1. Genetics: Mendel and Beyond
Chapter 10

2. Gregor Mendel Developed the fundamental laws of heredity
He studied science and mathematics 
Mendel chose garden peas (Pisum sativum) as his subjects as they are easily grown and their pollination is easily controlled. He controlled pollination by manually moving pollen between plants 
Developed true-breeding plants by self-pollination 
Funfact: Mendel originally wanted to breed mice, but wasn't allowed to because it was considered scandalous
He could also allow the plants to self-pollinate. 
Mendel examined varieties of peas for heritable characters and traits for his study. (stem length, pod shape, seed shape, seed color..etc)

3. Mendel's Law of Segregation (MONOHYBRID CROSS)
Mendel crossed true-breeding plants that differed for a given character
A monohybrid cross involves one (mono) character and different (hybrid) traits.
Pollen from true-breeding pea plants with purple flowers (one trait) was placed on stigmas of true-breeding plants with white flowers (another trait).
The F1 seeds were all purple; the white flower trait failed to appear at all.
Because the purple flower trait completely masks the white flower trait when true-breeding plants are crossed, the purple flower trait is called dominant, and the white flower trait is called recessive.

4. The F1 plants were allowed to self-pollinate.
The progeny, called F2, were examined: roughly 1/4 were white, and 3/4 were purple.
Mendel proposed that the units responsible for inheritance were discrete particles - particulate theory `

5. The same pattern occurred over and over, for seven different traits. 

6. As Viewed by Modern Genetics
During production of gametes, only one of the pair members for a given character passes to the gamete. (LAW OF SEGREGATION)
When fertilization occurs, the zygote gets one from each parent, restoring the pair.
Mendel's units of inheritance are now called genes.
Different forms of a gene are called alleles.
Each allele is given a symbol: In the case of purple flowers, P represents purple and p white. By convention, uppercase P represents the dominant; lowercase p represents the recessive. Never mix your letters! Choose one letter and use a capital to denote dominate and a lowercase to denote recessive.
                                                                                                           
Parental Cross 
PP  x  pp
purple x white

7. The F1 cross Pp x Pp purple x purple
True-breeding individuals would have two copies of the same allele: Purple would be PP. Two copies of same allele = homozygous. Homo means "the same" 
White true-breeding would be pp. Two copies of same allele = homozygous.   Therefore both PP and pp are considered homozygous, just one is purple and the other is white.
Some purple-flowered plants could be Pp, although they would not be true-breeding. Individuals that are purple, but had a white parent, are heterozygous or hybrid: Pp. Hetero means "different".
The F1 cross
Pp  x Pp   
purple x purple

8. When an organism is studied for three different genes and has the alleles AABbCC, it is homozygous for A and C genes but heterozygous for the B gene.
A = antenna a = no antenna
B = black
b = purple
C = chompers c = no chompers

9. Practice picking letters
Practice picking letters.... the following traits are found in the common Shirtus americanus.
1.  Polka dots are dominant to stripes.
2.  Long sleeves are dominant to short sleeves.
3.  Collared shirts are recessive.
4.  Buttons are dominant over snaps.
5.  Pockets are recessive.   

10. Practice with Punnett Squares
1.  A  round seeded plant (RR) is crossed with a wrinkle seeded plant (rr).  What are the phenotypes of the offspring?
2.  Two heterozygous purple flowered pea plants are crossed.  What are the phenotypes of their offspring and in what proportion?
3.  A plant with green seeds (yy) is crossed with a heterozygous plant.  What percentage of their offspring have yellow seeds?

11. Wings are a dominant trait, but some dragons are born wingless.
In dragons...
Wings are a dominant trait, but some dragons are born wingless.
What are the chances that two heterozygous dragons have a whelp that is wingless?
If a wingless dragon is crossed with one that is heterozygous, how many of its offspring will also be wingless?

