Bio 309 - 0

NATIONAL OPEN UNIVERSITY OF NIGERIA
SCHOOL OF SCIENCE AND TECHNOLOGY
COURSE CODE :BIO 309
COURSE TITLE: PLANT BREEDING

BIO 309 PLANT BREEDING ( 1 unit)
Course outline: Importance of plant breeding, Cytological principles of breeding,

Heterosis, Inbreeding and its consequences, Incompatibility mechanisms, sterility,
Breeding methods, Disease and pest resistance and their inheritance, Major farm
and domestic plants and the practices used to sustain desired qualities.
COURSE UNITS: Plant breeding is the art and science of changing the traits of plants in
order to produce desired characteristics. Plant breeding can be accomplished through many
different techniques ranging from simply selecting plants with desirable characteristics for
propagation, to more complex molecular techniques. The course will cover the following
outline: -
1. Importance of plant breeding

2. Cytological principles of breeding
3. Heterosis
4. Inbreeding and its consequences
5. Incompatibility mechanisms
6. Sterility
7. Breeding methods
8. Disease and pest resistance and their inheritance
9. Major farm and domestic plants and the practices used to sustain desired
qualities
UNIT 1: IMPORTANCE OF PLANT BREEDING
1.0. INTRODUCTION
Plant breeding is the art and science of changing the genetics of plants in
order to produce desired characteristics. Plant breeding can be accomplished
through many different techniques ranging from simply selecting plants with
desirable characteristics for propagation, to more complex molecular
techniques. Plant breeding has been practiced for thousands of years, since
near the beginning of human civilization. It is now practiced worldwide by
individuals such as gardeners and farmers, or by professional plant breeders
employed by organizations such as government institutions, universities, crop-
specific industry associations or research centres.
2.0. Objective
 At the end of this unit, student should be clear of the importance of
plant breeding
 Should be able to define plant breeding terms
 Understands and differentiate between the conventional and the
modern plant breeding methods and
 Select plant breeding applications
3.0. History and developments of Plant Breeding
Intra-specific hybridization within a plant species was demonstrated by Charles

Darwin and Gregor Mendel, and was further developed by geneticists and plant
breeders. In the United Kingdom in the 1880s, it was the pioneering work of Gartons
Agricultural Plant Breeders. In the early 20th century, plant breeders realized that
Mendel's findings on the non-random nature of inheritance could be applied to
seedling populations produced through deliberate pollinations to predict the
frequencies of different types.
From 1904 to World War II in Italy NazarenoStrampelli created a number of wheat

hybrids. His work allowed Italy to increase hugely crop production during the so
called "Battle for Grain" (1925–1940) and some varieties was exported in foreign
countries, as Argentina, Mexico, China and others. After the war, the work of
Strampelli was quickly forgotten, but thanks to the hybrids he created, Norman
Borlaug was able to move the very first steps of the Green Revolution.
In 1908, George Harrison Shull described heterosis, also known as hybrid vigor.
Heterosis describes the tendency of the progeny of a specific cross to outperform
both parents. The detection of the usefulness of heterosis for plant breeding has led
to the development of inbred lines that reveal a heterotic yield advantage when they
are crossed. Maize was the first species where heterosis was widely used to
produce hybrids.
By the 1920s, statistical methods were developed to analyze gene action and
distinguish heritable variation from variation caused by environment. In 1933,
another important breeding technique, cytoplasmic male sterility (CMS), developed
in maize, was described by Marcus Morton Rhoades. CMS is a maternally inherited
trait that makes the plant produce sterile pollen. This enables the production of
hybrids without the need for labour intensive detasseling.
These early breeding techniques resulted in large yield increase in the United States
in the early 20th century. Similar yield increases were not produced elsewhere until
after World War II, the Green Revolution increased crop production in the developing
world in the 1960s.
After the World War II, a number of techniques were developed that allowed plant
breeders to hybridize distantly related species, and artificially induce genetic
diversity.
When distantly related species are crossed, plant breeders make use of a number of
plant tissue culture techniques to produce progeny from otherwise fruitless mating.
Interspecific and intergeneric hybrids are produced from a cross of related species or
genera that do not normally sexually reproduce with each other. These crosses are
referred to as Wide crosses. For example, the cereal triticale is a wheat and rye
hybrid. The cells in the plants derived from the first generation created from the cross
contained an uneven number of chromosomes and as result was sterile. The cell
division inhibitor colchicine was used to double the number of chromosomes in the
cell and thus allow the production of a fertile line.
Failure to produce a hybrid may be due to pre- or post-fertilization incompatibility. If

fertilization is possible between two species or genera, the hybrid embryo may abort
before maturation. If this does occur the embryo resulting from an interspecific or
intergeneric cross can sometimes be rescued and cultured to produce a whole plant.
Such a method is referred to as Embryo Rescue. This technique has been used to
produce new rice for Africa (NERICA), an interspecific cross of Asian rice
(Oryzasativa) and African rice (Oryzaglaberrima).
Hybrids may also be produced by a technique called protoplast fusion. In this case
protoplasts are fused, usually in an electric field. Viable recombinants can be
regenerated in culture.
Chemical mutagens like Ethyl Methyl Sulphonate and Di Methyl Sulphonate,

radiation and transposons are used to generate mutants with desirable traits to be
bred with other cultivars in a process called Mutation Breeding. Classical plant
breeders also generate genetic diversity within a species by exploiting a process
called somaclonal variation, which occurs in plants produced from tissue culture,
particularly plants derived from callus. Induced polyploidy, and the addition or
removal of chromosomes using a technique called chromosome engineering may
also be used.
When a desirable trait has been bred into a species, a number of crosses to the
favored parent are made to make the new plant as similar to the favored parent as
possible. Returning to the example of the mildew resistant maize being crossed with
a high-yielding but susceptible maize, to make the mildew resistant progeny of the
cross most like the high-yielding parent, the progeny will be crossed back to that
parent for several generations. This process removes most of the genetic
contribution of the mildew resistant parent. Conventional or classical breeding is
therefore a cyclical process.
With conventional breeding techniques, the breeder does not know exactly what
genes have been introduced to the new cultivars. Some scientists therefore argue
that plants produced by these methods should undergo the same safety testing
regime as genetically modified plants. There have been instances where plants bred
using conventional techniques have been unsuitable for human consumption, for
example the poison solanine was unintentionally increased to unacceptable levels in
certain varieties of potato through plant breeding. New potato varieties are often
screened for solanine levels before reaching the marketplace
4.0 Importance of Plant breeding
It is believed that breeding new crops is important for:

Ensuring food security by developing new varieties that are higher-yielding, resistant
to pests and diseases, drought-resistant or regionally adapted to different
environments and growing conditions and that have uniformity in maturity time and
other desirable qualities.
Plant breeding in certain situations may lead to the domestication of wild plants.
Domestication of plants is an artificial selection process conducted by humans to
produce plants that have more desirable traits than wild plants, and which renders
them dependent on artificial (usually enhanced) environments for their continued
existence. The practice is estimated to date back to about 9,000-11,000 years. Many
crops in present day cultivation are the result of domestication in ancient times,
about 5,000 years ago. In the past, domestication took a minimum of about 1,000
years and a maximum of about 7,000 years. Today, all of our principal food crops
are products of domesticated varieties. Almost all the domesticated plants used
today for food and agriculture were domesticated in centres of origin that have been
identified as centres that host a great diversity of closely related crop wild plants or
relatives, which today can also be used for improving modern cultivars by plant
breeding.
A plant whose origin or selection is due primarily to intentional human activity is

called a cultigen, and a cultivated crop species that has evolved from wild
populations due to selective pressures from traditional farmers is called a landrace.
Landraces, which can be the result of natural forces or domestication, are plants (or
animals) that are ideally suited to a particular region or environment. An example are
the landraces of rice, Oryzasativa subspecies indica, which was developed in South
Asia, and Oryzasativa subspecies japonica, which was developed in China and
subspecies glaberrima which is the African rice.
5.0. Conventional plant breeding
Conventional or Classical plant breeding uses deliberate interbreeding (crossing) of

closely or distantly related individuals to produce new crop varieties or lines with
desirable properties. Plants are crossbred to introduce traits/genes from one variety
or line into a new genetic background. For example, a mildew-resistant maize Zea
mays may be crossed with a high-yielding but susceptible maize, the goal of the
cross being to introduce mildew resistance without losing the high-yield
characteristics. Progeny from the cross would then be crossed with the high-yielding
parent to ensure that the progeny were most like the high-yielding parent in a
process called backcrossing. The progeny from that cross would then be tested for
yield and mildew resistance and high-yielding resistant plants would be further
developed. Plants may also be crossed with themselves to produce inbred varieties
for breeding.
Classical breeding relies largely on homologous recombination between

chromosomes to generate genetic diversity. The classical plant breeder may also
makes use of a number of in vitro techniques such as protoplast fusion, embryo
rescue or mutagenesis to generate diversity and produce hybrid plants that would
not exist in nature.
Traits that breeders have tried to incorporate into crop plants in the last 100 years
include:
i Increased quality and yield of the crop
ii Increased tolerance of environmental pressures (salinity, extreme

temperature, drought)
iii Resistance to viruses, fungi and bacteria
iv Increased tolerance to insect pests
v Increased tolerance of herbicides
6.0. Modern plant breeding
Modern plant breeding may use techniques of molecular biology to select, or in the
case of genetic modification, to insert, desirable traits into plants.
Modern facilities in molecular biology has converted classical plant breeding to

molecular plant breeding
6.1. Marker assisted selection
Sometimes many different genes can influence a desirable trait in plant breeding.
The use of tools such as molecular markers or DNA fingerprinting can map
thousands of genes. This allows plant breeders to screen large populations of plants
for those that possess the trait of interest. The screening is based on the presence or
absence of a certain gene as determined by laboratory procedures, rather than on
the visual identification of the expressed trait in the plant.
6.2. Reverse Breeding and Doubled Haploids (DH)
A method for efficiently producinghomozygous plants from heterozygous starting

plants which has all desirable traits. This starting plant is induced to produce doubled
haploid from haploid cells, and later on creating homozygous/doubled haploid plants
from those cells. While in natural offspring genetic recombination occurs and traits
can be unlinked from each other, in doubled haploid cells and in the resulting DH
plants recombination is no longer an issue. There, a recombination between two
corresponding chromosomes does not lead to un-linkage of alleles or traits, since it
just leads to recombination with its identical copy. Thus, traits on one chromosome
stay linked. Selecting those offspring having the desired set of chromosomes and
crossing them will result in a final F1 hybrid plant, having exactly the same set of
chromosomes, genes and traits as the starting hybrid plant. The homozygous
parental lines can reconstitute the original heterozygous plant by crossing, if desired
even in a large quantity. An individual heterozygous plant can be converted into a
heterozygous variety (F1 hybrid) without the necessity of vegetative propagation but
as the result of the cross of two homozygous/doubled haploid lines derived from the
originally selected plant.
6.3. Genetic modification
Genetic modification of plants is achieved by adding a specific gene or genes to a

plant, or by knocking down a gene with RNAi, to produce a desirable phenotype. The
plants resulting from adding a gene are often referred to as transgenic plants. If for
genetic modification genes of the species or of a crossable plant are used under
control of their native promoter, then they are called cisgenic plants. Genetic
modification can produce a plant with the desired trait or traits faster than classical
breeding because the majority of the plant's genome is not altered.
To genetically modify a plant, a genetic construct must be designed so that the gene
to be added or removed will be expressed by the plant. To do this, a promoter to
drive transcription and a termination sequence to stop transcription of the new gene,
and the gene or genes of interest must be introduced to the plant. A marker for the
selection of transformed plants is also included. In the laboratory, antibiotic
resistance is a commonly used marker: Plants that have been successfully
transformed will grow on media containing antibiotics; plants that have not been
transformed will die. In some instances markers for selection are removed by
backcrossing with the parent plant prior to commercial release.
The construct can be inserted in the plant genome by genetic recombination using
the bacteria Agro bacteriumtumefaciens or A. rhizogenes, or by direct methods like
the gene gun or microinjection. Using plant viruses to insert genetic constructs into
plants is also a possibility, but the technique is limited by the host range of the virus.
For example, Cassava mosaic virus (CMV) only infects cassava and related species.
Another limitation of viral vectors is that the virus is not usually passed on to the
progeny, so every plant has to be inoculated.
The majority of commercially released transgenic plants are currently limited to

plants that have introduced resistance to insectpests and herbicides. Insect
resistance is achieved through incorporation of a gene from Bacillus thuringiensis
(Bt) that encodes a protein that is toxic to some insects. For example, the cotton
bollworm, a common cotton pest, feeds on Bt cotton it will ingest the toxin and die.
Herbicides usually work by binding to certain plant enzymes and inhibiting their
action. The enzymes that the herbicide inhibits are known as the herbicides target
site. Herbicide resistance can be engineered into crops by expressing a version of
target site protein that is not inhibited by the herbicide. This is the method used to
produce glyphosate resistant crop plants. Genetic modification of plants that can
produce pharmaceuticals (and industrial chemicals), sometimes called pharmacrops,
is a rather radical new area of plant breeding.
6.4. Issues and concerns on modern plant breeding
Modern plant breeding, whether classical or through genetic engineering, comes with
issues of concern, particularly with regard to food crops. The question of whether
breeding can have a negative effect on nutritional value is central in this respect.
Although relatively little direct research in this area has been done, there are
scientific indications that, by favoring certain aspects of a plant's development, other
aspects may be retarded. A study published in the Journal of the American College
of Nutrition in 2004, entitled Changes in USDA Food Composition Data for 43
Garden Crops, 1950 to 1999, compared nutritional analysis of vegetables done in
1950 and in 1999, and found substantial decreases in six of 13 nutrients measured,
including 6% of protein and 38% of riboflavin. Reductions in calcium, phosphorus,
iron and ascorbic acid were also found. The study, conducted at the Biochemical
Institute, University of Texas at Austin, concluded in summary: "We suggest that any
real declines are generally most easily explained by changes in cultivated varieties
between 1950 and 1999, in which there may be trade-offs between yield and nutrient
content."
The debate surrounding genetically modified food during the 1990s peaked in early
2000 in terms of media coverage and risk perception, and continues today - for
example, "Germany has thrown its weight behind a growing European mutiny over
genetically modified crops by banning the planting of a widely grown pest-resistant
corn variety.".The debate encompasses the ecological impact of genetically modified
plants, the safety of genetically modified food and concepts used for safety
evaluation like substantial equivalence. Such concerns are not new to plant
breeding. Most countries have regulatory processes in place to help ensure that new
crop varieties entering the marketplace are both safe and meet farmers' needs.
Examples include variety registration, seed schemes, regulatory authorizations for
GM plants, etc.
Plant breeders' rights are also a major and controversial issue. Today, production of
new varieties is dominated by commercial plant breeders, who seek to protect their
work and collect royalties through national and international agreements based in
intellectual property rights. The range of related issues is complex. In the simplest
terms, critics of the increasingly restrictive regulations argue that, through a
combination of technical and economic pressures, commercial breeders are
reducing biodiversity and significantly constraining individuals (such as farmers) from
developing and trading seed on a regional level. Efforts to strengthen breeders'
rights, for example, by lengthening periods of variety protection, are on-going.
When new plant breeds or cultivars are bred, they must be maintained and
propagated. Some plants are propagated by asexual means while others are
propagated by seeds. Seed propagated cultivars require specific control over seed
source and production procedures to maintain the integrity of the plant breeds
results. Isolation is necessary to prevent cross contamination with related plants or
the mixing of seeds after harvesting. Isolation is normally accomplished by planting
distance but in certain crops, plants are enclosed in greenhouses or cages (most
commonly used when producing F1 hybrids.)
7.0Steps of Plant Breeding
The following are the major activities of plant breeding;
i Creation of variation
ii Selection
iii Evaluation
iv Release
v Multiplication
vi Distribution of the new variety
8.0. Participatory Plant Breeding
The development of agricultural science, with phenomenon like the Green

Revolution arising, have left millions of farmers in developing countries, most of
whom operate small farms under unstable and difficult growing conditions, in a
precarious situation. The adoption of new plant varieties by this group has been
hampered by the constraints of poverty and the international policies promoting an
industrialized model of agriculture. Their response has been the creation of a novel
and promising set of research methods collectively known as participatory plant
breeding. Participatory means that farmers are more involved in the breeding
process and breeding goals are defined by farmers instead of international seed
companies with their large-scale breeding programs. Farmers' groups and NGOs, for
example, may wish to affirm local people's rights over genetic resources produce
seeds themselves, build farmers' technical expertise, or develop new products for
niche markets, like organically grown food.
9.0 summary
i) Plant breeding ensure food security by developing new varieties that are
higher-yielding, resistant to pests and diseases,
ii) Drought-resistant or regionally adapted to different environments and growing
conditions can be established through
iii) With plant breeding crops uniformity in maturity time and other desirable
qualities can be selected.
iv) Plant breeding in certain situations may lead to the domestication of wild
plants.
10.0 Conclusion
Plant breeding can increasedquality and yield of the crops through the
following:i) Increased tolerance of environmental pressures (salinity,
extreme temperature, drought)
ii) Resistance to viruses, fungi and bacteria
iii) Increased tolerance to insect pests
iv) Increased tolerance of herbicides
11.Self-assessment Assignments
a Why is plant breeding important?
b Explain the role of GMOs in modern plant breeding
c Why is participatory plant breeding important?

