Materi Kuliah Dasar2 Genetika Fakultas Pertanian UGM

1. Plant Meiosis

2. Plant Meiosis

3. Animals vs. Plants
Plant Reproduction Animal Reproduction
Life cycle
Alternation of
generations
No alternation of
generations
Gametes Haploid gametes Haploid gametes
Spores Haploid spores No spores
Gametes made
by
Haploid gametophyte, by
mitosis
Diploid organism, by
meiosis
Spores made by
Diploid sporophyte, by
meiosis
No spores

4. Alternation of Generations
• Plants have a double life cycle with two
distinct forms:
• Sporophyte: diploid, produce haploid cells
by meiosis.
• Gametophyte: haploid, produce gametes by
mitosis.

5. Non-flowering plants
Mosses, ferns, and related plants
have motile, swimming sperm.

6. Moss Life Cycle

7. Fern Life Cycle

8. Flower Higher Plant

9. Angiosperm Life Cycle

10. Gametogenesis: Male

11. Gametogenesis: Female

12. Double Fertilization

13. Flower to Fruit

14. Ovule to Seed

15. Unique events in Meiosis
• Homologous
(matching)
chromosomes pair up
before 1st
cell division
Homologous
chromosomes:
-look alike
-code for same traits
-receive one from
each parent

16. • During 1st
division, homologous chromosomes
exchange genes during process called “crossing over”
Unique events in Meiosis

17. • These homologous chromosomes separate during 2nd
division of
meiosis – so chromosomes in gametes are different from each other
due to crossing over
• Crossing over increases genetic variation and is the reason why
siblings look different
Unique events in Meiosis

18. Crossing Over
Sometimes in meiosis, homologous chromosomes exchange parts
in a process called crossing-over, or recombination.

19. Process of Recombination
• Genes are on chromosomes. Meiosis is a
mechanism for re-shuffling the chromosomes:
each gamete gets a mixture of paternal and
maternal chromosomes.
• However, chromosomes are long and contain
many genes. To get individual genes re-
shuffled, there needs to be a mechanism of
recombining genes that are on the same
chromosome. This mechanism is called
“crossing over.

20. More Recombination
• Crossing over occurs in prophase of meiosis 1, when the
homologous chromosomes “synapse”, which means to
pair closely with each other. DNA strands from the two
chromosomes are matched with each other.
• During synapsis, an enzyme, “recombinase”, attaches to
each chromosome at several randomly chosen points.
The recombinase breaks both DNA molecules at the
same point, and re-attaches them to opposite partners.
• The result of crossing over can be seen in the microscope
as prophase continues, as X-shaped structures linking
the homologues.
• The genetic consequence of crossing over is that each
chromosome that goes into a gamete is a combination of
maternal and paternal chromosomes.

21. Recombination Process

22. Linkage
.
 Linkage occurs when two genes are close to each other on the
same chromosome.
 Two genes are syntenic, when they are on the same chromosome.
 Linked genes are syntenic, but syntenic genes are not always
linked. Genes far apart on the same chromosome assort
independently: they are not linked.
 Linkage is based on the frequency of crossing over between the
two genes. Crossing over occurs in prophase of meiosis I, where
homologous chromosomes break at identical locations and rejoin
with each other.
The failure of two genes to assort independently

23. Discovery of
Linkage
• In 1900, Mendel’s work was re-discovered, and
scientists were testing his theories with as many
different genes and organisms as possible.
• William Bateson and R.C. Punnett were working with
several traits in sweet peas, notably a gene for purple
(P) vs. red (p) flowers, and a gene for long pollen grains
(L) vs. round pollen grains (l).

