There are too many examples of the latter to list, since most traits (beyond the expression of an enzyme itself) are, at least to some degree, polygenic.

One cute example is the inheritance of fruit color in bell peppers. There are at least three genes involved here:

• Y - timing of chlorophyll elimination (Y - early; y - normal)
• R - color of carotenoids (R - red; r - yellow)
• C - regulation of carotenoid deposition (C - normal; c1, c2 - lowered concentration)
• This leads to a few possible genotypes producing interesting phenotypes:
  • Y- rr c1c2 - pale yellow
  • Y- rr Cc2 - darker yellow
  • yy rr CC - green
  • Y- R- CC - red
  • yy Rr CC - purple
  • Y- Rr Cc2 - pale yellow

Multiple Alleles at a Single Locus Some genes have more than two alleles, and not all the alleles have equal dominance/recessiveness. Different combinations of the various alleles can produce a range of phenotypes.

Example: coat color in rabbits (at the "C" locus, another one of the many controlling mammal coat color)

agouti (C) > chinchilla (silver) c^ch > Himalayan (c^h)> albino (c^a)


Another Example: white chevron pattern in Clover (Trifolium sp.).

Pleiotropy When a single gene affects the expression of more than one phenotypic character, the phenomenon is known as pleiotropy (from the Greek pleio meaning "more" and "trop).

• Example: Albinism.
  A single defect in one of the enzymes catalyzing tyrosine (through many intermediate products) to melanin can affect multiple phenotypic characters, from eye color to skin color to hair color.

• Another Example - Sickle Cell Anemia
  The mutation which changes the 6th amino acid from the terminal end of the Beta-protein chain is changed from glutamate to valine, making the chain hydrophobic rather than hydrophilic. Because the mutant hemoglobin precipitates readily in slightly acid conditions (as when the sufferer undergoes physical exertion, dissolving CO2 in the blood), and the malformed rbc's clog the capillaries, causing multiple phenotypic problems:
  • malformed red blood cells
  • slowed blood flow due to malformed rbc's
  • "tower skull" phenotype due to hypertrophy of red marrow in the cranium
  • stunted growth

  Recall the silver lining, however:

  There's a silver lining to every cloud...
  

• Homozygous normal people have a high incidence of malaria, which can be fatal.
• Homozygous recessive sickle cell sufferers die of the fatal anemia, but do not contract malaria.
• Heterozygotes suffer neither the symptoms of sickle cell anemia NOR contract malaria, as the abnormal blood cells somehow make an inhospitable environment for the protozoan parasite, Plasmodium
• This is one form of heterozygote advantage.

Genes Bossing Other Genes: Epistasis

• Example: Inheritance of comb shape in chickens
  Two loci, each with two alleles:
  
  • Rose gene: R or r
  • Pea gene: P or p
    • Rose gene, if present in RR or Rr will produce a "rose type" comb-- but ONLY if Pea gene is present in pp condition.
    • Pea gene, if present in PP or Pp will produce a "pea type" comb-- but ONLY if Rose gene is present in rr condition.
    • If one dominant allele is present for BOTH pea and rose, a "walnut type" comb results. R_P_ will give "walnut" comb.
    • If both alleles are present in double recessive condition, (rrpp), the wild type, single comb results.

Genetic Dissection via Analysis of Mutants

• Mutational analysis is the process of analyzing the phenotypes of organisms known to be mutant for a particular wild type allele.

• The genetic field of mutational dissection involves the intentional disruption of wild type alleles in study organisms, and the study of the effect of that mutation on the organism's phenotype.

• Phenotypes of interest can be generated by exposing study organisms to known mutagens, and observing the resulting phenotypes. (you never know, at the initial outset, what you might get.)

• If a particular genes locus is known, it can sometimes be targeted and "knocked out" so that its function in a normal organism can be studied.

• Gene function can also be studied by leaving the gene itself intact, but disrupting the function of its mRNA transcripts, or even its encoded protein product.

• Genes that eliminate or reduce the function of a wild type gene product are known as loss-of-function mutations
• Genes that increase or change the activity or function of a gene product are known as gain-of-function mutations

Protein Function and Malfunction: When Genes Go Bad Many metabolic pathways involve the products of several genes that work together to facilitate a given process. When one or more of these genes mutates, the result can be...

