CS-461-Plant-breeding - Section 2

Genetic/Molecular/DNA Markers
 A genetic marker is any difference in DNA, no matter how it is

detected, whose pattern of transmission from generation to generation
can be tracked
 Each individual who carries the marker also carries a length

of chromosome (DNA) on either side of it
 They mark a particular region of the genome – landmarks in chromosomes
– like signposts along highways
 Any difference in DNA sequence between two individuals can serve as

a genetic marker
 Genetic markers that are detected by direct analysis of DNA are called DNA
• markers
 DNA markers allow position of genes controlling biological traits of

agricultural importance to be located on chromosomes (genome
mapping) and their DNA isolated, identified, and studied
1
CS 461: PLANT BREEDING
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Genetic Markers Cont’d
 Genetic markers represent genetic differences between
individual organisms or species
 All genetic markers occupy specific genomic positions within

• chromosomes (like genes) called ‘loci’ (singular ‘locus’).
 There are three major types of genetic markers:

(1)morphological (also ‘classical’ or ‘visible’) markers which
themselves are phenotypic traits or characters
(2)biochemical markers, which include allelic variants of

enzymes called isozymes
(3)DNA (or molecular) markers, which reveal sites of variation

in DNA CS 461: PLANT BREEDING 2
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Genetic Markers cont’d
 The major disadvantages of morphological and biochemical
markers are that they may be limited in number and are
influenced by environmental factors or the developmental
stage of the plant
DNA markers are the most widely used type of markers,

predominantly due to their abundance.
They arise from different classes of DNA mutations such as

substitution mutations (point mutations), re-arrangements
(insertions or deletions) or errors in replication of tandemly
repeated DNA
3
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Genetic Markers cont’d
Unlike morphological and biochemical markers, DNA
markers are practically unlimited in number and are
not affected by environmental factors and/or the
developmental stage of the plant
DNA markers are particularly useful if they reveal

differences between individuals of the same or
different species.
These markers are called polymorphic markers,

whereas markers that do not discriminate between
genotypes are called monomorphic markers
4
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Uses of Molecular Markers
 Markers to tag useful genes for marker-assisted
selection
 Identification and transfer of genes from wild species
to crops
 Assessment of genetic diversity in gene banks and
management of collections
 Selection of diverse parents for potential hybrids
 DNA fingerprinting to protect varieties from being
“pirated”
 Testing the purity of hybrid seed for quality control
5
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Assignment
 Write short notes on any six (6) types of molecular markers
6
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Advantages of Marker-Assisted
Selection
 Plant breeders try to choose the best plants from
segregating populations usually based on phenotype
(appearance). Sometimes the best looking plants do not
always have the best genes
 Marker-assisted selection (MAS) help breeders select
directly for good genes
 MAS works best for simply inherited traits, traits conditioned
by recessive genes, characters expressed late in the plant
life cycle, or where conventional selection is not possible
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BREEDING METHODS FOR SELF-POLLINATED
SPECIES
CS 461: PLANT BREEDING 8

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Mass Selection
 Mass selection in a heterogeneous population is the oldest
method of breeding in self-pollinated species.
 Mass selection regarded as method of increasing the
frequency of desirable genotypes during inbreeding in
populations developed by hybridization or artificial
mutagenesis.
 Mass selection is based on plant phenotype.
 It is most effective if the trait of interest has high heritability.
 It is applicable to both self- and cross-pollinated species,
provided there is genetic variation.
 Mass selection can be used for cultivar development or
purification
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Mass Selection…
Generalized steps in breeding by mass selection: (a) for cultivar

development and (b) for purification of an existing cultivar
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Mass Selection…
Merits:
 Wide adaptability: Since a large number is
selected, the composite variety is more stable in
performance over different environments as it is
more adapted than a single pure line.
 Less time and labor consuming
 Mass selection retains considerable genetic

variability, so another mass selection after few
years improves the variety
11
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Mass Selection Cont’d
Demerits:
To be most effective, the traits of interest should
have high heritability.
 Because selection is based on phenotypic values,

optimal selection is achieved if it is conducted in a
uniform environment.
Phenotypic uniformity is less than in cultivars

produced by pure line selection.
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Pureline Selection in Landraces
 The theory of the pure line was developed in 1903 by the Danish
botanist Johannsen.
 Studying seed weight of beans, he demonstrated that a mixed

population of self-pollinated species could be sorted out into
genetically pure lines.
 The lines were subsequently non-responsive to selection within

each of them
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Pureline Selection…
The development of the pure line theory by Johannsen

