APPLIED BOTANY

Comprehensive Exam-Ready Notes

UNIT 2

Plant Breeding & Crop

Improvement

Principles · Methods · Selection · Hybridization · Inbreeding

Heterosis · Mutation Breeding · Polyploidy · Biotechnology

■ SYLLABUS COVERAGE — UNIT 2
✦ Principles and Methods of Plant Breeding
✦ Hybridization and Selection
✦ Inbreeding Depression · Heterosis · Hybrid Vigour
✦ Mutation Breeding
✦ Polyploidy and its Role in Crop Improvement
✦ Molecular Markers in Plant Breeding
✦ Role of Biotechnology in Improving Crops
 TOPIC 1: INTRODUCTION TO PLANT BREEDING

Definition · Objectives · Principles

1.1 What is Plant Breeding?

Definition: Plant Breeding is the science and art of improving plants by altering their
genetic makeup to develop new varieties with desirable characteristics such as higher
yield, better quality, and resistance to diseases and environmental stresses.

Plant breeding is based on genetic, biological, and agronomic principles. It deals primarily with crop production
and improvement. It operates through three fundamental pillars:
➤ Objectives — what traits to improve
➤ Principles — the scientific laws governing inheritance
➤ Methods — the practical techniques used

1.2 Objectives of Plant Breeding

The objectives of plant breeding vary depending on the crop species, but the following are universally important:

1. Higher Yield
The ultimate aim is to improve the yield of economic produce — grain, fodder, fiber, tuber, cane, or oil yield
depending on the crop. Achieved by evolving high-yielding varieties or hybrids.

2. Improved Quality
Quality characters vary crop to crop: grain size, color, milling & baking quality (wheat); cooking quality (rice);
malting quality (barley); fruit size & color (vegetables); protein content (pulses); oil content (oilseeds); fiber
length & fineness (cotton).

3. Abiotic Resistance
Development of varieties resistant to drought, soil salinity, extreme temperatures, heat, wind, cold, and frost.
Critical as climate change intensifies.

4. Biotic Resistance
Crop plants suffer from diseases and insect pests causing yield losses. Genetic resistance is the cheapest and
best method. Resistant varieties developed using resistant donor parents from the gene pool.

5. Change in Maturity Duration / Earliness

Early maturity → less crop management, fewer insecticidal sprays, new crop rotations, extended crop area.
Examples: Cotton — 270 to 170 days; Pigeon pea — 270 to 120 days; Sugarcane — 360 to 270 days.

6. Dormancy
Some crops (Green gram, Black gram, Barley, Pea) germinate before harvest if rains occur at maturity. A period
of dormancy must be introduced to prevent pre-harvest germination losses. In other cases, dormancy may need
to be removed.

7. Desirable Agronomic Characteristics

Includes plant height, branching, tillering capacity, growth habit. Dwarfness in cereals → lodging resistance +
better fertilizer response. Tallness, high tillering, profuse branching → desirable in fodder crops.

8. Elimination of Toxic Substances

Some crops contain harmful compounds: Neurotoxin in Khesari (Lathyrus sativus) → causes paralysis of lower
limbs; Erucic acid in Brassica → harmful for human health; Gossypol in cotton seed → unfit for human
consumption. Removing these increases nutritional value.

9. Non-Shattering Characteristics
Shattering of pods is a serious problem in Green gram. Resistance to shattering is an important breeding
objective.

10. Synchronous Maturity

Maturity of a crop species at one time — highly desirable in Green gram, Cowpea, and Cotton where several
pickings are normally required.

11. Photo and Thermo-Insensitivity

Development of varieties insensitive to light and temperature. Helps cross cultivation boundaries.
Photo/thermo-insensitive wheat and rice now cultivated in new areas — Rice in Punjab, Wheat as major rabi
crop in western areas.

12. Wider Adaptability

Suitability of a variety for general cultivation over a wide range of environmental conditions. Helps stabilize crop
production over regions and seasons.

13. Varieties for New Seasons

Traditionally Maize is a kharif crop. Scientists can now grow Maize as rabi and Zaid crops. Similarly, Mung is
grown as a summer crop in addition to the main kharif crop.
■ QUICK REVISION POINTS
✔ 13 key objectives of plant breeding — yield, quality, abiotic/biotic resistance, maturity, dormancy,
agronomic traits, toxin removal, non-shattering, synchrony, photo-insensitivity, adaptability, new
seasons.
✔ Cotton maturity reduced from 270 → 170 days; Pigeon pea 270 → 120 days.
✔ Neurotoxin in Khesari → paralysis; Erucic acid in Brassica → harmful; Gossypol in cotton → toxic.
✔ Mnemonic: HI-ABCDEA-NSPW (Higher yield, Improved quality, Abiotic, Biotic, Change maturity,
Dormancy, Elimination of toxins, Agronomic traits, Non-shattering, Synchrony, Photo-insensitivity,
Wider adaptability)
 TOPIC 2: PRINCIPLES OF PLANT BREEDING

The Scientific Foundation of Crop Improvement

The success of any breeding program depends on the proper application of these fundamental principles. These
principles define what is scientifically possible and guide the breeder's decisions.

1. Genetic Variability
Genetic variability is the FOUNDATION of plant breeding. Without variation, improvement is impossible.

Sources / Types:
■ Introduction of varieties from other regions
■ Hybridization between genetically different parents
■ Mutation (natural or induced)
■ Recombination during meiosis
■ Polyploidy
Importance / Criteria:
■ Provides raw material for selection
■ Enables breeders to combine desirable traits
■ Helps in adapting crops to changing environments

2. Heredity
Heredity refers to the transmission of traits from parents to offspring. It helps predict inheritance patterns and
assists in designing appropriate breeding methods.

3. Selection
Selection is the process of identifying and retaining superior plants from a population while eliminating inferior
ones.

Sources / Types:
■ Natural Selection — occurs in nature, driven by adaptation
■ Artificial Selection — practiced by breeders for desired traits

4. Hybridization
Hybridization involves crossing genetically dissimilar plants to combine desirable traits from different parents,
create new gene combinations, and exploit heterosis (hybrid vigor).

