of 1/9/971 PHENOTYPIC SELECTION THEORY AND APPLICATION PHENOTYPIC SELECTION THEORY AND APPLICATION...
1/9/97 1
PHENOTYPIC SELECTIONTHEORY AND APPLICATIONPHENOTYPIC SELECTION
THEORY AND APPLICATION
Kendall R. LamkeyUSDA-ARS
Department of AgronomyIowa State University
Ames, IA 50011
1/9/97 2
OUTLINE
• Mendelian vs. Quantitative Traits
• Genotypic Value
• Average Effect
• Breeding Value
• Heritability
• Genetic Gain
• Empirical Results
1/9/97 3
REFERENCES
Falconer, D. S. 1981. Introduction to quantitative genetics. 2nd ed. Longman, New York.
Lush, J. L. 1994. The genetics of populations. Iowa Agriculture and Home Economics Experiment Station, College of Agriculture, Iowa State University, Ames.
1/9/97 4
QUANTITATIVE GENETICS
ContinuousVariationMendelism
Fisher, R. A. 1918. The correlation between relatives on the supposition of Mendelian Inheritance. Trans. Roy. Soc. Edinburgh 52:399-433.
Haldane, J. B. S. 1932. The causes of evolution. Longmans, Green, London
Wright, S. 1921. Systems of Mating. Genetics 6:111-178
1/9/97 5
QUANTITATIVE GENETICS
Phenotype
Environment Genotype
Genes
TemperaturePrecipitation
Etc.
1/9/97 6
QUANTITATIVE GENETICS
SELECTION
• Selection Must Be on Phenotype or Some Function of Phenotype
• Breeders Only Rarely Know Genotypes for More Than a Few of the Loci an Individual Possesses
• Individuals Chosen As Parents Transmit Only a Sample of Half of the Genes It Has
1/9/97 7
QUANTITATIVE GENETICS
SELECTION
• Show Us How to Choose Individuals With the Best Merit (Breeding Value)
• Predict the Outcome of Selection to Compare Different Breeding Schemes
1/9/97 8
QUANTITATIVE GENETICS
P = G + E
PHENOTYPIC VALUE (P) = Value observed when the character is measured on an individual
GENOTYPIC VALUE (G) = Value attributable to the particular assemblage of genes possessed by an individual
ENVIRONMENTAL DEVIATION (E) = Value attributable to all nongenetic circumstances that influence phenotype
1/9/97 9
QUANTITATIVE GENETICS
Assumptions
• Random Mating Equilibrium
• No Linkage
• No Epistasis
• Diploid Inheritance
f(A) = pf(a) = qp + q = 1
p2AA + 2pqAa + q2aa
Random Mating Population
1/9/97 10
GENOTYPIC VALUE
aa Aa AA
-a-4
0 d2
a4
aa Aa AA
6 12 14Yield
MP = (14 + 6)/2 = 10 a = 14 - 10 = 4d = 12 - 10 = 2 d/a = 2/4 = 0.5
1/9/97 11
GENOTYPIC VALUE
Genotype Frequency Value Freq x Value
AA p2 a p2a
Aa 2pq d 2pqd
aa q2 -a -q2a
Mean = a(p-q) + 2pqd
1/9/97 12
GENOTYPIC VALUE
• With selection we are concerned with the transmission of value from parent to offspring.
• This cannot be determined based on genotypic value alone.
• Parents pass on their genes and not their genotypes to the next generation.
• Genotypes are created anew in each generation.
1/9/97 13
GENOTYPIC VALUE
• Individuals transmit genes (alleles) to their progeny.
• One result of this is that some aspects of the value of a particular genotype are unpredictable.
• Selection theory can work only with the predictable aspects of the union of two gametes.
• Therefore, we need to introduce the average effect of a gene.
1/9/97 14
AVERAGE EFFECT
P = ijij + E
i = Average (or additive) effect of allele i
ij = Dominance deviation
1/9/97 15
AVERAGE EFFECT
Average effect of a gene - the mean deviation from the population mean, of individuals that received the gene from one parent, the gene received from the other parent having come at random from the population.
Average effect of a gene - let a number of gametes carrying A unite at random with gametes from the population; then the mean of the genotypes so produced deviates from the population mean by an amount that is the average effect of the A gene.
1/9/97 16
AVERAGE EFFECT
p2AA + 2pqAa + q2aa
pA + qa
pA + qaA
pAA + qaa
Mean = a(p-q) + 2pqd
Mean = pa + qd
1/9/97 17
AVERAGE EFFECT
= q[a + d(q - p)]
a= -p[a + d(q - p)]
= a
Average effect of a gene substitution - The mean change in value produced by changing (a) genes at random into (A) genes.
