Materi Kuliah Dasar2 Genetika Fakultas Pertanian UGM

1. 1
Gregor Johann Mendel
Between 1856 and
1863, Mendel
cultivated and tested
some 28,000 pea
plants
He found that the
plants' offspring
retained traits of the
parents

2. Gregor Mendel
 Called the “Father of
Genetics
 Gregor Mendel
(1860’s) discovered
the fundamental
principles of
genetics by
breeding garden
peas.

3. Pea Garden (Pisum sativum)

4. Pea Garden (Pisum sativum)
Easy to grow and can be grown in a small areaan be grown in a small area
Produce lots of offspringProduce lots of offspring
Produce pure plants when allowed to self-Produce pure plants when allowed to self-
pollinate several generations (true breedingpollinate several generations (true breeding
varieties)varieties)
Clearly defined characteristics or traits
Easy to be crossed between parents

5. Pea Characteristics

6. Mendel cross-
pollinated pea
plants
• Mendel probably chose
to work with peas
because they are
available in many
varieties.
• The use of peas also
gave Mendel strict
control over which
plants mated.
• Fortunately, the pea
traits are distinct and
were clearly contrasting.

7. Mendel’s experimental design
 Statistical analyses:
 Worked with large numbers of plants
 counted all offspring
 made predictions and tested them
 Excellent experimentalist
 controlled growth conditions
 focused on traits that were easy to score
 chose to track only those characters that varied in an
“either-or” manner

8. Mendel’s Work

9. Mendel’s Work

10. Typical breeding experiment
P generation (parental
generation)
F1 generation (first filial
generation, the word filial
from the Latin word for
"son") are the hybrid
offspring.
Allowing these F1 hybrids
to self-pollinate produces:
F2 generation (second
filial generation).

11. Mendel Conclusion
Factors are passed from one generation to
the next.

12. 12
Law of Dominance
In a cross of parents that are pure for
contrasting traits, only one form of the trait
will appear in the next generation.
All the offspring will be heterozygous and
express only the dominant trait.
RR x rr yields all Rr (round seeds)

13. The Principle of Dominance
PaternalMaternal
eye color locus
B = brown eyes
eye color locus
b = blue eyes

14. Dominant and Recessive alleles
Dominant alleles – upper-case (B)
a. homozygous dominant (BB – Brown eyes)
Recessive alleles – lower case (b)
a. homozygous recessive (bb – blue eyes)
b. heterozygous dominant (Bb – Brown eyes)

15. Phenotype vs. Genotype
 Outward appearance
 Physical characteristics
 Examples:
1.Brown eyes
2.blue eyes
 Arrangement of genes
that produces the
phenotype
 Example:
1. TT, Tt
2. tt

16. Segregation:
Alleles separate during meiosis

17. 17
Law of Segregation
During theDuring the formation of gametesformation of gametes (eggs(eggs
or sperm), theor sperm), the two allelestwo alleles responsibleresponsible
for a traitfor a trait separateseparate from each other.from each other.
Alleles for a trait are thenAlleles for a trait are then
"recombined" at fertilization"recombined" at fertilization,,
producing the genotype for the traits ofproducing the genotype for the traits of
the offspringthe offspring.

18. 18
The Law of Segregation

19. Punnett Squares
 Diagram used to predict genetic
crosses
 Tool for calculating genetic
probabilities
 A tool to predict the probability of
certain traits in offspring that shows
the different ways alleles can
combine.
 Diagram showing the probabilities of
the possible outcomes of a genetic
cross

20. How to use Punnett
Squares
 Choose a letter to represent the alleles in the cross.
 Write the genotypes of the parents.
 Determine the possible gametes (reproductive cells)
that the parent can produce.
 Enter the possible gamete at the top and side of the
Punnett square.
 Complete the Punnett square by writing the alleles
from the gametes in the appropriate boxes.
 Determine the phenotypes of the offspring.

21. Punnet Square Process
1. Determine alleles of
each parent, these are
given as TT, and tt
respectively.
2. Take each possible
allele of each parent,
separate them, and
place each allele
either along the top,
or along the side of
the punnett square.

22. Punnett Square Process
 Lastly, write the letter for
each allele across each
column or down each
row. The resultant mix is
the genotype for the
offspring. In this case,
each offspring has a Tt
(heterozygous tall)
genotype, and simply a
"Tall" phenotype.

23. Punnett Square Process
 Lets take this a step further
and cross these F1
offspring (Tt) to see what
genotypes and phenotypes
we get.
 Since each parent can
contribute a T and a t to the
offspring, the punnett
square should look like
this….