Sources / Types:
■ Selection of suitable parents
■ Controlled pollination
■ Proper emasculation and isolation

5. Isolation
Isolation is necessary to prevent unwanted cross-pollination. It maintains genetic purity, is essential for seed
production, and prevents contamination.

Sources / Types:
■ Spatial isolation — maintaining distance between crops
■ Temporal isolation — difference in flowering time
■ Mechanical isolation — bagging, cages

6. Adaptation
Adaptation refers to the ability of a variety to perform well in a specific environment. Ensures stability of yield,
improves farmer acceptance, and increases survival and productivity.

Sources / Types:
■ General adaptation — wide range of environments
■ Specific adaptation — particular agro-climatic conditions

7. Evaluation and Testing

New varieties must be evaluated rigorously before release to ensure they meet the required standards of yield,
quality, and resistance.

Sources / Types:
■ Preliminary yield trials
■ Advanced yield trials
■ Multi-location trials
■ On-farm trials
Importance / Criteria:
■ Yield potential
■ Quality traits
■ Resistance to biotic and abiotic stresses
■ Uniformity and stability

■ QUICK REVISION POINTS

✔ 7 Principles: Genetic Variability → Heredity → Selection → Hybridization → Isolation →
Adaptation → Evaluation.
✔ Genetic Variability is the FOUNDATION — no variation = no improvement.
✔ Selection acts ONLY on heritable differences; cannot create new variation.
✔ Isolation types: Spatial, Temporal, Mechanical.
✔ Evaluation stages: Preliminary → Advanced → Multi-location → On-farm trials.
 TOPIC 3: METHODS OF SELECTION

Mass Selection · Pure Line Selection · Back-Cross Method

3.1 Concept of Selection

Definition: Isolation of desirable plant types from the population is known as SELECTION.
It is basic to any crop improvement and one of the two fundamental steps of any breeding
programme (the other being creation of variation).

Selection operates on existing variability — it CANNOT create new variation. It acts only through heritable
differences. Two agencies are involved:
➤ Natural Selection — occurs in nature; based on adaptation to environment
➤ Artificial Selection — practiced by man/breeders for desired traits

KEY RULE: Selection works only on heritable (genetic) differences. Environmental

variability CANNOT be utilized under selection. The effectiveness of selection depends on
how much the phenotype reflects the genotype.

Flow: General Selection Process

Plant Population

Observation & Evaluation

Identification of Superior Plants

Selection

Elimination of Inferior Plants

Improved Population / Variety

3.2 Mass Selection

 Definition: A method where a large number of plants of similar phenotype are selected
and their seeds are mixed together to constitute a new variety.

Key Features:
➤ Plants selected on basis of their PHENOTYPE (appearance)
➤ Selection for easily observable characters: plant height, ear type, grain color, grain size, disease
resistance, tillering ability, lodging resistance, shattering resistance
➤ Seeds of selected plants are MIXED to constitute a new variety
➤ The resulting population is more uniform than the original population
➤ Generally, plants selected in mass selection are NOT subjected to progeny tests
➤ However, Allard (1960) recommends progeny test be done; poor/defective progenies are then rejected
Applications:
➤ Improvement of desi or local varieties
➤ Purification of already existing pureline varieties
Procedure (Year-wise):

Flow: Mass Selection Procedure

YEAR 1: Select 200–2000 plants with similar desirable traits

→ Composite seeds

YEAR 2: Composite seed planted in preliminary yield trial →

Phenotype critically evaluated

YEARS 3–6: Promising selections evaluated in coordinated

yield trials at several locations

YEAR 7: If outstanding, released as a new variety → Seed

multiplication for distribution

3.3 Pure Line Selection

Definition: A pureline is the progeny of a single, homozygous, self-pollinated plant. All

individuals within a pureline have IDENTICAL GENOTYPE; any variation within a pureline
is solely due to the environment.

Key Features:
➤ In self-pollinated species, all plants are expected to be homozygous
➤ Large number of plants selected from self-pollinated crop and harvested individually
➤ Individual progenies are evaluated; best progeny released as pureline variety
➤ Also known as Individual Plant Selection
 ➤ A pureline variety is a variety obtained from a SINGLE HOMOZYGOUS PLANT
➤ In self-pollinated crops, pureline varieties are far more common than mixtures of purelines
Procedure (Year-wise):

Flow: Pure Line Selection Procedure

YEAR 1: Select 200–3000 plants on basis of phenotype

(from desi/old variety)

YEAR 2: Individual plant progenies grown → Undesirable

progenies rejected

YEAR 3: Remaining progenies in Preliminary Yield Trial →

Inferior progenies rejected

YEARS 4–7: Multi-location Yield Trials → Disease resistance

& quality tests

YEAR 8: Best progeny released as new variety → Seed

multiplied for distribution

Applications:
➤ Improvement of desi or local varieties
➤ Purification of already existing pureline varieties

Feature Mass Selection Pure Line Selection

Basis of selection Phenotype Individual plant progeny

Seeds Mixed together Evaluated separately

Progeny test Not usually done Essential

Result Mixture of several purelines Single homozygous pureline

Duration ~7 years ~8 years

3.4 Back-Cross Method

Definition: The Back-Cross Method involves transferring one or a few desirable traits (like
disease resistance) from a donor parent into an otherwise superior, high-yielding variety
(recipient/recurrent parent).

Two Cases:
 ➤ Dominant Gene Transfer — Variety A (susceptible, rr) × Variety B (resistant, RR)
➤ Recessive Gene Transfer — More complex; requires selfing to identify homozygous recessives

Backcross with Dominant Gene (Progressive % of Variety A traits):

Generation % Recurrent Parent (A) Traits Remark

F1 50% 50% A + 50% B traits

Backcross 1 75% Rr eliminated, Rr retained

Backcross 2 87.5% Increasing A characteristics

Backcross 3 93.7% —

Backcross 4 96.8% —

Backcross 5 98.4% —

Final hybrid — has all characters

of Variety A + rust resistance
Backcross 6 99.2% gene

Formula for % Recurrent Parent traits after 'n' backcrosses:

% Recurrent Parent = [1 - (1/2)n+1] × 100 where n = number of backcrosses

■ QUICK REVISION POINTS

✔ 3 selection methods: Mass Selection (phenotype-based), Pure Line Selection (individual plant
progeny), Back-Cross Method (trait transfer).
✔ Mass selection = seeds mixed; Pure line = seeds evaluated separately.
✔ Pureline = progeny of ONE homozygous self-pollinated plant.
✔ Back-cross transfers 1–2 genes from donor to superior recurrent parent.
✔ After 6 backcrosses → 99.2% recurrent parent characteristics.
✔ Mnemonic for selection: 'Masters Pure Back' = Mass, Pureline, Backcross.
 TOPIC 4: HYBRIDIZATION

Crossing Genetically Dissimilar Plants for Improvement

4.1 What is Hybridization?

Definition: Hybridization is the process of crossing genetically dissimilar plants (different

genotypes, varieties, or species) to combine desirable traits from different parents, create
new gene combinations, and exploit heterosis (hybrid vigor).