12. Tutor marked assignment:
a What are the objectives of plant breeding?
b Differentiate between traditional and modern plant breeding.
References
1. Chahal, G.S and Gosal, S.S., 2002. Principles and procedures of Plant
Breeding, Alpha Science International, United Kingdom.
2. Kwon-Ndung, E.H. 2008. Genetics for degree students. Afaku Publishers,
Abuja.
3. Holsinger, K.E., 2000. Reproductive systems and evolution in vascular plants.
PNAS. June 20, vol. 97, no. 13: 7037-7042.
4. Kohli, M.M. and Francis, M., 2000. Application of biotechnologies to wheat
breeding. Proceedings of a conference at La Estanzuela, Uruguay, November
19–20, 1998. Montevideo, Uruguay: CIMMYT.
5. KWV, South Africa. (2005). Setting new global standards for vine plant
improvement. Vititec.
6. Franklin, F. C. H., M. J. Lawrence, and V. E. Franklin-Tong (1995). "Cell and
molecular biology of self-incompatibility in flowering plants". Int. Rev. Cytol.
Unit 2 Cytological principles of plant breeding
2.0 Cytological principles of plant breeding
2.0 Introduction
E. Strasburger in 1875 first discovered thread-like structures which appeared during

cell division. These thread like structures were called chromosomes due to their
affinity for basic dyes. The term chromosome is derived from two Greek words;
chrom = colour, soma=body. This term was first used by Waldeyer in 1888.
2.0.1 Objectives
At the end of this unit,
 students will understand the cytological principles of plant breeding

 Should visualise the chromosomes as the basis
 Should be able to describe the structure, composition and function of
chromosomes in relation to plant breeding
2.1. Chromosomes
Of all components of cell, the chromosomes have been studied most extensively and
perhaps more is known about them than any other cell organelle. The chromosome
has greater constancy than any other cell component and it maintains it special
qualities from one cell generation to another.
Chromosomes contributed to the division of cells and they are of prime importance
as they carry the genes which are the hereditary material.
2.1.1. Chromosome number:
The number of chromosomes in a given species is generally constant. All the

members of the species ordinarily have definite and generally a constant somatic
and gametic chromosome number. Somatic chromosome number is the number of
chromosomes found in somatic cells of a species and is represented by 2n.
Generally somatic cells contain two copies of each chromosome except the sex
chromosomes. Both the copies are ordinarily identical in morphology, gene content
and gene order and hence known as homologous chromosomes. Gametic
chromosome number is exactly half of somatic chromosome number and is
represented by n. it denotes the number of chromosomes found in gametes of a
species. The number of chromosomes varies greatly from 2n = 4 (n = 2) in
Haplopappusgracilis(Compositae) to 2n = > 1200 in some Pteridophytes.
Name of the Chromosome

organism number (2n)
Rice 24
Tomato 24
Wheat 42
Onion 16
Maize 20
Garden pea 14
Cotton 52
Humans 46
Drosophila 8
2.1.2. Chromosome Size:
The size of the chromosome shows a remarkable variation depending upon the
stage of cell division. The chromosomes are the longest and thinnest during
interphase (resting stage) and hence not visible under light microscope.
Chromosomes are the smallest and thickest during mitotic metaphase. In general,
plants have longer chromosomes than animals and species having lower
chromosome number have longer chromosomes than those having a higher
chromosome number. Among plants, dicots in general have shorter and higher
number of chromosomes than monocots. Among the higher plants, the longest
mitotic chromosomes are those of Trillium spp., which may reach 32 μ in size. In
most fungi all chromosomes are extremely minute. Chromosome size is not
proportional to the number of genes present on the chromosome.
2.1.3. Chromosome Morphology:
The outer covering or sheath of a chromosome is known as pellicle, which encloses

the matrix. Within the matrix lies the chromatin. Flemming introduced the term
chromatin in 1879. The term chromatin refers to the Feulgen positive materials
observed in interphase nucleus and later during nuclear division. Chromatin readily
stains with basic dyes especially Basic Fuchsin, which is specific for DNA which in
turn is a major constituent of chromosomes. The chromosome morphology changes
during cell division and mitotic metaphase is the most suitable stage for studies on
chromosome morphology. In mitotic metaphase chromosomes, the following
structural features can be seen under the light microscope.
I. Chromatid: Each metaphase chromosome appears to be longitudinally

divided into two identical parts each of which is called chromatid. Both the
chromatids of a chromosome appear to be joined together at a point known as
centromere. The two chromatids of chromosome separate from each other
during mitotic anaphase (and during anaphase II of meiosis) and move
towards opposite poles. Since the two chromatids making up a chromosome
are produced through replication of a single chromatid during synthesis (S)
phase of interphase, they are referred to as sister chromatids. In contrast, the
chromatids of homologous chromosomes are known as non-sister
chromatids.
II. Centromere: Centromere and telomere are the most stable parts of
chromosomes. The region where two sister chromatids appear to be joined
during mitotic metaphase is known as centromere. It generally appears as
constriction and hence called primary constriction. Centromere is a localized
and easily detectable morphological region of the chromosomes which helps
in the movement of the chromosomes to opposite poles during anaphase of
cell division. The centromere divides the chromosomes into two transverse
parts called arms. The centromere consists of two disk shaped bodies called
kinetochores. The kinetochores do not form part of the chromatid but lie one
on each side of the chromosome such that each chromatid is having its own
kinetochore. One kinetochore is attached to the spindle fibres towards one
pole and the other similarly towards the other pole. Depending on position of
the centromeres, chromosomes can be grouped as:
a) Metacentric: Centromere is located exactly at the centre of chromosome,
i.e. both arms are equal in size. Such chromosomes assume ‘V’ shape at
anaphase.
b) Submetacentric: The centromere is located on one side of the centre
point such that one arm is longer than the other. These chromosomes
become ‘J’ or ‘L’ shaped at anaphase.
c) Acrocentric: Centromere is located close to one end of the chromosome
and thus giving a very chort arm and a very long arm. These chromosomes
acquire ‘ J’ shape or rod shape during anaphase.
d) Telocentric: Centromere is located at one end of the chromosome so that
the chromosome has only one arm. These chromosomes are ‘I” shaped or rod
shaped. Normally chromosomes are monocentric having one centromere
each. Acentric (without centromere) and dicentric (with two centromeres)
chromosomes, if produced due to chromosomal aberrations, cannot orient
properly on the equatorial plate and lag behind other chromosomes during
anaphase movements. In certain organisms, centromere does not occupy a
specific position, but is diffused trough out the body of chromosome. Such
chromosomes, which do not have a localized centromere, are found in Luzula
spp. and insects belonging to the order Hemiptera.
3. Telomere: The two ends of chromosomes are known as telomeres. They are
highly stable and do not fuse or unite with telomeres of other chromosomes due to
polarity effect. Any broken end of a chromosome is unstable and can join with a
piece of any other chromosome. But the telomeres impart stability to the
chromosome, which retains its identity and individuality through cell cycle and for
many cell generations.
4. Secondary constriction: The constricted or narrow region other than that of

centromere is called secondary constriction and the chromosomes having secondary
constriction are known as satellite chromosomes or sat chromosomes. Chromosome
may possess secondary constriction in one or both arms of it. Chromosomal end
distal to the secondary constriction is known as satellite. Production of nucleolus is
associated with secondary constriction and therefore it is also called nucleolus
organizer region and satellite chromosomes are often referred to as nucleolus
organizer chromosomes.
5. Chromomere: In some species like maize, rye etc. chromosomes in pachytene

stage of meiosis show small bead like structures called chromomeres. Chromomeres
are visible during meiotic prophase (pachytene) and invisible in mitotic metaphase
chromosomes. The distribution of chromomeres in chromosomes is highly
characteristic and constant. The pattern of distribution being different for different
chromosomes. They are clearly visible as dark staining bands in the giant salivary
gland chromosomes. Chromomeres are regions of tightly folded DNA. Chromomeres
of single chromosome show considerable variation in size. They may differ in size as
in the case of maize or they may be of uniform size as in the case of rye.
6. Chromonema: A chromosome consists of two chromatids and each chromatid

consists of thread like coiled structures called chromonema (plural chromonemata).
The term chromonema was coined by Vejdovsky in 1912. The chromonemata form
the gene bearing portion of chromosomes.
7. Matrix: The mass of acromatic material which surrounds the chromonemata is

called matrix. The matrix is enclosed in a sheath which is known as pellicle. Both
matrix and pellicle are non genetic materials and appear only at metaphase, when
the nucleolus disappears.
2.1.4. Composition of chromosomes:
The material of which chromosomes are composed is called chromatin. N.Fleming

introduced the term chromatin in 1879. Chromatin was classified into two groups by
cytologists on the basis of its affinity to basic dyes like acetocarmine or feulgen
(basic fuchsin) reagent at prophase. The darkly stained regions were called
heterochromatin, while lightly stained regions were called euchromatin. This
differential staining capacity of different parts of a chromosomes is known as
‘heteropycnosis’. In general heterochromatin is found in centromeric and telomeric
regions and these regions of chromosome generally replicate later than the
euchromatic regions of chromosomes. The genes within the heterochromatic regions
are usually inactive. Most of the genome of an active cell is euchromatic and the
genes with in this euchromatic region are expressed. Heterochromatin is further
classified into two groups: a) Constitutive and b)Facultative
a) Constitutive heterochromatin: It is present in all cells at identical positions on both
homologous chromosomes of a pair.
b) Facultative heterochromatin: It varies in state in different cell types, at different
stages or sometimes, from one homologous chromosome to another. A well known
example of facultative heterochromatin is the Barr body, an inactivated X
chromosome in somatic cells of mammalian female(XX).
Differences between Heterochromatin and Euchromatin:
Heterochromatin Euchromatin
1 Represent darkly stained Lightly stained regions

regions
2 Contains few inactive genes Contains lot of active genes
3 Covers small region of Larger region of
chromosome chromosome
4 Usually found near Found in the middle of

centromere chromosome between
and telomere centromere and telomere
5 Two types – Constitutive and Only one type

facultative
6 Late replicating Normal replicating

7 Usually no active part in Plays active role in
transcription transcription
30 nm fibre 3-8 nm fibre
2.1.5. Karyotype and Ideogram: The general morphology (size of chromosomes,

position of centromere, presence of secondary constriction and size of satellite
bodies) of somatic chromosomal complement of an individual constitutes its
karyotype. It can be defined as “the characteristic features by which a set of
chromosomes of a species is identified”. Generally, karyotype is represented by
arranging the chromosomes in descending order of size, keeping their centromeres
in the same line. Thus the largest chromosome is placed on extreme left and the
shortest on extreme right. The karyotype of a species can be represented
diagrammatically showing all the morphological features of chromosomes. Such a
diagram is known as ideogram or ideotype.
1.2. Special types of Chromosomes

Some tissues of certain organisms contain chromosomes which differ significantly
from normal chromosomes in terms of either morphology or function. Such
chromosomes are referred to as special chromosomes. The following are included
under this category:
1. Giant chromosomes or polytene chromosomes: These were first discovered
by E. G. Balbiani in 1882 in Dipteran salivary glands and hence commonly called
salivary gland chromosomes. These chromosomes replicate repeatedly but the
daughter chromatids do not separate from one another and the cell also does not
divide. This phenomenon is known as endomitosis or endoreduplication. It results in
the formation of many stranded giant chromosomes known as polytene
chromosomes and the condition is known as polyteny. Their size is 200 times or
more than the normal somatic chromosomes (autosomes) and very thick. Hence
they are known as giant chromosomes. These chromosomes are somatically paired
and their number in the salivary gland cells always appear to be half of that in the
normal somatic cells. Along the length of chromosomes, a series of dark bands are
present alternate with clear bands known as interbands. These bands have greatly
helped in mapping of the chromosomes in cytogenetic studies. In the dark band
region, the DNA is tightly coiled while in the interband region, DNA is less tightly
coiled. The morphological expression of such sites is represented by local
enlargements of certain regions called puffs. These puffs are also known as balbiani
rings. Puffs are the sites of active RNA synthesis.
2. Lamp brush chromosomes: These were first observed by W. Flemming in 1882
and were described in detail in oocytes of sharks by Rukert in 1892. They occur at
diplotene stage of meiotic prophase in oocytes of all animal species. Since they are
found in meiotic prophase, they are present in the form of bivalents in which the
maternal and paternal chromosomes are held together by chiasmata at those sites
where crossing over has previously occurred. Each bivalent has four chromatids, two
in each homologue. The axis of each homologue consists of a row of granules or
chromomeres, each of which have two loop like lateral extensions, one for each
chromatid. Thus each loop represents one chromatid of a chromosome and is
composed of one DNA double helix. One end of each loop is thinner than other
which is known as thickened. There is extensive RNA synthesis at thin ends of the
loop while there is little or no RNA synthesis at the thick ends.
3. Accessory chromosomes: In many species some chromosomes are found in

addition to normal somatic chromosomes. These extra chromosomes are called
accessory chromosomes or B-chromosomes or supernumerary chromos omes.
These chromosomes are broadly similar to normal somatic chromosomes in their
morphology, but have some peculiar functional aspects. For instance, presence of
several such chromosomes often leads to reduction in vigour and fertility in males.
These chromosomes are generally smaller in size than the normal somatic
complement. They are believed to be generally inactive genetically. However they
may not be completely devoid of genes. Origin of these chromosomes in most
species is unknown.
4. Isochromosomes: An isochromosome is the one in which two arms are identical
with each other in gene content and morphology. Such a chromosome is in essence
a reverse duplication with centromeres separating the two arms. Every
isochromosome is metacentric. The attached ‘x’ chromosome of Drosophila is a
classical example of an isochromosome. However its origin is uncertain. There is no
evidence that isochromosomes had any evolutionary significane.
5. Allosomes / sex chromosomes: Chromosomes differing in morphology and
number in male and female are called allosomes. They are responsible for
determination of sex. Eg: X and Y chromosomes in human beings and Drosophila.
Chromosomes which have no relation with determination of sex and contain genes
which determine somatic characters of individuals are called autosomes and are
represented by letter ‘A’.
6. Summary
Plants are made of chromosomes. The number of chromosomes in a species is

constant. Somatic chromosome number is the number of chromosomes found in
somatic cells of a species and two copies of each chromosome except the sex
chromosomes.The size of the chromosome varieswith stage of cell division being
longest and thinnest during interphase (resting stage) but smallest and thickest
during mitotic metaphase. Plants have longer chromosomes than animals and
species having lower chromosome number have longer chromosomes than those
having a higher chromosome number. Dicots in general have shorter and higher
number of chromosomes than monocots.
7. Conclusion
Cytological principles of plant breeding are based on the chromosomal

structure, composition and function of chromosomes of the plant.
8. Self-assessment Assignments
1. What is a chromosome and how is it important in plant breeding?