24. Punnett Square Process
 Here we have some more
interesting results: First
we now have 3 genotypes
(TT, Tt, & tt) in a 1:2:1
genotypic ratio. We
now have 2 different
phenotypes (Tall &
short) in a 3:1
Phenotypic ratio. This
is the common outcome
from such crosses.
Monohybrid cross
(cross with only 1 trait)

25. Testcross
Cross the dominant phenotype (unknown genotype) with the
recessive phenotype (known genotype).

26. Dihybrid cross
The cross with a pure-breeding (homozygous)
two loci.
F1 generationF1 generation

27. Dihybrid cross
 Take the offspring and cross them since they are
donating alleles for 2 traits, each parent in the f1
generation can give 4 possible combination of alleles.
TW, Tw, tW, or tw.
F2 Generation

28. Dihybrid cross
 Note that there is a 9:3:3:1
phenotypic ratio. 9/16
showing both dominant
traits, 3/16 & 3/16 showing
one of the recessive traits,
and 1/16 showing both
recessive traits.
 Also note that this also
indicates that these alleles are
separating independently of
each other. This is evidence
of Mendel's Law of
independent assortment

29. Mendel’s Principles
 The inheritance of biological characteristics are
determined by genes.
 For two or more forms of a gene, dominance
and recessive forms may exist.
 Most sexually reproductive organisms have two
sets of genes that separate during gamete
formation.
 Alleles segregate independently.

30. Law of Independent
Assortment
 Alleles forAlleles for differentdifferent traits aretraits are
distributed to sex cells (& offspring)distributed to sex cells (& offspring)
independently of one another.independently of one another.
 Different genes on different
chromosomes segregate into
gametes independently of each other

31. E
n
e
N
Father
M
other
N
eE
n
e
n
E
N
e
n
E
N
e
N
E
n
Telophase II
Replication
Independent Assortment
N
E
n
e e
n
E
N
OR
Alignment of
Homologs at
Metaphase I

32. Segregation and
Independent Assortment

33. Hypothetical example of
independent Assortment
Gene
for
brown
eyes
Eye color
Gene
for
blue
eyes
Gene
for
black
hair
Gene
for
red
hair
Hair
color

34. Independent Assortment
OR
Brown eyes
Black hair
Blue eyes
Red hair
Brown
eyes
Red hair
Blue eyes
Black hair
Meiosis I & II

35. Three Conclusions of
Mendel Experiment
1. Principle of Dominance and Recessiveness
One allele in a pair may mask the effect of the other
1. Principle of Segregation
The two alleles for a characteristic separate during
the formation of eggs and sperm
1. Principle of Independent Assortment
The alleles for different characteristics are distributed
to reproductive cells independently.

36. Variations on Mendel’s
Laws
The relationship of genotype to phenotype is rarely
simple
Mendel’s principles are valid for all sexually
reproducing species
But genotype often does not dictate
phenotype in the simple way his laws
describe
 There is an exceptional to Mendel Laws

37. Exceptions To Mendel’s
Original Principles
 Incomplete
dominance
 Codominance
 Multiple alleles
 Polygenic traits
 Epistasis
 Pleiotropy
 Environmental effects on
gene expression
 Linkage
 Sex linkage

38. Incomplete dominance
 The phenotype of the
heterozygote is intermediate
between those of the two
homozygotes.
 Neither allele is dominant and
heterozygous individuals have an
intermediate phenotype
 For example, in Japanese “Four
o’clock”, plants with one red
allele and one white allele have
pink flowers:
P Generation
F1 Generation
F2 Generation
Red
CR
CR
Gametes CR
CW
×
White
CW
CW
Pink
CR
CW
Sperm
CR
CR
CR
Cw
CR
CRGametes
1
⁄2 1
⁄2
1
⁄2
1
⁄2
1
⁄2
Eggs
1
⁄2
CR
CR
CR
CW
CW
CW
CR
CW

39. F1 generation
F2 generation
CR
CR
All CR
CW
CW
CW
1 : 2 : 1
Gametes
Gametes
CR
CW
CR
CW
CR
CR
CR
CW
CR
CW
CW
CW
Incomplete Dominance

40. Co-dominance
Phenotype of both
homozygotes are
produced in
heterozygotes
individuals.
Both alleles are
expressed equally.
Examples:
Roan Cattle
White-feathered birds
are both homozygotes
for both B and W
alleles

41. Multiple Alleles
 More than three alleles for a gene
 Found among all individuals in a population
 Diploid individuals only have two of the alleles
 Phenotype depends on relationship
between different pairs of alleles
 Still follows Mendel’s principles

