Genes, Alleles and Genotypes

    There is no standard for the designation of genes and alleles.  Scientists working with specific organisms may have informal standards for naming a gene or a new allele of that gene.  Alleles may be designated by a single capital or lower case letter (e.g., L is the symbol of Lobe eye in Drosophila) or by two , three or more letter or letter/number combinations (Wr - Wrinkled, per - periodicity).  Alleles may have superscripts (w^a) or subscripts (A₁) or both. In teaching examples,  alleles are often designated by capital and lower cases pairs (A & a; B &b).

In dealing with eukaryotic, diploid organisms, the genotype for each autosomal gene is designed by a pair of alleles.  Thus, the A gene might have genotypes  AA, Aa or aa.   The B gene might have genotypes BB,  Bb, and bb.  

      If you are interested in looking at A and B genes jointly,  the genotypes are written together (e.g., AABB. AaBB, aaBb,  etc.).  Each pair of letters represents the genotype of a single gene. The dominance relationship of the alleles of a single gene must  be investigated by the appropriate experimenal crosses. 

When a problem is assigned in a genetic course, genetics dominance relationships are often specified by the instructor.  In research situations, geneticists maintain enormous databases with this type of information.

     In many situations we only know a partial genotype.  That is, we know from the phenotype that the individual has at least one dominant allele. In that case, the genotype might be written with a blank space (e.g., A_bb) where the blank might be either the B or the b allele.

Phenotypes

Phenotypes are observed at the organism level or other levels of organization.  Phenotypes are given names like tall and short, yellow or green and so forth.  For instructional purposes,  and when calculating expected values,  phenotypes may be refereed to by their allele designation.

For example: Let Tall be dominant to short (A > a);

                                 green pods dominant to yellow pods (B > b), and

                                purple flowers dominant to white flowers (C > c).  

In an F₂ cross, there are 27 genotypes and 8 phenotypes.   The genotypes AABBCC, AABBCc, AABbCC, AABbCc, AaBBCC, AaBBCc, AaBbCC, AaBbCc would have phenotype TALL, GREEN PODS, PURPLE FLOWERS.  

 The genotype aabbc would have the phenotype SHORT, YELLOW POD, WHITE FLOWERS.  Saying or writing the complete phenotype each time is quite tedious and confusing.  

In order to simplify discussion,  we might designate all eight of these genotypes associates with tall, green pods and purple flowers  as A_B_C_ and the corresponding phenotype as ABC.  The phenotype for short, yellow pod and white flowers would be abc.

Under this system phenotypes designated by a capital letter such as A would correspond to either a homozygous dominant (AA) or heterozygous (Aa) genotype while  phenotypes designated by a lower case letter such as a would correspond to  homozygous recessive genotype (aa).