Plant Breeding
Lecture 3
Objectives
Know essential terminology
 Know some examples of traits targeted by
breeding for genetic improvement of crops
 Understand the foundations of plant
breeding
 Know breeding techniques

Gamete
A mature reproductive cell that is
specialized for sexual fusion
Haploid (n)
Cells that have only one set of
chromosomes (n). Each gamete
is haploid
Cross
A mating between two
individuals, leading to the fusion
of gametes and progeny
Diploid (2n)
Cells with two copies of each
chromosome. The diploid state is
attained by the fusion of two
gametes
Zygote
The cell produced by the fusion
of the male and female gametes
Gene
The inherited segment of
DNA that determines a
specific characteristic in
an organism
Locus
The specific place on the
chromosome where a gene
is located
Alleles
Alternative forms of a gene
Genotype
The genetic
constitution of an
organism
Homozygous
An individual whose
genetic constitution
has both alleles the
same for a given
gene locus (i.e., AA
or aa)
An individual whose
genetic constitution
has different alleles
for a given gene
locus (i.e., Aa)
Heterozygous
Homogeneous
A population of individuals having
the same genetic constitution
(e.g., a field of pure-line soybean
or a field of hybrid corn)
Heterogeneous
A population of individuals having
different genetic constitutions
Phenotype
The physical manifestation of a
genetic trait that results from a
specific genotype and its
interaction with the environment
Trait goals
Yield = seeds, biomass, or fruit
size/number
 Quality traits, such as oil, flavor, color
 Stress tolerance, e.g., drought
 Insect and disease resistance
 Introgressing transgenes into plant
varieties

Yield
Figure 3.5 Yield of hybrid corn varieties versus year of release. Data were obtained
from Duvick and Cassman (1999), based on field experiments conducted at a plant
density of 79,000 plants per hectare at three locations in central Iowa in 1994.
Quality trait: oil quality
• Hydrogenation: flavor and oxidative stability
• Trans fats: health issues
• FDA label mandate
cis form
saturated
H H
H H
C C
trans form
H
Hydrogenation
C C
H H
;
C C
H
(Source: Wilson, 2004)
Environmental Stress Tolerance
Insect and disease
resistance
Soybean sudden death syndrome
Deployment of transgenic traits (e.g., transfer of
herbicide resistant genes in commercial varieties)
Foundations of plant breeding
Importance of genetic variation
and selection
What are the causes of biological
variation observed in plants?
1. Genetic causes (mode of inheritance)
 single genes
 multiple genes
2. Environmental
3. GxE: the interaction between the
genotype of the plant and the
environment in which it grows
Phenotype vs. Genotype
P = G + E + (GxE)
P is called the phenotypic value, i.e., the
measurement associated with a particular
individual
G is genotypic value, the effect of the genotype
(averaged across all environments)
E is the effect of the environment (averaged
across all genotypes)
Genetic variation: the basis for improvement
If we could measure P in all possible
environments and regard E as a
deviation, then the mean of E would be
The genotype responds more
zero and P = G.
strongly in some environments.
P1
Sets of environments tend to shift
E1
the trait value in one direction,
other environments in a different
direction.
P5
P2
E5
G
E4
P4
E2
E3
P3
Figure
3.8
Figure 3.8 In Sewall Wright’s
shifting balance theory, a
genotype or population is
defined by coordinates in Ndimensional space, and a
fitness value forms a surface
in the (N + 1)th-dimension.
Here, genotype coordinates
are defined in two
dimensions on the ground
beneath a mountainous
fitness surface (the third
dimension). The coordinates
of a given population can be
changed by selection, but
only in small increments.
Direct selection tends to
move a population toward
coordinates where fitness is
Methods and strategies: when
and why each is useful
Typically the goal is cultivar
production
How complex is selection?
• Qualitative traits, simple
inheritance, controlled by
major genes
• Quantitative traits, complex
inheritance controlled be
several gene loci
Qualitative traits