42. Multiple Alleles
Small
differences in
DNA
sequences
result in
multiple alleles

43. Human ABO Blood Group
 Antigens
 Glycoproteins on surface of red blood cells
 IA
allele produces A antigen (dominant)
 IB
allele produces B antigen (dominant)
 i allele produces neither A nor B (recessive)
 Blood types (phenotypes)
 IA
IA
or IA
i = type A blood
 IB
IB
or IB
i = type B blood
 ii = type O blood
 IA
IB
= type AB blood

44. Universal donors
Universalrecipients

45. Epistasis
 Type of polygenic inheritance where the alleles at one gene locus
can hide or prevent the expression of alleles at a second gene locus.
 Allele of one locus inhibits or masks effects of allele at a different
locus
 Some expected phenotypes do not appear among offspring
 Labrador retrievers one gene locus affects coat color by controlling
how densely the pigment eumelanin is deposited in the fur.
 A dominant allele (B) produces a black coat while the recessive allele
(b) produces a brown coat
 However, a second gene locus controls whether any eumelanin at all
is deposited in the fur. Dogs that are homozygous recessive at this
locus (ee) will have yellow fur no matter which alleles are at the first
locus:

46. Epistasis

47. Labrador Retrievers
 Melanin pigment gene
 B allele: black fur color (dominant)
 b allele: brown fur color (recessive)
 Pigment deposition gene
 E allele: pigment deposition normal (dominant)
 e allele: pigment deposition blocked (recessive)
 Phenotypes
 Black fur: BB EE, BB Ee, Bb EE, Bb Ee
 Brown fur: bb EE, bb Ee
 Yellow fur: BB ee, Bb ee, bb ee

48. Labrador Retrievers

50. Polygenic Inheritance
Most traits are not controlled by a single gene locus, but
by the combined interaction of many gene loci. These
are called polygenic traits.
Several genes at different loci interact to control the
same character
 Produces continuous variation
Phenotypic distribution: Bell-shaped curve
Often modified by environmental effects

51. Continuous Variation in
Human Height

52. Continuous Variation in
Plant Height

53. Pleiotropy
 One gene affects more than one character
 For example, in Labrador retrievers the gene
locus that controls how dark the pigment in the
hair will be also affects the color of the nose,
lips, and eye rims.

54. Environmental Effects
on Gene Expression
 The phenotype of
an organism
depends not only
on which genes it
has (genotype),
but also on the
environment
under which it
develops.

55. Environmental Effects
 . hydrangea color – affected by soil (pH, water,
temperature)

56. Extranuclear inheritance

Some genes are passed from parent to offspring without
being part of nuclear chromatin

Mitochondria (and chloroplasts in plants) are randomly
assorted into gametes and daughter cells

In animals, mitochondrial traits are maternally inherited

Example:

Leaf color in four o'clock plants

Human mitochondrial disorders

57. 
)

Examples:

Color blindness

Hemophilia
Linked Genes
Genes that tend to be inherited together on
the same chromosome due to their close
proximity)

58. A gene located on
either sex
chromosome (X in
humans)

Examples:

Color blindness

Hemophilia
Sex-linked traits

59. 6.Autosomal gene is present in both sexes but
expression depends on sex of individual (it’s dominant
in one sex but recessive in the other)

Example:

Baldness in males:
− Man with one copy of gene will be bald
− Female needs two copies of gene to be bald

Milk production in females
− Man with one copy does not lactate
− Female with one copy lactates
Sex-limited traits

60. Probability
The likelihood that a specific event
will occur.
The principles of probability can be
used to predict the outcomes of
genetic crosses.

61. Using probability in
Mendelian genetics
 Segregation and random assortment are random
events, and can thus be characterized by
probability
 The two rules of probability state that:
a. The probability of an outcome ranges from 0 to 1
b. The probabilities of all possible outcomes for an event
sum to 1
 The outcome of a random event is unaffected by
the outcome of previous events

62. Laws of Probability Govern
Mendelian Inheritance
Mendel’s laws of segregation and independent
assortment reflect the rules of probability
The multiplication rule
States that the probability that two or more
independent events will occur together is the
product of their individual probabilities
The rule of addition
States that the probability that any one of two or
more exclusive events will occur is calculated by
adding together their individual probabilities

63. Laws of Probability -
Multiplication Rule
 The probability of two or more independent events
occurring together is the product of the probabilities
that each event will occur by itself
 Following the self-hybridization of a heterozygous
purple pea plants (Pp), the probability of a homozygous
offspring such as the production of white flowers (pp):
a. Probability that a pollen seed will carry p: ½
b. Probability that an egg will carry p: ½
c. Probability that the offspring will be pp:
1/2 X 1/2 = 1/4

