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Choice of Parental Germplasm and Population Formation
The breeding method ultimately implemented is irrelevant if the
necessary genetic variation and overall level of adaptation and
yield have not been built into the population upon which you
impose selection.
• Knowledge of the evolution of the genus, plus a classification
of the
cultivated species and its relatives.
• A comprehensive history of cultivar development in the
species.
• Knowledge of the biotic and abiotic stresses found in your
target environments and their relative levels of importance to crop
production.
• Knowledge of the germplasm resources available. Of particular
importance is their adaptation to your target environments.
Classification of the cultivated species and its relatives
Variation patterns in cultivated plants can be very different from
those of wild species. Taxonomists have traditionally spent little time
on cultivated species, and those who did may have reached
remarkably different conclusions, even when working with the same
materials
For example, broccoli, brussel sprouts, cabbage and cauliflower
are grossly different morphologically but they are in the same
species in a biological sense--i.e., they can be crossed and the
hybrids are fertile.
Frustrated with this sort of vacillation and indecision among
taxonomists who cannot agree on species limits, breeders
have adopted Harlan and deWet’s more informal and intuitive
classifications as to what constitutes useful groupings based
on practical experience.
Harlan and deWet’s Gene Pool System
Informal genetic
perspective
Primary gene pool:
Biological species
Secondary gene pool :
Allele transfer a
struggle
Tertiary gene pool:
Outer limit of potential
genetic reach.
Every other plant and
animal?
A Comprehensive History of Cultivar Development in the
Species
The in-depth compilations published in the United States Department
of Agriculture Yearbooks of 1936 and 1937 provide a valuable starting
point for many species.
Species monographs published by The American Society of
Agronomy and similar organizations.
Pedigrees and methodologies utilized in cultivar development in a
diverse range of species can be found in Registration articles in
the journal Crop Science.
Biotic and Abiotic Stresses in Your Target Area
Resistance, or tolerance to all economically important biotic and
abiotic stresses must be incorporated into breeding populations
constructed for cultivar development. Although a thorough
knowledge of all the stresses that are found in your target areas is
vital, one needs to be aware of economic thresholds and the
frequency of occurrence of each stress when priorities are being
decided.
Life cycles - sexual or asexual - Races or Biotypes - virulence changes
(e.g. powdery mildew in wheat) - host resistance quantitative or
qualitative - - average life of qualitative allele – pyramids available effective alleles (Cereal Disease Lab)
Rust race
Attacks
Am I in trouble?
Cereal Disease Lab
USDA / U. Minn.
Track virulence
patterns of rust fungi
Isoline series?
Each isoline contains
a major gene in a
common genetic
background
Recessive
Knowledge of Available Germplasm Resources
An overwhelming majority of all germplasm incorporated
into cultivar development breeding populations comes
from cultivated species adapted to your target
environment
Note: ‘Exotic germplasm’ refers to not just wild or progenitor
species, but to cultivated types adapted to different target
environments.
Step 1: Adapted/Exotic Cross. An adapted, high yielding
cultivar with excellent baking quality, but poor fungal resistance, is
crossed to an exotic cultivar with excellent fungal resistance but poor
baking quality characteristics. The fungal resistance is controlled
qualitatively, so the breeder is only seeking a single resistance allele
. The inbred progeny from this cross will contain some excellent
fungal resistance, but none will contain the required baking quality,
which is quantitatively controlled
Step 2:
Adapted/Exotic/2/Adapted Backcross.
Next the
breeder backcrosses the F1 to an adapted parent. A step in the right
direction, but still one is unlikely to recover inbred progeny with
acceptable baking quality.
Step 3: Adapted/Exotic/2/Adapted/3/Adapted Backcross.
Thus an extended backcrossing program (prebreeding or parent
building) is required.
In general, when unadapted, exotic parents must be
utilized to provide the necessary genetic variation the
order of preference will be:
1. Improved cultivars and breeding lines
2. Landraces or older cultivars
3. Closely related species
4. More distantly related species and genera
A List of Parents for Cultivar Development.
1. The Reliables/Anchors
They serve as ‘anchors’ to provide the breeding population with
overall adaptation and high yield potential.
2. Elite Germplasm.
These genotypes are important because they may contain new
combinations of alleles that are superior to the Reliables
described above.