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Pure line Selection…
The pure-line selection in breeding involves repeated
cycles of selfing following the initial selection from a
mixture of homozygous lines.
Natural populations of self-pollinated species consist

of mixtures of homozygous lines with transient
heterozygosity originating from mutations and
outcrossing.
Developing a pure line from a landrace involves the

following steps:
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 The first step is to obtain a variable base population (e.g.,
introductions, segregating populations from crosses, land
race)
 Space plant it, select, and harvest desirable individuals
 Grow progeny rows of selected plants
 Rogue out any variants
 Harvest selected progenies individually
 Conduct preliminary yield trials for the selected progenies
and an appropriate check cultivars
 Conduct advanced yield trials at multilocations
 Release highest yielding line as new cultivar

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Pureline Selection…
Generalized steps in breeding by pure-line selection

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Merits:
 It is a rapid breeding method.
 The method is inexpensive to conduct. The base population
can be a landrace. The population size selected is variable
and can be small or large, depending on the objective.
 The cultivar developed by this method has great “eye
appeal” (because of the high uniformity of, e.g., harvesting
time, height, etc.).
 It is applicable to improving traits of low heritability, because
selection is based on progeny performance.
 In pure line selection, only the best pure line is selected for
maximum genetic advance.

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Demerits:
The cultivar has a narrow genetic base and, hence,
is susceptible to devastation from adverse
environmental factors because of uniform response.
 A new genotype is not created. Rather,
improvement is limited to the isolation of the most
desirable or best genotype from a mixed population.
The method promotes genetic erosion because
most superior pure lines are identified and
multiplied to the exclusion of other genetic variants.

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Single-Seed Descent
 The concept was first proposed by C.H. Goulden in 1941
 F1 plants from the cross between two parental lines are

allowed to naturally self-pollinate. The F2 seeds are grown,
the plants are self-pollinated and individual-plant selection is
conducted.
 A single F3 seed is harvested from each selected plant. F3

seeds are bulked and planted in the next season, and the
save-one-seed-per-plant procedure is repeated until the F4 or
F5 generation.
 Selfed seeds of individual F4 or F5 plants are saved

separately and are phenotyped in head rows.
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Single-Seed Descent…
Illustration of the procedure for the single-seed descent method

21
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Merits:
 It is an easy and rapid way to attain homozygosity (2–3
generations per year).
 Small spaces are required in early generations (e.g., can be
conducted in a greenhouse) to grow the selections.
 Natural selection has no effect (hence it can’t impose adverse
impact).
 The duration of the breeding program can be reduced by
several years by using single seed descent.
 Every plant originates from a different F2 plant, resulting in
greater genetic diversity in each generation.
22
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Demerits:
 Natural selection has no effect (hence no benefit from its
possible positive impact).
 Plants are selected based on individual phenotype not

progeny performance.
 Inability of seed to germinate or plant to set seed may prohibit

every F2 plant from being represented in the subsequent
population.
 The number of plants in the F2 is equal to the number of

plants in the F4. Selecting a single seed per plant runs the
risks of losing desirable genes.
23
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Pedigree Selection
Pedigree selection is a widely used method of
breeding self-pollinated species
F1 plants from a cross between two parental lines
are allowed to self-pollinate. The resulting F2 seeds
are also self-pollinated to produce F3 seeds. The F3
seeds are then planted in head rows.
Best F3 lines based on phenotypic measurements

are selected as a whole.
Selfed seeds (F4 ) are kept from one or more plants

judged as best within each selected row.
24
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Pedigree Selection…
All of F4 lines and sublines are grown in head
rows or progeny rows, the best rows are
selected, and seeds from the best few plants
within each selected row are harvested.
The procedure is repeated until the F6 or F7

generation.
Records are more extensive for pedigree

selection than for any other method of
inbreeding.
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Generalized steps in breeding by pedigree selection

26
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Merits:
 Record keeping provides a catalog of genetic information of
the cultivar unavailable from other methods.
 Selection is based not only on phenotype but also on
genotype (progeny row) making it an effective method for
selecting superior lines from among segregating.
 Using the records, the breeder is able to advance only the
progeny lines in which plants that carry the genes for the
target traits occur.
 A high degree of genetic purity is produced in the cultivar, an
advantage where such property is desirable (e.g., certification
of products for certain markets).
27
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Demerits:
Record keeping is slow, tedious, time consuming,
and expensive.
Pedigree selection is a long procedure, requiring

about 10–12 years or more to complete, if only one
growing season is possible.
28
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Backcross Breeding
 To initiate a backcross breeding program, the breeder
crosses the recurrent parent with the donor parent.
 The adapted and highly desirable parent is called the

recurrent parent in the crossing program, while the source
of the desirable gene missing in the adapted parent is
called the donor parent.
 The F1 is grown and crossed with the recurrent parent

again. The second step is repeated for as long as it takes to
recover the characteristics of the recurrent parent
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Backcross Breeding…
 This may vary from two to five cycles (or more in some
cases) depending on how much of the recurrent parental
genotype the breeder wants to recover, and the overall
acceptability of the donor parent.
 A selection pressure is imposed after each backcross to

identify and discard the homozygous recessive individuals.
 Where the desired trait is recessive, it will be necessary to

conduct a progeny test to determine the genotype of a
backcross progeny before continuing with the next cross.
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Generalized steps in breeding a recessive trait by the backcross method