4.2 Steps in Hybridization

Step 1: Selection of Parents

Choose parents with complementary desirable traits. At least one parent should possess the trait to be
transferred.

Step 2: Emasculation
Removal of anthers from the flower that will serve as the female parent, before the pollen is shed. Prevents
self-pollination.

Step 3: Bagging
The emasculated flower is covered with a bag to prevent contamination from unwanted pollen.

Step 4: Pollination / Controlled Crossing

Pollen from the selected male parent is transferred to the stigma of the emasculated female parent at the right
time.

Step 5: F1 Generation
Seeds are harvested from the pollinated flower. F1 plants show combination of traits from both parents.

Step 6: Subsequent Generations

F1 plants are allowed to self-pollinate or backcross as per breeding objectives.

Flow: Hybridization Process

Parent A (Trait X) × Parent B (Trait Y)

Emasculation of female parent

Controlled Pollination

F■ Hybrid (Combination of Traits)

Selfing / Backcross / Selection

Improved Variety / Inbred Line

 TOPIC 5: INBREEDING DEPRESSION

Effects of Close Mating on Plant Vigor

5.1 What is Inbreeding?

Inbreeding: Mating between individuals related by descent or ancestry. The highest

degree of inbreeding is achieved by SELFING. The chief effect is an increase in
homozygosity in the progeny, proportionate to the degree of inbreeding.

5.2 Definition of Inbreeding Depression

Inbreeding Depression: The reduction or loss in vigour and fertility as a result of

inbreeding. When individuals are closely related (e.g., brother-sister mating or sib
mating), the degree of inbreeding is high and depression is severe.

5.3 Effects of Inbreeding

1. Appearance of Lethal and Sublethal Alleles

Inbreeding results in appearance of lethal (causing death), sublethal and subvital characteristics. Includes:
chlorophyll deficiencies (albina, chlorina), rootless seedlings, defects in flower structure. Such plants cannot be
maintained and are lost from the population.

2. Reduction in Vigour
General reduction in the vigour of the population. Plants become shorter and weaker due to a general reduction
in the size of various plant parts.

3. Reduction in Reproductive Ability

Reproductive ability decreases rapidly. Many lines reproduce so poorly they cannot be maintained. In most
crops, only a small number of inbred lines have enough fertility to be useful in breeding programmes.

4. Separation into Distinct Lines

The population rapidly separates into phenotypically distinct lines due to increase in homozygosity, causing
random fixation of various alleles in different lines. This leads to increased variance of the population as a
whole.

5. Increase in Homozygosity
Each line becomes increasingly homozygous. After 7–8 generations of selfing, lines become almost uniform
(>99% homozygosity). Such highly homozygous lines maintained through close inbreeding are called INBRED
LINES.

6. Reduction in Yield
The best inbred lines in maize yield about half as much as the open-pollinated varieties from which they were
produced. In alfalfa and carrot, the reduction is much greater. In onions and many cucurbits, reduction is very
small.

5.4 Degrees of Inbreeding Depression

Degree Crops Characteristics

HIGH Alfalfa (M. sativa), Carrot (D. Large proportion show lethal traits; very
carota) few lines survive 3–4 generations; yield
<25% of open-pollinated varieties

MODERATE Maize (Z. mays), Jowar (S. Moderate reduction in vigour and fertility
bicolor), Bajra (P. americanum)

LOW Onion (A. cepa), Cucurbits, Rye, Small degree of depression; some
Sunflower, Hemp, Timothy grass inbred lines may yield as much as
open-pollinated varieties

NIL Some species No inbreeding depression observed

■ QUICK REVISION POINTS

✔ Inbreeding = mating between related individuals; selfing = highest degree.
✔ 6 effects: Lethal alleles, Reduced vigour, Reduced reproduction, Distinct lines, Homozygosity,
Reduced yield.
✔ After 7–8 generations of selfing → >99% homozygosity → INBRED LINES.
✔ Maize inbred lines yield ~50% of open-pollinated varieties.
✔ High depression: Alfalfa, Carrot | Moderate: Maize, Jowar | Low: Onion, Rye.
 TOPIC 6: HETEROSIS AND HYBRID VIGOUR

The Superiority of F■ Hybrids over Their Parents

6.1 Definitions

Heterosis (Shull, 1914): The superiority of an F■ hybrid over BOTH its parents in terms of
yield or some other character. Generally manifested as an increase in vigour, size, growth
rate, yield, or some other characteristic.

Hybrid Vigour: Often used as a synonym of heterosis. Hybrid vigour describes only the
superiority of hybrids OVER THEIR PARENTS, while heterosis describes other situations
as well. Use of the two terms as synonyms seems reasonably justified.

Luxuriance: The increased vigour and size of interspecific hybrids. The principal
difference between heterosis and luxuriance lies in the reproductive ability of the hybrids.
Heterosis is accompanied with increased FERTILITY, while luxuriance is expressed by
interspecific hybrids that are generally STERILE or poorly fertile.

6.2 Types of Heterosis

Average Heterosis
Superiority of F■ hybrid over the mid-parent (average of two parents). Of limited use in practical plant breeding
since it offers no advantage over the better parent.

Heterobeltiosis
Superiority of F■ over the SUPERIOR parent. Most breeders regard this as the only true case of heterosis.

Economic / Useful Heterosis

Superiority of F■ over the BEST COMMERCIAL VARIETY of the crop. This is the ONLY estimate of
practical/commercial value in plant breeding.