Inborn Errors of Metabolism

Protein function depends largely on the amino acids of which it is composed, and their precise order. This, in turn, is controlled by the nucleotide sequence of the DNA encoding that particular protein.
There are

• active proteins (e.g. enzymes, microtubule proteins, membrane pump proteins, antibodies) - these perform chemical functions
  
• structural proteins (e.g., silk, keratin, collagen) - these make up the physical structure of the organism

Archibald Garrod first wrote in 1909 that a number of human diseases were probably caused by "Inborn Errors of Metabolism": some fault in a metabolic pathway due to (almost always) deleterious mutation of a normal enzyme.

• Most often (not always), wild type is encoded by a dominant allele
• It usually codes for a functional form of an enzyme

• Most often (not always), mutations result in a recessive allele
• It usually (not always!) codes for a non-functional form of the wild type enzyme

The first scientists to study this phenomenon in detail were George Beadle and Edward Tatum, who initially worked on an ascomycete fungus, Neurospora, and later on Drosophila. By selecting mutants known to have faulty enzymes in a given metabolic pathway (auxotrophs), Beadle and Tatum were able to compare them to metabolically normal organisms (prototrophs) to discover the enzymes mediating entire metabolic pathways.

They did this by using known auxotrophic Neurospora . As you will recall,

• alter the way introns and exons are excised and spliced
• change the promoter of a gene, resulting in altered gene expression.
• alter the nature (and stability of the header and/or leader of the mRNA transcript.
• Let's have a LOOK.

In most wild populations, the two alleles carried by most individuals are wild type. Mutations may occur spontaneously, but rarely the same way in any two individuals, if the process is random.

This means that if a mutation occurs in a particular member of the species, and it passes on that mutation to its offspring, then inbreeding between those two related individuals is far more likely to result in homozygosity of recessive, mutant alleles than outbreeding with unrelated individuals would.

The field of Biochemical Genetics is devoted to the study of genetic control of biochemical pathways.

Many human disorders are known to be inborn and due to flaws in the enzymes that convert one cellular substance into another. For example, an error in any number of enzymes in the phenylalanine pathway can result in a several different types of disorders, like SO.

phenylalanine (aa) is a precursor to tyrosine, and aa which serves as a precursor to many different celllular products.

• In a normal metabolism, phenylalanine is converted to tyrosine by an enzyme phenylalanine hydroxylase (p.h.)

• A mutant form of p.h. is unable to change phe to tyr.
• In humans with this faulty enzyme, phe eventually breaks down into toxic, lipophilic waste products (phenylpyruvate) that deposit in the nervous tissue and damage the CNS.
• Result: severe mental retardation due to phenylketonuria.

But there's a happy sidelight to this discovery...

New problem!

• A common mutation that causes this disorder can be seen HERE.
• The mutation shown results in deletion of phenylalanine from a chloride-permeable channel membrane protein.
• Deletion of the phe disrupts normal chloride channel function.
• The resulting imbalance of chloride and sodium ions results in abnormally dehydrated mucus which causes a multitude of physical problems, from sterility to respiratory failure.

• a single base pair substitution can cause the normal aa, glutamate (hydrophilic and polar) to be replaced with valine (hydrophobic and non-polar).
• Result: hemoglobin is less water-soluble, especially under acidic conditions. It crystalizes when the blood becomes acidic (as from carbonic acid, during exertion).
• This disorder is ultimately fatal, due to extensive organ damage and anemia.
• One in twelve African Americans is heterozygous for the mutant form of the gene.
• Sidelight: heterozygote advantage: Malaria vs. Sickle Cell.

Complementation: Inferring Gene Interaction

Petal color in Harebells

• Wild type Harebells have blue flowers (produced by anthocyanin pigments)
• In the lab, you irradiated the flowers --> mutant gametes
• By breeding your mutant's seedlings together, you got three different true-breeding strains, X Y and Z
• Only recessive mutants will work in a complementation test
• So the first step is a back-cross to the wild type parent to get F1 for each mutant strain.
• F2 for each strain gives typical Mendelian ratios
• But where are the mutations? Are they all in one gene? Or more than one? You can tell by doing complementation matings.
• Let's have a look at the mutant HareBell flowers
• turns out that in our made-up example, there are two genes, each of which codes for an enzyme in the anthocyanin pathway.

Sometimes, the alleles of a single gene can interact in ways that result in phenotypic ratios in offspring that are not predicted by Mendel's Laws. Two such phenomena, not to be confused with one another are

Two alleles both produce proteins, but one is non-functional. This results in heterozygotes producing only half the amount of protein produced by a homozygous dominant individual.

