Unit 2: Alleles, Gene Interactions and Cytoplasmic Inheritance - Subjective Questions

Multiple Alleles: When a gene exists in more than two allelic forms in a population, the condition is called multiple allelism, and the alternative forms are called multiple alleles.

Characteristic Features:

• Multiple alleles occupy the same locus on homologous chromosomes.
• They are always related to the same character/trait.
• An individual (being diploid) can carry only two of the multiple alleles at a time.
• Gametes (being haploid) carry only one allele.
• There is no crossing over within the alleles of a multiple allele series.
• The wild type is usually dominant, while others may show a dominance hierarchy.

ABO Blood Group Example:

• The gene has three alleles: , , and .
• and are codominant to each other.
• Both and are dominant over .

Thus, three alleles produce four phenotypes, demonstrating multiple allelism.

Both are exceptions to Mendel's law of dominance, but they differ in how heterozygotes express the phenotype.

Example of Incomplete Dominance:

• In Mirabilis jalapa (Four O'clock plant), crossing red (RR) × white (rr) flowers gives pink (Rr) in F1.
• F2 gives Red Pink White.

Example of Codominance:

• In the AB blood group, individuals express both A and B antigens on RBCs.
• In cattle, roan coat color = mixture of red and white hairs.

Key point: In incomplete dominance the phenotype is a blend; in codominance both phenotypes appear side by side.

Allelic Series: A group of three or more alleles of the same gene arranged in a dominance hierarchy constitutes an allelic series. Each allele in the series produces a distinct phenotype and shows a graded dominance relationship.

Coat Color in Rabbits:
The coat color gene has four alleles arranged in the following dominance order:

Dominance Relationships:

• is dominant over all others.
• is dominant over and .
• is dominant over .
• (albino) is recessive to all.

Significance:

• Demonstrates that a gene can have more than two alleles.
• Each allele results from a different mutation of the same locus.
• The phenotype of heterozygotes depends on the dominance hierarchy.

Epistasis: The interaction between two or more different genes (non-allelic) in which one gene masks or modifies the phenotypic expression of another gene at a different locus. The masking gene is epistatic; the masked gene is hypostatic.

Types of Epistasis (modifications of the dihybrid ratio):

• 1. Dominant Epistasis (): A dominant allele at one locus masks the expression of alleles at another locus. Example: Fruit color in summer squash.

• 2. Recessive Epistasis (): The homozygous recessive condition at one locus masks the expression of the other gene. Example: Coat color in mice (agouti).

• 3. Duplicate Dominant Epistasis / Duplicate Gene Action (): A dominant allele at either locus produces the same phenotype. Example: Fruit shape in Capsella.

• 4. Duplicate Recessive Epistasis / Complementary Gene Action (): Dominant alleles at both loci are required for the phenotype; recessive at either locus gives the same phenotype. Example: Flower color in sweet pea.

• 5. Dominant and Recessive (Inhibitory) Epistasis (): A dominant allele at one locus and recessive at another produce the same phenotype. Example: Plumage color in poultry.

• 6. Duplicate Genes with Cumulative Effect (): Both dominant genes together give one phenotype, each alone gives another. Example: Fruit shape in summer squash.

Summary Table:

Recessive Epistasis: Occurs when the homozygous recessive condition at one locus masks the phenotypic expression of the alleles at a second locus. The ratio is modified from to .

Coat Color in Mice:
Two genes are involved:

• Gene A (agouti): = agouti (banded hair), = black.
• Gene C (color): = allows pigment production, = albino (no pigment).

The cc genotype is epistatic — when present, no pigment is formed, so the mouse is albino regardless of the A gene.

Cross:

F2 Genotypes and Phenotypes:

Resulting phenotypic ratio:

• Agouti : Black : Albino =

Here, the recessive combines the (3) and (1) classes into a single albino class of , illustrating recessive epistasis.

Pleiotropy: The phenomenon in which a single gene influences multiple, seemingly unrelated phenotypic traits. Such a gene is called a pleiotropic gene.

Mechanism: A single gene product (protein/enzyme) may be involved in multiple biochemical pathways or in the development of several organs, so a mutation affects many characters.

Example 1 — Sickle Cell Anemia:

• Caused by a single mutation in the β-globin gene (HbA → HbS), substituting glutamic acid with valine.
• This single change causes multiple effects:
  • Sickle-shaped RBCs
  • Anemia
  • Blockage of blood vessels
  • Damage to spleen, kidney, heart, brain
  • Joint pain, weakness

Example 2 — Phenylketonuria (PKU):

• Caused by a defect in the gene coding for phenylalanine hydroxylase.
• Multiple effects: mental retardation, reduced skin/hair pigmentation, eczema, seizures.