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Generalized steps in breeding a dominant trait by the backcross

method
32
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Merits:
The method reduces the amount of field testing
needed, as the new cultivar will be adapted to the
same area as the original cultivar (especially true
when both parents are adapted).
 Backcross breeding is repeatable. If the same
parents are used, the same backcrossed cultivar can
be recovered.
It is useful for introgressing specific genes from wide
crosses.
It is applicable to breeding both self-pollinated and
cross-pollinated species.
33
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Demerits:
Backcrossing is not effective for transferring quantitative traits.
The trait should be highly heritable and readily identifiable in
each generation. However, the application of molecular
markers is helping to change the application of backcrossing to
improving quantitative traits.
The presence of undesirable linkages may prevent the cultivar

being improved from attaining the performance of the original
recurrent parent.
Recessive traits are more time consuming to transfer.
34
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Bulk Method
Bulk method is a strategy of crop improvement in
which natural selection effect is solicited more
directly in the early generations of the procedure
by delaying stringent artificial selection until later
generations.
The method was developed by H. Nilsson-Ehle in

1908.
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Bulk Method…
Generalized steps in breeding by bulk selection

36
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Bulk Method…
Merits:
It is simple and convenient to conduct.
It is less labor intensive and less expensive in early
generations.
Natural selection may increase frequency of
desirable genotypes by the end of the bulking period.
Bulk breeding allows large amounts of segregating
materials to be handled. Consequently, the breeder
can make and evaluate more crosses.
The cultivar developed would be adapted to the
environment, having been derived from material that
had gone through years of natural selection.
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Bulk Method…
Demerits:
Superior genotypes may be lost to natural selection, while
undesirable ones are promoted during the early generations.
Genetic characteristics of the populations are difficult to

ascertain from one generation to the next.
Genotypes are not equally represented in each generation

because all plants in one generation are not advanced to the
next generation. Improper sampling may lead to genetic drift.
The procedure is lengthy.
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Breeding Methods for Cross-pollinated
Species
 Breeding cross-pollinated crop rather focuses on the
improvement of the population rather than improvement of
the individual plants as in self-pollinated crops
 The breeding methods for cross-pollinated crops may be
grouped into two broad categories: (i) Population
improvement (ii) Hybrids and synthetic varieties
 A population is a large group of interbreeding individuals
 Application of principles and concepts in population genetics
are use to change the genetic structure of a population of
plants.
 The breeder’s goal is to change the gene frequency such
that desirable genotypes predominate in the population.

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Breeding Methods for Cross-pollinated
Species…
To improve the population, breeders generally
assemble germplasm,
- evaluate,
- self-selected plants,
- cross the progenies of the selected selfed plants in
all possible combinations, and
- Self to develop inbred lines from the populations.
Some of the common methods for breeding cross-
pollinated crops are:
- Mass selection
- Recurrent selection
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Recurrent Selection
 A cyclical and systematic technique where desirable individuals are

selected from a population and mated to form a new population. The
cycle is then repeated.
 The purpose of recurrent selection is to improve the performance of the

population with regard to the trait(s) of interest such that the population
will be superior to original population in mean performance.
 The success of recurrent selection depends on the genetic nature of

the starting population.

AWK/BA
Recurrent Selection…
Factors to be considered in the development of a
base population are:
i. The parents should have high performance

regarding the traits of interest and not closely
related
ii. Many parents should be included in the base
population to in crease genetic diversity
iii. More cycles of mating should done to increase the
opportunity for recombination

AWK/BA
A recurrent selection cycle consists of three
main phases:-
i. Individual families are created for evaluation.
Parents are crossed in all possible
combinations
ii. The plants are evaluated and a new set of
parents selected
iii. The selected parents are intermated to produce
the population for the next cycle of selection.
This pattern or cycle is repeated several times
(3-5)
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The first cycle is labeled C0, and it is called base
population. The subsequent cycles are named C1,
C2-----Cn.
The concept of recurrent selection