2. Differentiate between euchromatin and hetrochromatin
3. List the special types of chromosomes and explain each
9 Tutor marked assignment:
1. Describe how you can distinguish chromosomes depending on position of the

centromeres.
References
1 Chahal, G.S and Gosal, S.S., 2002. Principles and procedures of Plant
2 Falconer, D.S., 1989. Introduction to Quantitative Genetics. 3rd Ed.
Longman. Burnt Mill.
3 Kwon-Ndung, E.H. 2008. Genetics for degree students. Afaku Publishers,
Abuja.
4 FrishM., and Elchinger, A.E., 2005. Selection Theory for Marker-assisted
Backcrossing. Genetics: Published Articles Ahead of Print, published on
March 31, 2005 as 10.1534/genetics.104.035451
5 Holsinger, K.E., 2000. Reproductive systems and evolution in vascular
plants. PNAS. June 20, vol. 97, no. 13: 7037-7042.
6 Kohli, M.M. and Francis, M., 2000. Application of biotechnologies to wheat
breeding. Proceedings of a conference at La Estanzuela, Uruguay,
November 19–20, 1998. Montevideo, Uruguay: CIMMYT.
7 KWV, South Africa. (2005). Setting new global standards for vine plant
8 Takebayashi, N and Morell, P.L., 2001. Is self-fertilization an evolutionary
dead end? Revisiting an old hypothesis with genetic theories and a
macroevolutionary approach. American Journal of Botany. 88:1143-115
9 Charlesworth, D., X. Vekemans, V. Castric and S. Glemin (2005). "Plant
self-incompatibility systems: a molecular evolutionary perspective". New
Phytologist168 (1): 61–69.
10 Franklin, F. C. H., M. J. Lawrence, and V. E. Franklin-Tong (1995). "Cell
and molecular biology of self-incompatibility in flowering plants". Int. Rev.
Cytol.
11 Qiao, H., H. Wang, L. Zhao, J. Zhou, J. Huang, Y. Zhang, and Y. Xue
(2004). "The F-box protein AhSLF-S2 physically interacts with S-RNases
that may be inhibited by the ubiquitin/26S proteasome pathway of protein
degradation during compatible pollination in Antirrhinum". Plant Cell 16 (3):
582–95.
Unit 3.
3.0. Heterosis
Introduction:
Heterosis, or hybrid vigor, or outbreeding enhancement, is the improved or

function of any biological quality in a hybrid offspring. It is the occurrence of a
genetically superior offspring from mixing the genes of its parents.
Heterosis is the opposite of inbreeding depression. Inbreeding depression

leads to offspring with deleterious traits due to homozygosity. The term
heterosis often causes controversy, particularly in selective breeding of
domestic animals, because it is sometimes claimed that all crossbred plants
and animals are genetically superior to their parents. This is untrue, as only
some hybrids are genetically superior. The inverse of heterosis, when a hybrid
inherits traits from its parents that are not fully compatible, with deleterious
results, is outbreeding depression.
3.1. Genetic basis of heterosis
Two competing hypotheses, not necessarily mutually exclusive, have been to

explain hybrid vigor. The dominance hypothesis attributes the superiority of
hybrids to the suppression of undesirable (deleterious) recessive alleles from
one parent by dominant alleles from the other. It attributes the poor
performance of inbred strains to the loss of genetic diversity, with the strains
becoming purely homozygous deleterious alleles at many loci. The
overdominance hypothesis states that some combinations of alleles (which
can be obtained by crossing two inbred strains) are especially advantageous
when paired in a heterozygous individual. The concept of heterozygote
advantage/overdominance is not restricted to hybrid lineages. This hypothesis
is commonly invoked to explain the persistence of many alleles (most
famously the erythrocyte-sickling allele) that are harmful in homozygotes; in
normal circumstances, such harmful alleles would be removed from a
population through the process of natural selection. Like the dominance
hypothesis, it attributes the poor performance of many inbred strains to a high
frequency of these harmful recessive alleles and the associated high
frequency of homozygous-recessive genotypes.
3.2. Hybrid corn
Nearly all field corn (maize) grown in most developed nations exhibits .
Modern corn hybrids substantially outyield conventional cultivars and respond
better to fertilizer.
Corn heterosis was famously demonstrated in the early 20th century by

George H. Shull and Edward M. East after hybrid corn was invented by Dr.
William James Beal of Michigan State University based on work begun in
1879 at the urging of Charles Darwin. Dr. Beal's work led to the first published
account of a field experiment demonstrating hybrid vigor in corn, by Eugene
Davenport and Perry Holden, 1881. These various pioneers of botany and
related fields showed that crosses of inbred lines made from a Southern dent
and a Northern flint, respectively, showed substantial heterosis and outyielded
conventional cultivars of that era. However, at that time such hybrids could not
be economically made on a large scale for use by farmers. Donald F. Jones at
the Connecticut Agricultural Experiment Station, New Haven invented the first
practical method of producing high-yielding hybrid maize in 1914-1917. Jones'
method produced a double-cross hybrid, which requires two crossing steps
working from four distinct original inbred lines. Later work by corn breeders
produced inbred lines with sufficient vigor for practical production of a
commercial hybrid in a single step, the single-cross hybrids. Single-cross
hybrids are made from just two original parent inbreds. They are generally
more vigorous and also more uniform than the earlier double-cross hybrids.
The process of creating these hybrids often involves detasseling.
3.3. Hybrid livestock
The concept of heterosis is also applied in the production of commercial

livestock. In cattle, hybrids between Black Angus and Hereford produce a
hybrid known as a "Black Baldy". In swine, "blue butts" are produced by the
cross of Hampshire and Yorkshire. Other, more exotic hybrids such as
"beefalo" are also used for specialty markets.
Within poultry, sex-linked genes have been used to create hybrids in which
males and females can be sorted at one day old by color. Specific genes used
for this are genes for barring and wing feather growth. Crosses of this sort
create what are sold as Black Sex-links, Red Sex-links, and various other
crosses that are known by trade names.
Commercial broilers are produced by crossing different strains of White Rocks

and White Cornish, the Cornish providing a large frame and the Rocks
providing the fast rate of gain. The hybrid vigor produced allows the
production of uniform birds with a marketable carcass at 6–9 weeks of age.
Likewise, hybrids between different strains of White Leghorn are used to

produce laying flocks that provide the majority white eggs for sale in the
United States.
3.4. Heterosis Effect in Animals
Purebreds and inbreeds often carry genetic disease. Heterosis is a theory,

where the phenomenon of crossing two inbred lines can produce descendants
with superior genetic foundation. In addition to the absence of inbreeding
depressing, present in inbreed and purebred dogs in general, there is some
remote inbreeding in any breed. Heterosis is also produced by over
dominance, i.e. better combined function of two diverse genes (alleles) on a
gene site (locus), compared to two identical (but harmless) ones. This
increased health and vigor does not create a superior breed, but the
advantages obtained from it are what produce hybrid vigor. This goal in this
scenario is not to create a new breed, but to create a happy and healthy pet.
Heterosis effect results in a healthier, more vigorous dog with a reduced

chance of genetic disease. It is well known in all domestic animal breeding,
hybrids, 50%-50% mixes of two different breeds, will raise the chances of
having less genetic diseases because all doubling of detrimental effects will
stop in the first generation. The genetic term for this is HETEROSIS EFFECT.
This effect often gives non-related individuals stronger descendants than
inbreeds.
Breeders who breed hybrid dogs have stated their goal was to get healthy and
happy dogs without genetic problems. Most breeders crossing with the poodle
are looking for a soft silky non-shedding coat good for allergy sufferers.
The purpose of these hybrids is not and should never be to develop a new
breed. Once one goes beyond first generation purebred to purebred, you lose
the heterosis effect, which is the goal for most hybrid breeders. The mother
should always be the bigger of the two, to avoid puppies getting too big and
complicating the delivery for the mother. Heterosis is said to not only occur in
the first generation, but also mating to a non related hybrid of same (or other)
type will also show this effect, though the aspect of the offspring will be
different. The hope is that the dogs will get the benefit of the greatly
demanded HETEROSIS effect, and avoid genetic diseases which are
common among purebreds and inbreeds.
8. Summary
Heterosisis the occurrence of a genetically superior offspring from mixing the genes
of its parents. The genetic explanation is that there is superiority of hybrids to the
suppression of undesirable (deleterious) recessive alleles from one parent by
dominant alleles from the other. It is found in plants, such as corn, and the production
of commercial livestock. In animals, heterosis results in a healthier, more
vigorous with a reduced chance of genetic disease.
9. Conclusion
Heterosis is the method of breeding desirable traits for high agricultural yield.
Self-assessment Assignments
1. Describe the genetic basis of heterosis

2. Explain the concept of hybrid corn and hybrid livestock
Tutor – Marked Assessment
1. Discuss on Heterosis in plants and animals

2. Give a concise account of how hybrid vigour is explained by two hypotheses.
References
2 Falconer, D.S., 1989. Introduction to Quantitative Genetics. 3rd Ed.

Longman. Burnt Mill.
3 Kwon-Ndung, E.H. 2008. Genetics for degree students. Afaku
Publishers, Abuja.
4 Frish M., and Elchinger, A.E., 2005. Selection Theory for Marker-
assisted Backcrossing. Genetics: Published Articles Ahead of Print,
published on March 31, 2005 as 10.1534/genetics.104.035451
5 Goussard, P.G. 2004. Improving grape vine material through selection.
Department of Viticulture. Stellenbosch University. Lecture notes.
6 Holsinger, K.E., 2000. Reproductive systems and evolution in vascular
plants. PNAS. June 20, vol. 97, no. 13: 7037-7042.
7 Kohli, M.M. and Francis, M., 2000. Application of biotechnologies to
wheat breeding. Proceedings of a conference at La Estanzuela,
Uruguay, November 19–20, 1998. Montevideo, Uruguay: CIMMYT.
9 Takebayashi, N and Morell, P.L., 2001. Is self-fertilization an
evolutionary dead end? Revisiting an old hypothesis with genetic
theories and a macroevolutionary approach. American Journal of
Botany. 88:1143-115
10 Charlesworth, D., X. Vekemans, V. Castric and S. Glemin (2005).
"Plant self-incompatibility systems: a molecular evolutionary
perspective". New Phytologist168 (1): 61–69.
11 Franklin, F. C. H., M. J. Lawrence, and V. E. Franklin-Tong (1995).
"Cell and molecular biology of self-incompatibility in flowering plants".
Int. Rev. Cytol.
12 Qiao, H., H. Wang, L. Zhao, J. Zhou, J. Huang, Y. Zhang, and Y. Xue
(2004). "The F-box protein AhSLF-S2 physically interacts with S-
RNases that may be inhibited by the ubiquitin/26S proteasome
pathway of protein degradation during compatible pollination in
Antirrhinum". Plant Cell 16 (3): 582–95.
13 Green EL. Genetics and probability in animal breeding experiments.
271pp. London and Basingstoke: The Macmillan Press Ltd., 1981.
14 McGregor, M.C. 1999. Hybrid vigor in plants and its relationship to
insect pollination — a section from Insect Pollination Of Cultivated Crop
Plants by, USDA
Unit 4
4.0. Inbreeding (F) and its consequences or applications
The broad scientific definition of inbreeding is that it is the mating of individuals more
closely related to each other than the average relationship within the population
concerned. This statement is really only valid for large populations, since with small
populations inbreeding is inevitable, even with random mating. To be more precise,
an inbred person is defined as someone whose parents are related. In practice this
means close direct relationship or, more usually, related throughrecent common
ancestors, since all members of the same species are related to some extent.
The adverse effects of inbreeding in animals are well known. The incidence of
metabolic disorders, structural abnormalities and inherited disease conditions,
caused by harmful recessive genes, increases following inbreeding. Performance in
several characters, particularly those concerned with reproduction and survival,
declines following the mating of close relatives. This is known as inbreeding
depression. These effects are mainly due to an increase in the frequency of
homozygous genotypes (AA and aa) at the expense of heterozygotes (Aa), which is
caused by inbreeding. It is only harmful, however, when the dominance is directional,
which means that the undesirable member of a pair of genes is usually recessive.
When a high proportion of these harmful genes are present in the heterozygous
state (Aa) the animal is protected from their debilitating effects by the dominance of
the normal gene; but when some of the heterozygotes are replaced by homozygous
recessives (aa), following inbreeding, their harmful effects become manifest. Other
types of gene action are sometimes responsible for inbreeding damage, but are
thought to be less important. These are: overdominance, epistatic interaction and the
overall level of heterozygosity.
Overdominance occurs when the heterozygote (A1A2) is superior in performance to

either of the two homozygotes (A1A1 or A2A2). In this situation, an increase in
homozygosity following inbreeding also causes inbreeding depression.
Epistatic interaction between different pairs of genes occurs when one pair affects
the expression of another pair at a different locus. With one particular type, called
complementary epistasis, two dominants, one from each of two separate loci, are
necessary for normal development or metabolism. Thus, AABB, AaBB, AABb and
AaBb will be normal, but AAbb, aaBBAabb, aaBb and aabb will be defective. This
situation arises when a metabolic pathway requires two enzymes for the essential
end-product to be synthesised. Since each enzyme requires a different dominant
gene for its synthesis, the absence of one or both will result in a defective individual.
Inbreeding in a population with a mixture of the above genotypes will lead to a break-
up of the favourable gene combinations, with more inferior genotypes, particularly
aaBB, AAbb and aabb, being produced.
Finally, Lerner (1954) found evidence that some abnormal conditions in animals
were not caused by single genes but by a drop in the general level of heterozygosity
throughout the whole genome. His theory of developmental homeostasis suggests
that for an animal to be able to cope with developmental accidents and
environmental stress there is a minimum or obligate level of heterozygosity for
normal development. The implication being that heterozygotes in general are more
versatile because they can produce a greater variety of enzymes and other proteins.
This means that the heterozygosity level per se, as well as the effects of the genes
themselves, may be a contributing factor.
The opposite of inbreeding depression is known as heterosis or hybrid vigour and

can result from the crossing of unrelated inbred animals or lines with different genetic
backgrounds. What is lost from inbreeding is usually restored when several inbred
lines are crossed randomly. Deliberate inbreeding and crossing, followed by
selection between lines, is sometimes used with farm plants and animals to improve
yields. Its significance in humans is that greater mobility means that people travel
further to find a spouse and are less likely to marry a person from the same locality
with a similargenotype. Thus, although most of the increase in height and improved
survival is the result of better nutrition and disease control, a small part may also be
due toheterosis following a change in the mating system.
4.1.Introduction
The coefficient of inbreeding (F) measures the probability that two genes at any
locus in an individual are identical by descent from the common ancestor(s) of the
two parents. This means the degree to which two alleles are more likely to be
homozygous (AA or aa) rather than heterozygous (Aa) in an individual, because the
parents are related. Like R,F is a relative measure, in that there will be a certain level
of homozygosity within the base population; F simply estimates the increase from
that initial level as a result of recentinbreeding.
The inbreeding coefficient of an individual is approximately half the relationship (R)

between the two parents.This equivalence only applies to low levels of inbreeding
in an otherwise outbred population.e.g.Two single first cousins normally have a
relationship (R) of 1/8.If there has been no previous inbreeding, their children will
have a coefficient of inbreeding of 1/16.With high levels of continuous inbreeding
this relationship breaks down. e.g. some strains of laboratory rats and mice have
reached an F value of 1.0, resulting from a long history of close inbreeding; but the
coefficient of relationship (R) between any two members of the strain can never
exceed 1.0. The mathematical reason for this is that although the basic formulae for
R and F are Σ(1/2)n and Σ(1/2)n+1, respectively, as inbreeding within a line
progresses, the correction terms applied to R for inbreedinggradually become more
important and start to reduce the value of R below Σ(1/2)n. As F approaches 1.0,
the correction terms for R also approach a maximum of (x 1/2); so that when F
reaches 1.0 (complete homozygosity), R also becomes 1.0 and all members of the
inbred line are identical.
The method of calculating the F coefficient of an individual is similar to that for the
coefficient of relationship (R) between two collateral relatives, and involves the
tracing of paths between the two parents via a common ancestor. The formula is as
follows:-
Equation 1:Method of calculating the F coefficient of an individual-
1[14]
Where FX is the coefficient of inbreeding of individual X,
n is the number of connecting links between the two parents of X through common
ancestors and FA is the coefficient of inbreeding of the common ancestor A. Thus, if
the common ancestor is inbred, a minor calculation must be performed first to
determine FA, before the main calculation can take place.In the main calculation any
coefficients of paths through inbred common ancestors can then be multiplied by
(1+ FA).
Example with an Inbred CommonAncestor:
Find FQ
The only inbred common ancestor of the two parents (O and P) is I (his parents are
single first cousins).
a) First Find FI
Common Ancestors Paths (1/2)n+1 (1+FA)

