Genetics glossary

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The words you meet in Punnett squares and genetic crosses, each with a plain definition, the level it’s first needed at, and an example in the notation our calculators use. Hover or tab to a dotted-underlined term anywhere on CrossCalc to see its definition.

These definitions describe the simple Mendelian model taught in school and introductory college biology. Real inheritance is often more complicated; where a term depends on the model, the entry says so. Updated 7 November 2026.

Allele School

One of the different versions of a gene. A plant might carry an allele for purple flowers and an allele for white flowers.

Alleles exist because the DNA sequence of a gene can differ slightly between individuals. In pea plants, humans and other organisms with paired chromosomes, body cells carry two alleles of each gene, one from each parent. The two can be the same (homozygous) or different (heterozygous), and together they make up the genotype. Under complete dominance one allele masks the other; see dominant allele. In the calculators, every letter you pick is an allele: A and a belong to one gene, B and b to another.

Example: In Aa, A and a are two alleles of the same gene.

Chromosome School

A thread-like structure of DNA and protein that carries many genes. In humans and many other organisms, body cells hold chromosomes in pairs, one from each parent.

Genes are arranged along chromosomes, each at its own locus. The two chromosomes of a pair carry the same genes in the same order, but not necessarily the same alleles. When gametes form, each gamete receives one chromosome from every pair, which is why it carries one allele of each gene. Mendel’s laws of segregation and independent assortment follow from how chromosome pairs are shared out in meiosis.

Dihybrid cross High school

A cross that follows two genes at once, such as seed colour and seed shape. A cross of two double heterozygotes uses a 4×4 Punnett square.

Each AaBb parent can make four kinds of gamete (AB, Ab, aB and ab), so the Punnett square has 4 × 4 = 16 boxes. The 9:3:3:1 phenotypic ratio is two 3:1 ratios multiplied together, which works only when the two genes assort independently. It extends the monohybrid cross to two genes, and a trihybrid cross adds a third. For the method step by step, see how to do a dihybrid cross; for a plain explanation, dihybrid cross explained; to try one, the dihybrid cross calculator.

Example: AaBb × AaBb gives a 9:3:3:1 phenotypic ratio when both genes show complete dominance and assort independently.

Dominant allele School

An allele whose trait shows even with only one copy, because it masks the other allele (complete dominance, the simple Mendelian model). Usually written with a capital letter.

Dominance describes how two alleles interact in a heterozygous individual. It says nothing about how common or how “strong” an allele is: a dominant allele can be rare in a population. Some genes don’t show complete dominance at all; in incomplete dominance or codominance the heterozygote looks different from both homozygotes. The allele it masks is the recessive allele. The CrossCalc calculators treat capital letters as completely dominant, so AA (homozygous) and Aa look the same.

Example: AA and Aa both show the dominant trait.

F1 generation High school

The first filial generation: the offspring of the parental (P) cross. When Mendel crossed true-breeding parents with different traits, every F1 plant was heterozygous.

Coming straight from the P generation, the F1 is where Mendel saw only one of the two parental traits, which led him to the idea of dominance. Because every F1 offspring of a cross like AA × aa is Aa, crossing F1 individuals with each other gives the F2 generation.

Example: AA × aa gives an F1 that is all Aa.

F2 generation High school

The offspring of F1 individuals crossed with each other (or self-fertilised). In Mendel’s crosses, this is where the recessive trait reappeared.

When both F1 parents are Aa, a quarter of the F2 are expected to be aa, so the recessive trait reappears in about one offspring in four, and the genotypic ratio is 1:2:1. Real counts vary around these expected numbers: Mendel’s F2 seeds came out 5,474 round to 1,850 wrinkled, close to 3:1 but not exact.

Example: Aa × Aa gives a 3:1 phenotypic ratio when one allele is completely dominant.

Gamete School

A reproductive cell, such as an egg or sperm. It has one set of chromosomes, so it normally carries one allele of each gene instead of two.

Gametes are made by meiosis, which halves the number of chromosomes; the two alleles of each gene separate into different gametes, as Mendel’s law of segregation describes. When two gametes fuse at fertilisation, the new cell gets one allele of each gene from each parent, restoring the pair. Listing each parent’s possible gametes is the first step of every Punnett square: an Aa parent gives A or a, and an AaBb parent gives four types. Gametes are written with one letter per gene, such as AB or ab.

Example: An Aa parent is expected to make A and a gametes in equal proportions.

Gene School

A section of DNA that carries the instructions for a product, usually a protein, that affects a trait. Genes are passed from parents to offspring.