6.3 Manifestations of Heterosis

1. Increased Fertility / Reproductive Ability

Hybrids show increase in fertility, expressed as higher yield of seeds or fruits or other propagules (e.g., tuber in
potato, stem in sugarcane).

2. Increased Yield
Most common expression. Hybrid yields significantly more than both parents.

3. Increase in Size and General Vigour

Hybrids are generally more vigorous, healthier, faster-growing, and larger in size. The increase is usually due to
increase in number and size of cells. Examples: fruit size in tomato, head size in cabbage, cob size in maize.

4. Better Quality
Many hybrids show improved quality — may or may not be accompanied by higher yields. Example: Onion
hybrids show better keeping quality but not higher yield.

5. Earlier Flowering and Maturity

In many cases, hybrids are earlier in flowering and maturity than the parents. Earliness is highly desirable,
particularly in vegetables. Many tomato hybrids are earlier than their parents.

6. Greater Resistance to Diseases and Pests

Some hybrids exhibit greater resistance to insects or diseases than their parents.

7. Greater Adaptability
Hybrids are generally more adapted to environmental changes than inbreds. The variance of hybrids is
significantly smaller than that of inbreds.

8. Faster Growth Rate

In some cases, hybrids show faster growth rate than their parents, though total plant size may be comparable.

■ QUICK REVISION POINTS

✔ Heterosis coined by Shull in 1914 — superiority of F1 over BOTH parents.
✔ Hybrid vigour ≈ heterosis (superiority over parents only).
✔ Luxuriance = vigour in interspecific hybrids that are STERILE.
✔ 3 types: Average heterosis, Heterobeltiosis, Economic heterosis (only economic heterosis has
commercial value).
✔ 8 manifestations: Fertility, Yield, Size/Vigour, Quality, Earlier maturity, Disease resistance,
Adaptability, Faster growth.
✔ Mnemonic: 'FYSEQUAD-F' = Fertility, Yield, Size, Earliness, Quality, dUrability (adaptability),
Adaptability, Disease resistance, Faster growth.
 TOPIC 7: MUTATION BREEDING

Induced Mutations for Crop Improvement

7.1 What is Mutation?

Mutation: A sudden, heritable change in the genetic material (DNA) of an organism.

Mutations can occur naturally (spontaneous) or can be artificially induced by physical or
chemical agents called MUTAGENS.

7.2 Mutation Breeding

Mutation Breeding: The deliberate use of mutagens to induce mutations in crop plants
and then select useful mutants for crop improvement. It creates new genetic variability
that may not exist in nature.

7.3 Types of Mutagens

A. Physical Mutagens:
➤ X-rays — first used by H.J. Muller (1927) on Drosophila
➤ Gamma rays — commonly used in crop plants
➤ UV rays — effective on microorganisms
➤ Neutrons — fast and thermal neutrons
➤ Alpha particles, Beta particles
B. Chemical Mutagens:
➤ EMS (Ethyl Methane Sulphonate) — most commonly used
➤ Nitrous acid, Hydroxylamine
➤ Alkylating agents — cause base substitution
➤ Acridine dyes — cause frameshift mutations

7.4 Procedure of Mutation Breeding

Flow: Mutation Breeding Procedure

 Select crop variety for improvement

Treat seeds/pollen/tissue with mutagen (physical or

chemical)

Grow M1 generation — chimeric plants

Self M1 → grow M2 generation (mutations become

homozygous)

Screen M2 for desirable mutant phenotypes

Select and grow superior mutants (M3, M4...)

Evaluate in yield trials → Release as new variety

7.5 Role of Mutation Breeding in Crop Improvement

➤ Creates new alleles not present in nature

➤ Useful when desirable traits are absent in the germplasm
➤ Can improve specific traits without disturbing the rest of the genome
➤ Particularly useful for: dwarfness, disease resistance, improved quality, early maturity
➤ Most mutations are recessive and deleterious; only rare useful mutants are selected

7.6 Notable Examples

➤ Sharbati Sonora wheat — developed through mutation from Sonora 64; amber-colored grain with
improved quality
➤ NP 836 (rice) — early-maturing mutant
➤ Atomita 2 (rice) — developed through mutation; high-yielding, early-maturing
➤ Mutation in barley — produced semi-dwarf varieties
■ QUICK REVISION POINTS
✔ Mutation = sudden heritable change in DNA.
✔ Physical mutagens: X-rays (Muller 1927), Gamma rays, UV, Neutrons.
✔ Chemical mutagens: EMS (most common), Nitrous acid, Alkylating agents.
✔ M1 → chimeric; M2 → mutations become homozygous (main screening generation).
✔ Sharbati Sonora wheat = most famous mutation breeding success.
✔ Most mutations are recessive, deleterious — rare useful ones are selected.
 TOPIC 8: POLYPLOIDY

Multiple Chromosome Sets and Their Role in Crop Improvement

8.1 What is Polyploidy?

Polyploidy: The condition in which a plant has more than two complete sets of
chromosomes. It naturally occurs due to irregularities in mitotic or meiotic divisions.
Polyploidy plays a pivotal role in plant breeding, especially in enhancing genetic diversity
and adaptability of crops.

Polyploidy is particularly valuable because it can create novel genetic combinations and traits that contribute to
crop improvement. It represents a major evolutionary mechanism in plants.

8.2 Types of Polyploidy

1. Autopolyploidy

Arise when chromosome duplication occurs WITHIN the SAME SPECIES, leading to
multiple copies of the same genome. Example: AA → AAAA (tetraploid). Induced by:
Colchicine treatment, Physical agents (heat, cold shock).

2. Allopolyploidy

Occur when chromosomes from DIFFERENT SPECIES are combined, usually through
hybridization followed by chromosome doubling. Example: Triticale, Raphanobrassica.
Important: Facilitates merging of desirable traits from two different species; overcomes
sterility resulting from hybridization.