(of parents G and H)
A G_1_D_2_A_3_E_4_H 1/32 x 1.0 = 1/32
B G_1_D_2_B_3_E_4_H 1/32 x 1.0 = 1/32
Therefore FI = Σ [(1/2)n+1(1 + FA) = 1/16
i.e. FI = 0.0625 = 6.25%
b) Main Calculation (To find FQ)
Common Ancestors Paths (1/2)n+1 (1+FA)

(of parents O and P)
I O_1_L_2_I_3_M_4_P 0.03125 x 1.0625 = 0.03220
J O_1_L_2_J_3_M_4_P 0.03125 x 1.0 = 0.03125
Therefore FQ = Σ[(1/2)n+1 (1 + FA)] = 0.06445
i.e. FQ = 0.06445 = 6.45%
Example without Inbred Common Ancestors:
Find FO
None of the common ancestors A, B, G or H are inbred. Therefore, no corrections

are necessary.
Common Paths (1/2)n+1

Ancestors
(of parents M
and N)
G M_1_J_2_G_3_K_4_N 1/32 = 0.03125
H M_1_J_2_H_3_K_4_N 1/32 = 0.03125
A M_1_J_2_G_3_D_4_A_5_E_6_H_7_K_8_N
M_1_J_2_H_3_E_4_A_5_D_6_G_7_K_8_N
1/512 x 4 = 0.0078125
B M_1_J_2_G_3_D_4_B_5_E_6_H_7_K_8_N
M_1_J_2_H_3_E_4_B_5_D_6_G_7_K_8_N
Therefore FO = Σ(1/2)n+1 = .0703125
i.e. FO = 7.03%
Close Inbreeding as used for Animals (3 generations of full sib mating):
Find FI
Common ancestors of G and H are A, B, C, D, E and F.The only two that are inbred
are E and F (related parents).Therefore, first calculate FE and FF (the same).
a) Find FE and FF
Common ancestors(of parents C Paths (1/2)n+1

and D)
A C_1_A_2_D 1/8 Therefore,
B C_1_B_2_D 1/8 FE = FF = 1/4 = 25%
b) Main Calculation (To Find FI)
Common ancestors
(of parents G and Paths (1/2)n+1 (1 + FA)
H)
E G_1_E_2_H (1/2)3 * 1.25 = 15625
F G_1_F_2_H (1/2)3 * 1.25 = 15625

G_1_E_2_C_3_F_4_H (1/2)5 * 1.0 = 03125
C
G_1_F_2_C_3_E_4_H (1/2)5 * 1.0 = 03125
G_1_E_2_D_3_F_4_H (1/2)5 * 1.0 = 03125

D
G_1_F_2_D_3_E_4_H (1/2)5 * 1.0 = 03125
G_1_E_2_C_3_A_4_D_5_F_6_H
G_1_F_2_C_3_A_4_D_5_E_6_H
A
G_1_E_2_D_3_A_4_C_5_F_6_H
G_1_F_2_D_3_A_4_C_5_E_6_H
(1/2)7 x 8 * 1.0 = 06250
_1_ _2_ _3_ _4_ _5_ _6_
G E C B D F H
G_1_F_2_C_3_B_4_D_5_E_6_H
B
G_1_E_2_D_3_B_4_C_5_F_6_H
G_1_F_2_D_3_B_4_C_5_E_6_H
FI=Σ[(1/2)n+1 (1 + FA)] =.50000
i.e FI =50%
4.2. The Closest Form of Inbreeding
The closest form of inbreeding is self-fertilisation which normally only occurs in

monoecious plants and animals which are hermaphrodites,, e.g. garden peas and
slugs.The equivalent situation has been experimentally produced in turkeys where a
rare form of parthenogenesis occurs.Parthenogenesis (virgin birth) is the production
of viable embryos (always males in birds) from haploid infertile eggs by the artificial
doubling of chromosome numbers. The embryos are highly homozygous.If one of
these parthenogenetic males is mated back to his mother this is equivalent to self-
fertilisation.One generation of self-fertilisation produces the same coefficient of
inbreeding (F) as three generations of full sib mating, i.e. 0.5.This follows from the
formula for F, which is Σ(1/2)n+1 where n is the number of connecting links between
the two parents via a common ancestor. With selfing, both parents are the same
individual so that the number of links (n) is 0 and, therefore Σ(1/2)n+1 = 0.5.
4.3. Sib Marriages in Humans
In some societies close consanguineous marriages have been encouraged.For

example, the ancient Egyptians and the Incas favoured marriages of brothers and
sisters of the reigning dynasty.
Marriages between Sibs and Half-sibs in the 18th Dynasty of Egypt, c. 1580 – 1350.
4.3. Inbreeding Coefficients

F
a) Amenhotep I and Aahotep II 25%

b) Aames 37.5%
c) Hatsheput 25%
d) The rest of the individuals in the pedigree are
not inbred, i.e. F = 0.
4.3.1. Double Grandchildren - The offspring of a full sib mating are sometimes
referred to as double grandchildren because they only have two grandparents
instead of the usual four.
4.3.2. The Special Case of Directly Related Parents
In an incestuous situation where there is a close direct relationship between the two
parents, such as father-daughter, mother-son or grandparent-grandchild, they may
have no common ancestors in any previous generation, even though they have a
strong genetic link. This is because one parent is the direct ancestor of the other. In
these situations, despite having no common ancestors, the correction term (1 + FA)
must still be applied to the path coefficient between an inbred ancestor (A) and
his/her descendant partner.
A Father-daughter mating:
The reason is that, taking a father-daughter mating as an example; if the father (A)
is inbred, his extra homozygosity will make it more likely that he will transmit to his
grandson (D) further copies of the same alleles which his daughter (C) has already
received from him. Since about one half of the genes the daughter receives from her
father will also be passed on to the grandson, the latter's inbreeding coefficient (F)
will rise above the normally expected level (0.25) and its value should be adjusted
accordingly.
Directly Related Parents Only:

Find FH FE = 0.25
Common ancestors
Path (1/2)n+1 (1 + FA) *
(of parents E and G
None E-G (1/2)2 x 1.25 = 0.3125
Therefore, FH= Σ[(1/2)n+1(1 + FA)] = 31.3%
However, there are cases (usually only found in animal breeding) where directly
related parents do share common ancestors. If any of these common ancestors are
also inbred, the correction term
(1 + FA) will be required in both situations.
Directly and Collaterally Related Parents:

Find FO
Common ancestors
(1 + FA)
(of parents L and Paths (1/2)n+1
*
N)
None L-N (1/2)2 x 1.03125 = 0.2578125
J L-J-M-N (1/2)4 x 1.125 = 0.0703125
L-I-F-B-G-J-M-
B (1/2)8 x 1.0 = 0.00390625
N
0.33203125
Therefore FO = ∑[(1/2)n+1(1 + FA)] = 33.2%
*A refers to any relevant inbred direct ancestor or common ancestor.
Alternative Methods of Calculating the coefficient of inbreeding:
An alternative method of computing F is to use the technique of

'Coancestries'.Instead of working from the present back to common ancestors we
work forward, keeping a running tally, generation by generation, and compute the
inbreeding that will result from the matings now being made.This method is easier
than path coefficients for animal breeding programmes where the paths are often
numerous and complex but unnecessary for normal human pedigrees.
For regular systems of inbreeding, as used in the 'inbred-hybrid' system for breeding
chickens and maize, 'recurrence equations' are the only easy method for calculating
F. A regular system of inbreeding is where a certain type of mating such as brother-
sister, is repeated indefinitely. A recurrence equation calculates the F value of the
present generation from those of recent previous ones. e.g. the recurrence equation
for repeated full sib mating is:
Ft = 0.25 (1 + 2Ft-1+ Ft-2)
Where Ft is the coefficient of the present generation, Ft-1 is the coefficient of the
previous generation and Ft-2 is the coefficient of the generation before that. It is
important to note that recurrence equations can only be used for regular systems of
inbreeding. e.g. Three generations of full sib mating:-
First generation - F1 = 0.25 (1 + 0 + 0) = 0.25
Second generation - F2 = 0.25 (1 + 0.5 + 0) = 0.375
Third generation - F3 = 0.25 (1 + 0.75 + 0.25) = 0.5
Values of F for ConsanguinousMatings (One generation, no previous inbreeding).

Self fertilisation 1/2
Full sibs, Parent-child, Double first cousins (first degree) 1/4
Half sibs, Grandparent-grandchild, Uncle-niece, Double first cousins 1/8
First cousins 1/16
First cousins (once removed) 1/32
Second cousins 1/64
Second cousins (once removed) 1/128
Third cousins 1/256
4.4. Practical Uses of F
F is a very valuable parameter in both population and quantitative genetics.From the

genealogists point of view the following are perhaps the two most interesting
applications:
a) Predicting the Effects of Inbreeding Depression
A decline in performance in certain economic characters in domestic animals is well

known following inbreeding. A similar depression has also been observed in
humans.e.g.
Inbreeding Depression for Every 10% Increase in F:

Animal Characteristic Inbreeding Reference
Depression
Chickens Hatchability 4.36% Shoffner
(1948)
Annual egg production 9.26 eggs Shoffner
(1948)
Man Height at age 10 2.0 cm Falconer
(1989)
I.Q. score 4.4% Falconer
(1989)
Pigs Body weight (154 2.6 kg Falconer
days) (1989)
Litter size 0.24 piglets Falconer
(1989)
Cattle Annual milk yield 135 kg Falconer
(1989)
Sheep Fleece weight (1 year) 0.29 kg Falconer
(1989)
Thus, 3 generations of full sib matings, as shown above, would lead to an expected
decrease in egg production in chickens of 9.26 x 5 = 46.3 i.e 46 eggs, compared with
other hens from the same population who were not inbred.
b) Assessing the Risk of Inheriting Genetic Defects
In a large random-mating population, where the frequency of a harmful recessive

gene (a) is q, the proportions of affected individuals and 'carriers' can be estimated
from the Hardy-Weinberg Lawas follows:
Aa (carriers) aa (affected)
2q(1 − q) q2
However, if any inbreeding has occurred,Wright's Equilibrium Lawenables a further

prediction to be made about the increased risk of inheriting any harmful conditions
caused by homozygous recessive genes.The expected frequency following
inbreeding rises to:
aa (affected)
q2 + Fq(1 - q)
The following table shows how inbreeding increases the likelihood of inheriting three
harmful recessive conditions in humans: phenylketonuria, albinism and
alkaptonuria.The first and last of these three are serious metabolic disorders.
Effects of Inbreeding on the Frequency of Inherited Defects:
Conditions Frequency Random Mating Proportion of
Caused by of Affected(aa)
Homozygous Recessive Following
Recessive Gene (a) Inbreeding
Genes q q2 + Fq(1 - q)2 [16]
Proportion Proportion First Full Sib
of of Affected Cousin Mating
Carriers Marriage (F = 1/4)
(aa) (F =
(Aa) 1/16)
q2
2q(1 - q)3
[16]
Phenylketonuria 1/100 1/50 1/10,000 1/1,380 1/385

Albinism 1/141 1/70 1/20,000 1/2,000 1/550
Alkaptonuria 1/1,000 1/500 1/1,000,000 1/16,000 1/4,000
Therefore, with albinism for example, a first cousin marriage increases the risk of
inheriting the condition ten-fold, and with alkaptonuria the increase following a full sib
mating is 250 fold. It also comes as quite a shock to most people that, even without
inbreeding, the proportion of normal people carrying phenylketonuria is as high as 1
in 50.
Inbreeding is a result of the mating of individuals which are related to one another by
having one or more common ancestors. If the mated individuals are related, their
offspring will to some extent be inbred.
4.5. The coefficient of inbreeding
The coefficient of inbreeding, is the probability that the two genes at any locus are
identical by descent.i.e. that the two genes are copies of one of the genes carried by
the common ancestor a few generations back. The coefficient of inbreeding,
symbolised by F, is a property of an individual, but inbreeding profoundly effects the
genetic composition of a population and in appropriate circumstances can lead to
the formation of inbred strains in which all individuals are virtually genetically
identical.
4.5.1. The rate of inbreeding depends on the degree of relationship
The closest relationship is that of an individual with itself, or self- fertilisation.