1/9/97 18
AVERAGE EFFECT
• Dependent on genotypic value.
• Dependent on gene frequencies.
• Property of the population as well as the genes concerned.
• Average effect of a gene cannot be measured.
• So, we introduce the concept of breeding value.
1/9/97 19
BREEDING VALUE
Breeding value is the value of an individual judged by the mean value of its progeny.
The Breeding Value of an individual is equal to the sum of the average effects of the genes it carries. The summation is over pairs of alleles at a locus and over all loci.
Genotype Breeding ValueAA 2
Aa A + a
aa 2a
1/9/97 20
0 1 2aa Aa AA
-a
0
d+a
-2p
(q - p)
0
2q
BREEDING VALUE
p =3
4
q =1
4
d =3
4a
q2 2pq p2
1/9/97 21
p s
Z
c
P
PHENOTYPIC SELECTION
1/9/97 22
Parents
Offs
prin
g
S
R
R = ResponseS = Selection Differential
R = bopS
PHENOTYPIC SELECTION
1/9/97 23
BaseBasePopulationPopulation
DevelopDevelopProgenieProgenie
ss
EvaluateEvaluateProgeniesProgenies
IntermateIntermateSelectionsSelections
C1C2..
Cn
C1C2..
Cn
PHENOTYPIC SELECTION
1/9/97 24
PHENOTYPIC SELECTION
OBJECTIVES OF SELECTION
• Increase the Frequency of Favorable Alleles, Which Is to Increase the Mean of the Population in the Favorable Direction
• Maintain Genetic Variability for Continued Selection by Intermating Superior Progenies for Each Cycle of Selection.
• Therefore, Enhancing the Probability of Obtaining Superior Genotypes (Lines or Hybrids) From the Population.
1/9/97 25
-5 -4 -3 -2 -1 0 1 2 3 4 5 6 7
PHENOTYPIC SELECTION
OriginalPopulation
ImprovedPopulation
Best Hybrid FromOriginal Population
Best Hybrid FromImproved Population
XC0 XCn
1/9/97 26
• Plant Breeders Determine Merit Based on Phenotypes.
• The Goal of Plant Breeding Is to Separate the Environment From the Breeding Value.
• From a Quantitative Genetic Point of View This Is Equivalent to Maximizing the Heritability.
• From a Statistics/Regression Point of View This Is Equivalent to Maximizing the Correlation Between Phenotype and Breeding Value.
PHENOTYPIC SELECTION
1/9/97 27
HERITABILITY
V(P) = V(G) + V(E)
V(P) = V(i)V(j)V(ij) + V(E)
V(P) = V(A) + V(D) + V(E)
1/9/97 28
HERITABILITY
V(P) = Variance among phenotypes Phenotypic variance
V(A) = Variance among breeding values Additive variance
V(D) = Variance among dominance deviations Dominance Variance
1/9/97 29
HERITABILITY
Heritability = The extent to which phenotypes are determined by genes transmitted from the parents.
h2 = V(A)/V(P)
The goal of an artificial selection program is to maximize heritability
1/9/97 30
GENETIC GAIN
( )b
op=
covop
12
V P
R = b Sop S = X XS P-
( )cov =1
2V A
op
( )( )
b =V A
V P= h
op2 R = h S2
1/9/97 31
GENETIC GAIN
R = h S2
Z
p
Xp Xs
R = ih2p i =
X XS P
p
-
1/9/97 32
GENETIC GAIN
G =ic
yre e
G2
e2
GE2
G2
where,
i = Standardized selection differentialc = parental controly = years per cycler = number of replications per environmente = number of environments
1/9/97 33
INCREASING GENETIC GAIN
• Increase Selection Intensity
• Increase Genetic Variance
