Breeding for resistance to disease and insect pests(biotic stress)

BREEDING FOR RESISTANCE
TO DISEASE AND INSECT
PESTS
(BIOTIC STRESS)
PRESENTED BY:
Pawan Nagar
Reg. no.: 04-2690-2015
M.Sc.(Fruit Science)

GROUPS OF PESTS TARGETED BY PLANT
BREEDERS
 Plant diseases are caused by pathogens that vary in nature
and may be microscopic or readily visible (e.g., virus, plant,
animal).
 Six general groups of causal agents of disease, which
represent six general approaches to breeding for pest
resistance, may be identified as: airborne fungi, soil-borne
fungi, bacteria, viruses, nematodes, and insects.
 Through an understanding of the biology, epidemics, spread,
and damage caused by these organisms in each category,
breeders have developed certain strategies and methods for
breeding cultivars to resist certain types of biotic stress in plant
production.

 Plant species vary in their susceptibility to diseases
caused by pathogens or pests in each group.
 Cereal crops tend to have significant airborne fungal
disease problems, while solanaceous species tend to
experience viral attacks.
 Breeding for resistance to fungi, especially airborne fungi,
is the most prominent resistance breeding activity.
 N. W. Simmonds has suggested that the relative
importance of the six groups of pathogens of importance
to plant breeders, might be something like this: airborne
fungi > soil-borne fungi > viruses > bacteria =
nematodes= insects.

BIOLOGICAL AND ECONOMIC
EFFECTS OF PLANT PESTS
 1 Complete plant death. Certain parasites sooner or later will
completely kill the afflicted plant; include those that cause mildews,
vascular wilts, and insects such as cutworms that cause a seedling
to fall over and die.
 2 Stunted growth. Viruses are known to reduce the metabolic
performance of plants without killing them outright.
 3 Partial plant death. Some diseases that afflict adult plants do not
completely kill them. Rather, only certain parts of the plant (e.g.,
branches) are killed(e.g., as observed in fungal diebacks).
 4 Direct product damage Some pests directly injure these products
completely (e.g., by causing rotting of tissue) or reducing quality
(e.g., by causing blemishes, holes).

OVERVIEW OF THE METHODS OF
CONTROL OF PLANT PARASITES
1. Exclusion of pathogen from the host. This strategy may use
methods such as legislation (plant quarantine, crop inspection) or
crop isolation to prevent the pathogen or pest from making initial
contact with the host plant.
2. Reduction or elimination of the pathogen’s inoculum. A
method such as crop rotation reduces disease buildup in the field,
while observance of sanitation (e.g., removing diseased plants and
burning them) reduces the spread of the pathogen.
3. Improvement of host resistance. This is the strategy of most
concern to plant breeders. It entails breeding to introduce genetic
resistance into adapted cultivars
4. Protection of the host. Economic plants may be protected from
parasites by using chemicals (pesticides).

PATHOGEN AND HOST
 The pathogen is a living organism that is capable of
inflicting a distinct disease or disorder in another
organism (the host).
 The capacity of the pathogen to cause disease or
disorder in a member of a host species is called its
pathogenecity.
 The extent of disease development pathogen causes is
its virulence.
 The pathogenecity and virulence of a pathogen vary
among pathogen types (races or pathotypes).

 Races or pathotypes that fail to cause disease symptoms or
successfully attack a given host are said to be avirulent.
 A third factor – favorable environment – is needed, the trio
(pathogen plus susceptible host plus favorable environment)
referred to as the disease triangle.
 Pathotypes or races of pathogens may also be described in
terms of aggressiveness or non-aggressiveness in relation
to the rate at which they produce disease symptoms.

