Who Was Mendel?

• Gregor Johann Mendel (1822-1884) was an Augustinian friar and scientist who conducted his famous inheritance experiments at the monastery of St. Thomas in Brno (now in the Czech Republic).
• His foundational paper 'Versuche uber Pflanzen-Hybriden' (Experiments on Plant Hybridization) was published in 1866 in the Proceedings of the Natural History Society of Brno.
• The paper was ignored for approximately 35 years until its simultaneous rediscovery in 1900 by three botanists working independently:

  • Hugo de Vries (Netherlands) — working on inheritance in Oenothera and other plants

  • Carl Correns (Germany) — working on maize
  • Erich von Tschermak (Austria) — working on crosses between pea varieties

Why Mendel Chose Garden Pea (Pisum sativum)

The choice of Pisum sativum was critical to Mendel's success.

• Clearly distinct, contrasting characters available — Mendel needed traits that were unambiguously one state or another, not a continuum.
• Bisexual, self-pollinating flowers — pea flowers are normally self-pollinating due to their keel structure enclosing stamens and stigma, so each variety breeds true over generations.
• Easy artificial cross-pollination — despite natural self-pollination, controlled crosses can be made by opening the keel petals and transferring pollen manually.
• Short generation time — two or three generations per year possible in greenhouse conditions, allowing many generations to be studied.
• Large number of seeds per plant — provides adequate progeny for counting and statistical analysis.
• Several distinct, stable varieties available — essential for developing homozygous true-breeding lines as parental stocks.
• Plants easy to grow, maintain, and protect from foreign pollen — low contamination risk.
• Mendel also had the advantage of mathematical training, which allowed him to recognise the numerical ratios in his progeny — something previous hybridizers like Koelreuter and Knight had noticed vaguely but never quantified.

1.3  Mendel's Seven Pairs of Contrasting Characters

• Mendel selected seven pairs of characters in pea, each showing two distinct, contrasting forms.
• Crucially, he worked with characters whose genes happen to be on different chromosomes — meaning they showed independent assortment.

Mendel's Experimental Approach — Cross Scheme

Mendel's approach was systematic and replicable. For each character, he:

• Developed true-breeding (homozygous) parental lines by repeated self-pollination over two or more years — confirming each line bred uniformly for the trait.
• Made reciprocal crosses (A female x B male; AND B female x A male) to check whether the result depended on which parent was female and which was male. For all seven characters, reciprocal crosses gave identical results — confirming nuclear (not cytoplasmic) inheritance.
• Allowed F1 plants to self-pollinate to produce F2.
• Allowed F2 plants to self-pollinate to produce F3, enabling him to determine genotypes from progeny behaviour.
• Counted large numbers — his total data involved tens of thousands of plants, giving him reliable ratios.

MENDELIAN TERMINOLOGY 

These terms are foundational to all of genetics and plant breeding. Questions specifically testing definitions (e.g., 'distinguish between genotype and phenotype', 'what is codominance') appear regularly in IFoS paper.

Gene, Allele, and Locus

• Gene: A unit of heredity; a segment of DNA that encodes for a specific product (protein or RNA) and contributes to a specific phenotype. The functional unit of inheritance.
• Allele (allelomorph): Alternative forms of a gene occupying the same locus on homologous chromosomes. Example: T (tall) and t (dwarf) are alleles of the height gene. Mendel called them 'allelomorphs'; the shortened form 'allele' is now universally used.
• Locus (plural: loci): The specific, fixed position of a gene on a chromosome. All members of a species carry their genes at the same relative loci on their chromosomes.
• Multiple alleles: When a gene has more than two allelic forms in the population (though any diploid individual carries only two alleles at a locus). Examples: ABO blood group system (I^A, I^B, i alleles); self-incompatibility S-locus in crops (often 30+ alleles).