• Decrease Years per Cycle
• Decrease Phenotypic Variance
1/9/97 34
INCREASING GENETIC GAIN
Increase Selection Intensity
G =ic
yre e
G2
e2
GE2
G2
Proportion Selected I
30 of 100 1.149
20 of 100 1.386
10 of 100 1.730
5 of 100 2.018
1 of 100 2.508
1/9/97 35
INCREASING GENETIC GAIN
Increase Genetic Variance
G =ic
yre e
G2
e2
GE2
G2
TC-I HS TC-B FS FR S1 S2 Method
0
10
20
30
40
50
60
70
80
Her
itabi
lity
(%)
1/9/97 36
INCREASING GENETIC GAIN
G =ic
yre e
G2
e2
GE2
G2
Decrease Years per Cycle
1/9/97 37
INCREASING GENETIC GAIN
Decrease Phenotypic Variance
G =ic
yre e
G2
e2
GE2
G2
1 2 3 4 5 6 7 8 9 10Number of Environmnets
0.3
0.4
0.5
0.6
0.7
0.8
Her
itabi
lity
One Rep per EnvironmentTwo Reps per EnvironmentFour Reps per Environment
1/9/97 38
PHENOTYPIC SELECTION
APPLICATIONEMPIRICAL RESULTS
1/9/97 39
RECIPROCAL RECURRENT SELECTION
BSSSC0 BSCB1C0
HS Families
HS Families
BSSS(R)C1 BSCB1(R)C1
BSSS(R)C9 BSCB1(R)C9
BSSS(R)C12 BSCB1(R)C12
BSSS(R)C1 X BSCB1(R)C1
FS Families
BSSS(R)C12 X BSCB1(R)C12
S1
S1
S1
S1
1/9/97 40
RECIPROCAL RECURRENT SELECTION
BSSS - Iowa Stiff Stalk Synthetic
- 16 Inbred Line Synthetic
- Synthesized in Early 1930s
BSCB1 - Iowa Corn Borer Synthetic #1
- 12 Inbred Line Synthetic
- Synthesized in 1940s
1/9/97 41
IOWA STIFF STALK SYNTHETIC
Os WD Ind Ill CI CI Ill Oh Ind TR A3G- CI LeI159 I224 420 456 461-3 12E 617 540 HY 3167B AH83 9116 F1B1 313 187-2 23
SingleCrosses
DoubleCrosses
Double-Double Crosses
Bulk Equal Quantities Seed
BSSSC0
1/9/97 42
0 2 4 6 8 10 12Cycle
3
4
5
6
7
8
Gra
in Y
ield
(M
g/h
a)
BSSS(R)Cn b = 0.06 Mg/haBSCB1(R)Cn b = 0.06 Mg/haCn x Cn b = 0.28 Mg/ha
IOWA STIFF STALK SYNTHETIC
1/9/97 43
C0 C11Cycle
0.0
0.1
0.2
0.3
0.4
0.5
0.6
0.7
Gra
in Y
ield
(M
g/h
a)
Total Genetic VarianceAdditive Genetic VarianceDominance Genetic Variance
IOWA STIFF STALK SYNTHETIC
1/9/97 44
1.44 2.88 4.32 5.76 7.20 8.64
0
5
10
15
20
25
30
35
Fre
qu
ency
1.44 2.88 4.32 5.76 7.20 8.64
0
5
10
15
20
25
30
35
Fre
qu
ency
1.44 2.88 4.32 5.76 7.20 8.64
0
5
10
15
20
25
30
35
Fre
qu
ency
Grain Yield Mg ha-1
BSSS(R)C0X
BSCB1(R)C0
BSSS(R)C5X
BSCB1(R)C5
BSSS(R)C11X
BSCB1(R)C11
X = 3.87
= 0.72ph
X = 5.01
= 0.73ph
X = 6.64
= 0.63ph
IOWA STIFF STALK SYNTHETIC
1/9/97 45
-4
-3
-2
-1
0
1
2
3
4
PC
A2
-4 -3 -2 -1 0 1 2 3 4PCA1
C0
C4
C7C9
C11
BSSS(R) BSCB1(R)
C0 C4
C7
C9
C11
IOWA STIFF STALK SYNTHETIC
1/9/97 46
0
10
20
30
40
50
60
70
80
90
Fre
qu
en
cy
0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0
Heterozygosity
Observed HeterozygosityExpected Heterozygosity
BSSS(R)C0
0
10
20
30
40
50
60
70
80
90
Fre
qu
en
cy
0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0
Heterozygosity
Observed HeterozygosityExpected Heterozygosity
BSSS Progenitors
0
10
20
30
40
50
60
70
80
90
Fre
qu
en
cy
0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0
Heterozygosity
Observed HeterozygosityExpected Heterozygosity
BSSS(R)C12
IOWA STIFF STALK SYNTHETIC
Heterozygosity
Population Observed Expected
Progenitors 0.01 0.59
C0 0.44 0.49
C12 0.31 0.34