8.3 Role of Autopolyploidy (Effects)

➤ Effect 1: Larger cell size than diploids; Guard cells of stomata are larger; fewer stomata per unit area
➤ Effect 2: Pollen grains are generally larger than those of corresponding diploids
➤ Effect 3: Generally slower in growth and later in flowering
➤ Effect 4: Usually have larger and thicker leaves, larger flowers and fruits (fewer in number than diploids)
➤ Effect 5: Generally show reduced fertility due to irregularities during meiosis and genotypic imbalance
➤ Effect 6: Often leads to increase in general vigour and vegetative growth (but some polyploids may be
smaller)
 ➤ Effect 7: Different species have different levels of optimum ploidy: Sugarbeet (Beta vulgaris) = 3x
optimum; Timothy grass (Phleum pratense) = 8–10x optimum
➤ Effect 8: Autopolyploids generally have LOWER dry matter content than diploids; increased size does
not always represent increased dry matter production (e.g., tetraploid turnip, cabbage)

8.4 Examples of Polyploid Crops

Crop Polyploid Type Benefit

Wheat Allopolyploid (Hexaploid) High yield, adaptability

Cotton Allopolyploid (Tetraploid) Fiber quality

Potato Autopolyploid (Tetraploid) Larger tubers

Banana Triploid (3x) Seedless fruits

Coffee Autopolyploid Flavor and disease resistance

High yield + disease resistance

Triticale Allohexaploid (Wheat × Rye) of rye

8.5 Benefits of Polyploidy in Plant Breeding

1. Increased Genetic Diversity

Polyploidy introduces new genetic combinations, enhancing adaptability and resilience. Essential for developing
new cultivars with improved traits.

2. Enhanced Stress Tolerance

Polyploid plants often exhibit greater resilience to drought, disease, and extreme temperatures. Attributed to
redundancy in genetic material, providing more adaptation options.

3. Improved Crop Traits

Leads to desirable agronomic traits: increased yield, larger fruit size, improved nutritional quality. Example:
Tetraploid durum wheat has superior pasta-making qualities compared to diploid varieties.

4. Facilitation of Hybridization
Polyploidy helps overcome sterility associated with hybridization between different species. Creates polyploid
hybrids combining beneficial traits from diverse genetic backgrounds.

5. Novel Phenotypic Expressions

Can result in unique physical characteristics not present in diploid plants: variations in flower color, size, and
overall plant morphology.

8.6 Triticale — A Classic Allopolyploid Example

 Triticale = Triticum turgidum (wheat, AABB genome, 2n=28) × Secale cereale (rye, RR
genome, 2n=14) → Sterile hybrid (ABR, 2n=21) → Colchicine treatment (chromosome
doubling) → Triticale Hexaploid AABBR (2n=42, Allohexaploid). Combines the HIGH
YIELD and bread-making quality of wheat with the DISEASE RESISTANCE and hardiness
of rye.

8.7 Hexaploid Wheat — Natural Allopolyploidy

Triticum monococcum (AA, n=7) × Aegilops speltoides (BB, n=7) → Sterile (AB) →
Spontaneous chromosome doubling → Tetraploid emmer wheat (AABB, n=14) × Aegilops
squarrosa (DD, n=7) → Sterile (ABD) → Spontaneous doubling → Hexaploid wheat
AABBDD (n=21). Modern bread wheat is a natural allohexaploid.

■ QUICK REVISION POINTS

✔ Polyploidy = more than 2 complete chromosome sets.
✔ Autopolyploidy = same species (AA→AAAA); Allopolyploidy = different species.
✔ Colchicine inhibits spindle formation → prevents chromosome separation → polyploidy.
✔ Triticale = Wheat (AABB) × Rye (RR) → AABBRR (allohexaploid).
✔ Modern bread wheat (AABBDD) = natural allohexaploid from 3 species.
✔ Benefits: Genetic diversity, Stress tolerance, Better traits, Overcomes sterility, Novel expressions.
✔ Banana = Triploid (seedless); Potato = Autotetraploid (larger tubers).
 TOPIC 9: MOLECULAR MARKERS IN PLANT
BREEDING

DNA-Based Tools for Precise and Efficient Crop Improvement

9.1 What are Molecular Markers?

Molecular Markers: DNA sequences at specific locations in the genome that can be
detected using laboratory techniques. They serve as 'DNA fingerprints' and can be used
to identify desired traits at the seedling stage without waiting for the plant to mature.

9.2 Types of Molecular Markers

RFLP (Restriction Fragment Length Polymorphism)

First-generation molecular marker. Detects variation in fragment sizes produced by restriction enzymes.
Labor-intensive but highly informative.

RAPD (Random Amplified Polymorphic DNA)

Uses short random primers to amplify DNA by PCR. Simple and inexpensive. Less reproducible than other
markers.

AFLP (Amplified Fragment Length Polymorphism)

Combines restriction digestion and PCR amplification. Highly informative and reproducible. Useful for genome
mapping.

SSR / Microsatellites (Simple Sequence Repeats)

Short tandem repeats of 1–6 bp. Highly polymorphic, co-dominant, and very useful in breeding. Can distinguish
closely related varieties.

SNP (Single Nucleotide Polymorphism)

Variation at a single nucleotide position. Most abundant type of variation in the genome. Most widely used in
modern breeding programs.

DArT (Diversity Arrays Technology)

Array-based technology for high-throughput genotyping. Useful for crop improvement and germplasm
characterization.
9.3 Marker-Assisted Selection (MAS)

MAS: The use of molecular markers linked to genes of interest to assist in the selection
process. Allows breeders to select plants with target genes at the seedling stage,
dramatically SPEEDING UP the breeding process.