Genotype and Phenotype

• Genotype: The genetic constitution (combination of alleles) of an organism for a given gene or set of genes. Example: TT, Tt, tt are three possible genotypes for height in pea. The genotype is fixed at conception and does not change with environment.
• Phenotype: The observable, measurable expression of the genotype — the appearance or character of the organism. Example: 'Tall' and 'Dwarf' are phenotypes. The phenotype is determined by both genotype and environment.
• Relationship: Phenotype = Genotype + Environment interaction. Two plants with the same genotype may show different phenotypes in different environments; two plants with different genotypes may show the same phenotype (e.g., TT and Tt are both phenotypically tall).
• The terms genotype and phenotype were introduced by Wilhelm Johannsen in 1903 as part of his pure line theory. 

Homozygous and Heterozygous

• Homozygous: An individual carrying two identical alleles for a gene (TT or tt). A homozygous individual breeds true — all progeny from selfing are identical to the parent for that gene. Also called 'pure breeding'.
• Heterozygous: An individual carrying two different alleles for a gene (Tt). A heterozygous individual does NOT breed true — selfing produces a segregating progeny with multiple genotypic classes. Also called 'hybrid' for that particular gene.
• Hemizygous: Condition where a gene is present in only one copy — either because the organism is haploid, or because a gene is on the X chromosome in an XY organism (the Y has no corresponding locus), or due to a deletion.

Dominant and Recessive

• Dominant allele: An allele that is expressed in phenotype when present in one copy (heterozygous) or two copies (homozygous). Expressed in Aa individuals.
• Recessive allele: An allele that is expressed in phenotype only when present in two copies (homozygous recessive: aa). Masked when a dominant allele is also present.
• Complete dominance: Heterozygote (Tt) is phenotypically identical to the dominant homozygote (TT). Classic Mendelian dominance. F2 shows 3:1 phenotypic ratio.
• Incomplete / Partial dominance: Heterozygote (Rr) shows an intermediate phenotype between the two homozygotes (RR full red; rr white; Rr pink). F2 shows 1:2:1 phenotypic ratio (same as genotypic ratio). Example: flower colour in Mirabilis jalapa (Four O'Clock plant).
• Codominance: Both alleles are fully and equally expressed in the heterozygote — the phenotype is not intermediate but shows both parental phenotypes simultaneously. Example: AB blood group in ABO system (both A antigen and B antigen present on red blood cells); roan coat colour in Shorthorn cattle (both red and white hairs present in a single coat).

Test Cross vs Back Cross

This is a frequently tested distinction. 

• A back cross made to the recessive parent is simultaneously a test cross. However, not all test crosses are back crosses — if the F1 is crossed with a homozygous recessive individual that is neither of its parents, it is a test cross but not a back cross.

Other Important Terms

• Pure line: The progeny of a single self-fertilised homozygous plant. All plants in a pure line have the same genotype. Variation within a pure line is entirely environmental. Concept proposed by Johannsen (1903) based on studies with Princess bean (Phaseolus vulgaris). Critically important — it demonstrates that selection within a pure line is ineffective because there is no heritable genetic variation to select.
• Epistasis: Interaction between genes at different loci (non-allelic genes) where one gene masks or modifies the expression of another. Detailed in Part 4.
• Penetrance: The percentage of individuals with a given genotype that show the expected phenotype. If a dominant gene has 80% penetrance, 20% of individuals with the gene do not express it at all. Example: polydactyly in humans (extra fingers) — not all carriers of the dominant allele show the extra digit.
• Expressivity: The degree or extent to which a phenotype is expressed in individuals that DO show the phenotype. Variable expressivity means the trait is expressed differently (mildly, moderately, severely) in different individuals carrying the same genotype.
• Pleiotropy: A single gene affects multiple, apparently unrelated phenotypic traits. Example: sickle cell anemia gene — causes abnormal haemoglobin, anaemia, increased malaria resistance, blood vessel blockage, bone deformation. Important example: the dwarfing gene sd1 in rice causes not only dwarfism but also changes in leaf angle, tillering pattern, and response to nitrogen fertiliser.

2.1 Law I — The Law of Dominance

When two homozygous individuals differing in a single pair of contrasting characters are crossed, the character that expresses itself in the F1 (first filial) generation is termed dominant, while the character that remains unexpressed or hidden is termed recessive.