44
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Types of Recurrent Selection
Simple recurrent selection: This is similar to mass
selection with one or two years per cycle. The
procedure does not involve the use of a tester.
Selection is based on phenotypic scores. This
procedure is also called phenotypic recurrent
selection.
Recurrent selection for general combining ability:

This is a half-sib progeny test procedure in which a
wide genetic based genotype (e.g., a cultivar) is used
as a tester. The test cross performance is evaluated
in replicated trials prior to selection.
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Types of Recurrent Selection…
 Recurrent selection for specific combining ability: This
scheme uses an inbred line (narrow genetic base) for a tester.
The test cross performance is evaluated in replicated trials
before selection. This method is useful only for those
characters which have high heritability
 Reciprocal recurrent selection: This scheme is capable of

exploiting both general and specific combining ability. It
entails two heterozygous populations, each serving as a
tester for the other. Two genetically different populations are
altered to improve their crossbred mean. To achieve this,
individual plants from two populations (A and B) are selfed
and also crossed with plants from the reciprocal female tester
population (B and A, respectively).
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Synthetic Variety
A variety developed by selecting a number of inbred
lines with good GCA, intercrossing them in all
possible combinations and mixing the seeds of all
the crosses conducted, in equal quantity

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Breeding Methods for Clonal Crops
 Clonal Selection
Selection in an asexually propagated species involves
saving vegetative propagules (buds, stem cuttings,
corms, etc.) from individual plants.
Selection among clones on individual-plant basis is

first conducted for traits of high h2 on an individual-
plant basis.
The individual plants retained after selection are then

vegetatively propagated and subjected to rigorous
phenotyping as seen in pureline selection.
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Breeding Methods for Clonal Crops…
Example of clonal selection in an asexually propagated species

49
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Release and Distribution of
Cultivars

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Release and Distribution of Cultivars
National Variety Release and Registration Committee
(NVRC) is responsible the release and registration of
varieties in Ghana
At least two years on-station data, two years on-farm

data, consumer preference data, physicochemical
and economic analysis are required for the release of
a variety.
An application for the release of the variety is

submitted to the NVRC after all the required data for
the release of a variety have been assembled
CS 461: PRINCIPLES OF PLANT 51
BREEDING
Release and Distribution of Cultivars…
 The members of the NVRC visit the breeder seed field twice
during the growing season.
 The first visit is at the flowering stage and the second is at

harvesting.
 Based on these visits, the committee decides whether or not

the process for the release of the variety should go on.
 If the committee is happy with the performance of the variety

in the breeder seed plot, a date is fixed for a committee
meeting to consider the release of the variety.
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Release and Distribution of Cultivars
 The breeder of the candidate variety is responsible for the
presentation of the necessary data during the meeting of the
NVRC to support the release of the variety.
Variety release channel in Ghana

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Intellectual Property Rights
Intellectual property rights (IPRs) are the rights given
to persons over the creations of their minds. They
usually give the creator an exclusive right over the
use of his/her creation for a certain period of time.
The main purpose is to encourage and reward

creativity.

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Intellectual Property Rights for Crop
Varieties
 IPR for crop varieties also known as Plant breeders'
rights (PBR), or plant variety rights (PVR), are rights granted
to the developer (breeder) of a new crop variety that
guarantee the breeder exclusive control over the propagating
material and harvested material of the bred variety for a
specified number of years
 These rights empower the breeder to become the sole
marketer of the variety, or to license the variety to others
under contractual agreements
 Breeders can thus, bring suit to enforce their rights and can
recover damages for infringement on these rights
 Crop varieties, thus enjoy patent protection!
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Why is it important to protect new
crop varieties?
 Plant breeding takes a long time and expensive, BUT
 Plant varieties can be easily and quickly reproduced/multiplied

 Breeders need protection to recover investment
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UPOV
UPOV is an intergovernmental organisation based in
Geneva, Switzerland.
The acronym, UPOV, stands for Union for the
Protection of New Varieties of Plants.
The system came into being with the adoption of the
“International Convention for the Protection of New
Varieties of Plants” by a Diplomatic Conference in
Paris on December 2, 1961.
Gave birth to the international recognition of the IPR
of Plant Breeders.
UPOV
The objective: To provide and promote an effective
system of plant variety protection, with the aim of
encouraging the development of new varieties of
plants, for the benefit of society.
The UPOV Convention provides the basis for

