Plant Breeding –
an Overview
Objective 1: know basic plant
genetics and breeding
terminology
Gamete
A mature reproductive cell that is
specialized for sexual fusion
Haploid (n)
Containing only one set of
chromosomes (n). Each gamete
is haploid
Cross
A
mating
between
two
individuals, leading to the fusion
of gametes
Diploid (2n)
Two copies of each type of
chromosome in the nuclei,
formed 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 (eg, AA)
Heterozygous
An individual whose
genetic constitution
has different alleles
for a given gene
locus (eg, Aa)
Homogeneous
A population of individuals having
the same genetic constitution (eg,
a field of pure-line soybean; 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
What is Plant Breeding?

The genetic adjustment of plants to the
service of humankind
---Sir Otto Frankel
Source: http://www.ars.usda.gov/is/graphics/photos/
Objective 2: know why plant
breeding is important and useful
Several examples in soybean
Why Plant Breeding
Increased global human population (shown here in billions of people)
will lead to increased demand for food, fiber and energy: improving
plant genetics is one tool
10
9
8
7
6
5
4
3
2
1
0
1950
1970
1990
2010
2030
2050
Adapted from http://www.census.gov/population/popclockworld.html
Plant
Breeding
Targets
1. Yield
Source: USB photo disc 0976
Plant breeding
has contributed
to more than
50% of increased
USA crop
productivity
during the last 30
years
Source: http://www.ars.usda.gov/is/graphics/photos/
Plant Breeding Targets
Improved product quality
Source: http://www.ars.usda.gov/is/graphics/photos/
• 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)
Plant Breeding Targets
3. Pest and Disease Resistance
Soybean sudden death syndrome
Joint Germplasm Release
(Drs. Arelli, Pantalone, Allen, Mengistu)
USDA-ARS and
Tennessee Agricultural Exp. Stn.
Release of JTN-5303 Soybean
Resistant to multiple diseases:
Soybean cyst nematode
Sudden death syndrome
Stem canker
Frogeye leaf spot
Charcoal rot
Plant Breeding Targets
4. Environmental Stress Tolerance
Plant Breeding Targets
5. Ease of Management
Deployment of transgenic traits (e.g., transfer of
herbicide resistant genes in commercial varieties)
Plant Breeding Targets
6. Adaptation to Mechanization
Source: http://www.ars.usda.gov/is/graphics/photos/
Plant Breeding Targets
7. Environmental sustainability
Conservation Tillage
Source: http://www.ars.usda.gov/is/graphics/photos/
Objective 3: know the basic
principles 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
A plant breeder needs to:
be observant of phenotypic
differences among plants
 understand the genetics
 have the imagination to visualize final
product
 foresight to predict demand for future
plant products

