1. Haixu Tang School of Informatics
Basic genetics
Haixu Tang
School of Informatics

2. Mendel’s two innovations
Developed pure lines
a population that breeds true for a particular trait
Counted his results and kept statistical notes

3. Phenotypes of Mendel's pea plants
round or wrinkled seed phenotype
yellow or green seed phenotype
red or white flower phenotype
tall or dwarf plant phenotype

4. Results from Mendel's Experiments
Parental Cross
F1 Phenotype
F2 Phenotypic Ratio
F2 Ratio
Round x Wrinkled Seed
Round
5474 Round:1850 Wrinkled
2.96:1
Yellow x Green Seeds
Yellow
6022 Yellow:2001 Green
3.01:1
Red x White Flowers
Red
705 Red:224 White
3.15:1
Tall x Dwarf Plants
Tall
l787 Tall:227 Dwarf
2.84:1

5. Phenotypes
Dominant - the allele that expresses itself at the expense of an alternate allele; the phenotype that is expressed in the F1 generation from the cross of two pure lines
Recessive - an allele whose expression is suppressed in the presence of a dominant allele; the phenotype that disappears in the F1 generation from the cross of two pure lines and reappears in the F2 generation

6. Conclusion
The hereditary determinants are of a particulate nature. These determinants are called genes.
Each parent has a gene pair in each cell for each trait studied. The F1 from a cross of two pure lines contains one allele for the dominant phenotype and one for the recessive phenotype. These two alleles comprise the gene pair.
One member of the gene pair segregates into a gamete, thus each gamete only carries one member of the gene pair.
Gametes unite at random and irrespective of the other gene pairs involved.

7. Some terms
Allele - one alternative form of a given allelic pair; tall and dwarf are the alleles for the height of a pea plant; more than two alleles can exist for any specific gene, but only two of them will be found within any individual
Allelic pair - the combination of two alleles which comprise the gene pair
Homozygote - an individual which contains only one allele at the allelic pair; for example DD is homozygous dominant and dd is homozygous recessive; pure lines are homozygous for the gene of interest
Heterozygote - an individual which contains one of each member of the gene pair; for example the Dd heterozygote
Genotype - the specific allelic combination for a certain gene or set of genes

8. F1: Symbol representation

9. F2: Punnett Square Union of Gametes At Random D d DD (Tall) Dd (Tall)
dd (Short)

10. Mendel's First Law
The law of segregation: during gamete formation each member of the allelic pair separates from the other member to form the genetic constitution of the gamete

11. Test the hypothesis

12. Genotype of the F2 individuals
Phenotypes
Genotypes
Genetic Description
F2 Tall Plants
1/3 DD 2/3 Dd
Pure line homozygote dominant Heterozygotes
F2 Dwarf Plants
all dd
Pure line homozygote recessive
Thus the F2 is genotypically 1/4 Dd : 1/2 Dd : 1/4 dd

13. Backcross: Dd x dd
The cross of an F1 hybrid to one of the homozygous parents; for pea plant height the cross would be Dd x DD or Dd x dd; most often, though a backcross is a cross to a fully recessive parent
Backcross One or (BC1) Phenotypes: 1 Tall : 1 Dwarf
BC1 Genotypes: 1 Dd : 1 dd

14. Monohybrid
Monohybrid cross - a cross between parents that differ at a single gene pair (usually AA x aa)
Monohybrid - the offspring of two parents that are homozygous for alternate alleles of a gene pair
Remember --- a monohybrid cross is not the cross of two monohybrids.

15. Variations to Mendel's First Law of Genetics
Codominance - a relationship among alleles where both alleles contribute to the phenotype of the heterozygote
Incomplete dominance - the F1 produces a phenotype quantitatively intermediate between the two homozygous parents;

16. Pedigree Analysis

17. Traits exhibiting dominant gene action
affected individuals have at least one affected parent
the phenotype generally appears every generation
two unaffected parents only have unaffected offspring

19. Traits exhibiting recessive gene action
unaffected parents can have affected offspring
affected progeny are both male and female

21. Mendel's Law of Independent Assortment
We have followed the expression of only one gene. Mendel also performed crosses in which he followed the segregation of two genes. These experiments formed the basis of his discovery of his second law, the law of independent assortment.

22. Dihybrid cross
Dihybrid cross - a cross between two parents that differ by two pairs of alleles (AABB x aabb)
Dihybrid- an individual heterozygous for two pairs of alleles (AaBb)

23. Mendel’s experiment
Parental Cross: Yellow, Round Seed x Green, Wrinkled Seed
F1 Generation: All yellow, round
F2 Generation: 9 Yellow, Round, 3 Yellow, Wrinkled, 3 Green, Round, 1 Green, Wrinkled
Seed Color: Yellow = G; Green = g
Seed Shape: Round = W; Wrinkled = w

24. Parental cross

25. GGww (Yellow, wrinkled) Ggww (Yellow, wrinkled)
Female Gametes GW Gw gW gw
GGWW (Yellow, round)
GGWw (Yellow, round)
GgWW (Yellow, round)
GgWw (Yellow, round)
Male
GGww (Yellow, wrinkled)
Ggww (Yellow, wrinkled)
Gametes
ggWW (Green, round)
ggWw (Green,ROUND)
ggWw (Green, round)
ggww (Green, wrinkled)

26. Phenotype
General Genotype
9 Yellow, Round Seed
G_W_
3 Yellow, Wrinkled Seed
G_ww
3 Green, Round Seed
ggW_
1 Green, Wrinkled Seed
ggww

27. Mendel's Second Law - the law of independent assortment
During gamete formation the segregation of the alleles of one allelic pair is independent of the segregation of the alleles of another allelic pair.