Two alleles of the same gene are expressed, and both products are functional, though different.

There are two alleles of a gene for flower petal red pigmentation.

• R1: red pigment produced
• R2: no pigment produced

• R1R1: red petals
• R2R2: white flowers
• R1R2: pink flowers

The mutant R2 allele produces an enzyme incapable of catalyzing the reaction.

This recalls the importance of Inborn Errors of Metabolism:

• normal (wild type) allele - functional enzyme
• mutant allele - nonfunctional enzyme

Tay Sachs Disease

A defective allele, found most often in populations of Ashkenazi Jews (Eastern Europe), results in a wild type enzyme (hexosaminidase-A) being produced in a non-functional form.

hexosaminidase-A is responsible for breaking down lipids. In its absence, sphingolipids accumulate in the developing brain and peripheral nervous system of affected fetuses/young children

Result: brain damage, mental impairment, death by age five.

• TT: normal
• Tt: half the amount of enzyme produced, but sufficient for normal development
• tt: no functional enzyme; expression of Tay Sachs disease.
• This is Incomplete Dominance because both alleles are expressed (i.e., a protein is made from each allele), but only one is functional.

Examples of Codominance

Human ABo blood groups

Humans with type AB blood have two different immunoglobins (I^A and I^B) inserted into the blood cell membrane. Types A or B have either one or the other, and type o has neither.

Note: The A & B alleles operate by modifying a wild type mucopolysaccharide terminal sugars.

type o:

fucose--galactose--N-acetylglucosamine (glunac)...

type A individuals have a modified enzyme (alpha-3-N-acetyl-D-galactosaminyl transferase), which modifies the terminal sugars like so:

fucose--galactose--glunac...
|
N-acetylgalactosamine (galnac)

type B individuals produce alpha-3-D galactosyl tranferase, which modifies the terminal sugars of the "o" type like so::


fucose--galactose--glunac...
|
galactose

Coat Color in Horses
Coat color in horses is a complex affair, and some mutations are specific to certain breeds of horses. Murindu!

Lethal Alleles Certain alleles, when present in homozygous recessive condition, cause inviability/death of the homozygous individual. By definition, the gene that has mutated is said to be an essential gene, since its "demise" causes death of the organism that doesn't get its product.
EXAMPLES:

• dwarfing gene in rabbits
• yellow coat color in mice
• manx allele in cats
• Duchenne Muscular Dystrophy
• Tay Sachs disease
• cystic fibrosis
• Overo Lethal White Syndrome in horses.

Let's have a look at skin color in Corn snakes (Elaphe guttata). Two pigments are involved, each manufactured by a different set of enzymes.

• Orange (carotenoid) pigment is produced by the o+ allele. The recessive mutation is o, and it encodes a non-functional enzyme in the orange pigment pathway. Hence, no orange pigment is made by an oo snake.
• Black/brown (melanin) pigment is encoded by the b+ allele. Recessive mutation b encodes a non-functional enzyme in the melanin pathway. Hence, no brown pigment is made by a bb snake.

  But you get unexpected phenotypes, even though the typical dihybrid genotype ratios are found in the offpring of a dihybrid cross:

  • o+_ b+_ - wild type
  • oo b+_ - grey
  • o+_ bb - orange
  • oo bb - albino

Epistasis and Hypostasis in Metabolic Pathways Two different genes can also affect the same enzymatic pathway.

Epistasis indicates that genes often interact in some biochemical or develomental sequence, and that gene actions are not always simultaneous. In many cases (as described in the Labrador Retriever coat color phenomenon in your text), this indicates that an epistatic gene operates "developmentally downstream" from its hypostatic gene.)

• B- E- will be black (fur and skin)
• B- ee will be yellow fur, dark skin
• bb E- will be brown fur, brown skin
• bb ee will be yellow with brown skin

This is an allele that reverses the effects of a recessive mutation at another locus, causing the organism to revert to wild type phenotype.

But how? There are several ways...

Mammal Coat Color At least five genes interact to determine the coat color of mice, and it is believed that similar genes may exist in other mammals.

• if dominant, in either the homozygous or heterozygous condition
  
• if recessive, if homozygous

This is not always the case.
Penetrance

is the proportion of individuals with a specific genotype who manifest that genotype at the phenotypic level. (Some individuals may not express a gene if modifiers, epistatic genes or suppressors are also present in the genome, which thwart expression.