12. What is a test cross? Help, help! I don't know what my genotype is!!
I can help you!  Let's have offspring!
Help, help!  I don't know what my genotype is!!
Am I Dd or DD?

13. R T R t r T r t Why does the punnett square work?
It all goes back to meiosis.. each side represents a sperm or egg.  The boxes filled out simply give you the statistical chance that a certain sperm will fertilize a certain egg. 
Consider a pea plant that is RrTt  (round seed, tall)
When this plant's cells go through MEIOSIS, the alleles segregate - each sperm receives a random combination...
Possible Gametes:
R T   R t r T      r t

14. What are the gametes possible for an organism that is AaBbRr?
Mendel’s Three Laws 1. Dominance & Recessiveness 2. Segregation
 3. Independent Assortment

15. Mendel's Law of Independent Assortment – Illustrated by the DIHYBRID cross
The second law describes the outcome of dihybrid (two character) crosses, or hybrid crosses involving additional characters.
A dihybrid is an individual that is a double heterozygote (e.g., with the genotype RrYy - round seed, yellow seed).
What are the gametes that can be produced by this individual?

16. Dihybrid Cross: RrYy x RrYy

17. BEYOND MENDEL
Conditions that Mendel didn't explore - genetic traits that are inherited in new and interesting patterns.
Codominance / Incomplete dominance / Multiple Allele Traits / Polygenic Inheritance /  Lethal Alleles / Epistatic Alleles

18. Incomplete Dominance
Traits appear to "blend" in offspring
RR x WW
      RW  (pink)
Show:
Pink x Red
Pink x Pink
White x White

19. This illustrates another style of "letters" to denote genotypes
R1 and R2

20. Sickle Cell Trait in Humans
Genotypes  & Phenotypes

21. Coloration in Rodents
Black x White = Gray
BB   x   WW  =  BW

22. ROAN COW - What happens when you cross a white and a red cow?
Roan is codominant - both alleles R and W are expressed

23. What happens when two Roan Cows are Crossed?

24. Blood Types - Multiple Alleles

25. When doing blood type crosses, you will need to know whether at type A or B person is heterozygous or homozygous. Type O's are automatically OO and type AB is automatically AB. Crosses are performed the same as any other.
Show Crosses:
A B   x   A O                        A O  x  B O                         A A  x  A B

26. A woman who is type A is married to a man who is type B, what are ALL of the possible blood types of their children?

27. Mix Those Genes Many Genes Have Multiple Alleles
A population might have more than two alleles for a given gene.
In Labrador retriever, coat color is determined by one gene with four different alleles. Five different colors result from the combinations of these alleles.  (More on labradors later)
Eye color is also controlled by multiple alleles
Try this activity on Eye Color
     Mix Those Genes

28. If you played "Mix Those Genes"  you saw how the eye color of the parents determines the eye color of their offspring.
The simulation is a bit simplified, but the idea is that MULTIPLE ALLELES control a single trait (eye color)
It is likely that more than 2 alleles control eye color, the simulation just made it simple to understand.

29. Determine the genotypes of these aliens given that the trait is controlled by multiple alleles. 

30. Polygenic Traits
Individual heritable characters are often found to be controlled by groups of several genes, called polygenes.
Each allele intensifies or diminishes the phenotype.
Variation is continuous or quantitative (adding up) - also called quantitative inheritance
Seed Color in wheat - aabbcc, Aabbcc, AaBbcc, AaBbCc, AABbCc, AABBCC (light, intermediate colors, dark)
In humans - hair color, height, skin color

31. Polygenic Inheritance
AABBCC x aabbcc (P)
AaBbCc x AaBbCc (F1)
Seven Possible Phenotypes in the F2

34. Environment and Phenotype Temperature, water, food sources can have an affect on how a gene is expressed
Rabbits have a gene that codes for darker pigments - this gene is more active at low temperatures. Parts of the body that are colder will develop the darker pigmentation - ears and feet 

36. SIAMESE CATS

37. LEGHORN CHICKEN – SINGLE COMB
Multiple Alleles control the combs of chickens.
Assignment:
Multiple Alleles in Chickens
LEGHORN CHICKEN – SINGLE COMB

38. Lethal Genes 
Some genes are lethal when both alleles are present. Lethality can occur before or after birth
Huntington's disease in humans is caused by a lethal allele, death occurs later in life
Other examples: Mouse coat color (yellow), Creeper legs in chickens, Manx Cats (no tails)
An example is the "creeper" allele in chickens, which causes the legs to be short and stunted.