➤ Example: Sub1 Rice — Submergence-tolerant rice developed using MAS. The 'Sub1' gene for flood
tolerance was identified and introduced using molecular markers.
➤ MAS eliminates the need to wait for phenotypic expression
➤ Particularly useful for traits that are difficult to evaluate phenotypically (e.g., disease resistance, drought
tolerance)
➤ Reduces time and cost of breeding by selecting only plants with the target genes

9.4 Applications of Molecular Markers

➤ Gene mapping and genome sequencing

➤ Identification of QTLs (Quantitative Trait Loci) for complex traits
➤ Marker-Assisted Backcrossing (MABC) for precise gene introgression
➤ Fingerprinting of varieties for intellectual property protection
➤ Assessment of genetic diversity in germplasm collections
➤ Marker-assisted pyramiding of multiple resistance genes
➤ Phylogenetic analysis and taxonomy

■ QUICK REVISION POINTS

✔ Molecular markers = DNA fingerprints at specific genome locations.
✔ Types: RFLP (1st gen), RAPD, AFLP, SSR/Microsatellites, SNP (most abundant/used).
✔ MAS = Marker-Assisted Selection — selects plants at seedling stage.
✔ Sub1 rice = classic MAS success (flood-tolerant gene identified and used).
✔ SNPs are most abundant genetic markers in any genome.
✔ SSR/Microsatellites = most useful in plant breeding (co-dominant, polymorphic).
 TOPIC 10: ROLE OF BIOTECHNOLOGY IN PLANT
BREEDING

Modern Molecular Tools for Precise Crop Improvement

10.1 What is Biotechnology in Plant Breeding?

Biotechnology in Plant Breeding: The use of modern molecular tools and techniques
(genetic engineering, tissue culture, marker-assisted selection, etc.) to enhance, modify,
or introduce specific genes into plants much faster and more precisely than traditional
methods.

Traditionally, plant breeding involved cross-breeding plants over many generations — a slow and imprecise
method. Biotechnology has revolutionized this by enabling targeted, precise, and rapid genetic improvement.

10.2 Major Roles of Biotechnology in Plant Breeding

1. Genetic Engineering (Transgenic Plants)

➤ Involves inserting genes from another organism into a plant's genome
➤ Can create GMO crops with traits NOT naturally present in the species
➤ Uses vectors (like Agrobacterium tumefaciens) or gene gun for gene transfer
➤ Allows precise addition of a specific functional gene

Example: Bt Cotton — A gene from the bacterium Bacillus thuringiensis (Bt) is inserted
into cotton. This gene produces a protein (Cry toxin) TOXIC to bollworms (a major pest),
drastically reducing the need for chemical pesticides. First GM crop widely
commercialized in India; also widely adopted in USA, China.

2. Tissue Culture and Micropropagation

➤ Produces identical copies (clones) of plants under sterile lab conditions
➤ Useful for rapid multiplication of disease-free elite varieties
➤ Enables production of thousands of plants from a small amount of tissue
➤ Important in horticulture for mass propagation

Example: Banana and Orchid propagation — Tissue culture is widely used to produce
large numbers of uniform, disease-free banana plants. Essential for somatic hybridization.

3. Marker-Assisted Selection (MAS)

 ➤ Molecular markers (DNA fingerprints) used to identify desired traits at seedling stage
➤ Speeds up breeding by selecting ONLY plants with target genes
➤ Eliminates the need to grow plants to maturity before selection
➤ Can identify multiple traits simultaneously

Example: Sub1 Rice — Submergence-tolerant rice developed using MAS by identifying

and introducing the 'Sub1' gene for flood tolerance.

4. CRISPR and Genome Editing

➤ CRISPR/Cas9 allows PRECISE editing of specific genes WITHOUT introducing foreign DNA
➤ Considered more natural and safer than traditional GMOs
➤ Can knock out (disable), knock in (add), or edit specific genes
➤ Targets only the desired gene with high precision

Example: CRISPR-edited mushrooms that resist browning by turning off a single gene —
without adding any new DNA. Also used to develop disease-resistant crops and improve
nutritional profiles.

5. Molecular Diagnostics
➤ Helps detect plant diseases at an early stage using DNA/RNA-based tools
➤ Uses PCR, ELISA, gene probes for pathogen detection
➤ Ensures timely treatment and reduces crop loss
➤ Essential for quarantine and seed health testing

Example: PCR-based detection of viral diseases in seed lots before planting.

10.3 Bt Cotton — A Detailed Case Study

Bt Cotton: Genetically engineered cotton expressing the Cry toxin gene from Bacillus
thuringiensis bacterium. IMPACT: • Pest resistance without chemical pesticides • Higher
yield and profit for farmers • Reduced environmental impact from pesticide use • Widely
adopted in India, USA, China, etc. • First genetically modified crop widely commercialized
in India • Has significantly changed cotton farming practices globally

10.4 Advantages of Using Biotechnology in Plant Breeding

Dimension Advantage

Speed Faster development of new varieties; more plant generations per year
(speed breeding); accelerated trait selection
 Precision Specific genes/traits modified without bringing unwanted traits; CRISPR and
molecular markers allow targeted genetic changes

Resilience Development of crops tolerant to climate-change stresses (drought, flooding,

heat, salinity); better pest and disease resistance

Sustainability Reduces dependence on pesticides, fertilizers, excessive water; conserves

land; reduces GHG emissions; improves yield per input

10.5 Challenges and Concerns

➤ Public resistance to GMO crops — ethical and safety concerns

➤ Regulatory hurdles — different regulations in different countries
➤ Potential risks to biodiversity — gene flow to wild relatives
➤ Intellectual property and seed patent issues — corporate control of food supply
➤ High initial cost of biotechnological research and development
➤ Limited access for small farmers in developing countries

■ QUICK REVISION POINTS

✔ 5 major biotech roles: Genetic Engineering, Tissue Culture, MAS, CRISPR, Molecular
Diagnostics.
✔ Bt Cotton = Bacillus thuringiensis gene → Cry toxin → kills bollworms; 1st GM crop in India.
✔ CRISPR = precise editing without foreign DNA; safer than traditional GMOs.
✔ Tissue culture = rapid clonal multiplication of disease-free elite varieties.
✔ Advantages: Speed, Precision, Resilience, Sustainability.
✔ Concerns: GMO resistance, Regulatory issues, Biodiversity risk, Patents, Cost.
✔ Mnemonic for biotech roles: 'GT-MCC' = Genetic engineering, Tissue culture, MAS, CRISPR,
diagnostiCs.
 MASTER SUMMARY — UNIT 2

Complete Quick Revision at a Glance

■ PLANT BREEDING
✦ Science + Art of improving plants by altering genetic makeup
✦ Based on genetic, biological, and agronomic principles
✦ 3 pillars: Objectives, Principles, Methods