Classified into discrete classes

Individuals in each class counted

Some environmental influence on
phenotype

Controlled by a few (<3) major genes
Figure 2.3
Mendel’s seven traits showing simple inheritance
Often single gene traits
are easy to see or
measure, since
environment typically has
limited control over their
expression
Tawny (TT or Tt) versus gray (tt) single gene locus on soybean chromosome 6
Figure 2.4.
A. Monohybrid Cross
B. F1 Self Fertilization
Parent 1
Parent 2
Parent 1
YY
Y
yy
Y
Parent 2
X
X
Gametes:
=
y
Yy
Yy
y
F1 Fertilization:
Gametes:
Y
F2 Fertilization:
y
Y
Parent 1
Parent 1
Y
Y
Y
y
y
Yy
Yy
YY
Yy
y
Yy
Y
YY & Yy
Parent 2
Parent 2
Yy
F1 Hybrid Plants: 100% yellow
Yy
y
y
Yy
yy
F2 Plants: 75% yellow
25% green
yy
Gene and Genotype Frequencies
Example: Self pollinated diploid species
Upon selfing F2 population; 25% homozygous ‘YY’ will produce only ‘YY’
genotypes, and 25% homozygous ‘cc’ will produce only ‘yy’ genotypes. So
only ‘Yy’ will segregate to produce genotypes in proportion of 0.25 (YY):0.50:
(Yy):0.25(yy).
F2 population:
0.25(YY ) 0.50
(Cc) 0.25 (cc )
YY
0.25
Produce
all CC
plants
Resulting F3
population
will have
0.25 + ½ (0.25) =
0.375 CC plants
Yy
Yy
0.50
Segregate into
0.25(CC ) 0.50%
(Cc) and 0.25 (cc)
½ (0.50) = 0.25
Cc plants
yy
0.25
Produce
all cc
plants
½ (0.25) + (0.25)
= 0.375 cc plants
Heterozygosity reduced by half
in each selfing generation
YY
Yy
yy
F2
25%
50%
25%
F3
37.5%
25%
37.5%
F4
43.75%
F5
46.88%
F6
48.44%
F7
49.22%
F8
49.61%
12.5%
6.25%
43.75%
46.88%
48.44%
3.135
1.56
0.78%
49.22%
49.61%
When should
we select?
Questions based on F5 single plant derived
progeny rows from one population formed
from crossing two pure line parents:
Selfing a double het (AaBb × AaBb)
produces a 9:3:3:1 phenotypic ratio only if
trait governed by complete dominance
Freq Genotype
Phenotypic Ratio
Underlying
Genotypes
9
AABB = AABb =
AaBB = AaBb
1/16
AABB
2/16
AABb
1/16
AAbb
2/16
AaBB
3
AAbb = Aabb
4/16
AaBb
3
aaBB = aaBb
2/16
Aabb
1
aabb
1/16
aaBB
2/16
aaBb
1/16
aabb
Note: only 1 out of 16 is
homozygous favorable
allele for both gene loci
Selfing a double het (AaBb × AaBb)
produces 9 genotypic classes
Figure 3.1
Freq Genotype No. of CAP
alleles
1/16
AABB
4
2/16
AABb
3
1/16
AAbb
2
2/16
AaBB
3
4/16
AaBb
2
2/16
Aabb
1
Freq
No. of CAP
alleles
1/16
aaBB
2
1
0
2/16
aaBb
1
4
1
1/16
aabb
0
6
2
4
3
1
4
1
4 kg
4
6
4
5 kg
6 kg
7 kg
1
8 kg
Quantitative traits

Express continuous variation
(normal distribution)