24. Bateson and Punnett’s Results
• PP LL x pp ll
• selfed F1: Pp Ll
• F2 results in table
• Very significant deviation from
expected Mendelian ratio: chi-
square = 97.4, with 3 d.f.
Critical chi square value =
7.815.
• The null hypothesis for chi
square test with 2 genes is that
the genes assort independently.
These genes do not assort
independently.
phenot
ype
obs exp
ratio
exp
num
P_ L_ 284 9/16 215
P_ ll 21 3/16 71
pp L_ 21 3/16 71
pp ll 55 1/16 24

25. Linkage Mapping
• Each gene is found at a fixed position on a particular chromosome. Making a map of their
locations allows us to identify and study them better. In modern times, we can use the locations
to clone the genes so we can better understand what they do and why they cause genetic
diseases when mutated.
• The basis of linkage mapping is that since crossing over occurs at random locations, the closer
two genes are to each other, the less likely it is that a crossover will occur between them. Thus,
the percentage of gametes that had a crossover between two genes is a measure of how far
apart those two genes are.
• As pointed out by T. H. Morgan and Alfred Sturtevant, who produced the first Drosophila gene
map in 1913. Morgan was the founder of Drosophila genetics, and in his honor a recombination
map unit is called a centiMorgan (cM).
• A map unit, or centiMorgan, is equal to crossing over between 2 genes in 1% of the gametes.

26. Gene Mapping
• Gene mapping determines the order of genes and the
relative distances between them in map units
• 1 map unit = 1 cM (centimorgan)
In double heterozyote:
• Cis configuration = mutant alleles of both genes are on the
same chromosome = ab/AB
• Trans configuration = mutant alleles are on different
homologues of the same chromosome = Ab/aB

27. Gene Mapping
• Gene mapping methods use recombination
frequencies between alleles in order to
determine the relative distances between them
• Recombination frequencies between genes
are inversely proportional to their distance
apart
• Distance measurement: 1 map unit = 1
percent recombination (true for short
distances)

28. Recombination

29. 29
Gene Mapping
• Genes with recombination frequencies less than 50 percent are on the
same chromosome = linked)
• Linkage group = all known genes on a chromosome
• Two genes that undergo independent assortment have recombination
frequency of 50 percent and are located on nonhomologous
chromosomes or far apart on the same chromosome = unlinked
Recombination

30. Recombination
• Recombination between linked genes occurs at the
same frequency whether alleles are in cis or trans
configuration
• Recombination frequency is specific for a particular
pair of genes
• Recombination frequency increases with increasing
distances between genes
• No matter how far apart two genes may be, the
maximum frequency of recombination between any
two genes is 50 percent.
Recombination

31. 31
Gene Mapping
• Recombination
results from
crossing-over
between linked
alleles.
• Recombination
changes the allelic
arrangement on
homologous
chromosomes
Recombination

32. Genetic Mapping
• The map distance (cM) between two genes equals one half the
average number of crossovers in that region per meiotic cell
• The recombination frequency between two genes indicates how
much recombination is actually observed in a particular
experiment; it is a measure of recombination
• Over an interval so short that multiple crossovers are precluded
(~ 10 percent recombination or less), the map distance equals
the recombination frequency because all crossovers result in
recombinant gametes.
• Genetic map = linkage map = chromosome map
Recombination

33. Gene Mapping: Crossing Over
Two exchanges taking place
between genes, and both
involving the same pair of
chromatids, result in a
nonrecombinant
chromosomes

34. Gene Mapping: Crossing Over
• Crossovers which occur outside the region between
two genes will not alter their arrangement
• The result of double crossovers between two
genes is indistinguishable from independent
assortment of the genes
• Crossovers involving three pairs of alleles
specify gene order = linear sequence of genes

35. 35
Gene Mapping: Crossing Over

36. Genetic vs. Physical Distance
• Map distances based on recombination
frequencies are not a direct measurement of
physical distance along a chromosome
• Recombination “hot spots” overestimate
physical length
• Low rates in heterochromatin and centromeres
underestimate actual physical length

37. Genetic vs. Physical Distance

38. Discovery of Genetic
Linkage
• Classical genetics analyzes the frequency of allele
recombination in progeny of genetic crosses
• New associations of parental alleles are
recombinants, produced by genetic
recombination.
• Tests crosses determine which genes are linked,
and a linkage map (genetic map) is constructed
for each chromosome.

39. MORGAN’s
EXPERIMENTS
• Both the white eye gene (w) and a gene for miniature
wings (m) are on the X chromosome.
• Morgan (1911) crossed a female white miniature (w
m/w m) with a wild-type male (w+ m+/ Y).
• In the F1, all males were white-eyed with miniature
wings (w m/Y), and all females were wild-type for
eye color and wing size (w+ m+/w m).