members to encourage plant breeding by granting
breeders of new plant varieties an intellectual
property: THE PLANT BREEDERS’ RIGHT.
Membership of UPOV: Africa Details
 ARIPO (African Regional Intellectual Property
Organisation)
 Has 18 member countries predominantly English
speaking.
 Headquarters is in Harare, Zimbabwe.
 ARIPO Protocol for the Protection of New Varieties of
Plants was adopted by its Diplomatic Conference in
Arusha Tanzania in July, 2015.
 This is based on UPOV’91 framework, but ARIPO is not
yet a member of UPOV.
 Ghana is among the countries that have signed this
Protocol.
 Ghana signed in Dec. 2015.
Guidelines for Seeking PBR (Under
UPOV 1991 Act)…
New (Novelty): To be eligible for protection, a
variety must not have been sold, or otherwise
disposed of, in the territory of the member of the
Union concerned for more than one year prior to the
application for a breeders’ right, or more than four
years (six years for trees or vines) in a territory other
than that of the member of the Union in which the
application has been filed.
UPOV 1991 Act)…
Distinct (Distinctness): A variety is deemed to
be distinct if it is clearly distinguishable from any
other variety whose existence is a matter of
common knowledge at the time of filing of the
application.
Uniform (Uniformity): A variety is deemed to be

uniform if, subject to the variation that may be
expected from the particular features of its
propagation, it is sufficiently uniform in its relevant
characteristics.
UPOV 1991 Act)…
The new plant must Uniformity means the
be distinct from plants must display
other available homogeneity in the
varieties field
62
Guidelines for seeking PBR (Under
UPOV 1991 Act)
 Stable (Stability): A variety is deemed to be stable if its
relevant characteristics remain unchanged after repeated
propagation or, in the case of a particular cycle of
propagation, at the end of each such cycle.
 The grant of protection shall not be subject to any further

conditions.
 UPOV provides the necessary guidelines for the

examination of the DUS characteristics to its members.
UPOV 1991 Act)…
Stability
64
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Genetic/Molecular/DNA Markers

 A genetic marker is any difference in DNA, no matter how it is

 Each individual who carries the marker also carries a length

 Any difference in DNA sequence between two individuals can serve as

 DNA markers allow position of genes controlling biological traits of

 All genetic markers occupy specific genomic positions within

 There are three major types of genetic markers:

(2)biochemical markers, which include allelic variants of

(3)DNA (or molecular) markers, which reveal sites of variation

DNA markers are the most widely used type of markers,

They arise from different classes of DNA mutations such as

DNA markers are particularly useful if they reveal

These markers are called polymorphic markers,

CS 461: PLANT BREEDING 8

Generalized steps in breeding by mass selection: (a) for cultivar

 Less time and labor consuming

 Mass selection retains considerable genetic

 Because selection is based on phenotypic values,

Phenotypic uniformity is less than in cultivars

 Studying seed weight of beans, he demonstrated that a mixed

 The lines were subsequently non-responsive to selection within

The development of the pure line theory by Johannsen

Natural populations of self-pollinated species consist

Developing a pure line from a landrace involves the

CS 461: PLANT BREEDING 16

Generalized steps in breeding by pure-line selection

CS 461: PLANT BREEDING 18

CS 461: PLANT BREEDING 19

 F1 plants from the cross between two parental lines are

 A single F3 seed is harvested from each selected plant. F3

 Selfed seeds of individual F4 or F5 plants are saved

Illustration of the procedure for the single-seed descent method

 Plants are selected based on individual phenotype not

 Inability of seed to germinate or plant to set seed may prohibit

 The number of plants in the F2 is equal to the number of

Best F3 lines based on phenotypic measurements

Selfed seeds (F4 ) are kept from one or more plants

The procedure is repeated until the F6 or F7

Records are more extensive for pedigree

Generalized steps in breeding by pedigree selection

Pedigree selection is a long procedure, requiring

 The adapted and highly desirable parent is called the

 The F1 is grown and crossed with the recurrent parent

 A selection pressure is imposed after each backcross to

 Where the desired trait is recessive, it will be necessary to

Generalized steps in breeding a recessive trait by the backcross method

Generalized steps in breeding a dominant trait by the backcross

The presence of undesirable linkages may prevent the cultivar

Recessive traits are more time consuming to transfer.

The method was developed by H. Nilsson-Ehle in

Generalized steps in breeding by bulk selection

Genetic characteristics of the populations are difficult to

Genotypes are not equally represented in each generation

The procedure is lengthy.

CS 461: PLANT BREEDING 39

 A cyclical and systematic technique where desirable individuals are

 The purpose of recurrent selection is to improve the performance of the

 The success of recurrent selection depends on the genetic nature of

CS 461: PLANT BREEDING 41

i. The parents should have high performance

CS 461: PLANT BREEDING 42

The concept of recurrent selection