Example 3 — In pea plants (Mendel):

• A single gene controls flower color, seed coat color, and axil spots simultaneously.

Significance: Pleiotropy shows that genes do not work in isolation and that one gene can have widespread developmental and physiological consequences.

Genomic Imprinting: An epigenetic phenomenon in which the expression of a gene depends on whether it is inherited from the mother or the father. Certain genes are expressed only from the maternally-inherited allele or only from the paternally-inherited allele, while the other allele is silenced.

Mechanism:

• Imprinting occurs mainly through DNA methylation (addition of methyl groups to cytosine residues) and histone modifications.
• Methylation silences the gene without changing the DNA sequence.
• Imprints are erased and re-established during gametogenesis according to the sex of the individual.

Key Features:

• It is reversible and does not alter the DNA sequence (epigenetic).
• Only a small subset of genes are imprinted.

Examples — Chromosome 15q region:

• Prader-Willi Syndrome: Results from loss/deletion of the paternal copy of genes on chromosome 15. Symptoms: obesity, short stature, hypotonia, intellectual disability.

• Angelman Syndrome: Results from loss/deletion of the maternal copy of genes in the same region. Symptoms: severe intellectual disability, ataxia, seizures, inappropriate laughter.

Significance:

• Explains parent-of-origin effects in disease.
• Important in embryonic development and growth regulation.

Both terms describe variations in the phenotypic expression of a genotype, but they refer to different aspects.

Penetrance Example:

• Polydactyly (extra fingers/toes) shows incomplete penetrance — some individuals carrying the dominant allele have normal digits.
• If 80 out of 100 individuals with the genotype show the trait, penetrance = 80%.

Expressivity Example:

• In polydactyly, expressivity varies — some individuals have one extra finger, others have extra fingers on all four limbs.
• Camptodactyly (bent fingers) shows variable expressivity in different fingers.

Factors affecting both: environment, modifier genes, age, sex, and genetic background.

Cytoplasmic Inheritance: Also called extranuclear or extrachromosomal inheritance, it is the transmission of characters controlled by genes located in cytoplasmic organelles — chiefly mitochondria and chloroplasts — rather than in the nuclear chromosomes.

Salient Features:

• 1. Uniparental (Maternal) Inheritance: Traits are usually inherited from the female parent, because the egg contributes most of the cytoplasm to the zygote.

• 2. No Mendelian Segregation Ratios: Reciprocal crosses give different results; classical or ratios are not obtained.

• 3. Non-nuclear location: Genes are present in mtDNA / cpDNA, which are typically circular.

• 4. Irregular / non-Mendelian segregation: Organelles are distributed randomly (cytoplasmic segregation) during cell division.

• 5. Reciprocal cross differences: Phenotype of offspring depends on the maternal parent, not the paternal.

• 6. Not linked to any chromosome: Genes cannot be mapped to nuclear linkage groups.

Comparison Summary:

Mitochondrial DNA (mtDNA):

• Mitochondria contain their own circular, double-stranded DNA (~16.5 kb in humans).
• mtDNA encodes 37 genes: 13 proteins (electron transport chain components), 22 tRNAs, and 2 rRNAs.
• Each mitochondrion contains multiple copies; each cell contains many mitochondria.

Maternal Inheritance:

• mtDNA is inherited almost exclusively from the mother because the ovum contributes the cytoplasm (and mitochondria) to the zygote.
• Sperm mitochondria are usually destroyed after fertilization.
• Therefore, an affected mother transmits the trait to all her children, but affected fathers do not transmit it.

Heteroplasmy vs. Homoplasmy:

• Homoplasmy: All mtDNA copies in a cell are identical.
• Heteroplasmy: A mixture of normal and mutant mtDNA exists in the same cell.
• The threshold effect: disease appears only when the proportion of mutant mtDNA exceeds a critical level.

Example Diseases:

• Leber's Hereditary Optic Neuropathy (LHON): sudden loss of vision due to optic nerve degeneration.
• MELAS (Mitochondrial Encephalomyopathy, Lactic Acidosis, Stroke-like episodes).

Pedigree feature: All children of affected females may be affected; children of affected males are never affected.

