crosscalc

How to write genotypes: Allele letters and notation rules

Published

Table of contents
  1. The three genotypes for one gene
  2. Choosing a letter
  3. Two or more genes
  4. Writing phenotypes
  5. Notation you’ll meet later
  6. Common mistakes
  7. Quick check
  8. Related
  9. Sources

Level: School · You’ll need: nothing. Start here.

In introductory genetics, each allele of a gene is written as a single letter. A capital letter is the dominant allele and the same letter in lowercase is the recessive allele. A genotype is the pair of letters an organism carries, one from each parent.

So for height in pea plants, where tall is dominant to short, you might use T for tall and t for short.

The three genotypes for one gene

GenotypeNamePhenotype (complete dominance)
TTHomozygous dominantTall
TtHeterozygousTall
ttHomozygous recessiveShort
  • Homozygous dominant is two capital letters (TT).
  • Heterozygous is one of each, with the capital written first by convention (Tt, not tT).
  • Homozygous recessive is two lowercase letters (tt).

That answers two common questions. Is Rr homozygous or heterozygous? Heterozygous, because the two letters differ. What is the genotype rr? Homozygous recessive. More on homozygous vs heterozygous.

Choosing a letter

There’s no single official rule for classroom problems, and textbooks don’t all do it the same way, so follow your teacher’s or exam board’s convention if they have one. These habits help:

  • Use one letter per gene, the same letter for both alleles. T and t, not T and s.
  • Many courses take the letter from the dominant trait (T for tall, t for short).
  • When writing by hand, pick a letter whose capital and lowercase look different. A/a, B/b, D/d, E/e, G/g and T/t are easy to tell apart. C/c, K/k, O/o, P/p, S/s, W/w and Z/z are easy to mix up on paper (typed text, like this site, can use any letter).
  • Use a different letter for each gene in the same problem.

Many problems simply use A, B and C for the first, second and third gene, which is what the CrossCalc calculators do.

Two or more genes

Write the alleles gene by gene, keeping each pair together and the dominant allele first:

  • AaBb, not ABab or aBbA
  • AABb is homozygous dominant for gene A and heterozygous for gene B

A gamete carries one allele of each gene, so gametes are written with one letter per gene: AB, Ab, aB, ab. In normal gametes there is never more than one allele per gene, so writing Aa as a gamete is a mistake. See how gametes become a Punnett square.

Writing phenotypes

A phenotype is what you observe, so describe it in words: “tall”, “white flowers”, “round yellow seeds”.

The one accepted letter shorthand is for a phenotype class: when you mean “dominant, whatever the second allele is”, use an underscore. T_ means TT or Tt, both of which are tall. In a dihybrid cross, A_B_ is the class showing both dominant traits.

Notation you’ll meet later

Plain capital/lowercase letters work best for complete dominance. Other patterns often add superscripts to a shared base letter:

SituationExample notation
Incomplete dominance or codominanceC^R C^W (red and white alleles of gene C)
Multiple alleles, such as ABO blood groupsI^A, I^B, i
Genes on the X chromosomeX^H X^h, X^h Y
Wild-type (normal) allele in research genetics+ or a superscript +, e.g. a^+

In formal writing, gene and allele symbols are usually printed in italics. Exact conventions differ between organisms.

Common mistakes

  1. Using different letters for the two alleles of one gene.
  2. Writing the recessive allele first (aA).
  3. Splitting a gene’s pair in a two-gene genotype (ABab).
  4. Two alleles of one gene in a gamete.
  5. Writing a phenotype as a genotype (“the phenotype is Tt”) instead of describing the trait.

Quick check

Write the genotype for each:

  1. A short pea plant (tall T is dominant).
  2. A tall plant whose mother was short.
  3. A plant heterozygous for height and homozygous recessive for seed shape (R round, r wrinkled).
Answers
  1. tt. Short is recessive, so both alleles must be t.
  2. Tt. It’s tall, so it has at least one T, and the short mother could only pass on t.
  3. Ttrr.

Sources

Try it: check any cross instantly with the dihybrid cross calculator, or use the monohybrid and trihybrid versions.