• The "Plant System": Gene abbreviations begin with an upper case (dominant allele) or lower case letter.

• The "Drosophila System": Gene abbreviations are represented by letters with (wild-type allele) or without (mutant allele) a + symbol. The mutant allele begins with a capital letter if the mutant is dominant to the wild type and with a lower case letter if the mutant is recessive to the wild type allele (w+ is dominant to w; B is dominant to B+).

• Incomplete Dominance (Partial Dominance, Lack of Dominance): In some cases, one allele is not completely dominant to the other and the phenotype is an intermediate. Example: Flower color in snapdragons.

• Codominance: In some cases, one allele is not completely dominant to the other and the phenotype shows the expression of both alleles. Examples: ABO blood group (I^A, I^B) and MN group (L^M, L^N).

• Variable Expressivity: This exception is closely related to incomplete penetrance but is seen with quantitative traits. In variable expressivity, the degree of expression (color, height, etc.) varies among individuals with the same genotype. Variable expressivity and incomplete penetrance have been explained in the past as "due to differences in the genetic background." With the advent of genomics, the actual contributing genes in this background may be discovered.

• Overdominance: In some cases, the most extreme phenotype is seen in the heterozygote, not the homozygous dominant. Cases of overdominance for the trait height have been discovered in wheat and other plants.
  
• Sickle-Cell Anemia: A Case Study: Sickle-cell anemia is an inherited form of anemia caused a mutant β-globin allele. (Normal hemoglobin has 2 β- and 2 α-globins.) Several mutations have apparently arisen independently in malaria-prone regions of the world. The most common mutant is due to a single nucleotide change (A to T) of the β-globin gene, which results in glutamic acid being substituted by valine at position 6. This causes hemoglobin molecules to polymerize and causes red blood cells to sickle (elongate). These sickled cells are destroyed, causing anemia, and also clog up organs, causing various severe conditions. People with two copies of the mutant allele (homozygotes) have sickle-cell disease. People with just one copy of the allele (heterozygotes) have sickle-cell trait. Their red blood cells may sickle but this is much rarer, so they have slight anemia and other problems, but not as severely. However, in an environment where malaria is a major health problem, people with sickle-cell trait are actually fitter (less likely to die). This is because the malaria parasite (a sporozoan--which is a protist) infects red blood cells during its multiplication stage. Cells that are invaded by the parasite are much more likely to sickle and therefore be destroyed--also destroying the parasite. So, these people have much less severe malaria attacks and are much less likely to die from malaria. This is an example of what is called heterozygote advantage. The term heterosis is also used to describe cases where the heterozygote is actually more fit than either homozygote. (Summary: sickle-cell disease people are more likely to die of sickle-cell disease, people with no sickle-cell alleles are more likely to die of malaria if they are in a malaria environment, so the  fittest are the people with sickle-cell trait.)
  
• Problem: In this case, there are several phenotypes including: 1) how sick from anemia the person is; 2) how likely the person is to experience organ failure from sickling; 3) the person's fitness in a malaria environment. How would you characterize the relationship between these two alleles with respect to these three phenotypes? (Completely dominant, incompletely dominant, overdominant, ... ?)
  

• Multiple Alleles: Some genes (actually all genes) have more than just two alleles, although each individual has only two. Example: ABO Blood Group (I^A, I^B, i). Although this is a complication of Mendel's ideas, it does not alter how you would predict outcomes of crosses.
• A problem using multiple alleles in the rabbit.
  
• Multiple alleles in the Drosophila white gene:

• Multiple Genes, Polygenes, Quantitative Traits, Mutiple-Factor Traits, Multifactorial Traits: Some traits are determined by more than one gene. (Theoretical) Example: Plant height (determined by two or three genes with incomplete dominance). These are usually continuous (vs. discontinuous) traits. (Continuous traits=quantitative traits; discontinuous traits=qualitative traits). With environmental influence and variable expressivity, these traits can truly become continuous. The color of wheat grain is determined by a polygene (3 genes, 7 phenotypes, 1:6:15:20:15:6:1 ratio in the F2. Quantitative traits (including human intelligence) are determined by heredity and environment. The quotient called heritability (h2) measure the proportion genetics contributes to a trait (h2 = 1.0 means the trait is completely determined by genetics; h2=0 means the trait is completely determined by the environment). (Human multifactorial traits, twin studies, and DNA methylation: intelligence, psoriasis, Genetics Society of America statement on race and intelligence--scroll down to 1975.)(Equally additive genes problem)
  
• Human complex multifactorial traits: Many human traits (other than intelligence) are multifactorial traits and also have an environmental component.
• Autism has been shown to be influenced by a number of genes (AUTS1, AUTS3, AUTS4, and AUTS6 through AUTS17, all of which are autosomal, in addition to 4 X-linked susceptibility loci).
• New Research on Educational Achievement:   The General Certificate of Secondary Education (GCSE) exam is administered at the end of compulsory education at age 16 in Great Britain. GCSE scores were obtained for 13,306 twins at age 16 and assessed on 83 scales that were condensed to nine broad psychological domains, including intelligence, self-efficacy, personality, well-being, and behavior problems. The mean of GCSE core subjects (English, mathematics, science) is more heritable (62%) than the nine predictor domains (35-58%). Each of the domains correlates significantly with GCSE results, and these correlations are largely mediated genetically. The main finding is that, although intelligence accounts for more of the heritability of GCSE than any other single domain, the other domains collectively account for about as much GCSE heritability as intelligence. Together with intelligence, these domains account for 75% of the heritability of GCSE. We conclude that the high heritability of educational achievement reflects many genetically influenced traits, not just intelligence. (PNAS, October 21, 2014)
  

• Gene Interactions: Sometimes multiple genes produce unusual phenotypes. To solve problems with two gene interactions, remember the F2 genotypic ratio: 1 AABB: 2 AABb: 1 AAbb: 2 AaBB: 4 AaBb: 2 Aabb: 1 aaBB: 2 aaBb: 1 aabb
• Various Interactions: Two genes can interact to give various F2 phenotypic ratios.

Gene Interactions in fowl comb shape:

• Epistasis: This type of gene interaction occurs when one gene masks the effect of another. The gene that is doing the masking is the epistatic gene and the one that is being masked is the hypostatic gene. Example: Albinism is an example of recessive epistasis (C_ is pigmented, cc is albino; B_ is agouti, bb is black--note cc is albino regardless of which B/b genes are present). Example cross: agouti x white (P) ---> agouti (F1) ---> 9 agouti : 3 black : 4 white. Albinism is often a mutation in the tyrosinase gene. Tyrosinase catalyzes an initial step in the synthesis of melanin (tyrosine -->  ).
• Gene Suppression: A special type of epistasis is gene suppression where a second mutation reverses the effect of a first mutation. Example: Drosophila: f⁺/_ females have normal bristles and f/f females have short, bent bristles but f/f su(f)/su(f) females have normal bristles.