Chromosomal & Biochemical Basis

In a diploid organism, chromosomes exist in homologous pairs, meaning the organism possesses two alleles for every gene locus.

• The Wild-Type Allele: The dominant allele generally represents the normal, "wild-type" DNA sequence. It actively transcribes RNA to produce a fully functional protein or enzyme (e.g., an enzyme that synthesizes a growth hormone for Tallness).
• The Mutant Allele: The recessive allele is typically a mutated DNA sequence. It either produces a defective, non-functional protein or produces no protein at all.
• Haplosufficiency: In a heterozygous condition (Tt), the alleles do not physically blend. The phenomenon of dominance occurs because of haplosufficiency—a single copy of the dominant (functional) allele on one homologous chromosome is entirely sufficient to produce enough functional protein to manifest the normal phenotype. The defective recessive allele on the other homolog is simply masked by the abundance of the normal protein.

Example: Monohybrid Cross for Flower Colour

Cross between pure-breeding purple-flowered and white-flowered pea plants:

Monohybrid Cross — F1 Generation

P = Purple (Dominant),

p = White (Recessive).

F1 Result: All purple — dominance of P allele

All F1 progeny show the dominant trait (purple).

The white character is not lost; it is merely hidden. When F1 plants are selfed to obtain F2:

F2 Generation — Selfing of F1 (Pp × Pp)

Phenotypic Ratio: 3 Purple : 1 White | Genotypic Ratio: 1 PP : 2 Pp : 1 pp

The 3:1 ratio in F2 confirms that the recessive allele was preserved intact through F1 and re-expressed in homozygous condition in F2.

Significance in Plant Breeding

• Phenotypic Predictability: Enables breeders to definitively predict the F1 hybrid phenotype.
• Selection for Resistance: Many disease-resistance genes are dominant (e.g., the Xa21 gene for bacterial blight in rice). Because of haplosufficiency, the resistance is fully expressed and can be actively selected even in the heterozygous state during backcross generations.

Law II — The Law of Segregation (Law of Purity of Gametes)

During the formation of gametes (meiosis), the two alleles of a gene pair present in a heterozygous individual segregate (separate) from each other without blending, such that each gamete receives only one allele of the pair. Consequently, gametes are always pure for a particular trait.

Chromosomal Basis (Meiotic Disjunction)

The Law of Segregation is the direct phenotypic result of chromosomal behavior during the first division of meiosis (Meiosis I).

• Prophase I (Synapsis): The homologous chromosomes (one carrying the dominant allele 'T', the other carrying the recessive allele 't') physically pair up.
• Anaphase I (Disjunction): The spindle fibers contract and physically pull the homologous chromosomes to opposite poles of the dividing cell.
• Result: Because the 'T' allele is located on one chromosome and the 't' allele is located on its homolog, the physical separation of the chromosomes absolutely guarantees the separation of the alleles. The resulting haploid gametes receive only one chromosome from the homologous pair, thereby receiving only one allele. This cytological event proves why gametes are permanently "pure."

Example: Seed Shape — Round (R) vs. Wrinkled (r)

Monohybrid Cross — Seed Shape (RR × rr)

F1: All Rr (Round). The R and r alleles remain separate within the F1 heterozygote

F2 from selfing F1 (Rr × Rr) — Law of Segregation demonstrated

Phenotypic Ratio: 3 Round : 1 Wrinkled | Genotypic Ratio: 1 RR : 2 Rr : 1 rr

The re-appearance of the wrinkled trait in F2 in a predictable 3:1 ratio proves that alleles segregate cleanly during gamete formation — they never blend or contaminate each other.

Backcross vs. Test Cross (Crucial Distinction)

• Backcross: A cross between the F1 hybrid and either of its original parents. Used to transfer a specific trait into a recurrent parent.
• Test Cross: A specific backcross where the F1 hybrid is crossed only with the homozygous recessive parent.

  • Cross: F1 Tall (Tt) x Dwarf Parent (tt)

  • Result: 50% Tall (Tt) and 50% Dwarf (tt).
  • Significance: The 1:1 ratio mathematically verifies that the F1 parent was heterozygous and that meiotic segregation occurred perfectly.