Chloroplast DNA (cpDNA):

• Chloroplasts possess their own circular DNA (120–160 kb), encoding rRNAs, tRNAs, and proteins for photosynthesis.
• cpDNA is generally inherited maternally in most angiosperms.

Correns' Experiment on Mirabilis jalapa (1908):
The Four O'clock plant shows variegation — branches may be green, white, or variegated (patches of green and white). This is due to plastids being normal (green, with chlorophyll) or mutant (white, lacking chlorophyll).

Cross results depend ONLY on the maternal (seed-bearing) branch:

Interpretation:

• The phenotype of offspring is determined entirely by the female parent, irrespective of pollen source.
• This proves maternal cytoplasmic inheritance through chloroplasts.
• Variegated branches contain both plastid types, and random sorting (cytoplasmic segregation) during cell division distributes them unevenly, producing mixed progeny.

Conclusion: Leaf color in Mirabilis is controlled by plastid (chloroplast) genes, not nuclear genes.

Chloroplast-controlled Drug Resistance in Chlamydomonas reinhardtii:

Chlamydomonas is a unicellular green alga used to study chloroplast inheritance. It has a single large chloroplast and shows two mating types, and .

Streptomycin Resistance:

• Resistance to the antibiotic streptomycin () is controlled by a chloroplast gene.
• Sensitivity is denoted and resistance .

Uniparental Inheritance Pattern:

• Although both mating types contribute equal cytoplasm, chloroplast genes are inherited only from the parent.
• The chloroplast DNA of the parent is degraded after zygote formation.

Cross Results (Ruth Sager's work):

Interpretation:

• The progeny always resemble the parent for streptomycin phenotype.
• This uniparental inheritance (functionally maternal) confirms that the resistance gene is located in the chloroplast, not in the nucleus.

Significance: It provides direct evidence that antibiotic resistance can be encoded by organellar (cpDNA) genes and inherited cytoplasmically.

Kappa Particles in Paramecium aurelia:

Some strains of Paramecium called killer strains produce a toxic substance (paramecin) that kills sensitive strains. This trait shows the interaction between cytoplasmic particles and a nuclear gene.

Kappa Particles:

• Kappa are self-replicating, DNA-containing cytoplasmic particles (bacterial endosymbionts, later identified as Caedibacter).
• They produce the toxin paramecin, lethal to sensitive Paramecia.
• Killers are immune to their own toxin.

Role of Nuclear Gene K:

• The maintenance and multiplication of kappa particles require the dominant nuclear gene .
• Genotype or with kappa in cytoplasm → Killer.
• Genotype → cannot maintain kappa; particles are lost → Sensitive.

Conjugation Crosses:

• Case 1 — Short conjugation (no cytoplasmic exchange):

  • Killer ( + kappa) × Sensitive ()
  • Exconjugants: one killer (retains kappa), one sensitive (no kappa).

• Case 2 — Prolonged conjugation (cytoplasmic bridge forms):

  • Kappa passes to both partners → both exconjugants become killers ( + kappa).

Conclusion:

• The killer trait requires both the cytoplasmic kappa particles and the nuclear gene .
• This is a classic example of nucleo-cytoplasmic interaction in inheritance.

Shell Coiling in Limnaea peregra:

The direction of shell coiling in this snail shows a maternal effect — the phenotype of the offspring is determined by the genotype of the mother, not by the offspring's own genotype.

Two Phenotypes:

• Dextral (right-handed coiling) — dominant, controlled by allele .
• Sinistral (left-handed coiling) — recessive, controlled by allele .

Genetic Control (Maternal Effect):

• Coiling direction is determined by the orientation of the spindle during early cleavage, which is set by substances (mRNA/proteins) deposited in the egg cytoplasm by the mother's genotype.
• Therefore, an individual's phenotype reflects its mother's genotype, delayed by one generation.

Cross Example:

• Mother (sinistral) × Father (dextral) → F1 = , but they are sinistral (because mother was ).
• Reciprocal: Mother × Father → F1 = , all dextral.
• In F2, all snails are dextral regardless of genotype (because F1 mothers were , dextral-determining).
• In F3, a (dextral : sinistral) pattern appears, delayed by a generation.

Difference from True Cytoplasmic Inheritance:

Conclusion: Shell coiling is a maternal effect governed by nuclear genes, not true cytoplasmic (organellar) inheritance.

Complementary Gene Interaction (Duplicate Recessive Epistasis):

When two dominant genes at different loci are both required together to produce a phenotype, and the absence of a dominant allele at either locus results in the same (default) phenotype, the modified dihybrid ratio is .