28. backcross - F1 dihybrid x
Female Gametes GW Gw gW gw
Male Gametes
GgWw (Yellow,
round)
Ggww (Yellow,
wrinkled)
ggWw (Green,
ggww (Green,
The phenotypic ratio of the test cross is:
1 Yellow, Round Seed
1 Yellow, Wrinkled Seed
1 Green, Round Seed
1 Green, Wrinkled Seed

29. The Chi-Square Test
An important question to answer in any genetic experiment is how can we decide if our data fits any of the Mendelian ratios we have discussed. A statistical test that can test out ratios is the Chi-Square or Goodness of Fit test.
Degrees of freedom (df) = n-1, where n is the number of classes

30. An example
Let's test the following data to determine if it fits a 9:3:3:1 ratio.
Observed Values
Expected Values
315 Round, Yellow Seed
(9/16)(556) = Round, Yellow Seed
108 Round, Green Seed
(3/16)(556) = Round, Green Seed
101 Wrinkled, Yellow Seed
(3/16)(556) = Wrinkled, Yellow
  32 Wrinkled, Green
(1/16)(556) =   Wrinkled, Green
556 Total Seeds
                        Total Seeds
                                                 
Number of classes (n) = 4
df = n = 3
Chi-square value = 0.47

31. A Chi-Square Table Probability Degrees of Freedom 0.9 0.5 0.1 0.05
0.01 1
0.02
0.46
2.71
3.84
6.64 2
0.21
1.39
4.61
5.99
9.21 3
0.58
2.37
6.25
7.82
11.35 4
1.06
3.36
7.78
9.49
13.28 5
1.61
4.35
9.24
11.07
15.09

32. Pleiotropic Effects and Lethal Genes
In 1904, a cross was made between a yellow-coated mouse and a mouse with a gray coat. The gray- coated mouse was extensively inbred and therefore was considered to be pure bred.

33. Next a cross was made between two yellow mice
Next a cross was made between two yellow mice. What genetic ratio would we expect to see? Yy x Yy should give a ratio of 3 yellow:1 gray. The result, though, was a ratio of 2 yellow to 1 gray mice. How can this result be explained? Let's first set up a Punnett Square.

34. Testcross
All testcross data with the yellow mice give a 1:1 ratio. This ratio is typical of what is seen with heterozygous individuals.
All of the yellow mice from the cross of two heterozygous yellow mice are genotypically Yy. Somehow the YY genotype is lethal. The 2:1 ratio is the typical ratio for a lethal gene.

35. Lethal gene
Lethal Gene - a gene that leads to the death of an individual; these can be either dominant or recessive in nature.
Pleiotropic gene - a gene that affects more than one phenotype

36. Gene Interactions
Rose                                              Pea
Single                                               
Walnut

37. Phenotypes
Genotypes
Frequency
Walnut
R_P_
9/16
Rose
R_pp
3/16
Pea
rrP_
Single
rrpp
1/16

38. Epistasis
The interaction between two or more genes to control a single phenotype

39. Modifier Genes
Instead of masking the effects of another gene, a gene can modify the expression of a second gene. In mice, coat color is controlled by the B gene. The B allele conditions black coat color and is dominant to the b allele that produces a brown coat. The intensity of the color, either black or brown is controlled by another gene, the D gene. At this gene, the dominant D allele controls full color whereas the recessive d allele conditions a dilute or faded expression of the color expression at the B gene. Therefore, if a cross is made among mice that are BdDd, the following phenotypic distribution will be seen:
9 B_D_ (black)
3 B_dd (dilute black)
3 bbD_ (brown)
1 bbdd (dilute brown)
The D gene does not mask the effect of the B gene, rather it modifies its expression.

40. Gene linkage
One experiment was performed by Bateson and Punnett with sweet peas. They performed a typical dihybrid cross between one pure line with purple flowers and long pollen grains and a second pure line with red flowers and round pollen grains. Because they knew that purple flowers and long pollen grains were both dominant, they expected a typical 9:3:3:1 ratio when the F1 plants were crossed.

41. Observed
Expected
Purple, long (P_L_)
284
215
Purple, round (P_ll) 21 71
Red, long (ppL_)
Red, round (ppll) 55 24
Total
381

42. Linked Genes On The Same Chromosome
F1 Gamete
Testcross Distribution
Gamete Type
pr+ vg+
1339
Parental
pr+ vg
151
Recombinant
pr vg+
154
pr vg
1195

43. Coupling and repulsion
F1 Gamete
Testcross Distribution
Gamete Type
pr+ vg+
1339
Parental
pr+ vg
151
Recombinant
pr vg+
154
pr vg
1195

45. Genotype
Observed
Type of Gamete
ABC
390
Parental
abc
374
AbC 27
Single-crossover between genes C and B
aBc 30
ABc 5
Double-crossover
abC 8
Abc 81
Single-crossover between genes A and C
aBC 85
Total
1000