40. MORGAN’s
EXPERIMENTS
• F1 interbreeding is the equivalent of a test cross for these X-linked genes,
since the male is hemizygous recessive, passing on recessive alleles to
daughters and no X-linked alleles at all to sons.
• What is the expected ratio of phenotypes in F2, if white and miniature are on
different chromosomes?
In F2, the most frequent phenotypes for both sexes were the phenotypes of the
parents in the original cross (white eyes with miniature wings, and red eyes
with normal wings).
Non-parental phenotypes (white eyes with normal wings or red eyes with
miniature wings) occurred in about 37% of the F2 flies. Well below the 50%
predicted for independent assortment, this indicates that non-parental flies
result from recombination of linked genes.

41. Peter J. Russell, iGenetics: Copyright © Pearson Education, Inc., publishing as Benjamin Cummings.
Morgan’s experimental crosses of white-eye
and miniature-wing variants of Fruit fly

42. MORGAN’S PROPOSAL
• During meiosis alleles
of some genes assort
together because they
are near each other on
the same
chromosome.
• Recombination occurs
when genes are
exchanged between X
chromosomes of the
F1 females
• Parental phenotypes occur most
frequently, while recombinants less.
• Terminology
• Chiasma: site of crossover
• Crossing over: reciprocal exchange of
homologous chromatid segments
• Crossing-over occurs at prophase I in
meiosis; each event involves two of
the four chromatids. Any chromatids
may be involved in crossing over.

43. Mechanism of crossing-over

44. Detecting Linkage
through Testcrosses
• Linked genes are used for mapping. They are
found by looking for deviation from the
frequencies expected from independent
assortment.
• A testcross (one parent is homozygous recessive)
works well for analyzing linkage
• If the alleles are not linked, and the second parent is
heterozygous, all four possible combinations of traits
will be present in equal numbers in the progeny.
• A significant deviation in this ratio (more parental and
fewer recombinant types) indicates linkage.

45. Testcross to show that two genes are
linked

46. Testcross to show that two genes are
linked

47. Chi-square for analysis
of linkage
• A null hypothesis (‘the genes independently assort’) is used
because it is not possible to predict the phenotype
frequencies produced by linked genes.
• If two genes are not linked, a testcross should yield a 1:1 ratio of
parentals: recombinants.
• Formula is X2 = sum (Obs-Exp)^2/Exp
• If P>0.05, deviation between Obs and Exp is not significant
• If P<=0.05, deviation is statistically significant; such that genes
may be linked.

48. Concept of Genetic Map
• In an individual heterozygous at two loci, there are two
arrangements of alleles:
• Cis (coupling) arrangement: has both wild type alleles on one
homologous chromosome, and both mutants on the other (e.g., w+
m+ and w m).
• Trans (repulsion) arrangement: has one mutant and one wild-type
on each chromosome (e.g., w+ m and w m+)
• A crossover between homologs in cis arrangement results in a
homologous pair with the trans arrangement. A crossover between
homologs in the trans arrangement results in cis homologs.

49. Drosophila Crosses
• They showed that cross over frequency for linked genes
(measured by recombinants) is characteristics for each
gene pair. The frequency stays the same, whether the
genes are in coupling or in repulsion.
• Morgan and Sturtevant (1913) used recombination
frequencies to make a genetic map.
• A 1% crossover rate is a genetic distance of 1 map unit (mu). A map unit
is also called a centimorgan (cM). Geneticists use recombination
frequency as a way to estimate crossover frequency. The farther apart
the two genes are on the chromosome, the more likely it is that crossover
will occur between them, and therefore the greater their crossover
frequency.

50. Drosophila Crosses

51. First Genetic Map
• Three X-linked genes
• White (w): white eyes
• Miniature (m): miniature wings
• Yellow (y): yellow body
• Crosses gave the following recombination frequencies:
• White x miniature was 32.6
• White x yellow was 1.3
• Miniature x yellow was 33.9
MAP: m-----------------------------------w---y

52. Gene Mapping Using
Two-Point Testcrosses
With autosomal recessive alleles, when a
double heterozygote is testcrossed, four
phenotypic classes are expected. If the genes
are linked, the two parental phenotypes will be
about equally frequent and more abundant than
the two recombinant phenotypes.