Each gene sits at a particular locus on a chromosome, and the different versions of a gene are its alleles. In a cross, each gene gets its own letter, so a dihybrid cross follows two genes with two letters. Many real traits depend on several genes and on the environment, so one gene rarely tells the whole story.

Genotype School

The alleles an organism has for a gene. In crosses we write the genotype with letters, such as Aa.

The genotype is the cause and the phenotype is what you observe. Different genotypes can give the same phenotype: under complete dominance, AA and Aa look alike, and only a test cross tells them apart. For more than one gene, write the genotype gene by gene, as in AaBb. See genotype vs phenotype and how to write genotypes and alleles.

Example: AA, Aa and aa are the three possible genotypes for one gene with two alleles.

See also: genotypic ratio

Genotypic ratio High school

The expected proportion of each genotype among the offspring of a cross, counted from the Punnett square.

Count the boxes of the Punnett square that hold each genotype and write the counts as a ratio. Because it counts genotypes rather than traits, it doesn’t depend on dominance: Aa × Aa always gives 1:2:1. It differs from the phenotypic ratio whenever two genotypes look alike. To turn it into fractions or percentages, see ratios as percentages and fractions; to work backwards from a ratio to the parents, see the reverse Punnett square.

Example: Aa × Aa gives AA : Aa : aa = 1:2:1.

Heterozygous School

Having two different alleles of a gene.

Because of segregation, a heterozygous individual is expected to make two kinds of gamete, A and a, in equal proportions. Under complete dominance it shows the dominant trait but can still pass on the recessive allele, so two heterozygous parents can have a recessive offspring. A test cross shows whether a dominant-looking individual is heterozygous. Its opposite is homozygous. More in homozygous vs heterozygous.

Example: Aa is heterozygous.

Homozygous School

Having two identical alleles of a gene. In a simple dominant/recessive model, that means both dominant or both recessive.

An individual can be homozygous dominant (AA) or homozygous recessive (aa); the opposite is heterozygous. A homozygous individual makes only one kind of gamete for that gene, so it passes the same allele to every offspring. That is why true-breeding plants are homozygous, and why crossing AA × aa gives an F1 generation that is all Aa. Compare with heterozygous in homozygous vs heterozygous.

Example: AA is homozygous dominant; aa is homozygous recessive.

Independent assortment High school

Mendel’s second law: alleles of different genes go into gametes independently. It holds for genes on different chromosomes; genes close together on one chromosome tend to be inherited together.

Independent assortment extends the law of segregation from one gene to several. It is why an AaBb parent is expected to make four gamete types in equal proportions, and why a dihybrid cross gives 9:3:3:1. The physical reason is that chromosome pairs line up independently of each other in meiosis. Genes close together on the same chromosome are linked and break the rule. Shortcut methods for crosses of three or more genes, which multiply each gene’s ratio, depend on it.

Example: An AaBb parent is expected to make AB, Ab, aB and ab gametes in equal proportions.

Locus High school

The position of a gene on a chromosome. A gene’s two alleles sit at the same locus on the two chromosomes of a pair.

The two chromosomes of a pair carry the same genes in the same order, so a gene’s two alleles are found at matching positions. If the two alleles differ, the individual is heterozygous at that locus. The plural is loci. The idea matters when genes are close together: genes at nearby loci on one chromosome tend to be inherited together instead of assorting independently.

Monohybrid cross High school

A cross that follows one gene, such as flower colour. Each parent passes on one of its two alleles, so the offspring fit in a 2×2 Punnett square.

The classic example is Mendel’s cross of true-breeding tall and dwarf pea plants: the F1 were all tall, and the F2 were about three tall to one dwarf. Each parent makes at most two kinds of gamete, so the Punnett square has four boxes. Try it in the monohybrid cross calculator, and compare with monohybrid vs dihybrid crosses. Following two genes at once is a dihybrid cross; three, a trihybrid cross.

Example: Aa × Aa gives a 3:1 phenotypic ratio when one allele is completely dominant.

P generation High school

The parental generation: the individuals crossed at the start of a breeding experiment. In Mendel’s work they were true-breeding plants.

Starting with true-breeding parents means their genotypes are known, so the results of later generations can be predicted and tested. A typical sequence is P → F1 → F2. The monohybrid cross calculator page works through this sequence with Mendel’s tall and dwarf peas.

Example: AA × aa is a typical P cross.

Phenotype School

The observable characteristics of an organism, such as flower colour. It results from the genotype and, for many traits, the environment too.