 The host
The host (genotype, plant) is the organism in which a pathogen may
produce disease symptoms.
 A susceptible host is one in which a pathotype or race can manifest a
disease symptom.
 A host may employ one of several mechanisms (defense mechanisms)
to resist pathogens.
1 Pre-existing defense mechanisms. These include morphological
features that pose as barriers to the penetration of the pathogen into the
plant (e.g., presence of lignin, cork layer, callose layers), or secondary
metabolites (phenols, alkaloids, glycosides) that have antimicrobial
properties.
2 Infection-induced defense mechanisms. Upon infection, the host
quickly produces chemical products (e.g., peroxidases, hydrolases,
phytoalexins, etc.) to combat the infection.

MECHANISMS OF DEFENSE IN PLANTS
AGAINST PESTS
 Mechanisms of defense in plants against pests Plants exhibit a wide variety
of strategies and mechanisms of defense against pathogens and insects pest
that may be classified into three major groups – avoidance, resistance, and
tolerance.
 Avoidance Also described as escape, avoidance is a mechanism that reduces
the probability of contact between pathogens or insect pests and the plant.
 Resistance The mechanism of resistance manifests after a host has been
attacked by a pathogen or insect pest. The mechanism operates to curtail the
invasion or to reduce the growth and/or development of the pathogen.
 Tolerance Unlike avoidance and resistance mechanisms that operate to reduce
the levels of infection by the pathogen or pest, tolerance (or endurance) operates
to reduce the extent of damage inflicted. The afflicted host attempts to perform
normally in spite of the biotic stress.

TYPES OF GENETIC RESISTANCE
 The complexity of host–pathogen interaction makes it
difficult to categorize resistance into finite types.
 A large number of host–pathogen interaction systems
occur at various stages of coevolution.
 Resistance reactions may be generally categorized into
two major kinds – vertical or horizontal – based on
their epidemiological status and stability of resistance.

VERTICAL RESISTANCE / RACE OR PATHOTYPE-SPECIFIC
RESISTANCE/ OLIGOGENIC RESISTANCE /NONDURABLE
/QUALITATIVE
RESISTANCE/NON-UNIFORM RESISTANCE
 This reaction is said to occur when a race of a pathogen
produces disease symptoms on some cultivars of a host but
fails to do so on others.
 This type of resistance is relatively easy to breed because the
major genes are easy to identify and transfer through simple
crosses.
 These genes control specific races or genotypes of pests and
hence do not protect against new races of the pests.

HORIZONTAL RESISTANCE/PARTIAL RESISTANCE/ RACE-NON-
SPECIFIC RESISTANCE/MINOR GENE REACTIONS/ POLYGENIC
RESISTANCE.
 The resistance is effective against all genotypes of the parasite
species without cultivar × isolate interaction (i.e., race-non-specific).
 Horizontal resistance is controlled by polygenes. Each of the genes
that condition the disease contributes toward the level of resistance,
and hence resistance is also called minor gene resistance.
 Breeding polygenic resistance is more challenging. The many minor
genes cannot be individually identified and consequently cannot be
transferred through crossing in a predictable fashion.

GENETICS OF HOST–PATHOGEN REACTIONS
 R. H. Biffen is credited with providing the first report on
the genetics of resistance. Working on stripe rust
(Puccinia striiformis), he reported that resistance to
disease was controlled by a single Mendelian gene.
 However, it is known that resistance may be controlled
by any number of genes whose effects may be large or
small.
 Further, the genes may interact epistatically or
additively.

GENE-FOR-GENE REACTIONS (GENETICS OF
SPECIFICITY)
 Working on flax rust (caused by Melamspora lini), H. H. Flor
discovered that the major genes for resistance in the host interacted
specifically with major genes for avirulence in the pathogen.
 For each gene conditioning resistance in the host, there is a specific
gene conditioning virulence in the parasite.
 In the host the genes for resistance are Dominant(R) , however gene
for susceptibility are recessive(r).
 In the pathogen genes for avirulence ( inability to infect) are usually
dominant(A) whereas genes for virulence are recessive(a).