Penetrance = 1.0 (100%) when all homozygous recessive individuals express the recessive form of the allele, and all homozygous dominant individuals and heterozygous individuals express the alternate form of the allele.

Penetrance < 1.0 if not all homozygous recessive individuals express the recessive allele.

Example: Brachydactyly in humans

Expressivity

is the degree to which a particular genotype is expressed in the phenotype of a particular individual. (That is, phenotype may be altered by heterogeneity of other genes which affect the expression of the particular locus in question, or by environmental influence.)

Neurofibromatosis in humans causes tumorlike growths to appear all over the surface of the body if it is fully expressed. In mildly expressed cases, the person with this genotype may never have anything more severe than a few cafe au lai spots on the skin.

Piebald spotting in beagles (and some other mammals): dogs who have the same genotype for the piebald locus often express various patterns and total coverage of white fur patches.

Essentially, penetrance describes what happens in a population, and expressivity describes what happens in a particular individual.

Internal Environment Can Affect Gene Expression

Age-dependent Expression As an organism passes through its life cycle, the expression of its genes changes. This means that some genes are not expressed until later in life. Examples:

• Huntington's disease (age usu. 30 or over)
  
• Male pattern baldness (age usu. 20 or over)
  
• Duchenne Muscular Dystrophy (age 2-5)
• Grey coat color in horses (progressive lightening of the coat with age)

Sex-Dependent Gene Expression

In sex-influenced traits, expression varies depending on the sex of the individual carrying the alleles.

e.g. - finger length (we already did this one)

In other cases, autosomal genes cause the expression of a trait ONLY in one sex or the other.

Example: Feathering morphology in chickens:
h+ - hen-feathering in male or female (short, erect tail, short body plumage)
h - cock-feathering in male, if homozygous (long tail, long body plumage)

Females express hen feathering, no matter what their genotype.

Other examples of sex-limited traits:

Presence of rubella virus during the first 12 weeks of pregnancy in humans can mimic the phenotypic effects of certain rare, recessive alleles (at several different loci) which can cause deafness, cataracts and defects in cardiac development.

Thalidomide (a drug administered in the 1950's to woman at risk of miscarriage) mimicked a rare genetic mutation causing a disorder known as phocomelia--failure of the long bones of the limbs to develop. (Note that thalidomide did not produce a phenocopy effect in the test mammal, Rattus norvegicus.)

The formation of birth defects due to environmental agents (viruses, chemicals, etc.) is known as teratogenesis.

The answer may turn out to be....it depends.

The genotype may set the limits for a particular organism's phenotypic potential. The environment works on the plasticity of expression to produce different phenotypes from similar genotypes. This is evident even in identical twins.
Norm of Reaction: The degree to which phenotype varies with environmental influence.
We will return to this in more detail, in the Quantitative Genetics portion of the course.

Maternal Effect There's more to maternal inheritance than mitochondria and chloroplasts.

Direction of Shell Coiling in Limnaea, a freshwater snail.

The type of inheritance we're about to cover is known as maternal effect--not maternal inheritance.

In these snails, there are two directions the shell can coil (when you look at it with the opening facing you:

• dextral (right-handed) is the more common coiling direction
• sinistral (left-handed) is the rarer direction

If you cross...

• female dex x male sin the F1 will be 100% dextral
• If you allow the F1 to self-fertilize, the F2 is 100% dextral.
• What you'd expect, though, if this were a normal, Mendelian trait, is a 3:1 ratio of dex: sin.

If you cross...

• male dex x female sin the F1 will be 100% sinistral
• If you allow these to self-fertilize, the F2 will be 100% dextral!

Turns out that the phenotype of the offspring depends on the genotype of the mother snail. This is known as maternal effect.

The coiling direction of a particular individual's shell is governed by its mother's genotype. Let's view the results of the snail shell coiling breedings.

Why does this happen?

the ovum contains maternal cytoplasm. Hence, the direction of the baby snail's shell coiling is determined, not by its own genes, but by the mitotic spindle of it's mother's cytoplasmic legacy.

Maternal effect is also seen in larval development of Ephestia kuehniella, the Flour Moth:

• pigmented male x nonpigmented female, offspring exhibit typical Mendelian ratios (depending on the genotype of the male)

• pigmented female x nonpigmented male, offspring are 100% pigmented.

Why?