Phenotypes include visible traits, such as flower colour, and less visible ones, such as blood type. Under complete dominance two genotypes (AA and Aa) share one phenotype, so you can’t always read the genotype from the phenotype. Many real traits are shaped by several genes and by the environment. See genotype vs phenotype.

Phenotypic ratio High school

The expected proportion of each observable trait among the offspring of a cross.

Group the Punnett square boxes by the trait they show, then count. Unlike the genotypic ratio, it depends on dominance: Aa × Aa gives 3:1 under complete dominance but 1:2:1 under incomplete dominance. A test cross (Aa × aa) gives 1:1. A ratio is a set of expected probabilities, so small families or samples rarely match it exactly. More in ratios as percentages and fractions.

Example: Aa × Aa gives 3 dominant : 1 recessive under complete dominance.

Punnett square School

A grid that pairs every gamete from one parent with every gamete from the other, showing each possible offspring genotype and how likely it is.

Write one parent’s gametes across the top and the other’s down the side, then fill each box with the combined genotype. Assuming every gamete type is equally likely, each box is equally likely, so counting boxes gives the genotypic and phenotypic ratios. One gene needs a 2 × 2 grid, two genes 4 × 4, three genes 8 × 8. Build one with the dihybrid cross calculator, or follow how to do a dihybrid cross. Working from the offspring back to the parents is a reverse Punnett square.

Recessive allele School

An allele whose trait is masked by a dominant allele, so it usually shows only when two copies are present (simple Mendelian model). Usually written in lowercase.

Because the dominant allele masks it, a recessive allele can be carried, hidden, by heterozygous individuals for many generations and reappear in homozygous aa offspring when two carriers are crossed. “Recessive” doesn’t mean rare or harmful. The two-copy rule has exceptions: for genes on the X chromosome, males have only one copy, so a single recessive allele can show.

Example: Only aa shows the recessive trait.

Segregation High school

Mendel’s first law: the two alleles of a gene separate when gametes form, so each gamete gets one of them, with equal chance.

Segregation happens in meiosis, when the two chromosomes of each pair move into different cells. It is why a heterozygous Aa parent passes A to about half its offspring and a to the other half, and why the F2 generation shows a 3:1 ratio under complete dominance. With two or more genes, segregation works together with independent assortment.

See also: gamete

Test cross High school

Crossing an individual that shows the dominant trait with a homozygous recessive one, to find out whether it is AA or Aa from the offspring.

In its simplest form, a test cross is a monohybrid cross set up to reveal an unknown genotype, read from the offspring’s phenotypic ratio. It uses a homozygous recessive partner because it can only pass on a, so each offspring’s phenotype reveals the allele it got from the other parent. One recessive offspring proves the tested parent is Aa; a small all-dominant litter suggests, but doesn’t prove, AA.

Example: Aa × aa gives a 1:1 ratio; AA × aa gives all dominant.

See also: recessive allele

Trihybrid cross High school

A cross that follows three genes at once. A cross of two triple heterozygotes has 64 boxes in its Punnett square.

A trihybrid cross extends the monohybrid and dihybrid cross to three genes. Each AaBbCc parent makes 2 × 2 × 2 = 8 gamete types, so the Punnett square has 64 boxes. Rather than drawing it, you can multiply three 3:1 ratios together (the forked-line or branching method). See trihybrid cross without a Punnett square, or check your answer in the trihybrid cross calculator.

Example: AaBbCc × AaBbCc gives a 27:9:9:9:3:3:3:1 phenotypic ratio under complete dominance and independent assortment.

True-breeding High school

Always producing offspring with the same trait when self-fertilised or bred with others of the same true-breeding type. True-breeding individuals are homozygous for that gene.

Mendel worked with true-breeding pea lines, which peas maintain naturally because they self-fertilise. Being homozygous, a true-breeding plant makes only one kind of gamete for the gene, so crossing two true-breeding lines with different traits gives a uniform, heterozygous F1.

Use the terms

Every term above appears in a calculator result. Try a monohybrid cross to see genotypes, phenotypes and a 3:1 ratio, or the dihybrid cross calculator to see gametes and independent assortment at work. For how to write genotypes yourself, read how to write genotypes and alleles.

Sources

1. Biology 2e, chapter 12: Mendel’s Experiments and Heredity, OpenStax, Rice University. Accessed 7 November 2026.
2. Talking Glossary of Genomic and Genetic Terms, National Human Genome Research Institute (NIH). Accessed 7 November 2026.