Breeding for resistance to disease and insect pests(biotic stress)

GENERAL CONSIDERATIONS FOR BREEDING
RESISTANCE TO PARASITES
1. Breeding is an expensive and long-duration undertaking that makes it only
justifiable for major pests that impact crops that are widely produced or have
significant benefit to society.
2. Natural resistance is not available for all pests. Sometimes, the resistance is
available in unadapted gene pools, requiring additional costs of prebreeding.
3. Breeding for resistance varies in ease and level of success from one pest to
another. Resistance to vascular pathogens, viruses, smuts, rusts, and mildews
is relatively easier to breed than breeding against pathogens that cause rots
(root rot, crown rot, storage rot) and ectoparasitic nematodes. Similarly, it is
relatively easier to have success with breeding resistance to aphids, green
bugs, and hoppers, than to breed resistance to root-chewing or grain-storage
pests.

4. Instability of pest resistance is a key consideration breeding for pest control
because diseases and insect.pests continue to change. New pathogenic races
may arise, or the cultural environment may modify the resistance of the
cultivar.
5. The techniques of biotechnology may be effective in addressing some
breeding problems more readily than traditional methods.
6. After being satisfied that breeding for disease resistance is economical, the
breeder should select the defense mechanism that would be most effective for
the crop, taking into account the market demands. For example, horticultural
products and produce for export usually require that the product to be free
from blemish. In these cases, breeding for major gene resistance with
complete expression is desirable. It is also easy to breed for this type of
reaction. However, the breeders should note that this resistance is not
durable.
7. When a crop is grown for food or feed, breeding for mechanisms that increase
the levels of chemical toxins in plant tissues is not suitable.

RESISTANCE BREEDING STRATEGIES
 Disease breeding is a major objective for plant breeders.
 It is estimated that 95–98% of cultivars of small grains grown
in the USA have at least one gene for disease resistance.
 It should be pointed out that a combination of traits rather than
just one trait, makes a cultivar desirable.
 Yield and resistance to disease are top considerations in
breeding programs.

1. SPECIFICITY IN THE PARASITE
 When pathogen genotypes share a group of cultivars to which they are virulent, they are
said to belong to a physiological race.
 Physiological races of pathogens occur in rusts, powdery mildew, and some insects.
 The physiological races may be identified by using differential cultivars (contain known
genes for disease reaction).
 Breeders use a series of differentials to determine what genes would be most effective to
incorporate into a cultivar.
 The concept of differentials stems from the ability of a cultivar to differentiate between races
of a parasite on the basis of disease reaction.
 If a cultivar has resistance to one race but is susceptible to another, it has differential
properties to identify two races of a pathogen and hence is called a differential.

 In that case, four races of a pathogen can be differentiated
 The ideal set of differential cultivars is one in which each cultivar carries
a gene for resistance to only one race.
 The differential cultivars provide some information on the virulence
characteristics present in resistance to which the pathogen population
carries avirulent genes, and, similarly, the genes for resistance of the
host that would fail because the pathogen possesses the necessary
genes for virulence.

2. PLANNED RELEASE OF RESISTANCE GENES
 It is recommended to have a planned release (consecutive
release of different resistance genes) of resistance genes so
that only one or a few are used in agricultural production at
one time.
 Once a current cultivar succumbs to a new race of a pathogen
(i.e., a new race that is virulent with the resistance gene in
use), breeders then release new cultivars that carry another
effective gene. This way, plant breeding stays ahead of the
pathogen

3. APPLICATION OF GENE PYRAMIDING
 The concept of transferring several specific genes into one plant is
called gene pyramiding.
 Because there are different races of pathogens, plant breeders may
want to transfer a number of genes for conferring resistance to
different races of a disease into a cultivar.
 Functional stacking of three resistance genes against Phytophthora
infestans in potato.
Three broad spectrum potato R genes (Rpi), Rpi-sto1 (Solanum
stoloniferum), Rpi-vnt1.1 (S. venturii) and Rpi-blb3 (S. bulbocastanum)
were selected, combined and transformed into the susceptible cultivar
to exhibit durable resistance.