Significance in Plant Breeding

• Basis of Segregating Populations: Explains the biological mechanism behind the segregation of parental traits in the F2 generation, forming the absolute basis of pure-line and pedigree selection methods.
• Genotypic Verification: The test cross determines whether a selected dominant plant is homozygous (pure line) or heterozygous (segregating).

Law III — The Law of Independent Assortment

When two or more pairs of contrasting characters are considered simultaneously in a cross, the segregation of one pair of alleles occurs completely independently of the segregation of the other pair during gamete formation.

Crucial Condition: This law is valid only if the genes governing the distinct characters are located on non-homologous chromosomes (different chromosome pairs).

Chromosomal Basis (Independent Bivalent Alignment)

The Law of Independent Assortment is the direct phenotypic result of chromosomal behavior during Metaphase I of Meiosis.

• The Metaphase Plate: During Metaphase I, paired homologous chromosomes (called bivalents) line up along the equatorial plate of the cell.
• Random Orientation: The orientation of these bivalents is entirely random. For example, the maternal chromosome carrying gene 'R' might face the "North" pole of the cell, while the paternal homolog carrying 'r' faces the "South" pole.
• Independence: The alignment of Chromosome Pair 1 (carrying genes for seed shape) has absolutely zero physical or biochemical influence on the alignment of Chromosome Pair 2 (carrying genes for seed color).
• Result: When the cell divides in Anaphase I, the chromosomes assort into gametes in random combinations. Mathematically, a plant with pairs of chromosomes can produce different types of gametes due strictly to this independent metaphase alignment.

The Cross Demonstration (Dihybrid Cross)

Characters considered: Seed Shape (Round R vs. Wrinkled r) and Seed Cotyledon Color (Yellow Y vs. Green y).

• Parents (P): Homozygous Round Yellow (RRYY) x Homozygous Wrinkled Green (rryy)
• F1 Generation: 100% RrYy (Phenotype: Round Yellow).

When the F1 (RrYy) is selfed, the independent assortment of chromosomes results in four distinct gamete types in equal frequencies (1:1:1:1): RY, Ry, rY, and ry.

The Dihybrid Punnett Square (F2 Generation):

Gametes	RY	Ry	rY	ry
RY	RRYY (Round Yellow)	RRYy (Round Yellow)	RrYY (Round Yellow)	RrYy (Round Yellow)
Ry	RRYy (Round Yellow)	RRyy (Round Green)	RrYy (Round Yellow)	Rryy (Round Green)
rY	RrYY (Round Yellow)	RrYy (Round Yellow)	rrYY (Wrinkled Yellow)	rrYy (Wrinkled Yellow)
ry	RrYy (Round Yellow)	Rryy (Round Green)	rrYy (Wrinkled Yellow)	rryy (Wrinkled Green)

F2 Phenotypic Ratio (9:3:3:1)

• 9/16: Round Yellow (Expressing both dominant traits: R_Y_)
• 3/16: Round Green (Dominant shape, recessive color: R_yy)
• 3/16: Wrinkled Yellow (Recessive shape, dominant color: rrY_)
• 1/16: Wrinkled Green (Expressing both recessive traits: rryy)

 

Exceptions / Deviations

• Genetic Linkage: Formulated by T.H. Morgan. If two genes are physically located close together on the same chromosome, they do not assort independently. They are physically linked and tend to be inherited together as a single unit, which drastically reduces the frequency of recombinant gametes and violates the 9:3:3:1 Mendelian ratio.

Significance in Plant Breeding

• Recombination Breeding: Provides the genetic foundation for combination breeding, allowing breeders to mathematically predict and extract recombinant genotypes (e.g., combining high yield from Parent A with disease resistance from Parent B).
• Population Size Calculations: Establishes the statistical framework for calculating the required size of an F2 field population. Because the probability of recovering a target double-recessive recombinant (rryy) is strictly 1/16, breeders know they must plant large populations to ensure its recovery