However, the closest relationship that is usually possible with mammals is full
brother x sister (known as full-sib) mating. Continuous mating of offspring to the
younger parent (which prevents repeated backcrossing to the same individual,
which would have different genetic consequences), or a single generation of parent
x offspring mating is genetically equivalent to full-sib mating.
Other regular mating systems which lead to a high level of inbreeding include half-
sib and cousin matings. Repeated backcrossing, say of a transgene or a new
mutation, to an inbred strain increases homozygosity as rapidly as self-fertilisation.
4.5.2. Inbreeding also arises as a result of restricted population size
In a closed colony it eventually becomes impossible to avoid the mating of related

individuals. Hence even “outbred” stocks maintained as a closed colony gradually
become inbred at a rate which depends on the size of the colony. Mathematical
explanations of the consequences of brother x sister mating and other regular
systems of inbreeding have been shown. Contrary to popular belief, avoiding
brother x sister mating in a small closed, random-mated population may reduce the
inbreeding of an individual but it does not reduce the over-all rate of inbreeding. This
is because the inbreeding will be undone in a subsequent generation.
Inbreeding is always expressed relative to an arbitrary starting point at which the

coefficient of inbreeding is assumed to be zero. Therefore, the magnitude of the
effects of inbreeding any specific population will depend on the previous history of
the stock, and the extent to which it has already been inbred.
Figure showing inbreeding as a result of restricted population size. A strain is

regarded as an “inbred strain” when the coefficient of inbreeding, F, is greater than
0.986, i.e. after 20 generations of sib-mating.
4.5.3. Full sib mating
Full sib inbreeding of a genetically heterogeneous stock doubles the total genetic
variation if all the sublines are kept. However, all the genetic variation will then be
due to differences betweensublines, with no genetic variation within sublines. The
phenotypic variation among sublines also increases. This is largely due to the
"uncovering" of recessive genes and genetic drift in which alleles at a particular
polymorphic locus become fixed in a homozygous state with plus or minus (with
respect to the character) alleles being fixed largely by chance. The phenotypic
variation among a set of inbred strains derived from an outbred stock is therefore
substantially greater than the phenotypic variation within the starting population.
The converse of this is also true. If several inbred strains are mixed together, then
the phenotypic variation in the combined population will be less than that of the
individual inbred strains taken together.
The coefficient of inbreeding never quite reaches 100 per cent. Therefore, no strain
is ever fully inbred. Moreover, the coefficient of inbreeding is calculated on the
assumption that the reproductive performance of heterozygotes is equal to that of
homozygotes, and that no mutation occurs. Both of these assumptions are incorrect,
and lead to a slight overestimate of the actual level of inbreeding. On the other hand,
it is assumed that the base population has a coefficient of inbreeding of zero. In
practice, many inbred strains are derived from outbred stocks which may have been
maintained as closed colonies with a restricted population size for many
generations, as a result of which they may already be highly inbred.
4.5.4. Inbreeding depression
Inbreeding depression is a decline in reproductive performance, ability to survive

and other characteristics associated with fitness as a result of inbreeding. It occurs
as a result of "uncovering" deleterious recessive genes by making them
homozygous and is a consequence of the evolution of dominance of loci concerned
with fitness characters. The direction of the change is towards the value of the more
recessive alleles. Inbreeding depression does not occur for those characters where
the heterozygote is intermediate between the two homozygotes.
The degree of inbreeding depression depends on the previous history of the stock. A
stock which has been kept as a closed population for many generations will already
be partly inbred; hence, full-sib mating may not result in much inbreeding
depression.
Inbreeding depression varies substantially among different lines. Anyone starting a

new inbreeding project should do so on a sufficiently large scale to allow for
extinction of a proportion of the lines during the first few generations. Once an inbred
strain has been established, no further inbreeding depression should occur. Any
decline in breeding performance will be due either to environmental influences
(particularly disease) or in some cases to new deleterious mutations becoming fixed
in the strain.
4.5.5. Inbred strains
The decision as to whether a strain is sufficiently inbred for any particular research
project is largely arbitrary. The Committee on Standardized Genetic Nomenclature
for Mice decided in 1952 that 20 generations of full-sib mating (or its genetic
equivalent), at which time F= 98.6 per cent, is the minimum level of inbreeding
required before a strain of mice can be designated as an inbred strain.
However, the coefficient of inbreeding never quite reaches 100 per cent so no strain
is ever fully inbred. Moreover, the coefficient of inbreeding is calculated on the
assumption that the reproductive performance of heterozygotes is equal to that of
homozygotes, and that no mutation occurs. Both of these assumptions are incorrect,
and lead to a slight overestimate of the actual level of inbreeding. But it is also
assumed that the base population has a coefficient of inbreeding of zero. Many
inbred strains are derived from outbred stocks which have been maintained as
closed colonies with a restricted population size for many generations, as a result of
which they may already be highly inbred.
Inbreeding is defined in terms of the probability of heterozygosity at a locus.

However, all inbred strains used in biomedical research should also be isogenic, i.e.
all individuals within an inbred strain should be genetically identical (apart from
residual segregation due to the impossibility of achieving fully inbred strains). In fact
it is isogenicity rather than homozygosity that is the most useful property of inbred
strains, and the two are distinct properties which should not be confused. Isogenicity
is achieved by ensuring that all individuals trace back to a common ancestral full-sib
breeding pair in the twentieth or a subsequent generation. All parallel substrains
should be eliminated. F1 hybrids, i.e. the first-generation cross between two inbred
strains, are isogenic but not homozygous. It is unfortunate that the terms inbred and
`outbred' which describe breeding methods rather than a genetic property of a group
of animals, have become so widely accepted.
Summary
Inbreeding is the mating of individuals more closely related to each other than the average
relationship within the population concerned. The incidence of metabolic disorders, structural
abnormalities and inherited disease conditions caused by harmful recessive genes increases
are results of inbreeding. Inbreeding can occur through self-fertilization and observed in
monoecious plants and hermaphrodite animals and also when parthenogenesis takes place.
Sibling marriages in humans, where marriage between brother and sister; or in cases where
there is direct relationship with parent (mating between father and daughter) and direct and
collaterally related parents. Inbreeding study is an important tool in predicting the effects of
inbreeding and assessing the risk of inheritable genetic defects. The rate of inbreeding
depends on the degree of relationship between the mating partners.
Conclusion
Inbreeding occur in both plants and animals. When they occur the results is
devastating. It has predictable effects and assessable risks in the populations. The
rate of which depend on how closely related the reproducing individuals are.
Selfassessment Assignments
1. Write short notes on the following:

i. Inbreeding depression
ii. Overdominance
iii. Epistasis
iv. Coefficient of inbreeding (F)
2. Comment on consangeinous marriages using the sibs and half sibs marriage
in the 18th dynasty of Egypt(1580-1350 BC)
3. Using 2 above, calculate the inbreeding coefficients for
i) Amenhotep I and Aahotep II

ii) Aames
iii) Hatsheput
Tutor Marked Assessment
1. How can you calculate the F coefficient for an individual?
References
2. Chahal, G.S and Gosal, S.S., 2002. Principles and procedures of Plant
3. Falconer, D.S., 1989. Introduction to Quantitative Genetics. 3rd Ed. Longman.
Burnt Mill.
4. Kwon-Ndung, E.H. 2008. Genetics for degree students. Afaku Publishers,
Abuja.
5. FrishM., and Elchinger, A.E., 2005. Selection Theory for Marker-assisted
6. Goussard, P.G. 2004. Improving grape vine material through selection.
7. Holsinger, K.E., 2000. Reproductive systems and evolution in vascular plants.
PNAS. June 20, vol. 97, no. 13: 7037-7042.
8. Kohli, M.M. and Francis, M., 2000. Application of biotechnologies to wheat
9. KWV, South Africa. (2005). Setting new global standards for vine plant
10. Takebayashi, N and Morell, P.L., 2001. Is self-fertilization an evolutionary
11. Charlesworth, D., X. Vekemans, V. Castric and S. Glemin (2005). "Plant self-
incompatibility systems: a molecular evolutionary perspective". New
12. Franklin, F. C. H., M. J. Lawrence, and V. E. Franklin-Tong (1995). "Cell and
13. Qiao, H., H. Wang, L. Zhao, J. Zhou, J. Huang, Y. Zhang, and Y. Xue (2004).
"The F-box protein AhSLF-S2 physically interacts with S-RNases that may be
inhibited by the ubiquitin/26S proteasome pathway of protein degradation
during compatible pollination in Antirrhinum". Plant Cell 16 (3): 582–95.
14. Green EL. Genetics and probability in animal breeding experiments. 271pp.
London and Basingstoke: The Macmillan Press Ltd., 1981.
15. McGregor, M.C. 1999. Hybrid vigor in plants and its relationship to insect
pollination — a section from Insect Pollination Of Cultivated Crop Plants by,
USDA
UNIT 5
5.0. Self-incompatibility in plants
Self-incompatibility (SI) is a general name for several genetic mechanisms in

angiosperms, which prevent self-fertilization and thus encourage outcrossing. In
plants with SI, when a pollen grain produced in a plant reaches a stigma of the same
plant or another plant with a similar genotype, the process of pollen germination,
pollen tube growth, ovulefertilization, and embryo development is halted at one of its
stages, and consequently no seeds are produced. SI is one of the most important
means to prevent selfing and promote the generation of new genotypes in plants,
and it is considered as one of the causes for the spread and success of the
angiosperms on the earth.
5.1. Mechanisms of self-incompatibility
The best studied mechanisms of SI act by. These mechanisms are based on protein-
protein interactions, each mechanism being controlled by a single locus termed S,
which has many different alleles in the species population. Despite their similar
morphological and genetic manifestations, these mechanisms have evolved
independently, and are based on different cellular components; therefore, each
mechanism has its own, unique S-genes.
The S-locus contains two basic protein coding regions - one expressed in the pistil,
and the other in the anther and/or pollen (referred to as the female and male
determinants, respectively). Because of their physical proximity, these are
genetically linked, and are inherited as a unit. The units are called S-haplotypes. The
translation products of the two regions of the S-locus are two proteins which, by
interacting with one another, lead to the arrest of pollen germination and/or pollen
tube elongation, and thereby generate an SI response, preventing fertilization.
However, when a female determinant interacts with a male determinant of a different
haplotype, no SI is created, and fertilization ensues. This is a simplistic description of
the general mechanism of SI, which is more complicated, and in some species the
S-haplotype contains more than two protein coding regions.
Following is a detailed description of the different known mechanisms of SI in plants.
5.2. Gametophytic self-incompatibility (GSI)
In gametophytic self-incompatibility (GSI), the SI phenotype of the pollen is

determined by its own gametophytichaploid genotype. This is the more common type
of SI, existing in the families: Solanaceae, Rosaceae, Plantaginaceae, Fabaceae,
Onagraeae, Campanulaceae, Papaveraceae and Poaceae. Two different
mechanisms of GSI have been described in detail at the molecular level, and their
description follows.
5.2.1. The RNase mechanism
The female component of GSI in the Solanaceae was found in 1989. Proteins in the
same family were subsequently discovered in the Rosaceae and Plantaginaceae.
Despite some early doubts about the common ancestry of GSI in these distantly
related families, phylogenetic studies and the finding of shared male determinants
(F-box proteins)clearly established homology. Consequently, this mechanism arose
approximately 90 million years ago, and is the inferred ancestral state for
approximately 50% of all plants.
In this mechanism, pollen tube elongation is halted when it has proceeded

approximately one third of the way through the style. The female component
ribonuclease, termed S-RNase probably causes degradation of the ribosomal RNA
(rRNA) inside the pollen tube, in the case of identical male and female S alleles, and
consequently pollen tube elongation is arrested, and the pollen grain dies.
The male component was only recently putatively identified as a member of the "F-
box" protein family. Despite some fairly convincing evidence that it may be the male
component, several features also make it an unlikely candidate.
5.2.2. The S-glycoprotein mechanism
The following mechanism was described in detail in Papaverrhoeas. In this

mechanism, pollen growth is inhibited within minutes of its placement on the stigma.
The female determinant is a small, extracellular molecule, expressed in the stigma;

mthe identity of the male determinant remains elusive, but it is probably some cell
membranereceptor. The interaction between male and female determinants
transmits a cellular signal into the pollen tube, resulting in strong influx of
calciumcations; this interferes with the intracellular concentration gradient of calcium
ions which exists inside the pollen tube, essential for its elongation.The influx of
calcium ions arrests tube elongation within 1-2 minutes. At this stage, pollen
inhibition is still reversible, and elongation can be resumed by applying certain
manipulations, resulting in ovule fertilization.
Subsequently, the cytosolic protein p26, a pyrophosphatase, is inhibited by

phosphorylation, possibly resulting in arrest of synthesis of molecular building blocks,
required for tube elongation. There is depolymerization and reorganization of actin
filaments, within the pollen cytoskeleton. Within 10 minutes from the placement on
the stigma, the pollen is committed to a process which ends in its death. At 3-4 hours
past pollination, fragmentation of pollen DNAbegins,and finally (at 10-14 hours), the
cell dies apoptotically.
5.2.3. Sporophytic self-incompatibility (SSI)
In sporophytic self-incompatibility (SSI), the SI phenotype of the pollen is

determined by the diploid genotype of the anther (the sporophyte) in which it was
created. This form of SI was identified in the families: Brassicaceae, Asteraceae,
Convolvulaceae, Betulaceae, Caryophyllaceae, Sterculiaceae and Polemoniaceae.
Up to this day, only one mechanism of SSI has been described in detail at the
molecular level, in Brassica (Brassicaceae).
Since SSI is determined by a diploid genotype, the pollen and pistil each express the
translation products of two different alleles, i.e. two male and two female
determinants. Dominance relationships often exist between pairs of alleles, resulting
in complicated patterns of compatibility/self-incompatibility. These dominance
relationships also allow the generation of individuals homozygous for a recessive S
allele.
Compared to a population in which all S alleles are co-dominant, the presence of

dominance relationships in the population, raises the chances of compatible mating
between individuals. The frequency ratio between recessive and dominant S alleles,
reflects a dynamic balance between reproduction assurance (favoured by recessive
alleles) and avoidance of selfing (favoured by dominant alleles).
5.2.4. The SI mechanism in Brassica
As previously mentioned, the SI phenotype of the pollen is determined by the diploid

genotype of the anther. In Brassica, the pollen coat, derived from the anther's
tapetumtissue, carries the translation products of the two S alleles. These are small,
cysteine-rich proteins. The male determinant is termed SCR or SP11, and is
expressed in the anther tapetum (i.e. sporophytically), as well as in the microspore
and pollen (i.e. gametophytically).There are possibly up to 100 polymorphs of the S-
haplotype in Brassica, and within these there is a dominance hierarchy.
The female determinant of the SI response in Brassica, is a transmembrane protein

termed SRK, which has an intracellular kinase domain, and a variable extracellular
domain. SRK is expressed in the stigma, and probably functions as a receptor for the
SCR/SP11 protein in the pollen coat. Another stigmatic protein, termed SLG, is
highly similar in sequence to the SRK protein, and seems to function as a co-
receptor for the male determinant, amplifying the SI response.
The interaction between the SRK and SCR/SP11 proteins results in

autophosphorylation of the intracellular kinase domain of SRK, and a signal is
transmitted into the papilla cell of the stigma. Another protein essential for the SI
response is MLPK, a serine-threonine kinase, which is anchored to the plasma
membrane from its intracellular side. The downstream cellular and molecular events,
leading eventually to pollen inhibition, are poorly described.
5.2.5. Other mechanisms of self-incompatibility
These mechanisms are less abundant and have received only limited attention in
scientific research. Therefore, they are still poorly understood.
5.3. Heteromorphic self-incompatibility
A distinct SI mechanism exists in heterostylous flowers, termedheteromorphic self-

incompatibility. This mechanism is probably not evolutionarily related to the more
familiar mechanisms, which are differentially defined as homomorphic self-
incompatibility.Almost all heterostylous taxa feature SI to some extent. The loci
responsible for SI in heterostylousflowers, are strongly linked to the loci responsible
for flower polymorphism, and these traits are inherited together. Distyly is determined
by a single locus, which has two alleles; tristyly is determined by two loci, each with
two alleles. Heteromorphic SI is sporophytic, i.e. both alleles in the male plant,
determine the SI response in the pollen. SI loci always contain only two alleles in the
population, one of which is dominant over the other, in both pollen and pistil.
Variance in SI alleles parallels the variance in flower morphs, thus pollen from one
morph can fertilize only pistils from the other morph. In tristylous flowers, each flower
contains two types of stamens; each stamen produces pollen capable of fertilizing
only one flower morph, out of the three existing morphs.
A population of a distylous plant contains only two SI genotypes: ss and Ss.