Individuals measured, not counted

Significant environmental influence on
phenotype

Controlled by many minor (or major) genes,
each with small (or large) effects
X
aa, BB
(6 kg)
AA, bb
(6 kg)
Aa, Bb
(6 kg)
Self-pollinate
4 kg:
aa, bb
5 kg:
Aa, bb (x2)
aa, Bb (x2)
1
4 kg
6 kg:
Aa, Bb (x4)
AA, bb
aa, BB
Note: Consider upper
case letter represents
the favorable allele for
each gene
7 kg:
Aa, BB (x2)
AA, Bb (x2)
4
6
4
5 kg
6 kg
7 kg
1
8 kg
8 kg:
AA, BB
Histogram depicts
dominant genotype
effect with yield:
“capital” alleles (0,
1, 2Figure 3.1
Frequency distribution of seed yield for 187 different recombinant
inbred lines (RIL) in the soybean population 5601T x Cx1834-1-2
(Scaboo et al., 2009)
[no transgressive segregates for this trait in this population]
45
40
40
36
Cx1834-1-3
Frequency
35
5601T = 3252
32
28
30
25
19
20
14
15
10
10
5
5
2
1
0
1300
1500
1700
1900
2100
2300
2500
2700
2900
3100
Yield kg ha -1
High yielding low-phytate parental lines is the goal
Proportion of homozygous individuals after various generations of selfing,
for 1, 5, 10, 20 independently inherited gene pairs = [1-(½)G]L
Adapted from Allard, 1999
1.25
Proportion of
homozygous individuals
1
15/16
7/8
0.75
0.5
3/4
1/2
(15/16)20
0.25
0
0
(1/2)20
Then find the
better individuals
among the
homozygous
plants (those
accumulating the
greatest number
of superior
alleles). Can be
done with DNA
technologies and
progeny row
testing.
1
2
20
(7/8)
3
4
1-Gene
5-Genes
10-Genes
20-Genes
5
6
7
8
9
Generations of self-fertilization
10
11
12
(3/4)20
Even if 20 genes are involved, using the power of inbreeding 5 generations, over half
the proportion of individuals will be completely homozygous!
The effect of reproductive
behavior
Reproductive Behavior
Self
pollinated
Perfect
flower
- Pure line variety
- Hybrid variety
Cross pollinated
Monoecy
Dioecy
Vegetative
reproduction
Self-incompatible
- Synthetic variety – heterogeneous
population (not a pure line)
- Hybrid variety, if inbred
development is possible
No flowering/limited
flowering
• Clonal variety
• Hybrid
Figure
3.9
Figure 3.9 The pedigree breeding method is used in self-pollinated species to derive
pure-line varieties when it is desirable to practice selection in early generations.
Cultivar development for self-pollinated species:
pedigree method
Germplasm
Cultivar, local or exotic
landraces, wild relatives
Hybridization
Parents are usually inbred
F1 Nursery, all
plants heterozygous
Homogeneous population if
parents were inbred
F2 Nursery, all
plants heterozygous
Every single plant is a
different genotype
F3: head rows
Select the best rows, select
best plant within selected rows,
proceed to F4 head rows
This is typical pedigree method of selection in self-pollinated crop. Each
head row is called line. Most F6 or F7 lines are uniform enough for
preliminary yield testing
Cultivar development for self-pollinated species: bulk
method
Germplasm
Cultivar, local or exotic
landraces, wild relatives
Hybridization
Parents are usually inbred
F1 Nursery, all
plants heterozygous
Homogeneous population if
parents were inbred
F2 population, all
plants heterozygous
Collect equal amount of
seed from each plant
F3: bulk population
Repeat one or two more
generation, then follow head
rows
This is bulk method of breeding self-pollinated crop. Most F6 or F7 lines
are uniform enough for preliminary yield testing. This is less resource
consuming.
Figure
3.10
Figure 3.10 The single-seed descent (SSD) breeding method is used in self-pollinated
species to derive pure-line varieties when it is desirable to select from random
homozygous lines in an advanced generation.
Backcross breeding and recurrent selection
Figure 3.11 The backcross
breeding method is used to transfer
alleles at a small number of loci
from a donor parent into the genetic
background of a reciprocal parent.
Each generation of backcrossing
reduces the proportion of alleles
from the donor (D) parent by half
(), as shown on the right.
Used extensively in cross-pollinating crops
Figure 3.13 An example of a recurrent selection strategy with progeny testing. Many variations
on this type of strategy have been devised.
Figure 3.14 Schematic simplification of the development of a synthetic plant variety in an
outcrossing species. The Syn-1 generation is produced by random mating of reproducible
components (inbred lines or clones). If it is found to be desirable as a new plant variety, it can
be reproduced and sold by repeating the identical crossing block. This type of breeding
method is most practical in a perennial forage species. If adequate seed cannot be produced
in Syn-1 generation, the Syn-2 generation (harvested from Syn-1) may be used instead.
Figure 3.15 Schematic simplification of the development of a hybrid plant variety. In corn, the
parents (i.e., A, B, and C) are inbred lines that have been derived through other breeding
methods. In other crops, the parents may be clonally propagated. Parents are grown in
adjacent rows for crossing, and the female parent is emasculated so that it will not selfpollinate. Seed harvested from the female parent is tested in performance trials. If a hybrid
variety is successful, the cross is repeated on a large scale for commercial production.
With Traditional Backcross Breeding
F1
BC1F1
BC2F1
BC3F1
BC4F1
BC5F1
BC6F1
Year 1
50
75
87.5
93.5
96.9
98.4
99.2
%
%
%
%
%
%
% Year 7
Molecular markers allow visualization of genotypes
RR
rr
RR
Rr rr
RR
rr
rr
Gel electrophoresis of DNA markers:
we can now ‘see’ genotypes to
accelerate breeding cycles
Figure 3.17
Figure 3.17 Visualization of SNP markers on chromosome-1 for a set of soybean varieties. Each column represents a locus position on the
chromosome, and each row represents a different soybean variety. Most loci have two alternate alleles, which are colored to represent the
DNA base present in a homozygous state in the corresponding soybean variety. The predicted value of each allele is determined by testing a
reference population where phenotypes are known, A predicted genotypic value of each soybean variety is then derived as a summation of
predicted allele values, and varieties with the highest overall genotypic values are selected.
Other breeding methods
•Vegetative reproduction and
apomixis
•Mutation breeding
Summary
• Plant breeding mostly uses sexual crosses to recombine genes and
alleles in crops
• Goal: usually a cultivar with improved traits
• Selfing crops are improved using the pedigree method or bulk
methods, such as single-seed descent
• Recurrent selection and backcrossing is a useful tool, especially for
outcrossing crops
• Synthetic varieties and hybrids are the product of breeding
outcrossing species
• Mutation, vegetative cloning and apomixes are sometimes used in
breeding
• Marker assisted selection can speed up breeding cycles
Figure 3.17
Figure 3.17 Visualization of SNP markers on chromosome-1 for a set of soybean varieties. Each column represents a locus position on the
chromosome, and each row represents a different soybean variety. Most loci have two alternate alleles, which are colored to represent the
DNA base present in a homozygous state in the corresponding soybean variety. The predicted value of each allele is determined by testing a
reference population where phenotypes are known, A predicted genotypic value of each soybean variety is then derived as a summation of
predicted allele values, and varieties with the highest overall genotypic values are selected.