53.  For autosomal dominants, a double heterozygotes (A
B/A+B+) is testcrossed with a homozygous wildtype
(recessive) individual (A+B+/A+B+)
 For X-linked recessives, a female double heterozygote (a+
b+/a b) is crossed with a hemizygous recessive male (a
b/Y).
 For X-linked dominants, a female double heterozygote (A
B/A+ B+) is crossed with a male hemizygous for the wild-
type (A+ B+).
 Phenotypes obtained in these crosses will depend on
whether the alleles are in cis or trans position.

54. GENETIC MAP
• Recombination frequency is used directly as
an estimate of map units.
• The measure is more accurate when alleles
are close together.
• Scoring large numbers of progeny
increases accuracy.

55. GENERATING A
LINKAGE MAP
• Genetic map is generated from estimating the crossover
rate in a particular segment of a the chromosome. It may
not exactly match the physical map because crossover is
not equally probable at all sites on the chromosome.
• Recombination frequency is also used to predict progeny
in genetic crosses. For example, a 20% crossover rate
between two pairs of alleles in a heterozygote (a+ b+/a b)
will give 10% gametes of each recombinant type (a+ b
and a b+).

56. MULTIPLE
CROSSOVERS
If the genes are on the same chromosome,
multiple crossovers can occur. The further apart
two loci are, the more likely they are to have
crossover events take place between them. The
chromatid pairing is not always the same in
crossover, so that 2,3, or 4 chromatids may
participate in multiple crossover.

57. Demonstration that the recombination frequency
between two genes located
far apart on the same chromosome cannot
exceed 50 percent

58. Demonstration that the recombination frequency
between two genes located
far apart on the same chromosome

59. Demonstration that the recombination
frequency between two genes located
far apart on the same chromosome
cannot exceed 50 percent

60. Three-point mapping, showing the
testcross used and the resultant progeny

61. Mapping using three-
point testcrosses
• Geneticists design experiments to gather data on several
traits in 1 testcross. An example of a three-point testcross
would be
• p+r+j+/p r j X p r j / p r j
• In the progeny, each gene has two possible phenotypes.
For three genes there are (2)^3=8 expected phenotypic
classes in the progeny.

62. Establishing the order of
genes
• The order of genes on the chromosome can be deduced
from results of the cross. Of the eight expected progeny
phenotypes:
• Two classes are parental (p+ r+ j+/ p r j and p r j / p r j)
and will be the most abundant.
• Of the six remaining phenotypic classes, two will be
present at the lowest frequency, resulting from apparent
double crossover (p+ r+ j / p r j and p r j+ / p r j). This
establishes the gene order as p j r.

63. Consequences of a double crossover in a
triple heterozygote for three linked
genes

64. Rearrangement of the three genesr

65. Rewritten form of the testcross and
testcross progeny based
on the actual gene order p j r

66. Calculating the
recombination frequencies
Cross data is organized to reflect the gene order, and
this example the region between genes p and j is
called region I, and that between j and r is region II.

67. Calculating recombination
frequencies
• Recombination frequencies are now calculated for two genes at
a time. It includes single crossovers in the region under study,
and double crossovers, since they occur in both regions.
• Recombination frequencies are used to position genes on the
genetic map (each 1% recombination frequency = 1 map unit)
for the chromosomal region.
• Recombination frequencies are not identical to crossover
frequencies, and typically underestimate the true map distance.

68. Genetic map of the p-j-r region of the
chromosome

69. Calculating accurate
map distances
• Recombination frequency generally underestimates the true map
distance:
• Double crossovers between two loci will restore the parental
genotype, as will any even number of crossovers. These will
not be counted as recombinants, even though crossovers take
place.
• A single crossover will produce recombinant chromosomes, as
will any odd number of crossovers. Progeny analysis assumes
that every recombinant was produced by a single crossover.
• Map distances for genes that are less than 7 mu apart are very
accurate. As distance increases, accuracy declines because
more crosses go uncounted.

70. Progeny of single and double
crossovers