3. Allele Sources for Specific Traits.
Consists of cultivars, breeding lines or germplasms that may or
may not be adapted to your target environments. Typically
contain pathogen resistance or novel physiological or
morphological characteristics. (http://www.ars-grin.gov/)
4. Remnant Single- and Two-Way Hybrids.
Remnant F1 hybrid seeds are found in most programs and can
serve as building blocks over many crossing seasons for
three- and four-way hybrid populations.
The Search for Alternative Methods of Parental
Selection
The approach whereby 'good by good' parental hybridizations are
made has shown time and again to have the highest probability of
producing superior progenies.
Breeders desire to increase the frequencies of parental
combinations that produce superior advanced generation lines.
The general objective of the studies is to measure the genetic
distance between all potential parents. By combining two parents
with high mean trait values and the maximum genetic distance,
one should be able to construct a breeding population that
maximizes the probability of containing high transgressive
segregates because the population mean would be high and the
trait would exhibit a broad genetic variance.
1. Coefficient of Parentage
A methodology that has received much attention is in-depth
pedigree analysis that measures the probability that two
parents have the same allele at any given locus (coefficient
of parentage).
2. Multivariate Analysis
 C3
Grain
yield
C2


C1
Heading date
The distance between the three cultivars on the plot is one measure
of their genetic distinctiveness, or genetic distance, based on the
traits grain yield and heading date.
Principal Component Analysis (PCA) Creates a new set of dimensions
(usually two or three) based on the best combination of the original set
of multiple dimensions. This permits the plotting of the cultivars in
two- or three-dimensional space to obtain estimates of genetic
distances between cultivars that are based on multiple variables
Bhatt (1973) conducted one of the original studies comparing the
use of multivariate analysis for selecting parents compared to the
conventional methods described above
Eleven parental combinations were made and he developed 27
random F4:5 progenies in each of the resulting 11 populations
•
Conventional basis, whereby parents were chosen on their
ability to complement weaknesses in each other.
•
Random basis, whereby parents were chosen at random.
This practice would be rare, for obvious reasons.
•
Multivariate analysis, whereby parents were chosen
on the basis of their genetic distance estimates.
•
Ecogeographical diversity, whereby parents were
chosen because they were adapted to different
ecogeographic zones. Such geographical diversity is a
reasonable index of genetic diversity.
Population number, basis on which parents were selected, estimated parental
divergence (rank), genetic variability among lines in cross (rank), and number of high
transgressive segregates for yield.
Rank
Basis for
Population parent selection
1
Parental
Mean
divergence1 yield
No. of
Variation
among lines
transgressive
segregates
1
Conventional
8
8
10
1
2
Conventional
10
11
8
0
3
Random
6
4
7
3
4
Random
11
7
11
0
5
M. Anal. – Distant
2
1
2
10
6
M. Anal. – Distant
1
6
1
9
7
M. Anal. – Close
5
10
6
4
8
M. Anal. – Close
7
9
9
2
9
M. Anal. – Close
9
3
5
0
10
Ecogeographical
4
5
4
7
11
Ecogeographical
3
2
3
5
all parental divergence estimates based on multivariate analysis
3. Molecular Markers
The development of marker technologies such as isozymes,
RFLPs, RAPDs, AFLPs, SSRs, etc., has provided the ability to
measure, not just infer, differences at the DNA level.
Heterotic groups are germplasm groupings, determined on the
basis of heterosis levels expressed in F1 progeny from crosses
between different parents.
The two most important heterotic groups in corn are Reid Yellow
Dent and Lancaster Sure Crop. One of the biggest selling hybrids
ever was the F1 from the cross between the inbreds B73 (a Reid type)
and MO17 (a Lancaster type).
Lee et al. (1989) examined the RFLP fingerprints of seven inbreds
and evaluated their F1 hybrids for yield in multienvironment tests.
Three of the inbreds were from the:
BSSS sub-set of the Reid group,
Three inbreds were from the:
C103 sub-set of the Lancaster group,
One inbred (B79) was of unknown heterotic group.
The more bands (alleles at RFLP loci) they had in common, the
closer their DNA structure.
Summary by heterotic group of hybrid yields, genetic distance between their inbred
parents, and number of heterozygous RFLP loci in F1 hybrids (after Lee et al., 1989).