4. BREEDING FOR HORIZONTAL RESISTANCE
 It is suitable for both annuals and perennials and is applicable to all
pathogens.
 Breeding for general resistance is more challenging because many
genes with minor effects are involved.
 It is laborious to develop breeding stocks with horizontal resistance.
 However, it is easy to improve on the very low level of horizontal
resistance that normally underlies a failed vertical resistance.
 Such improvements may be accomplished by using recurrent selection
methods.

5. BREEDING FOR VERTICAL RESISTANCE
 Vertical resistance is pathotype- specific and easy to breed.
 Boom and bust cycles
Arise when major genes for vertical resistance against a major economic
race of a pathogen are used in cultivar development for a region, leading
to widespread adoption of the resistant cultivars by most producers in the
region (boom phase).
Selection pressure on the races of the pathogen present in the cultivars
reduces the virulent ones.
However, the less virulent one against which the cultivars carry no major
genes continues to increase until it becomes epidemic in the vast region of
production of the crop (bust phase).

GENERAL STRATEGIES MAY BE USED TO MAKE VERTICAL
RESISTANCE A SUCCESS
1. Temporal deployment. A strategy for enhancing the success of vertical resistance is to
develop and release several cultivars in successive or cyclical fashion.
2. Geographic deployment. The application is of limited practical use because it requires a
special circumstance that one crop population protects another by acting as a filter to
delay the advance of disease.
3. Spatial deployment. In a situation where virulent pathogens are spatially localized, a
cultivar diversification strategy whereby the fields of different farmers are planted to
different cultivars , containing two or more virulent genes, would slow down disease
epidemics.
4. Multiline deployment. A multiline consisting of genotypes carrying different major genes
would also put a damping effect on epidemics just like in the case of spatial deployment.
5. Mixture deployment. A mixture of distinct cultivars with complementary vertical
resistance genes can be deployed.

6. COMBINING VERTICAL AND HORIZONTAL RESISTANCE
 It is tempting to think that combining vertical resistance and
horizontal resistance will provide the best of two worlds in the
protection of plants.
 The erosion of horizontal resistance while breeding for race-
specific vertical resistance is called the vertifolia effect (after the
potato cultivar “Vertifolia”) in which the major gene is so strong
that while the breeder focuses on vertical resistance, no
evaluation and selection for horizontal resistance is possible,
eventually leading to the loss of horizontal resistance.
 The vertifolia effect is not of universal occurrence.

 Some researchers have reported race-specific resistance in
addition to high-level polygenic resistance to leaf rust in barley.
 To reduce the incidence of Vertifolia effect, some suggest that
breeders select and discard susceptible plants in segregating
populations, rather than selecting highly resistant genotypes.
 Also, others suggest to first breed for a high level of horizontal
resistance in a genotype then cross it with one that has high
vertical resistance.

7. ROLE OF WILD GERMPLASM IN RESISTANCE
BREEDING
 The success and effectiveness of introgression of disease-resistance
genes into crop species from wild relatives varies by crop.
 The resistance to the devastating late blight of potato was found in a
wild species.
 Similarly, resistance to the root knot nematode in peanut was obtained
from three wild species.
 A wild relative of rice, Oryza nivara, growing in the wild in Uttar Pradesh
was found to have one single gene for resistance to the grassy stunt
virus, a disease that devastated the crop in South and South East Asia
in the 1970s.

8. APPLICATIONS OF BIOTECHNOLOGY IN
RESISTANCE BREEDING
A. Tissue culture:
 Meristem tip culture can be used to produce virus free plants.
 Haploid production has been used for introduction of disease resistance into the
cultivars.
eg: Resistance to barley YMV has been introduced into susceptible breeding lines
by haploid breeding,
Medium late maturing rice variety Hwacheongbyeo derived from anther culture
showed resistance to brown plant hopper.
 Somatic Hybridization : disease resistance genes like potato leaf roll virus , leaf
blight, have been transferred to Solanum tuberosum from other species.
 Somaclonal variation: resistance to Phytophthora infestans in potato
somaclones.