Fertilization is possible only between genotypes; each genotype cannot fertilize itself.
This restriction maintains a 1:1 ratio between the two genotypes in the population;
genotypes are usually randomly scattered in space. Tristylous plants contain, in
addition to the S locus, the M locus, also with two alleles.The number of possible
genotypes is greater here, but a 1:1 ratio exists between individuals of each SI type.
5.4. Cryptic self-incompatibility (CSI)
Cryptic self-incompatibility (CSI) exists in a limited number of taxa (for example,

there is evidence for CSI in Silene vulgaris, Caryophyllaceae. In this mechanism, the
simultaneous presence of cross and self pollen on the same stigma, results in higher
seed set from cross pollen, relative to self pollen. However, as opposed to 'complete'
or 'absolute' SI, in CSI, self-pollination without the presence of competing cross
pollen, results in successive fertilization and seed set; in this way, reproduction is
assured, even in the absence of cross-pollination. CSI acts, at least in some species,
at the stage of pollen tube elongation, and leads to faster elongation of cross pollen
tubes, relative to self pollen tubes. The cellular and molecular mechanisms of CSI
have not been described.
The strength of a CSI response can be defined, as the ratio of crossed to selfed
ovules, formed when equal amounts of cross and self pollen, are placed upon the
stigma.
5.5. Late-acting self-incompatibility (LSI)
Late-acting self-incompatibility (LSI) is also termed ovarian self-incompatibility (OSI).

In this mechanism, self pollen germinates and reaches the ovules, but no fruit is set.
LSI can be pre-zygotic (e.g. deterioration of the embryo sac prior to pollen tube
entry, as in Narcissus triandrus) or post-zygotic (malformation of the zygote or
embryo, as in certain species of Asclepias and in Spathodeacampanulata.
The existence of the LSI mechanism among different taxa and in general, is subject
for scientific debate. Criticizers claim, that absence of fruit set is due to genetic
defects (homozygosity for lethal recessive alleles), which are the direct result of self-
fertilization (inbreeding depression).Supporters, on the other hand, argue for the
existence of several basic criteria, which differentiate certain cases of LSI from the
inbreeding depression phenomenon.
5.6. Self-compatibility (SC)
SI is not universal in flowering plants. Indeed, a great many species are self-
compatible (SC). The best estimates indicate that approximately one half of
angiosperm species are SI. Pollinator decline, variability in pollinator service, and life
history traits that are associated with weediness, and the so-called "automatic
advantage" of self-fertilisation, among other factors, may favor the loss of SI. As a
result, mutations that break down SI (result in SC) may become common or entirely
dominate in natural populations. Similarly, human-mediated artificial selection
through selective breeding may be responsible for the commonly observed SC in
cultivated plants. SC enables more efficient breeding techniques to be employed for
crop improvement.
Summary
Self-incompatibility (SI) is a genetic mechanisms in angiosperms, which prevent self-

fertilization and thus encourage outcrossing. In plants with SI, the process of pollen
germination, pollen tube growth, ovulefertilization, and embryo development is halted
at one of its stages, and consequently no seeds are produced.SI is one of the most
important means to prevent selfing and promote the generation of new genotypes in
plants.This is achieved by inhibiting the germination of pollen on stigmas, or the
elongation of the pollen tube in the styles. These mechanisms are based on protein-
protein interactions, each being controlled by a single locus termed S, with many
different alleles in the species population.These mechanisms have evolved
independently, and are based on different cellular components thus, each
mechanism has its own, unique S-genes.
Conclusion
Self Incompatibility (SI) is one of the most important means to prevent selfing and
promote the generation of new genotypes in plants, and it is considered as one of
the causes for the spread and success of the angiosperms on the earth.
1. Enumerate the role of self-incompatibility in the evolution of plants
Tutor marked assessment
1. Differentiate between gametophytic and sporophyticself-incompatibility
References
2 Falconer, D.S., 1989. Introduction to Quantitative Genetics. 3rd Ed. Longman.
Burnt Mill.
Abuja.
6 Holsinger, K.E., 2000. Reproductive systems and evolution in vascular plants.
PNAS. June 20, vol. 97, no. 13: 7037-7042.
10 Charlesworth, D., X. Vekemans, V. Castric and S. Glemin (2005). "Plant self-
11 Franklin, F. C. H., M. J. Lawrence, and V. E. Franklin-Tong (1995). "Cell and
12 Qiao, H., H. Wang, L. Zhao, J. Zhou, J. Huang, Y. Zhang, and Y. Xue (2004).
13 Green EL. Genetics and probability in animal breeding experiments. 271pp.
14 McGregor, M.C. 1999. Hybrid vigor in plants and its relationship to insect
USDA
Unit 6
6.0. Cytoplasmic male sterility
Cytoplasmic male sterility is the total or partial male sterility associated with plant
biology as the result of specific nuclear and mitochondrial interactions. Male sterility
is the failure of plants to produce functional anthers, pollen, or male gametes.
The first documentation of male sterility came in Joseph Gottlieb Kölreuter observed
anther abortion within species and specific hybrids. Cytoplasmic male sterility has
now been identified in over 150 plant species. It is more prevalent than female
sterility, either because the male sporophyte and gametophyte are less protected
from the environment than the ovule and embryo sac, or because it results from
natural selection on mitochondrial genes which are maternally inherited and are thus
not concerned with pollen production. Male sterility is easy to detect because a large
number of pollen grains are produced and are easily studied. Male sterility is
assayed through staining techniques (carmine, lactophenol or iodine); while
detection of female sterility is detectable by the absence of seeds. Male sterility has
propagation potential in nature since it can still set seed and is important for crop
breeding, while female sterility does not. Male sterility can be aroused spontaneously
via mutations in nuclear and/or cytoplasmic genes.
Male sterility can be either cytoplasmic or cytoplasmic-genetic. Cytoplasmic male
sterility (CMS) is caused by the extranuclear genome (mitochondria or chloroplast)
and shows maternal inheritance. Manifestation of male sterility in CMS may be either
entirely controlled by cytoplasmic factors or by the interaction between cytoplasmic
and nuclear factors.
Cytoplasmic male sterility, as the name indicates, is under extra-nuclear genetic

control (under the control of the mitochondrial or plastid genomes). They show non-
Mendelian inheritance and are under the regulation of cytoplasmic factors. In this
type, male sterility is inherited maternally. In general there are two types of
cytoplasm: N (normal) and the aberrant S (sterile) cytoplasms. These types exhibit
reciprocal differences.
6.1. Cytoplasmic-genetic male sterility
While CMS is controlled by an extranuclear genome often times nuclear genes can
have the capability to restore fertility. When nuclear restorations of fertility genes
(“Rf”) are available for CMS system in any crop, it is cytoplasmic-genetic male
sterility; the sterility is manifested by the influence of both nuclear (Mendelian
inheritance) and cytoplasmic (maternally inherited) genes. There are also restorers
of fertility (Rf) genes, which are distinct from genetic male sterility genes. The Rf
genes do not have any expression of their own unless the sterile cytoplasm is
present. Rf genes are required to restore fertility in S cytoplasm which causes
sterility. Thus N cytoplasm is always fertile and S cytoplasm with genotype Rf-
produces fertiles; while S cytoplasm with rfrf produces only male steriles. Another
feature of these systems is that Rf mutations (i.e., mutations to rf or no fertility
restoration) are frequent, so N cytoplasm with Rfrf is best for stable fertility.
Cytoplasmic-genetic male sterility systems are widely exploited in crop plants for
hybrid breeding due to the convenience to control the sterility expression by
manipulating the gene–cytoplasm combinations in any selected genotype.
Incorporation of these systems for male sterility evades the need for emasculation in
cross-pollinated species, thus encouraging cross breeding producing only hybrid
seeds under natural conditions.
6.2. Cytoplasmic male sterility in hybrid breeding
Hybrid production requires a female plant in which no viable male gametes are
borne. Emasculation is done to make a plant devoid of pollen so that it is made
female. Another simple way to establish a female line for hybrid seed production is to
identify or create a line that is unable to produce viable pollen. This male sterile line
is therefore unable to self-pollinate, and seed formation is dependent upon pollen
from the male line.
Cytoplasmic male sterility is used in hybrid seed production. In this case, the sterility
is transmitted only through the female and all progeny will be sterile. This is not a
problem for crops such as onions or carrots where the commodity harvested from
the F1 generation is produced during vegetative growth. These CMS lines must be
maintained by repeated crossing to a sister line (known as the maintainer line) that is
genetically identical except that it possesses normal cytoplasm and is therefore male
fertile. In cytoplasmic-genetic male sterility restoration of fertility is done using
restorer lines carrying nuclear restorer genes in crops. The male sterile line is
maintained by crossing with a maintainer line which has the same genome as that of
the MS line but carrying normal fertile cytoplasm.
6.3. Cytoplasmic male sterility in hybrid maize breeding
Cytoplasmic male sterility is an important part of hybrid maize production. The first
commercial cytoplasmic male sterile, discovered in Texas, is known as CMS-T. The
use of CMS-T, starting in the 1950s, eliminated the need for detasseling. In the early
1970’s plants containing CMS-T genetics were susceptible to southern corn leaf
blight and suffered from widespread loss of yield. Since then CMS types C and S are
used instead.Unfortunately these types are prone to environmentally induced fertility
restoration and must be carefully monitored in the field. Environmentally induced
restoration is when certain environmental stimuli signal the plant to bypass sterility
restrictions and produce pollen anyway. Environmentally induced restoration differs
from genetic restoration in that it is rooted in external signals rather than genetic
DNA.The systematic sequencing of new plant species in recent years has uncovered
the existence of several novel RF genes and their encoded proteins. A unified
nomenclature for the RF extended protein families across all plant species,
fundamental in the context of comparative functional genomics. This unified
nomenclature accommodates functional RF genes and pseudogenes, and offers the
flexibility needed to incorporate additional RFs as they become available in future.
Summary
Male sterility is the failure of plants to produce functional anthers, pollen, or male
gametes.Cytoplasmic male sterility is the total or partial male sterility as the result of specific
nuclear and mitochondrial interactions. It is prevalent in males because the male sporophyte
and gametophyte are less protected from the environment than the ovule and embryo sac,
and the natural selection on mitochondrial genes which are maternally inherited and are thus
not concerned with pollen production. Cytoplasmic male sterility is used in hybrid seed
production
Conclusion
Cytoplasmic male sterility is used in hybrid seed production.
1. Differentiate between cytoplasmic male sterility and cytoplasmic-genetic male

sterility
1. Discuss the role of cytoplasmic male sterility in hybrid maize breeding

References
Burnt Mill.
Abuja.
PNAS. June 20, vol. 97, no. 13: 7037-7042.
USDA
Unit 7
7.0. Breeding methods
7.1. Mode of reproduction
The mode of reproduction of a crop determines its genetic composition, which, in

turn, is the deciding factor to develop suitable breeding and selection methods.
Knowledge of mode of reproduction is also essential for its artificial manipulation to
breed improved types. Only those breeding and selection methods are suitable for a
crop which does not interfere with its natural state or ensure the maintenance of
such a state. It is due to such reasons that imposition of self-fertilization on cross-
pollinating crops leads to drastic reduction in their performance.
For this teaching purpose, plant breeding methods are presented as four categories:
Line breeding (autogamous crops), population breeding (allogamous crops), hybrid
breeding (mostly allogamous crops, some autogamous crops), clone breeding
(vegetatively propagated crops).
7.1. Self fertilizing crops or autogamous crops.
Certain restrictions caused the mechanisms for self fertilization (partial and full self
fertilization) to develop in a number of plant species. Some of the reasons why a self
fertilizing method of reproduction is so effective are the efficacy of reproduction, as
well as decreasing genetic variation and thus the fixation of highly adapted
genotypes. Almost no inbreeding depression occurs in self fertilizing plants because
the mode of reproduction allows natural selection to take place in wild populations of
such plants.
Critical steps in the improvement of self fertilizing crops are the choice of parents
and the identification of the best plants in segregating generations. The breeder
should also have definite goals with the choice of parents. Self fertilizing are easier
to maintain, but this could lead to misuse of seed.
Some farm and domestic important, self fertilizing crops include rice, maize,
Sorghum, Millets, cowpea beans, soy beans, groundnuts, potatoes and tomatoes,
etc.
7.2. Mass selection
This method of selection depends mainly on selection of plants according to their

phenotype and performance. The seed from selected plants are bulked for the next
generation. This method is used to improve the overall population by positive or
negative mass selection. Mass selection is only applied to a limited degree in self
fertilizing plants and is an effective method for the improvement of land races. This
method of selection will only be effective for highly heritable traits. One shortage of
mass selection are the large influence that the environment has on the development,
phenotype and performance of single plants.
A plant developed by this method will be more uniform than those developed by
mass selection because all of the plants in such a variety will have the same
genotype. The seed from selected plants are not added together but are kept apart
and used to perform offspring tests. This is done to study the breeding behaviour of
the selected plant.
Stratified mass selection for ear size over 22 cycleshas drastically altered plant
phenotype in the maize population Zacatecas 58. Plants in the C22 cycle were
50 cm taller, had twice the leaf area index, reached anthesis 7 days later and had a
30% higher harvest index than C0. Differences in growth were detected early in
ontogeny. The root growth of C22 exceeded that of C0 and the ratio of shoot dry
mass to root dry mass was reduced by nearly 12%, from 8.0±0.2 to 7.1±0.1. Analysis
of yield components revealed that C22 was superior to C0 in grain weight, number of
rows per ear, number of grains per row, and total yield per unit area. Because the
two genotypes were phenologically different, planting density optima are probably
different for each population.
7.3. Selection of cross-pollinated crops
Plant species where normal mode of seed set is through a high degree of cross-
pollination have characteristic reproductive features and population structure.
Existence of self-sterility, self-incompatibility, imperfect flowers, and mechanical
obstructions make the plant dependent upon foreign pollen for normal seed set.
Each plant receives a blend of pollen from a large number of individuals each having
different genotypes. Such populations are characterized by a high degree of
heterozygosity with tremendous free and potential genetic variation, which is
maintained in a steady state by free gene flow among individuals within the
populations.
In the development of hybrid varieties, the aim is to identify the most productive
heterozygote from the population, which then is produced with the exclusion of other
members of the population.
7.4. Mass selection
It is the simplest, easiest and oldest method of selection where individual plants are
selected based on their phenotypic performance, and bulk seed is used to produce
the next generation by mixing it. Mass selection proved to be quite effective in maize
improvement at the initial stages but its efficacy especially for improvement of yield,
soon came under severe criticism that culminated in the refinement of the method of
mass selection. The selection after pollination does not provide any control over the
pollen parent as result of which effective selection is limited only to female parents.
The heritability estimates are reduced by half, since only parents are used to harvest
seed whereas the pollen source is not known after the cross pollination has taken
place.
7.5. Recurrent selection
This type of selection is a refined version of the mass selection procedure and differs
as follows:
 Visually selected individuals out of the base population undergo progeny testing
 Individuals selected on basis of the progeny test data are crossed with each
other in every possible way to produce seed to form the new base population.
7.5.1. Half-sib selection with progeny testing
Selections are made based on progeny test performance instead of phenotypic