■ OBJECTIVES (13)
✦ Higher Yield, Improved Quality, Abiotic Resistance, Biotic Resistance
✦ Change in Maturity/Earliness, Dormancy, Desirable Agronomic Traits
✦ Elimination of Toxins (Khesari → neurotoxin; Brassica → erucic acid; Cotton → gossypol)
✦ Non-Shattering, Synchronous Maturity, Photo/Thermo-Insensitivity
✦ Wider Adaptability, Varieties for New Seasons

■ PRINCIPLES (7)
✦ Genetic Variability (foundation), Heredity, Selection, Hybridization
✦ Isolation (Spatial, Temporal, Mechanical), Adaptation, Evaluation & Testing

■ SELECTION METHODS
✦ Mass Selection → phenotype-based, seeds mixed, ~7 years
✦ Pure Line Selection → individual plant progeny, ~8 years
✦ Back-Cross Method → transfers 1–2 genes; 6 backcrosses → 99.2% recurrent parent

■ HYBRIDIZATION
✦ Crossing genetically dissimilar plants
✦ Steps: Parent selection → Emasculation → Bagging → Pollination → F1 harvest
✦ Creates new gene combinations; exploits heterosis

■ INBREEDING DEPRESSION
✦ Reduction in vigour/fertility due to inbreeding
✦ Effects: Lethal alleles, Reduced vigour, Reduced reproduction, Distinct lines, Homozygosity (>99% after
7–8 selfing generations), Reduced yield
✦ Degrees: High (Alfalfa, Carrot), Moderate (Maize, Jowar), Low (Onion, Rye), None

■ HETEROSIS
 ✦ Coined by Shull (1914); superiority of F1 over both parents
✦ Types: Average heterosis, Heterobeltiosis, Economic heterosis (only commercially useful)
✦ Hybrid Vigour ≈ Heterosis; Luxuriance = vigour in sterile interspecific hybrids
✦ 8 manifestations: Fertility, Yield, Size/Vigour, Quality, Early maturity, Disease resistance, Adaptability,
Faster growth

■ MUTATION BREEDING
✦ Deliberate use of mutagens to induce heritable changes
✦ Physical: X-rays (Muller 1927), Gamma rays, UV, Neutrons
✦ Chemical: EMS (most common), Nitrous acid, Alkylating agents
✦ Main screening in M2 generation; M1 is chimeric
✦ Example: Sharbati Sonora wheat

■ POLYPLOIDY
✦ More than 2 complete chromosome sets
✦ Autopolyploidy = same species (colchicine); Allopolyploidy = different species
✦ Triticale = Wheat (AABB) × Rye (RR) → AABBRR (allohexaploid)
✦ Hexaploid wheat = AABBDD (natural allopolyploid)
✦ Benefits: Genetic diversity, Stress tolerance, Better traits, Hybridization facilitation

■ MOLECULAR MARKERS
✦ DNA fingerprints at specific genome locations
✦ Types: RFLP, RAPD, AFLP, SSR/Microsatellites, SNP (most common)
✦ MAS = Marker-Assisted Selection; Sub1 rice = classic example
✦ Applications: Gene mapping, QTL analysis, Variety fingerprinting

■ BIOTECHNOLOGY
✦ 5 roles: Genetic Engineering, Tissue Culture/Micropropagation, MAS, CRISPR, Molecular Diagnostics
✦ Bt Cotton = Bt gene → Cry toxin → kills bollworms; 1st GM crop in India
✦ CRISPR = precise editing without foreign DNA
✦ Advantages: Speed, Precision, Resilience, Sustainability
✦ Concerns: GMO resistance, Regulation, Biodiversity, Patents, Cost
 PRACTICE MCQs

Unit 2 — Plant Breeding & Crop Improvement

Q1. The term 'heterosis' was first coined by:

(A) Darwin
(B) Mendel
(C) Shull
(D) Muller
✔ Answer: (C) Shull (1914)
Explanation: Heterosis was first used by G.H. Shull in 1914 to describe the superiority of F1 over both parents.

Q2. Which type of selection involves mixing seeds from phenotypically similar superior plants?
(A) Pure Line Selection
(B) Mass Selection
(C) Back-Cross Selection
(D) Clonal Selection
✔ Answer: (B) Mass Selection
Explanation: In mass selection, 200–2000 plants of similar phenotype are selected and seeds mixed together.

Q3. Inbreeding depression is defined as:

(A) Increase in vigour due to selfing
(B) Reduction in vigour and fertility due to inbreeding
(C) Cross-pollination between related plants
(D) Increased homozygosity without any effect
✔ Answer: (B) Reduction in vigour and fertility due to inbreeding
Explanation: Inbreeding depression is the reduction or loss in vigour and fertility as a result of inbreeding.

Q4. Bt Cotton contains a gene from:

(A) Bacillus subtilis
(B) Bacillus thuringiensis
(C) E. coli
(D) Agrobacterium
✔ Answer: (B) Bacillus thuringiensis
Explanation: The Bt gene (Cry toxin gene) from Bacillus thuringiensis is inserted into cotton to control bollworms.

Q5. Polyploidy induced by colchicine primarily affects:

(A) Mitosis — inhibits spindle formation
(B) DNA replication
(C) Photosynthesis
(D) Respiration
✔ Answer: (A) Mitosis — inhibits spindle formation
Explanation: Colchicine inhibits spindle fiber formation, preventing chromosome separation, leading to polyploidy.

Q6. Triticale is a cross between:

(A) Wheat × Barley
 (B) Wheat × Rye
(C) Wheat × Oat
(D) Rye × Barley
✔ Answer: (B) Wheat × Rye
Explanation: Triticale = Triticum turgidum (wheat, AABB) × Secale cereale (rye, RR) → AABBRR allohexaploid.

Q7. In the backcross method, after 6 backcrosses, what percentage of recurrent parent traits is
recovered?
(A) 87.5%
(B) 93.7%
(C) 99.2%
(D) 96.8%
✔ Answer: (C) 99.2%
Explanation: After 6 backcrosses, approximately 99.2% of the recurrent parent characteristics are recovered.

Q8. CRISPR/Cas9 is considered safer than traditional GMOs because:

(A) It requires more DNA
(B) It introduces foreign DNA
(C) It edits specific genes without introducing foreign DNA
(D) It is less precise
✔ Answer: (C) It edits specific genes without introducing foreign DNA
Explanation: CRISPR allows precise gene editing without adding foreign DNA, making it closer to natural mutation.