C. MARKER ASSISTED SELECTION
There are five main considerations for the use of DNA markers in MAS:
1. Reliability. Markers should be tightly linked to target loci, preferably less than 5 cM
genetic distance. The use of flanking markers or intragenic markers will greatly increase
the reliability of the markers to predict phenotype.
2. DNA quantity and quality. Some marker techniques require large amounts and high
quality of DNA, which may sometimes be difficult to obtain in practice, and this adds to
the cost of the procedures.
3. Technical procedure. The level of simplicity and the time required for the technique are
critical considerations. High-throughput simple and quick methods are highly desirable.
4. Level of polymorphism. Ideally, the marker should be highly polymorphic in breeding
material (i.e. it should discriminate between different genotypes), especially in core
breeding material.
5. Cost. The marker assay must be cost-effective in order for MAS to be feasible.

QTL MAPPING AND MAS
 The detection of genes or QTLs controlling traits is possible due to
genetic linkage analysis, which is based on the principle of genetic
recombination during meiosis.
 Construction of linkage maps composed of genetic markers for a
specific population. Segregating populations such as F2, F3 or
backcross (BC) populations are frequently used.
 Using statistical methods such as single-marker analysis or interval
mapping to detect associations between DNA markers and phenotypic
data, genes or QTLs can be detected in relation to a linkage map.
 Once tightly linked markers that reliably predict a trait phenotype have
been identified, they may be used for MAS.

ADVANTAGES OF MAS
 It may be simpler than phenotypic screening, which can save time,
resources and effort.
 Selection can be carried out at the seedling stage. This may be
useful for many traits, but especially for traits that are expressed at
later developmental stages. Therefore, undesirable plant genotypes
can be quickly eliminated.
 With MAS, individual plants can be selected based on their
genotype. For most traits, homozygous and heterozygous plants
cannot be distinguished by conventional phenotypic screening.

MARKER-ASSISTED BACKCROSSING
 Three general levels of marker-assisted backcrossing (MAB) can be
described.
 In the first level, markers can be used in screening for the target gene
or QTL.
 This is referred to as ‘foreground selection’ .
 It can also be used to select for reproductive-stage traits in the seedling
stage, allowing the best plants to be identified for backcrossing.
 Furthermore, recessive alleles can be selected, which is difficult to do
using conventional methods

 The second level involves selecting BC progeny with the
target gene and recombination events between the target
locus and linked flanking ‘recombinant selection’.
 The purpose of recombinant selection is to reduce the size of
the donor chromosome segment containing the target locus
(i.e. size of the introgression).
 By using markers that flank a target gene (e.g. less than 5 cM
on either side), linkage drag can be minimized.

 The third level of MAB involves selecting BC progeny with the greatest
proportion of recurrent parent (RP) genome, using markers that are
unlinked to the target ‘background selection’.
 Background selection refers to the use of tightly linked flanking markers
for recombinant selection and unlinked markers to select for the RP .
 Background markers are markers that are unlinked to the target
gene/QTL on all other chromosomes, in other words, markers that can
be used to select against the donor genome.
 This is extremely useful because the RP recovery can be greatly
accelerated.

LOW IMPACT OF
MARKER-ASSISTED SELECTION
a) Still at the early stages of DNA marker technology development.
b) Reliability and accuracy of quantitative trait loci mapping studies.
c) Insufficient linkage between marker and gene/ quantitative trait locus.
d) Quantitative trait loci and environment effects.
e) High cost of marker-assisted selection.
f) ‘Application gap’ between research laboratories and plant breeding institutes.
g) ‘Knowledge gap’ among molecular biologists, plant breeders and other
disciplines

Breeding for resistance to disease and insect pests(biotic stress)

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