39. LABRADOR RETRIEVERS AND EPISTATIC ALLELES
A population might have more than two alleles for a given gene.
In labrador retriever, coat color is determined by one gene with four different alleles. Five different colors result from the combinations of these alleles.
Even if more than two alleles exist in a population, any given individual can have no more than two of them: one from the mother and one from the father.
Black is dominant to chocolate B or b Yellow is recessive epistatic (when present, it blocks the expression of the black and chocolate alleles) E or e

40. Black Lab Chocolate Lab Yellow Lab BBEE BbEE BBEe BbEe bbEE bbEe
BBee Bbee bbee

41. 1. A black lab (BBEe) x yellow lab (bbee)
2. A chocolate lab (bbEe) x black lab (BbEe)

42. 3. Two black labs (BBEE x BbEe)

44. Linkage Groups & Chromosome Maps
When Mendel crossed his F1 generation:  PpRr x PpRr, he got a 9:3:3:1 ratio.   He would have not seen this pattern if the alleles had been located on the same chromosome and inherited together.

45. A return to Drosophila.... Check out:
Different alleles exist because any gene is subject to mutation, or change, to a stable, heritable new form
Alleles can randomly mutate to become a different allele depending on DNA sequence changes.
Wild type is a term used for the most common allele in the population.
Other alleles, often called mutant alleles, may produce a phenotype different from that of the wild-type allele.
An alternate form of designating alleles. Alleles that are wild type are expressed with a +
Ex. Red eye color (w+) is dominant to white eye color (w). The red eye is the wild type. Don't let this confuse you, its just a different way to express alleles.
Check out:  

46. Many genes are located on the same chromosome, and they do not assort independently, instead, they are inherited together
Consider the following chromosome map of the fruit fly: All the alleles are located on chromosome 2 of the fruit fly, and are inherited together.

47. Punnett Squares with Linkage Groups 
When performing crosses with linkage groups, I find it best to draw a little picture of the chromosomes to show how they are inherited. Example: A fly that is heterozygous for long wings (Ll) and heteroyzygous for long aristae (Aa) is crossed with another fly of the same type. AaLl x AaLl. In both cases the dominant allele is located on the same chromosome. Before you set about making a 4x4 square, you need to consider the linkage groups. Sketch them!

48. The results of the cross will change if the alleles are arranged in a different way.  Show the cross if the dominant alleles were located on DIFFERENT chromosomes (don't forget to sketch)

49. How Chromosome Maps Are Determined
Alleles that are farther apart, like the gray body and the brown eye color allele are more likely to cross-over and exchange than ones closer together.

50. Biologists use the percent of crossing over to determine the locus of alleles on a chromosome. 
The distance between alleles is measures in MAP UNITS, or MU. On the diagram the long wing allele is 13MU from the aristae allele. The image above is a linkage map because it shows the distance between the alleles

53. Practice Questions (assume no crossing over occurs) 1
Practice Questions (assume no crossing over occurs) 1. A dumpy winged (ww) fruit fly with long aristae (AA) is crossed with a long winged (Ww) short aristae (aa). Show the cross and the phenotypic proportions.

54. 2. A fruit fly with short legs (ll) and vestigial wings (ww) is crossed with one that is heterozygous for both traits. Assuming the dominant alleles are on separate chromosomes, show the cross and the expected phenotypic proportions.