Q9. A pureline variety is derived from:

(A) Mixture of several plants
(B) A single homozygous self-pollinated plant
(C) Cross-pollinated plants
(D) Backcross generations
✔ Answer: (B) A single homozygous self-pollinated plant
Explanation: A pureline is the progeny of ONE homozygous, self-pollinated plant with identical genotype.

Q10. Which crop shows HIGH inbreeding depression?

(A) Onion
(B) Rye
(C) Alfalfa
(D) Maize
✔ Answer: (C) Alfalfa
Explanation: Alfalfa (Medicago sativa) shows very high inbreeding depression; yield drops below 25% of
open-pollinated varieties.

Q11. Economic heterosis is the superiority of F1 over:

(A) Mid-parent
(B) Superior parent
(C) Best commercial variety
(D) Inferior parent
✔ Answer: (C) Best commercial variety
Explanation: Economic/Useful heterosis = superiority over the best commercial variety. This is the ONLY
commercially valuable estimate.

Q12. Sub1 rice was developed using which biotechnological tool?

(A) Genetic engineering
 (B) CRISPR
(C) Marker-Assisted Selection (MAS)
(D) Tissue culture
✔ Answer: (C) Marker-Assisted Selection (MAS)
Explanation: Sub1 rice (flood-tolerant) was developed using MAS by identifying and introducing the Sub1 gene.

Q13. Which mutagen was first used by H.J. Muller in 1927?

(A) Gamma rays
(B) X-rays
(C) EMS
(D) Neutrons
✔ Answer: (B) X-rays
Explanation: H.J. Muller first demonstrated use of X-rays as mutagen in 1927 using Drosophila.

Q14. The neurotoxin causing paralysis of lower limbs is found in:

(A) Cotton (Gossypium)
(B) Brassica
(C) Khesari (Lathyrus sativus)
(D) Green gram
✔ Answer: (C) Khesari (Lathyrus sativus)
Explanation: Khesari (Lathyrus sativus) contains a neurotoxin that causes paralysis of lower limbs (lathyrism).

Q15. After how many generations of selfing does a population reach >99% homozygosity?
(A) 3–4 generations
(B) 5–6 generations
(C) 7–8 generations
(D) 10–12 generations
✔ Answer: (C) 7–8 generations
Explanation: After 7–8 generations of selfing, lines approach >99% homozygosity and are called inbred lines.
 MAINS PRACTICE QUESTIONS

Unit 2 — Plant Breeding & Crop Improvement

Q1. Describe the objectives of plant breeding with suitable examples. How have these objectives
contributed to the Green Revolution?
→ Introduction: Define plant breeding; mention its importance for food security
→ List and explain 13 objectives with examples (yield, quality, abiotic/biotic resistance, etc.)
→ Specific examples: Cotton (270→170 days), Pigeon pea (270→120 days)
→ Mention Green Revolution context: High-yielding varieties of wheat, rice
→ Conclusion: Role in food security and sustainable agriculture

Q2. Compare Mass Selection and Pure Line Selection as methods of plant breeding. Which is more
effective and why?
→ Introduction: Define selection as isolation of desirable plants
→ Mass Selection: Phenotype-based, seeds mixed, 7 years, no progeny test
→ Pure Line Selection: Individual plant, separate evaluation, 8 years, progeny test
→ Comparison table: Basis, seeds, test, result, duration
→ Effectiveness: Pureline more genetically pure; mass selection faster but less precise
→ Conclusion: Choice depends on crop and breeding objective

Q3. What is inbreeding depression? Explain its effects with examples from different crop species.
→ Definition: Reduction in vigour/fertility due to inbreeding
→ Mechanism: Increase in homozygosity → expression of harmful recessive alleles
→ 6 effects: Lethal alleles, Reduced vigour, Reduced reproduction, Distinct lines, Homozygosity, Reduced yield
→ Degrees: High (Alfalfa, Carrot), Moderate (Maize), Low (Onion, Rye)
→ Maize example: Inbred lines yield ~50% of open-pollinated varieties
→ Conclusion: Importance of understanding inbreeding in hybrid seed production

Q4. Explain heterosis and hybrid vigour. What are the different estimates of heterosis and their
significance?
→ Define heterosis (Shull, 1914) and hybrid vigour
→ Distinguish: Heterosis vs Hybrid vigour vs Luxuriance
→ 3 types: Average heterosis (mid-parent), Heterobeltiosis (superior parent), Economic heterosis (best
commercial variety)
→ 8 manifestations: Fertility, Yield, Size, Quality, Early maturity, Disease resistance, Adaptability, Growth rate
→ Commercial significance: Only economic heterosis is practically useful
→ Examples: Tomato hybrids (earlier maturity), Onion hybrids (better keeping quality)

Q5. Discuss the role of polyploidy in plant breeding with suitable examples. How are polyploids
artificially induced?
→ Definition: More than 2 complete chromosome sets
→ Types: Autopolyploidy (same species) vs Allopolyploidy (different species)
→ Induction: Colchicine treatment (inhibits spindle → prevents chromosome separation)
 → Triticale: Wheat (AABB) × Rye (RR) → AABBRR via colchicine
→ Hexaploid wheat: Natural allopolyploid (AABBDD) evolution
→ Benefits: 5 benefits (genetic diversity, stress tolerance, improved traits, etc.)
→ Autopolyploidy effects: 8 effects (size, fertility, dry matter, etc.)
→ Examples table: Wheat, Cotton, Potato, Banana, Coffee

Q6. Describe the role of biotechnology in plant breeding. How has it revolutionized crop improvement?
→ Introduction: Limitations of traditional breeding (slow, imprecise)
→ 5 major roles: Genetic Engineering, Tissue Culture, MAS, CRISPR, Molecular Diagnostics
→ Bt Cotton case study: Bt gene → Cry toxin → bollworm control; impact in India
→ CRISPR: Precise editing without foreign DNA; examples
→ MAS: Sub1 rice; selection at seedling stage
→ Advantages: Speed, Precision, Resilience, Sustainability (with examples)
→ Challenges: GMO concerns, regulation, patents, biodiversity risk
→ Conclusion: Biotechnology as the future of sustainable crop improvement