Plant selections to improve plant traits
are made by assessing plant phenotypes

In plants, examples include:
 plant
height
 plant and leaf morphology
 biomass yield
 seed yield
 chemical composition of plant tissues and
seeds
Genetic variation: the basis for improvement
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)
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
Cultivar Breeding: A Recurrent procedure
Utilization of
Germplasm Resources
Release of New
Improved Variety
Development of
Genetically Diverse Populations
Vigorous Yield Testing
Controlled Cross Pollination
Parent 1 × Parent 2
Stigma
Objective 4: know some basic
plant breeding methods and
strategies
How do we breed improved
crop cultivars?
1.Inheritance of trait
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 2.4
Mendel’s seven traits showing simple inheritance
Source: Halfhill and Warwick, 2008, Chapter 3, in C.N. Stewart, Jr. (ed.),
Available: http://www.wiley.com/WileyCDA/WileyTitle/productCd-0470043814.html
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 2.5.
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
Yy
y
Y
Yy
yy
F2 Plants: 75% yellow
yy
25% green
Source: Halfhill and Warwick, 2008, Chapter 3, in C.N. Stewart, Jr. (ed.),
Available: http://www.wiley.com/WileyCDA/WileyTitle/productCd-0470043814.html
F1 Hybrid Plants: 100% yellow
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
Source: Tinker, 2008, Chapter 3, in C.N.
Stewart, Jr. (ed.), Available:
http://www.wiley.com/WileyCDA/WileyTitle/
productCd-0470043814.html
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, 2,Figure
3, 4) 3.1
Source: Tinker, 2008, Chapter 3, in C.N. Stewart, Jr. (ed.),
Available: http://www.wiley.com/WileyCDA/WileyTitle/productCd-0470043814.html
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 is involved, using the power of inbreeding 5 generations, over half
the proportion of individuals will be completely homozygous!
How do we breed
improved crop cultivars?
2. Understand 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
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.
Cultivar development for cross-pollinated
species: recurrent phenotypic selection
Repeat cycle
Starting population cycle 0 (C0)
Select best plants (phenotypes)
Polycross selected plants
Eliminate unselected,
intercross selected &
harvest seed & bulk
Harvest seeds
from selected
plants & bulk
-
Produce cycle-1 (C1) seeds
-
Space-plant C1 population, select
the best plant (with respect to
target trait)
Field testing of seed in each cycle
Cultivar development for cross-pollinated species: recurrent
phenotypic selection, continued
Repeat cycle
Phenotypic selection
Progeny evaluation
- Genotypic selection among families
- Selection among-and-within families
Select superior
genotypes of
superior families
Select parents
producing
superior families
Intermate selected genotypes
Multilocation yield test
Synthetic seed production
Field testing of new synthetics:
evaluation
How cultivar development
can be accelerated
One method: backcross
breeding
With Traditional Backcross Breeding:
F1
BC1F1
BC2F1
BC3F1
BC4F1
BC5F1
BC6F1
2000
50
75
87.5
93.5
96.9
98.4
99.2
%
%
%
%
%
%
%
TN Line
TN Line
TN Line
TN Line
TN Line
TN Line
TN Line
2006 – just a few pods produced
Molecular markers allow visualization of genotypes
RR
rr
RR
Rr rr
RR
rr
rr
Gel electrophoresis of DNA markers:
we can now ‘see’ genotypes
Molecular genetic markers can accelerate
breeding with fewer generations needed
F1
BC1F1
BC2F1
BC3F1
50
80+
98+
99+
%
%
%
%
TN Line
TN Line
TN Line
TN Line
2002
2003 winter plant-row increase
2004 TN yield tests & re-selections:
2005 harvest 100+ bushels 5601T-RR
Phytate quantitative trait loci (Walker et al. 2006) now with
confirmed quantitative trail locus (QTL) designations (Scaboo et al., 2009)
LG L
♦ LG N Pha-001
Pha-002
Satt156
Satt530
Maximum
LOD: 6.4
Maximum
LOD: 25.5
2
2
R : 13%
R : 40%
Satt527
Satt387
Satt561
Sat_236
Satt229
10 cM
Satt339
Satt237
GMABAB
Satt373gs
Sat_091
10 cM
2008 phytate yield trial
33 new BC lines
Less agronomic
QTL for HT
QTL for MAT
a
BU/A
56
57.4 a
53.6
52
48
44
40
42.2 b
BC1
BC4
5601T
Biotechnology can be used
to improve crop cultivars?
3. Transgenic varieties
Source: http://en.wikipedia.org/wiki/Gm_crops
IMPACT
For every 1 bushel/acre increase in production,
largely through genetic gain,
increased income to
TN soybean producers of
15 Million $ annually
5601T
UT AgResearch soybean at Obion, TN
USG Allen #1 and better than average in every county
Yields of 18 Maturity Group V Roundup Ready soybean varieties in 9 County
Standard Tests in TN and KY during 2007.
MS
Brand/Variety
AvgYld
Moist
Carl
Dyer
Gibs 1
Gibs 2
Hayw
Laud
MREC
Obio
Weak
bu/a
%
planted 5/26
5/21
6/18
5/14
5/17
5/22
5/15
6/7
5/23
41.3
16.0
63.1
53.0
37.0
41.1
32.2
29.7
33.5
35.6
46.1
A
*USG Allen
AB
Delta King DK52K6
40.0
15.3
62.4
49.7
40.1
30.1
30.7
35.7
27.2
36.4
47.4
AB
***Delta King DK5567
39.9
16.0
67.4
50.5
34.1
37.8
34.5
33.6
27.4
34.2
39.9
ABC
**Armor 54-03
39.2
13.9
61.6
52.5
31.0
25.7
28.1
34.6
27.1
30.8
61.8
ABC
Ag Genetics South AGS 568
38.2
15.8
56.5
41.0
44.3
34.7
33.9
35.0
28.5
35.2
34.9
ABC
Dyna-Gro 33X55
38.0
15.6
56.7
51.6
33.2
34.1
26.4
31.5
26.5
37.6
44.8
BCD
**Dyna-Gro 33B52
35.6
13.3
56.7
46.0
36.5
22.8
26.5
33.5
28.4
27.8
42.1
CD
Pioneer 95M30
35.4
15.1
51.4
47.2
31.1
23.2
31.7
29.8
19.2
31.7
53.3
CD
Schillinger 557RC
35.3
15.2
56.9
54.1
41.0
17.3
21.5
30.0
23.9
31.9
41.3
DE
Stine 5482-4 RR/STS
33.3
15.4
54.1
47.8
39.1
22.3
20.4
28.7
24.4
31.7
31.3
EF
Vigoro V51N7RS
30.3
14.3
45.3
42.7
30.8
16.9
20.8
29.5
24.6
30.1
32.4
EFG
FFR 5116
30.2
14.1
46.5
37.8
30.1
18.2
29.2
27.8
20.6
34.3
27.3
EFG
Armor 52-U2
29.9
14.0
50.9
44.2
27.2
18.8
16.4
29.4
18.4
30.2
33.6
EFG
Dairyland 8512
29.7
14.6
44.5
37.8
30.8
19.0
19.3
27.1
19.5
31.3
38.5
FG
Progeny 5115
28.5
13.5
50.6
37.8
33.6
18.8
14.5
22.6
15.7
28.3
34.2
FG
Deltapine DP5115 RR/S
26.8
13.5
48.2
27.5
30.0
15.0
17.9
25.9
18.3
30.3
28.5
FG
Delta King DK5066
25.9
14.1
53.6
27.5
27.4
15.1
10.1
19.2
12.1
34.5
33.4
G
Dairyland 8509
25.8
13.6
54.0
21.8
34.2
16.1
14.6
25.9
14.9
26.0
24.6
33.5
14.6
54.5
42.8
34.0
23.7
23.8
29.4
22.8
32.1
38.6
Average (bu/a)
+7.8
+8.6 +10.2
+17.4 +8.4
+10.7
+7.5
For the plant breeder patience is a
virtue
…when working with new genetics
Key points
Know basic terminology in transmission
genetics and plant breeding
 Understand the goals of plant breeding
 Know plant reproductive syndromes, e.g.,
self-fertilization, and how they effect
breeding methods