64. Laws of Probability -
Addition Rule
 The probability of either of two mutually exclusive events occurring
is the sum of their individual probabilities
 Following the self-hybridization of a heterozygous purple pea plant
(Pp), the probability of purple offspring:
a. Probability of maternal P uniting with paternal P: 1/4
b. Probability of maternal p uniting with paternal P: 1/4
c. Probability of maternal P uniting with paternal p: 1/4
d. Probability that the offspring will be purple:
1/4 + 1/4 + 1/4 = 3/4

65. Probability in Mendel’s
Crosses
Purple-flowered × white-flowered (PP × pp)
 Probability of PP zygote = ½ × ½ = ¼
 Probability of pp zygote = ½ × ½ = ¼

66. Probability in Mendel’s
Crosses
Purple-flowered × white-flowered (PP × pp)
 Probability of Pp zygote = ½ × ½ = ¼
 Probability of pP zygote = ½ × ½ = ¼
 Total probability of heterozygote = ¼ + ¼ = ½

67. Probability in Mendel’s
Crosses
Heterozygous cross (Pp × Pp)
Genotype probabilities
PP zygote = ½ × ½ = ¼
pp zygote = ½ × ½ = ¼
Pp zygote = ¼ + ¼ = ½
Phenotype probabilities
Purple flowers = PP + Pp = ¼ + ½ = ¾
White flowers = pp = ¼

68. Monohybrid Cross
×Rr
Segregation of
alleles into eggs
Rr
Segregation of
alleles into sperm
R r
r
R
R
R
R1
⁄2
1
⁄2
1
⁄2
1
⁄4
1
⁄4
1
⁄4
1
⁄4
1
⁄2 r
r
R r
r
Sperm
×
Eggs

69. Dihybrid Crosses

70. Statistical Testing
 Used by biologists to find out if observed results
differ significantly from expected results.
 Biologists want more than 95% confidence which
means the probability that the deviation of the
observed from that expected is due to chance
alone (no other forces acting).
 In a genetic experiment, it can be used to decide if
observed data fits any of the expected Mendelian
ratios or if data is too “far off” and should be
rejected.

71. Observed Values Expected Values
315 Round, Yellow Seed (9/16)(556) = 312.75 Round, Yellow Seed
108 Round, Green Seed (3/16)(556) = 104.25 Round, Green Seed
101 Wrinkled, Yellow Seed (3/16)(556) = 104.25 Wrinkled, Yellow Seed
32 Wrinkled, Green (1/16)(556) = 34.75 Wrinkled, Green Seed
5556 Total Seeds 556.00 Total Seeds

72. • Xcalc 2
= 0.47 (this is the answer, do not √ it)
• Find the correct critical value on the following table.
• Find the degrees of freedom (n-1) in your data.
• Xtab 2
= 7.82 (Xcalc2
<<<< Xtab2
)
• If calculated chi-square is lower than the critical value,
this shows there is no significant difference between the
expected and observed values and the results are within
the range of acceptable deviation.
• If it is above, the difference is too great and the results
are outside the range of acceptable deviation and should
be rejected!

73. Degrees of
Freedom
(df)
Probability (p)
0.95 0.90 0.80 0.70 0.50 0.30 0.20 0.10 0.05 0.01 0.001
1
0.004 0.02 0.06 0.15 0.46 1.07 1.64 2.71 3.84 6.64 10.83
2
0.10 0.21 0.45 0.71 1.39 2.41 3.22 4.60 5.99 9.21 13.82
3
0.35 0.58 1.01 1.42 2.37 3.66 4.64 6.25 7.82 11.34 16.27
4
0.71 1.06 1.65 2.20 3.36 4.88 5.99 7.78 9.49 13.28 18.47
5
1.14 1.61 2.34 3.00 4.35 6.06 7.29 9.24 11.07 15.09 20.52
6
1.63 2.20 3.07 3.83 5.35 7.23 8.56 10.64 12.59 16.81 22.46
7
2.17 2.83 3.82 4.67 6.35 8.38 9.80 12.02 14.07 18.48 24.32
8
2.73 3.49 4.59 5.53 7.34 9.52 11.03 13.36 15.51 20.09 26.12
9
3.32 4.17 5.38 6.39 8.34 10.66 12.24 14.68 16.92 21.67 27.88
10
3.94 4.86 6.18 7.27 9.34 11.78 13.44 15.99 18.31 23.21 29.59
Nonsignificant. The differences are due to acceptable Significant. Reject! Differences are NOT due to
chance