1/9/97 47
IOWA CORN BORER SYNTHETIC #1
0
10
20
30
40
50
60
70
80
90
Fre
qu
en
cy
0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0
Heterozygosity
Observed HeterozygosityExpected Heterozygosity
BSCB1(R)C0
0
10
20
30
40
50
60
70
80
90
Fre
qu
en
cy
0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0
Heterozygosity
Observed HeterozygosityExpected Heterozygosity
BSCB1 Progenitors
0
10
20
30
40
50
60
70
80
90
Fre
qu
en
cy
0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0
Heterozygosity
Observed HeterozygosityExpected Heterozygosity
BSCB1(R)C12Heterozygosity
Population Observed Expected
Progenitors 0.05 0.61
C0 0.52 0.58
C12 0.30 0.32
1/9/97 48
BSSS(R)
BSCB1(R)
P
C12
P
C12
0.33
0.26
0.070.66
NEI’S GENETIC DISTANCE
1/9/97 49
GENE DIVERSITY
P
C12
C0
0.2
0.3
0.4
0.5
0.6
0.7
Gen
e d
iver
sity Total
Mean within
BSSS(R) and BSCB1(R)
1/9/97 50
Full-sib (FS) 5
Half-sib with Inbred Test. (HI) 4
Modified Ear-to-row (MER) 5
Mass selection (MASS) 10
Reciprocal Full-sib (FR) 5
S1 Progeny (S1) 5
S2 Progeny (S2) 4
Last Cycle Method Evaluated
BS11 SELECTION METHODS STUDY
1/9/97 51
FSFS BS11BS11 22 100 100 20 20 20 20
MERMER BS11BS11 22 100 100 20 20 20 20
HIHI B79B79 33 100 100 20 20 20 20
S2S2 BS11BS11 33 100 100 20 20 20 20
S1S1 BS11BS11 22 100 100 20 20 20 20
FRFR BS10BS10 22 175 175 20 20 11 11
MASSMASS BS11BS11 1 10000 1001 10000 100 1 1
CycleCycle # Progeny # Progeny Selection Selection Method Tester TimeMethod Tester Time Evaluated Evaluated ** Intermated Intermated Intensity Intensity
*Evaluations based on 2 Reps at 3 Locations
BS11 SELECTION METHODS STUDY
1/9/97 52
BS11 SELECTION METHODS STUDY
Grain Yield - Populations Per SeGrain Yield - Populations Per Se
00 11 22 33 44 554.64.6
4.84.8
5.05.0
5.25.2
5.45.4
5.65.6
5.85.8
Mg
ha
Mg
ha-1-1
CycleCycle
S2S2 MER
FR
S1S1
HIHI FS
MASS
ResponseResponse
S2S2 0.21**0.21** 4.54.5MERMER 0.17**0.17** 3.63.6FRFR 0.12**0.12** 2.62.6S1S1 0.09**0.09** 1.91.9HIHI 0.08**0.08** 1.61.6FSFS 0.07**0.07** 1.41.4MASSMASS 0.03**0.03** 0.60.6
Per Cycle %Per Cycle % RR22 = 0.83 = 0.83
1/9/97 53
BS11 SELECTION METHODS STUDYStalk Lodging - Populations Per SeStalk Lodging - Populations Per Se
00 11 22 33 44 558.08.0
10.010.0
12.012.0
14.014.0
16.016.0
18.018.0
20.020.0
22.022.0
%%
CycleCycle
ResponsResponsee
S2S2 -2.4** -2.4**MERMER -2.2** -2.2**FSFS -2.2** -2.2** HIHI -2.1** -2.1** S1S1 -2.0**-2.0** FRFR 0.0 0.0 MASSMASS 0.3** 0.3**
Per Cycle Per Cycle
S2S2MER
FR
S1S1
HIHI
FS
MASS24.024.0
RR22 = 0.85 = 0.85
1/9/97 54
ACKNOWLEDGEMENTS
Dr. Joanne LabateRoger WeyhrichJode EdwardsPeter GuzmanChris MackKebede MulatuJohn GoldenJim Sears
Dr. Arnel R. HallauerDr. Michael LeeDr. Howie SmithDr. Paul Scott
1/9/97 55
1860 1880 1900 1920 1940 1960 1980 2000Year
0102030405060708090
100110120130140150
Gra
in Y
ield
(b
u/a
c)
Open pollinatedOpen pollinatedb = -0.08b = -0.08
Double CrossesDouble Crossesb = 1.10b = 1.10
Single CrossesSingle Crossesb = 2.06b = 2.06
RR22 = 0.96 = 0.96
U.S. CORN YIELD - 1866 to 1996