Bateson and Punnett's Sweet Pea Experiment:

• Two different white-flowered varieties were crossed.
• Surprisingly, the F1 were all purple-flowered.
• The F2 gave purple : white = .

Explanation:
Purple pigment (anthocyanin) synthesis requires two enzymes coded by two genes:

• Gene C → produces a precursor.
• Gene P → converts precursor to purple pigment.

Both dominant alleles ( and ) must be present for color.

Cross: (white) × (white)

• F1 = → Purple (both dominants present).
• F1 × F1 → F2:

Result: Purple : White = .

Conclusion: Both genes complement each other; only their combined dominant presence produces color, demonstrating complementary gene action.

Dominant Epistasis: When a dominant allele at one locus masks the phenotypic expression of alleles at a second locus, the interaction is called dominant epistasis. The dihybrid ratio is modified to .

Fruit Color in Summer Squash:
Two genes control fruit color:

• Gene W: (white) is epistatic and dominant — it masks color. allows color.
• Gene Y: = yellow, = green (expressed only when ).

When the dominant is present, the fruit is white regardless of the Y gene.

Cross:

F2 Genotypes and Phenotypes:

Combining classes:

• White =
• Yellow =
• Green =

Resulting ratio: White : Yellow : Green = .

Conclusion: The dominant allele masks color expression, illustrating dominant epistasis.

Duplicate Dominant Epistasis (Duplicate Gene Action): When a dominant allele at either of two loci produces the same phenotype, and only the double recessive gives a different phenotype, the ratio becomes .

Example — Capsule shape in Capsella bursa-pastoris (shepherd's purse):
Two genes ( and ) control the triangular vs. ovoid seed capsule.

• A dominant allele at either locus ( or ) → triangular capsule.
• Only double recessive () → ovoid capsule.

Cross:

F2 Genotypes and Phenotypes:

Combining classes:

• Triangular =
• Ovoid =

Resulting ratio: Triangular : Ovoid = .

Interpretation: The two genes are duplicate — either one alone can produce the dominant phenotype, so their effects overlap. This redundancy explains the ratio.

Comparison of Nuclear and Cytoplasmic Inheritance:

Why Reciprocal Crosses Differ in Cytoplasmic Inheritance:

• In a reciprocal cross, the roles of male and female parents are exchanged (e.g., cross A♀ × B♂ vs. B♀ × A♂).
• In nuclear inheritance, both parents contribute equal nuclear genes, so both reciprocal crosses give the same offspring.
• In cytoplasmic inheritance, the offspring receive nearly all their cytoplasm (and hence organelles/mtDNA/cpDNA) from the female (egg) parent.
• Therefore, the phenotype of the offspring depends only on the maternal parent, and reversing the parental sexes changes the result.

Conclusion: The difference in reciprocal crosses is a diagnostic feature that reveals cytoplasmic (maternal) inheritance.

Modification of the Dihybrid Ratio ():

When two gene pairs interact (either through epistasis or complementary/duplicate action), the standard F2 dihybrid ratio of is modified. The nine, three, three, and one classes get combined in different ways depending on the interaction.

Summary Table of Gene Interactions:

Key Points:

• All modified ratios are rearrangements of the same 16 F2 individuals.
• The sum of the numbers always equals 16, confirming two gene pairs are involved.
• These interactions demonstrate that genes do not always act independently; the phenotype often results from interaction between products of different genes in a biochemical pathway.

Conclusion: Gene interactions expand Mendelian genetics, showing that a single character may be governed by two or more interacting genes.

Incomplete Dominance: A form of inheritance in which the heterozygote shows a phenotype intermediate between the two homozygous parents, because neither allele is completely dominant over the other.

Flower Color in Mirabilis jalapa:

• Red flowers = genotype
• White flowers = genotype
• Pink flowers = genotype (intermediate/blended)

Biochemical Basis: The allele produces a certain amount of red pigment. In , only one dose of pigment is produced, giving a diluted (pink) color. Two doses () give full red.

Cross (P generation): Red () × White ()

F1 Generation:

• All → Pink (intermediate).

F2 Generation (Rr × Rr):

Ratios:

• Genotypic ratio =
• Phenotypic ratio = Red Pink White

Key Observation:

• Unlike complete dominance (where phenotypic ratio is ), here the phenotypic ratio equals the genotypic ratio (), because each genotype has a distinct phenotype.
• This confirms that the alleles were not lost or blended permanently — the parental phenotypes reappear in F2, supporting the particulate nature of genes.