appearance of the parental plants. Seed from selected half-sibswhich have been
pollinated by random pollen from the population, is grown in unreplicated progeny
rows for the purpose of selection. A part of the seed is planted to determine the
yielding ability, or breeding value, for any character of each plant. The seed from the
most productive rows or remnant seed from the outstanding half-sibs is bulked to
complete one cycle of selection.
7.5.2. Full-sib selection with progeny testing
A number of full-sib families, each produced by making crosses between the two
plants from the base population are evaluated in replicated trials. A part of each full-
sib family is saved for recombination. Based on evaluation the remnant seed of
selected full-sib families is used to recombine the best families.
7.6. Breeding of Asexually Propagated Crops
Asexual reproduction covers all those modes of multiplication of plants where normal
gamete formation and fertilization does not take place making these distinctly
different from normal seed production crops. In the absence of sexual reproduction,
the genetic composition of plant material being multiplied remains essentially the
same as its source plant.
Clones of mother plants can be made with the exact genetic composition of the
mother plant. Superior plants are selected and propagated vegetatively; the
vegetative propagated offspring are used to develop stable varieties without any
deterioration due to segregation of gene combinations. This unique characteristic of
asexual reproduction helped to develop a number of cultivars of fruits and
vegetables including grapes, apples, pears and peaches.
7.6.1. Improving asexual plant material through selection
The selection in these crops is restricted to the material introduced from other
sources, such as field plantations. The improvement of asexually propagated plants
through induced mutations has distinct advantages and limitations. Any vegetative
propagule can be treated with mutagens and even a single desirable mutant or a
part of a mutated propagule (chimera) can be multiplied as an improved type of the
original variety.
7.6.2. Selection of asexual plants
Selection, in the case of asexual plants, can be defined as the selection of the best
performing plant and the vegetative propagation thereof. Because plants are not
totally genetically stable, it can be expected that deviations would occur through the
years. Selection is thus an ongoing process where deviants are selected or removed
from the selection program. The main purpose of selection is to better the quality and
yield of forthcoming plantations. Different approaches can be followed in the
selection process of asexual plants, such as mass selection and clone selection from
clone blocks.
In mass selection there are some factors that must be considered when selecting
plants in a mother block, e.g. vineyard. Time of selection is a big factor, because you
have to select when most of the characteristics of the plant are clearly showing. With
asexual perennials the best time is just before harvest. For the best results the
selected plant must be evaluated during the next season, when growth-
abnormalities, leave disfigurations and virus symptoms are best visualized. Mass
selection is done annually on the same plant for a minimum of three years. A plant
that does not conform to the requirements in any given year of the selection cycle is
discarded from the program.
7.6.3. New clone development
The development and registration of new clones take place by means of local clone
selection in old plantations, as well as the importation of high quality clones from
abroad, for local evaluation.
A clone is the vegetative offspring of one specific mother plant; it does not show any
genetic, morphologic or physiologic deviations from the mother plant. Evaluation
takes place with the different selected clones after selection.Some plants reproduce
by (more or less strict) self-fertilization where pollen from a plant will fertilise
reproductive cells or ovules of the same plant. Other plants only (mainly) allow cross-
pollination where pollen from one plant can only fertilize a different plant.
Asexual propagation (vegetative propagation) can also occur in plants (e.g. runners
from sweet potato Ipomeabatatasplant or suckers from Plantains or bananas Musa
spp.) which gives a new plant which is genetically identical to its parent plant. All
these differences change the way plant breeders work. Apomixis is the phenomenon
that seeds are produced, but in an essentially asexual way, so that parent and
offspring belong to one clonejust as in case of 'normal' asexual propagation.
Summary
Plant breeding methods are in four categories: Line breeding (autogamous crops),
population breeding (allogamous crops), hybrid breeding (mostly allogamous crops,
some autogamous crops) and clone breeding (vegetatively propagated crops). To
develop suitable breeding and selection methods the knowledge of the mode of
reproduction is essential for its artificial manipulation to breed improved types.
Conclusion
Breeding and selection methods are suitable for a crop production to ensure food
security.
1. Differentiate between autogamous, allogamous and clonal crops. Give

specific examples
2. Explain the breeding procedures for self pollinating and cross pollinating
crops
1. Write concise notes on:
i. Recurrent selection
ii. Mass selection
iii. Progeny testing
References

Burnt Mill.
Abuja.
PNAS. June 20, vol. 97, no. 13: 7037-7042.
USDA
UNIT 8
8.0. Disease and pest resistance and their inheritance
8.1. Plant Breeding for Disease Resistance
Plant breeders focus a significant part of their effort on selection and development of
disease-resistant plant lines. Plant diseases can also be partially controlled by use of
pesticides, and by cultivation practices such as crop rotation, tillage, planting density,
purchase of disease-free seeds and cleaning of equipment, but plant varieties with
inherent (genetically determined) disease resistance are generally the first choice for
disease control. Breeding for disease resistance has been underway since plants
were first domesticated, but it requires continual effort. This is because pathogen
populations are often under natural selection for increased virulence, new pathogens
can be introduced to an area, cultivation methods can favor increased disease
incidence over time, changes in cultivation practice can favor new diseases, and
plant breeding for other traits can disrupt the disease resistance that was present in
older plant varieties. A plant line with acceptable disease resistance against one
pathogen may still lack resistance against other pathogens.
8.1.1. Plant breeding for disease resistance typically includes:
 Identification of resistant breeding sources (plants that may be less desirable

in other ways, but which carry a useful disease resistance trait). Ancient plant
varieties and wild relatives are very important to preserve because they are
the most common sources of enhanced plant disease resistance.
 Crossing of a desirable but disease-susceptible plant variety to another
variety that is a source of resistance, to generate plant populations that mix
and segregate for the traits of the parents.
 Growth of the breeding populations in a disease-conducive setting. This may
require artificial inoculation of pathogen onto the plant population. Careful
attention must be paid to the types of pathogen isolates that are present, as
there can be significant variation the effectiveness of resistance against
different isolates of the same pathogen species.
 Selection of disease-resistant individuals. It is essential to note that breeders
are trying to sustain or improve numerous other plant traits related to plant
yield and quality, including other disease resistance traits, while they are
breeding for improved resistance to any particular pathogen.
Each of the above steps can be difficult to successfully accomplish, and many highly
refined methods in plant breeding and plant pathology are used to increase the
effectiveness and reduce the cost of resistance breeding.
Resistance is termed durable if it continues to be effective over multiple years of

widespread use, but some resistance “breaks down” as pathogen populations evolve
to overcome or escape the resistance. Resistance that is specific to certain races or
strains of a pathogen species is often controlled by single R genes and can be less
durable; broad-spectrum resistance against an entire pathogen species is often
quantitative and only incompletely effective, but more durable, and is often controlled
by many genes that segregate in breeding populations. However, there are
numerous exceptions to the above generalized trends, which were given the names
vertical resistance and horizontal resistance, respectively, by J.E. Vanderplank.
Crops such as potato, apple, banana and sugarcane are often propagated by
vegetative reproduction to preserve highly desirable plant varieties, because for
these species, outcrossing seriously disrupts the preferred plant varieties. See also
asexual propagation. Vegetatively propagated crops may be among the best targets
for resistance improvement by the biotechnology method of plant transformation to
add individual genes that improve disease resistance without causing large genetic
disruption of the preferred plant varieties.
8.1.2. Host Range
There are thousands of species of plant pathogenic microorganisms. Only a small

minority of these pathogens have the capacity to infect a broad range of plant
species. Most pathogens instead exhibit a high degree of host-specificity. Non-host
plant species are often said to express non-host resistance. The term host
resistance is used when a pathogen species can be pathogenic on the host species
but certain strains of that plant species resist certain strains of the pathogen species.
There can be overlap in the causes of host resistance and non-host resistance.
Pathogen host range can change quite suddenly if, for example, the capacity to
synthesize a host-specific toxin or effector is gained by gene shuffling/mutation, or by
horizontal gene transfer from a related or relatively unrelated organism.
8.1.3. Epidemics and Population Biology
Plants in native populations are often characterized by substantial genotype diversity

and dispersed populations (growth in a mixture with many other plant species). They
also have undergone millions of years of plant-pathogen coevolution. Hence as long
as novel pathogens are not introduced from other parts of the globe, natural plant
populations generally exhibit only a low incidence of severe disease epidemics. In
agricultural systems, humans often cultivate single plant species at high density, with
numerous fields of that species in a region, and with significantly reduced genetic
diversity both within fields and between fields. In addition, rapid travel of people and
cargo across large distances increases the risk of introducing pathogens against
which the plant has not been selected for resistance. These factors make modern
agriculture particularly prone to disease epidemics. Common solutions to this
problem include constant breeding for disease resistance, use of pesticides to
suppress recurrent potential epidemics, use of border inspections and plant import
restrictions, maintenance of significant genetic diversity within the crop gene pool.
Crop diversity, and constant surveillance for disease problems to facilitate early
initiation of appropriate responses. Some pathogen species are known to have a
much greater capacity to overcome plant disease resistance than others, often
because of their ability to evolve rapidly and to disperse broadly.
8.1.4. Epidemic
In epidemiology, an epidemic (epi- meaning "upon or above" and demic- meaning

"people"), occurs when new cases of a certain disease, in a given human population,
and during a given period, substantially exceed what is "expected," based on recent
experience (the number of new cases in the population during a specified period of
time is called the "incidence rate"). (An epizootic is the analogous circumstance
within an animal population.) In recent usages, the disease is not required to be
communicable; examples include cancer or heart disease. Another example includes
the infamous Black Plague of the Middle Ages.
8.1.5. Classification
Defining an epidemic can be subjective, depending in part on what is "expected". An

epidemic may be restricted to one locale (an outbreak), more general (an
"epidemic") or even global (pandemic). Because it is based on what is "expected" or
thought normal, a few cases of a very rare disease may be classified as an
"epidemic," while many cases of a common disease (such as the common cold)
would not.
8.1.6. Syndemics
The term syndemic refers to interacting epidemics that increase the health burden of
affected populations. Social conditions that heighten the health risk of populations
(e.g. poverty, discrimination and stigmatization, and marginalization) by increasing
stress, malnutrition, interpersonal violence, and the experience of deprivation,
increase the clustering of epidemic diseases and the likelihood of their interacting.
8.1.7. Non-infectious disease usage
The term "epidemic" is often used in a sense to refer to widespread and growing
societal problems, for example, in discussions of obesity or drug addiction. It can
also be used metaphorically to relate a type of problem like those mentioned above.
8.1.8. Factors stimulating new epidemics
Factors that have been described to stimulate the rise of new epidemics include:
1. Alterations in agricultural practices and land usage

2. Changes in society and human demographics
3. Poor population health (e.g., malnutrition, high prevalence of HIV)
4. Hospitals and medical procedures
5. Evolution of the pathogen (e.g., increased virulence, drug resistance)
6. Contamination of water supplies and food sources
7. International travel
8. Failure of public health programs
9. International trade
10. Climate change
11. Reduced levels of biodiversity (e.g. through environmental destruction)
12. Bad urban planning
8.2. Breeding for pest resistance

8.2.1. Resistance Breeding Before Mendel
Wild relatives of crop plants such as beans, wheat, and maize are not uniformly
resistant to insect and disease pests. This can be demonstrated in simple fashion—
when selections of these wild populations are set out in plant-rows, some of them
are highly susceptible, others are resistant, and some are intermediate in resistance
to the common pests of the region. The first plant breeders, those women and men
who domesticated crops such as beans, maize, and wheat, could save only those
genotypes that had some level of resistance, i.e., those individual plants that did not
succumb to pest depredation. In effect, therefore, they selected for pest resistance
and thus changed the population structure of their crop species in favor of resistance
genes. This change made it possible to grow the crops in monoculture, which was
convenient for food production and harvest. It was also convenient for multiplication
of disease and insect pests that might not be affected by the limited sample of
resistance genes.
Plant breeding thus set the stage for sequential cycles of pest resistance and pest
susceptibility of crop plants. We have no direct record of the consequences of this
ancient ecological meddling, but myth and historical accounts tell of disastrous
disease epidemics and insect outbreaks, so one can assume that from time to time
large plantings of crops that were uniformly susceptible to a new kind of insect or
disease fostered increases of that pest to epidemic proportions. Resistance genes
were essential for crop domestication and monoculture but they did not guarantee
perfect safety.
We have no record at all and little or no speculation about how the newly
domesticated crops might have affected their wild relatives, which no doubt were
growing in close proximity to the domesticates.
8.2.2. Resistance Breeding After Mendel
Genetics-based plant breeding, launched in the early years of the 20th century,
produced new crop varieties with improved resistance to major disease and insect
pests. Usually such resistance was developed as a second phase—a rescue
operation—after new varieties, selected primarily for high yield, were discovered to
be susceptible to a particular insect or disease. Breeders found early on that they
could identify single genes (usually dominant) that conferred essentially complete
resistance to the pest in question. Varieties containing such excellent resistance
were developed and released for large-scale farmer use. But breeders then
discovered, all too often, that the "perfect" resistance lost its effectiveness after a few
seasons. They soon learnt, with the aid of entomologists and plant pathologists, that
insect and disease pests are highly diverse genetically, and that almost without fail a
rare pest genotype will turn up (or perhaps be created de novo by natural mutation)
that is not affected by the newly-deployed resistance gene. The new pest genotype
multiplies and the crop variety’s resistance "breaks down."
As years went by, breeders found that some kinds of resistance did not fail, and that
such resistance often was less than complete; the plants suffered some damage but
gave performance overall. This longer lasting resistance was dubbed "durable"
resistance. Further, the breeders discovered that durable resistance usually (but not
always) was governed by several genes rather than by one major gene. The
multifactorial kind of resistance has been called "horizontal resistance." The major-
gene resistance has been called "vertical resistance."
The good news, then, was that breeders could identify and breed for durable
resistance. The bad news was that the breeding was more difficult because several
genes had to be transferred at one time, thus requiring larger populations for
selection, as well as multiplying the usual problems with "linkage drag" (undesirable
genes that are tightly linked to the desired ones). To this day, breeders use both
kinds of resistance in varying proportions, according to the crop and where it is
grown.
At first, breeders found and used resistance genes from the adapted, local landrace
populations that also were the initial gene pool as a source of resistance genes for
their new varieties. As years went by, these gene pools began to dry up and
breeders looked further afield, turning to exotic (unadapted) landraces, and even to
wild relatives of their crop. Sometimes they made extraordinary efforts to hybridize
the domestic crop with a very distant wild relative—making a cross that could not
succeed under natural conditions. Embryo rescue and even x-ray treatments were
used to make "unnatural" crosses and derive breeding progeny from them. The
breeders fooled around with Mother Nature; they moved genes farther than natural
processes would allow.
But the breeders as a whole preferred to not breed from exotic varieties or distant
and often wild relatives. They used exotic material only when there was no other
choice. This preference was due not only to the difficulty of wide hybridization, but
also to the fact that exotic germplasm exacerbates the problem of undesirable
linkages. Few or none of the foreign genes—except the desired resistance genes—
were suitable for the needs of high yielding, locally adapted varieties. But often the
breeders had no choice; either they got the needed resistance genes from a distant
relative, or they got nothing at all.
At about this time, breeders realized that it would be important to conserve remnant
seed of landraces from all around the world, but especially from the centers of
diversity of their crop. As farming worldwide grew more commercial, farmers turned
more and more to professionally bred varieties that were better suited to commercial
production, and in so doing they abandoned their landraces. If remnant seed of
those landraces was not collected and saved in special storage facilities, the genetic
base for crop breeding in the future would be drastically narrowed. Seed "banks"
were needed. Through the efforts (especially in the 1960s and 1970s) of a few far-
sighted plant breeders, seed banks were established in several countries and in
international research centers.
So at the end of the 20th century, plant breeding for pest resistance had laid out the
genetic framework of vertical and horizontal resistance, and identified important
sources of new resistance genes, i.e., plant germplasm from anywhere in the world.
Sources were limited, however, to the crop species itself or its relatives, either wild or
cultivated. All of the introduced genes therefore came from plants.
Plant breeders selected not only for tolerance or resistance to disease and insect
pests, they also selected for tolerance to abiotic stresses such as heat and drought,
cool temperatures, or nutrient imbalance. Much of this selection was involuntary; in
selecting varieties with top performance over many seasons and many locations the
breeders necessarily selected varieties with tolerance to the prevailing abiotic
stresses of the diverse seasons and localities. In selecting for tolerance to
environmental stresses, breeders necessarily changed the genetic makeup of the
crop species, altering it still further from that of the original wild species, which had
been restricted to certain environmental niches. Witness teosinte (the probable
parent of maize), restricted to certain habitats in Mexico as compared to maize that
now is grown in nearly every country of the world except Iceland.
Global distribution of crop plants often means that they are grown with no proximity
to wild relatives that might intercross with them. Teosinte is not found in Germany or
China, nor for that matter in the US Corn Belt. In other cases, however, wild species
with hybridization potential coexist with their cultivated crop relatives, often as
weeds. Canola, sunflower, and grain sorghum are examples of crops with
hybridization potential with either a related species (canola with wild mustards) or
with a weedy form of the same species (sorghum with shattercane, cultivated
sunflower with wild sunflower).
8.2.3. Four questions about pest resistance traits
The above discussion shows that plant breeders have changed the genetic
composition of crop species to a large degree as they selected for pest resistance
and also for resistance to environmental stresses. Such changes are in addition to
the major phenotypic changes (e.g., non-shattering, uniform and fast germination)
that were a consequence of domestication. What have been the consequences of
such alterations, either on the crop species and its near relatives or on the
ecosystems in which those species are grown? Experienced plant breeders have
addressed this question as they responded to four queries sent to them. The
questions were:
1. Have the resistance traits been stable over time?