Hybrid
combination
F1 hybrid
yield
Parental
F1 hybrid
genetic distance heterozygous loci
Mg ha-1
BSSS x BSSS
7.0
0.55
C103 x C103
6.9
0.64
44
8.6
0.79
68
BSSS x C103
BSSS x B79
7.4
C103 x B79
8.2
LSD (0.05)
0.8
0.72
0.77
33
56
65
Thus the RFLP data on inbreds and predictions for their crosses were
consistent with expectations based on known pedigrees.
These data suggest that B79 may be more closely related to BSSS
germplasm than C103 germplasm.
Burkhamer et al. (1998) utilized STS-PCR primer sets and AFLP
primer combinations to estimate genetic distances between 10
spring wheats.
They used this relationship data to predict genetic variance for
nine traits among 50 random F3:5 lines in 12 crosses involving the
parents.
The coverage of the genome was extensive in this study as 505
polymorphic bands were observed with the STS primers and an
additional 145 polymorphic fragments were observed with the
AFLPs.
Simple correlation between genetic variance and genetic distance based on
STS-PCR primer sets and AFLP primer combinations in 12 wheat populations
for nine traits.
Genetic distance based on
Trait
STS
AFLP
Tillers m-2
0.31
0.15
Plant height
0.33
0.22
Stem solidness
0.34
0.13
Grain yield
0.41
0.13
Test weight
0.44
0.34
Heading date
0.54
0.44
Maturity
0.56
0.20
Grain filling
0.54
0.55
Grain protein
0.50
0.36
The authors point out that one possible reason for this was that they
had no indication if any of the polymorphic markers were linked to
loci controlling any of the traits and that linkage relationships are
likely more important than absolute marker number.
The results seem to indicate that, for markers to be useful as
predictors, the effects of QTL 'alleles' linked to specific marker
alleles must be ascertained (Stuber et al., 1999).
Population Formation by Hybridization
Required reading: Chapter 12, Fehr, pp. 136-155.
Types of Crosses
•
•
•
•
Single cross
Three way cross
Four way cross
Complex cross
Single cross
• Easy to make good x good
• Choose parents to complement one another
• Choose parents from different “heterotic
groups”
• Some crops have many breeding targets
• Two parents unlikely to have all traits
Three Way Cross
• True or modified backcross
• Widely used in wheat
• Third parent is critical (50%)
Table 3. Summary of Percentage of Transgressive Segregates of RILs for Heading
Date (HD), Plant Height (PH), Grain Yie ld (GY) and Test Weight (TW) 1996-1998,
Lexington, KY
Set
Pedigree
1
T63 / Pionee r 2548 //
Madison
T63 / P2548
VA 85-54-290 / Karl // T441
VA 85-54-290 / Karl
SC 850236 / Karl // Pioneer
2510
SC 850236 / Karl
T63 / Pionee r 2548 //
Madison
T63 / P2548
VA 85-54-290 / Karl // T441
VA 85-54-290 / Karl
SC 850236 / Karl // Pioneer
2510
SC 850236 / Karl
2
3
1
2
3
Trait †
PH
GY
1996
<L.P. >H.P.
‡
0
4
1997
<L.P. >H.P.
1998
<L.P. >H.P.
0
20
0
23
3
0
0
0
10
0
0
45
0
0
5
0
0
2
71
12
0
0
59
18
0
5
30
23
0
0
8
0
0
13
63
0
0
0
11
0
13
0
0
0
0
0
0
0
0
0
0
0
0
4
0
5
0
0
0
2
0
2
15
0
0
0
0
0
0
0
---------1997----------
-------------1998----------
Set
Cross
Test
P
N Np P
N Np 1
Three-way
1
< 0.01
41
7
NS
41
12
Single
2
< 0.01
41
15
< 0.01
41
25
Three-way
3
< 0.01
30
14
NS
30
19
Single
4
NS
35
14
< 0.01
34
29
Three-way
5
NS
57
27
< 0.01
57
15
Single
6
< 0.01
57
21
< 0.01
57
20
2
3
Number of lines tested
Number of li nes exceeding parental mean
Four Way Cross
• Cross two single cross F1’s
• Not as successful as 3 way crosses in wheat
• One modification: Use two F1’s which
have one parent in common - same genetic
composition as 3 way, but increased
recombination
Complex Crosses
• > 4 parents
• See Fehr chapter 12 for methods of
combining parents
• Will discuss polycrosses with Dr. Phillips
Assessing Parental Value
• Can make crosses using parents to evaluate
their “combining ability”
• Typically we would cross parents in all
possible combinations - referred to as a
diallel
• Requires considerable time; most breeders
will not do this