AP Syllabus focus:
‘Traits controlled by chloroplast and mitochondrial DNA exhibit non-nuclear inheritance and do not follow simple Mendelian rules.’
Organelle genomes add an important “extra layer” to heredity. Because mitochondria and chloroplasts carry their own DNA and replicate independently, traits they encode often show inheritance patterns that differ from standard nuclear genetics.
What organelle DNA is (and why it matters)
Mitochondria and chloroplasts contain small, usually circular DNA molecules that encode a subset of proteins and RNAs essential for organelle function (for example, components of electron transport or photosynthesis). Most organelle proteins are still encoded by nuclear genes, but organelle-encoded variants can change phenotype.
Organelle DNA (organelle genome): Genetic material located in mitochondria or chloroplasts, separate from nuclear chromosomes, inherited through the cytoplasm rather than via Mendelian segregation.
Unlike nuclear chromosomes, organelle genomes:
Exist in many copies per cell (numerous organelles, multiple genomes per organelle)
Replicate and are distributed during cell division in ways that are not tightly coupled to the nuclear cell cycle
Can create inheritance patterns that do not produce classic Mendelian ratios
Non-nuclear (cytoplasmic) inheritance patterns
When a phenotype depends on alleles in organelle DNA, the trait shows non-nuclear inheritance because the relevant genetic information is outside the nucleus.
Key reasons Mendelian rules may not apply
Mendelian inheritance assumes:
Two alleles per gene per individual (diploid nuclear genes)
Segregation of allele pairs during meiosis
Independent assortment for genes on different chromosomes
Organelle traits often violate these assumptions because:
Cells may contain mixtures of organelle genotypes rather than a single allele pair.
During gamete formation and early development, the cytoplasm contributed to the zygote is unequal, so organelle DNA transmission can be biased.
Organelle genomes are inherited as cytoplasmic units, not as homologous chromosome pairs that segregate in meiosis.
Cytoplasmic inheritance: Inheritance of traits determined by genetic material in the cytoplasm (typically mitochondrial or chloroplast DNA), producing pedigree or cross outcomes that differ from Mendelian expectations.
A practical implication is that reciprocal crosses (switching which parent has the trait allele) can yield different offspring outcomes, which is unusual for autosomal nuclear genes.
Pedigree chart illustrating a mitochondrial inheritance pattern, where transmission follows the maternal line rather than Mendelian segregation. Both sexes can be affected, but only mothers pass the trait to their offspring, while affected fathers do not transmit it. This visual is useful for distinguishing organelle inheritance from autosomal or sex-linked patterns. Source
Heteroplasmy and variable expression
Because many mitochondria or chloroplasts are present in each cell, an individual can carry more than one organelle genotype.
Heteroplasmy and segregation effects
Heteroplasmy occurs when a cell contains both normal and mutant organelle genomes.
As cells divide, organelles are distributed to daughter cells through random sampling, which can shift the proportion of mutant genomes among tissues.
Schematic of mtDNA segregation through a developmental “bottleneck,” showing how daughter cells can inherit different proportions of wild-type and mutant mtDNA. The figure emphasizes that stochastic partitioning (and related processes) can amplify differences in heteroplasmy between cell lineages. This helps explain why organelle mutations can produce variable expression across tissues even when the mutation is inherited. Source
This can produce variable expressivity: different cells, tissues, or individuals show different trait severity even with the “same” inherited organelle mutation.
This sampling effect helps explain why some organelle-based traits can appear patchy (mosaic) across a tissue, especially in plants where chloroplast function strongly affects pigmentation and growth in particular cell lineages.
Photograph of a variegated Mirabilis jalapa plant showing patchy pigmentation, a classic phenotype used to discuss cytoplasmic (plastid/chloroplast) inheritance. Variegation reflects tissue mosaics that can arise when different cell lineages contain different chloroplast genotypes or functional states. This provides an intuitive visual link between heteroplasmy/segregation and visible plant traits. Source
Chloroplast traits: distinctive features
Chloroplast DNA variants can alter photosynthetic components, pigment pathways, or chloroplast gene expression, leading to phenotypes that may show:
Tissue mosaics if different cell lineages contain different chloroplast genotypes
Strong selection at the cellular level because nonfunctional chloroplasts can reduce cell performance
Because chloroplasts are abundant in leaf tissues, chloroplast-encoded defects often present as leaf colour or pattern changes, reflecting local chloroplast performance.
Mitochondrial traits: distinctive features
Mitochondrial DNA variants can change oxidative phosphorylation efficiency. Traits associated with mitochondrial genotypes often show:
High impact in energy-demanding tissues (e.g., muscle, nervous tissue)
Threshold-like effects driven by the proportion of dysfunctional mitochondria in a cell
Variable severity among siblings because organelle genomes can be partitioned unevenly into gametes and early embryonic cells
In all cases, these outcomes align with the syllabus emphasis: organelle DNA produces non-nuclear inheritance and does not follow simple Mendelian rules.
FAQ
During germline development, only a small subset of mitochondrial genomes may populate future eggs.
Random sampling can shift mutant loads markedly between siblings.
Some organisms show limited chloroplast recombination.
If recombination occurs, it can reshuffle chloroplast alleles and blur simple lineage-based expectations.
Rarely, organelles from the sperm/pollen contribute DNA to offspring.
This can create exceptions to the usual uniparental pattern and complicate pedigree interpretation.
They often compare reciprocal crosses and track whether offspring phenotypes depend on the cytoplasmic donor.
Molecular genotyping of organelle vs nuclear loci can confirm the source.
Different tissues can end up with different proportions of mutant organelles due to early developmental partitioning.
Energy demand can also amplify effects in particular organs.
Practice Questions
State two reasons why traits encoded by mitochondrial or chloroplast DNA may not follow Mendelian inheritance patterns. (2 marks)
Gene is located in organelle DNA in the cytoplasm rather than on nuclear chromosomes (1)
Organelle genomes are present in multiple copies and can be randomly partitioned, so there is no simple 1:1 segregation of allele pairs (1)
A student investigates a trait caused by a mutation in organelle DNA and observes variable severity among offspring. Explain how organelle inheritance can produce non-Mendelian ratios and variable expression. (5 marks)
Trait is determined by mitochondrial/chloroplast DNA, so inheritance is non-nuclear/cytoplasmic (1)
Organelle DNA is not packaged as homologous chromosome pairs that undergo Mendelian segregation in meiosis (1)
Cells contain many organelles and thus many genome copies (1)
Heteroplasmy (mixture of mutant and normal organelle genomes) can occur (1)
Random partitioning/sampling of organelles into gametes or daughter cells changes mutant proportions, causing variable severity (1)