2. Have they led to undesirable consequences with respect to weediness of the
crop or its relatives?
3. What have been the major sources of pest resistance genes as used in
classical breeding (e.g., same species, related species, mutation)?
4. Are there relevant differences between the resistance genes currently being
engineered into plants and those that have been transferred by conventional
breeding?
The summary of the responses from the breeders are stated below:
8.2.4. Have Resistance Traits Been Stable Over Time?
The breeders say that as a general rule, resistance traits governed by major
dominant genes have not been stable over time, whereas those governed by several
genes have been more durable. But there are exceptions to both statements. One
cannot say categorically that single gene resistance will always be undependable, or
that multiple factor resistance will always be durable.
It is important to remember that the phrase "stability of resistance" refers to whether

or not a previously resistant variety is overcome by a particular species of disease or
insect. It does not infer that individual resistance genes lose their power to hold
individual pest biotypes in check. The resistance genes are stable, but new (or
previously undetected) pest biotypes appear, with types of virulence that are not
curbed by the now-outdated resistance genes. The variety succumbs to the disease
or insect pest once again, albeit to a new race of the pest, and breeders say that the
variety’s resistance was unstable.
8.2.5. Has Introduction of Conventional Resistance Genes Led to Undesirable
Consequences with Respect to Weediness of the Crop or Its Relatives?
The breeders know of no undesirable consequences (such as enhanced competitive
ability in a related weed species following the unintended transfer of resistance
genes from crop to weed) from any introduction of resistance genes into crop plants
through classical breeding. Some of the introduced genes have come from very
distant relatives, but all have been derived from plants. Chances of introgression
from crop species to wild relatives vary by crop. Ease of hybridization and the
genetic complexity of transformation from wild to domesticated plant type (or vice
versa) are major determinants for the rate and amount of introgression that might be
expected. In the US, sunflower and sorghum are highly cross-compatible with related
weeds and would be the most likely crops to exhibit undesired movement of pest
resistance genes from crop to weed. Breeders, however, have not yet observed this
kind of introgression.
8.2.6. What Are the Major Sources of Resistance Genes in Classical Breeding?
The breeders say that resistance genes from within the crop species are preferred
when they can be found, because of ease of breeding with them, but they will go far
afield if they have to. The practice varies with the crop; e.g., tomato breeders
commonly use genes from wild relatives whereas sorghum breeders do not. The
amount of genetic diversity within the crop species and its ease of breeding with
alien species are major determinants of breeders’ actions.
8.2.7. Are There Important Differences Between Classical and Engineered

Resistance Genes?
The breeders say that engineered resistance genes now in use appear to have
different modes of action than traditional resistance genes, but they point out that we
know very little about structure and mode of operation of the traditional genes and so
have little basis for sweeping judgments about difference. Further, we have few
specifics about how a radically different genetic background might affect expression
of a transgene.
Genes for herbicide resistance (the archetype example of potentially dangerous

genetic transformation) are not necessarily imparted by means of genetic
transformation. Such genes are found within crop species or their relatives, or have
been created by means of mutation. These genes, bred into a specific crop variety,
theoretically could move from the crop to cross-compatible weed species and impart
unwanted herbicide resistance to the weeds. But in order to cause a new problem,
resistance genes would have to introgress into weeds that had not contributed the
resistance genes in the first place. This example shows how difficult it can be to
decide whether or not a given resistance gene in a crop plant will increase
competitiveness in weeds or make crop plants into weeds. Presence or absence of
genetic engineering is not the major determining factor.
The breeders look to a future generation of engineered plant genes that will provide
greater diversity and utility than genes presently available in any one crop. Genes
from related taxa, from very distant taxa, or from within the crop species may be
altered to provide improved resistance, but they will be plant genes rather than
genes from extremely different organisms. It may be difficult to identify the point at
which such new genes should be called "unnatural."
Until recently, plant breeders did not worry about how their breeding affected
weeds, or whether their crops could become weeds. Weeds were looked on as
potential sources of genes for pest resistance if they could hybridize with crop
species, but almost no one thought about whether or not the population genetics of
weeds could be altered by introgression from crop species. A very few students of
crop evolution studied the weeds that may have been ancestors of cultivated plants.
Plant taxonomists and ecologists usually ignored weeds because they weren’t
considered as parts of natural ecosystems.
Genetic engineering has changed all of that. If genes from far afield can be added to
crop plants, giving them marvelous gains in pest resistance, tolerance of
environmental stress, or enhanced seed production, one can imagine that those
transgenes could enhance the power of weeds in the same ways.
The analogy may not be as simple as it sounds, however. Two concepts must be
clarified and data need to be assembled before one can make firm predictions.
8.2.8. Do crop plants as a class have the same requirements for survival and
luxuriance as weeds as a class?
 To consider this question one must lay out the ways in which crop plants and
weeds are similar and ways in which they differ.
 Perhaps even before that, one must decide whether it is possible to make a
definitive description of crop plants as a class, and another one for weeds as
a class.
8.2.9. What is the functional role of resistance genes in weeds as compared to

their role in crop plants?
 Will a gene that greatly enhances survival chances for a crop plant perform
the same service for a weed? (Crops grow in crowded monocultures; weeds
usually grow in dispersed "polycultures.")
 Will the presence or absence of genetic diversity within a crop or weed
population, or among crop or weed species in a site, affect the utility of a
given resistance gene? (Crop varieties usually are genetically uniform, weed
populations are not.)
 Should one distinguish between dangers of imparting genes for resistance to
natural restraints, such as disease or insect attack, and resistance to man-
made restraints, such as herbicides?
 Do we have any reason to believe that selection for new (or previously
undetected) kinds of herbicide resistance in weed species operates on
different principles than selection for new (or previously undetected) kinds of
virulence in disease or insect species?
The breeders, in answering the above four questions, were considering these two
main points and the subsequent questions that they raise. It is possible that they did
not want to classify resistance genes into only two categories—natural or
engineered. Further, the breeders said we know so little about the molecular nature
of resistance genes that we cannot yet categorize them in any meaningful way. It is
possible they do not believe that mode of transfer or kingdom of origin is a
meaningful classification.
Despite their reluctance to sort genes into "engineered-bad" and "natural-good," the
breeders acknowledged that whenever we fool around with Mother Nature we get
surprises, some of them bad. Therefore we need to look with caution at any novel
breeding technology, predicting possible consequences as well as we can, with the
modicum of data we may have in hand.
We need to know more about the effects of genetic background on gene action.
Location within a genome seems important, and the entire genetic background
seems important. We have little or no understanding of these interactions.
We need to know more about the consequences of hybridization of crop species with
related weeds and the potential for introgression in both directions. Jointed
goatgrass hybridizes with common wheat and viable backcross offspring can be
produced. Have resistance genes from wheat moved into jointed goatgrass and
changed its survival potential? A similar question can be asked for sorghum and
shattercane, sunflower and wild sunflower, canola and mustards, or maize and
teosinte.
So we must ask ourselves, do we have data to answer either of these key

questions—effect of genetic background, or consequences of hybridization—or at
the least do we have enough data to let us speculate from a firmer foundation than
we have at present?
In my opinion, we have fragments of data for some crops and/or their weed relatives,
but rarely do we have enough for firm predictions about gene introgression or about
gene action in the genome or the population.
What are the consequences of adding new pest resistance genes to a wild species,
either a weed or otherwise? How plentiful and how powerful must the genes be to
change the genetic balance of the wild species, make it a stronger weed, transform a
non-weed into a weed, or, conversely, reduce the weed’s viability as a competing
population?
How about the "function" of related weeds as a reservoir of new biotypes of pest
species, disease, or insects? Are the weeds more dangerous to crop plants when
they lack resistance and so are a constant source of pest infection and infestation?
Or are they more threatening when they contain many of the same resistance genes
as carried in the crop species and therefore encourage the multiplication of new pest
biotypes (biotypes that are not bothered by the weeds’ resistance genes)?
The recommendation arising from these questions seems obvious. Whenever a

worrisome outcome seems likely but data are too sparse for firm conclusions,
scientists need to work hard to fill the void. They need to plan the right experiments,
gather the needed data, and publicize the results in both public and specialist media.
And the public needs to provide the fundsto support this work, since most of it will
need to be done by scientists in public institutions.
Finally, sometimes the odds of a bad outcome from not doing a particular action may
be much higher than the odds of a bad outcome from performing that action.
Sometimes it may be better to take action with uncertain outcome than to stand still.
Life always works on probabilities.
Summary
Plant diseases can also be partially controlled by use of pesticides, and by cultivation
practices. Plant varieties with inherent (genetically determined) disease resistance
are generally the first choice for disease control. Breeding for disease resistance has
been underway since plants were first domesticated, but it requires continual effort
because pathogen populations are often under natural selection for increased
virulence, new pathogens are introduced to an area, cultivation methods can favor
increased disease incidence over time, changes in cultivation practice can favor new
diseases, and plant breeding for other traits can disrupt the disease resistance that
was present in older plant varieties. Plant breeding for disease resistance typically
includes:
 Identification of resistant breeding sources.

 Crossing of a desirable but disease-susceptible plant variety to another
variety that is a source of resistance, to generate plant populations that mix
and segregate for the traits of the parents.
 Growth of the breeding populations in a disease-conducive setting.
 Selection of disease-resistant individuals.
Conclusion
Plant diseases can be controlled by selecting and breeding plant resistant species
1. List the components for plant breeding for disease resistance.

2. Distinguish between vertical and horizontal resistance
1. Identify the specific qualities required for breeding for pest resistance
References
1Chahal, G.S and Gosal, S.S., 2002.Principles and procedures of Plant

2Falconer, D.S., 1989.Introduction to Quantitative Genetics.3rd Ed.

Longman.Burnt Mill.
3Kwon-Ndung, E.H. 2008.Genetics for degree students.Afaku Publishers, Abuja.
4 Frish M., and Elchinger, A.E., 2005. Selection Theory for Marker-assisted
Backcrossing. Genetics: Published Articles Ahead of Print, published on March
31, 2005 as 10.1534/genetics.104.035451
PNAS. June 20, vol. 97, no. 13: 7037-7042.
9 Takebayashi, N and Morell, P.L., 2001. Is self-fertilization an evolutionary dead
end? Revisiting an old hypothesis with genetic theories and a macroevolutionary
approach. American Journal of Botany. 88:1143-115
inhibited by the ubiquitin/26S proteasome pathway of protein degradation during
compatible pollination in Antirrhinum". Plant Cell 16 (3): 582–95.
USDA

Bio 309 - 0

Uploaded by

Copyright:

Available Formats

Bio 309 - 0

Uploaded by

Document Information

Original Title

Copyright

Available Formats

Share this document

Share or Embed Document

Sharing Options

Did you find this document useful?

Is this content inappropriate?

Copyright:

Available Formats

Bio 309 - 0

Uploaded by

Copyright:

Available Formats

NATIONAL OPEN UNIVERSITY OF NIGERIA

SCHOOL OF SCIENCE AND TECHNOLOGY

COURSE CODE :BIO 309

COURSE TITLE: PLANT BREEDING

Course outline: Importance of plant breeding, Cytological principles of breeding,

1. Importance of plant breeding

UNIT 1: IMPORTANCE OF PLANT BREEDING

Intra-specific hybridization within a plant species was demonstrated by Charles

From 1904 to World War II in Italy NazarenoStrampelli created a number of wheat

Failure to produce a hybrid may be due to pre- or post-fertilization incompatibility. If

Chemical mutagens like Ethyl Methyl Sulphonate and Di Methyl Sulphonate,

4.0 Importance of Plant breeding

It is believed that breeding new crops is important for:

A plant whose origin or selection is due primarily to intentional human activity is

5.0. Conventional plant breeding

Conventional or Classical plant breeding uses deliberate interbreeding (crossing) of

Classical breeding relies largely on homologous recombination between

i Increased quality and yield of the crop

ii Increased tolerance of environmental pressures (salinity, extreme

iii Resistance to viruses, fungi and bacteria

iv Increased tolerance to insect pests

v Increased tolerance of herbicides

6.0. Modern plant breeding

Modern facilities in molecular biology has converted classical plant breeding to

6.1. Marker assisted selection

6.2. Reverse Breeding and Doubled Haploids (DH)

A method for efficiently producinghomozygous plants from heterozygous starting

6.3. Genetic modification

Genetic modification of plants is achieved by adding a specific gene or genes to a

The majority of commercially released transgenic plants are currently limited to

6.4. Issues and concerns on modern plant breeding

7.0Steps of Plant Breeding

The following are the major activities of plant breeding;

8.0. Participatory Plant Breeding

The development of agricultural science, with phenomenon like the Green

a Why is plant breeding important?

b Explain the role of GMOs in modern plant breeding

c Why is participatory plant breeding important?

a What are the objectives of plant breeding?

b Differentiate between traditional and modern plant breeding.

2.0 Cytological principles of plant breeding

E. Strasburger in 1875 first discovered thread-like structures which appeared during

At the end of this unit,

 students will understand the cytological principles of plant breeding

2.1.1. Chromosome number:

The number of chromosomes in a given species is generally constant. All the

Name of the Chromosome

2.1.2. Chromosome Size:

2.1.3. Chromosome Morphology:

The outer covering or sheath of a chromosome is known as pellicle, which encloses

I. Chromatid: Each metaphase chromosome appears to be longitudinally

4. Secondary constriction: The constricted or narrow region other than that of

5. Chromomere: In some species like maize, rye etc. chromosomes in pachytene

6. Chromonema: A chromosome consists of two chromatids and each chromatid

7. Matrix: The mass of acromatic material which surrounds the chromonemata is

2.1.4. Composition of chromosomes:

The material of which chromosomes are composed is called chromatin. N.Fleming

Differences between Heterochromatin and Euchromatin:

1 Represent darkly stained Lightly stained regions